RiceWiki - User contributions [en]

Os06g0706400

2014-12-30T16:50:05Z

Shijc:

OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os06g0706400-Fig1.png|right|thumb|200px|'' The effect of OsPTR9 on the formation of roots. (from reference <ref name="ref1" />).'']]
'''OsPTR9 expression is regulated by light and N source'''

OsPTR9 is closely related to the functional di/tripeptide transporters <ref name="ref2" /> and is localized at the plasma membrane. Members of the PTR/NRT1 family transport a wide range of substrates, including di/tripeptides, nitrate, histidine, carboxylates, other N-containing compounds such as IAA-amino acid conjugates, ABA, glutathione, and even the defence compound glucosinolate, and other substrate compounds might be identified <ref name="ref3" /><ref name="ref4" /><ref name="ref5" /><ref name="ref6" /><ref name="ref7" /><ref name="ref2" />.
OsPTR9 was found to be expressed in all organs analysed, but expression levels varied. The expression of OsPTR9 was high at night and low during the light period, which is different than the expression patterns of many ammonium and nitrate transporter genes <ref name="ref8" /><ref name="ref9" />. Inorganic N is usually used for metabolic synthesis in Arabidopsis under light, but organic N is usually used for long-distance transport and substance storage under dark conditions <ref name="ref10" />. Therefore, OsPTR9 might also be an organic N transporter. Similar to AMT1;3 <ref name="ref11" />, but different from other inorganic N transporters, OsPTR9 expression also affected root growth. The expression of OsPTR9 was repressed during N starvation and induced by ammonium, similar to the expression induction of the ammonium transporter OsAMT1;2 <ref name="ref12" />. The regulation of OsPTR9-expression by N sources and light/dark changes shows that there are common feedback regulatory pathways for C/N balance in rice, similar to reports from studies of Arabidopsis <ref name="ref13" /><ref name="ref14" />.
[[File: Shijc-Os06g0706400-Fig2.png|right|thumb|200px|'' Root architecture is affected by altered expression of OsPTR9. (from reference <ref name="ref1" />).'']]
'''The effect of OsPTR9 on the development of roots and stems may contribute to nutrient uptake and allocation'''

Biomass and photosynthesis rate differed most between altered-OsPTR9 expressing plants and the wild type, when ammonium or nitrate was the sole N source other than nitrate. Ammonium is the preferred N species taken up by rice <ref name="ref15" />. Root development is strongly affected by the plant's nutritional status and by the external availability of nutrients <ref name="ref16" /><ref name="ref17" />. Ammonium is complementary to nitrate in shaping lateral root development and, in Arabidopsis, the stimulation of lateral root branching by ammonium occurs in an AMT1;3-dependent manner <ref name="ref11" />. Increased expression of OsPTR9 promoted the growth of lateral roots, while a lower number of lateral roots were found in the osptr9 mutant and the OsPTR9-RNAi lines, suggesting that OsPTR9 contributes to ammonium-stimulated lateral root branching. In maize seedlings, the time required for the entire cap to be displaced by a new set of cells ranges from 24 h to 7 days, depending on growth conditions <ref name="ref18" />. Abnormal cell displacement of the root cap in the osptr9 mutant and the OsPTR9-RNAi lines might block root growth into soil, while the thickened cell wall of the osptr9 mutant and the OsPTR9-RNAi lines may hinder lateral root formation leading to reduced root surface area for N uptake. Dense cytoplasm accumulated in the cortical fibre cells of the OsPTR9-RNAi lines and the osptr9 mutant, which might suggest a transportation obstacle due to the down-expression of OsPTR9 leading to cytoplasm accumulation in cells on the outside of the cortex.
Rice roots in paddy soil prefer ammonium as the N source <ref name="ref15" />, and the major N forms in the xylem sap of rice plants are Gln and Asn <ref name="ref19" />. Down-regulation of OsPTR9 expression caused decreased concentrations of some amino acids in roots and leaves, while many amino acids accumulated in stems. These might be caused by the abnormal development of the stem, which resulted in short and slim plants, and a reduced and disordered arrangement of the outer vascular bundle. These may, finally, block N translocation from source organs (leaves and roots) to sink (seed) resulting in nutrient accumulation in the stems and a reduced number of filled seeds. Generally, N partitioning to leaves positively regulates photosynthesis and consequently improves allocation of carbohydrates to sink tissues for vegetative and reproductive growth <ref name="ref20" />. The changed levels and partitioning of amino acids and proteins might lead to the observed growth effects and reduced N translocation to seeds.

'''N recycling from leaves is important for increased grain yields in OsPTR9-over-expressing plants'''

The leaves are sinks for N during the vegetative stage; subsequently, this N is remobilized to the developing seeds. Up to 80% of grain N contents are derived from leaves in rice and wheat <ref name="ref21" /> <ref name="ref22" /> <ref name="ref23" />. The high transport rate of amino acids is an essential prerequisite for seed development. Down-regulation of OsPTR9 resulted in higher concentrations of amino acids in the stems, suggesting that OsPTR9 directly or indirectly affected the transport of amino acids to seeds. Over-expression of OsPTR9 also promoted ammonium uptake, which might be the reason for the up-regulation of OsAMT1;2 expression in the OsPTR9-over-expressing lines, as OsAMT1;2 expression was shown to be induced by ammonium <ref name="ref12" />.

===Mutation===
[[File: Shijc-Os06g0706400-Fig3.png|right|thumb|200px|'' Phenotypes of rice plants with altered expression of OsPTR9. (from reference <ref name="ref1" />).'']]
An OsPTR9 T-DNA insertion mutant (04Z11AH79, osptr9) was obtained from the Rice Mutant Database at Huazhong Agricultural University, China (http://rmd.ncpgr.cn/). One T-DNA copy was inserted in the first exon of OsPTR9, that is, 521 nucleotides downstream of the start codon of the OsPTR9 gene, as verified by sequencing the flanking region. The homozygous mutant (osptr9) was screened and used for analysis. RT-PCR analysis revealed that OsPTR9 mRNA is absent in the osptr9 at both day and night. OsPTR9-RNAi transgenic rice plants (RNAi) were generated under control of the rice Ubi-1 promoter <ref name="ref24" />. Nine independent OsPTR9-RNAi lines were obtained, 3 of which showed very low OsPTR9 transcript levels in panicles. To address the effect of increased OsPTR9 expression, OsPTR9 over-expressing (OE) rice was constructed under the control of the 35S promoter <ref name="ref25" />. Three of 11 independent OE lines were obtained that accumulated large amounts of OsPTR9 transcripts.

===Expression===
[[File: Shijc-Os06g0706400-Fig4.png|right|thumb|200px|'' Subcellular localization of OsPTR9-eGFP fusion protein. (from reference <ref name="ref1" />).'']]
OsPTR9 (LOC_06g49250) is most closely related to the members of subgroup II of the PTR/NRT1 family, containing the Arabidopsis di/tripeptide transporter AtPTR2 (At2g02040) <ref name="ref7" />. The OsPTR9 mRNA (AK064899) encodes a protein with the domain (LGTGGIKPXV) characteristic of the PTR proteins <ref name="ref26" /> <ref name="ref27" />. Transient expression of 35S:OsPTR9-eGFP in onion epidermal cells resulted in green fluorescence at the periphery of the cells, outside of the nucleus. In addition, stable expression of 35S:OsPTR9-eGFP in plasmolysed root cells of tobacco and roots of rice showed OsPTR9-eGFP localized to the plasma membrane.
[[File: Shijc-Os06g0706400-Fig5.png|right|thumb|200px|'' Expression analysis of OsPTR9. (from reference <ref name="ref1" />).'']]
In roots, GUS staining was mainly observed in young main root tips and in the cortical fibre cells of lateral roots. Furthermore, OsPTR9 expression was higher in leaves and panicles than in roots and stems.
[[File: Shijc-Os06g0706400-Fig6.png|right|thumb|200px|'' OsPTR9 expression is regulated by light and N source. (from reference <ref name="ref1" />).'']]
Higher transcript levels of OsPTR9 were observed where inorganic N (NO3−, NH4+ or NH4NO3) was the sole N source, compared with organic or mixed N sources (peptone or NH4NO3 + peptone). Preliminary experiments showed that the osptr9 mutant was more seriously affected by growth on ammonium than on nitrate (data not shown), and OsPTR9 expression was induced by both low (0.5 mm) and high (5 mm) ammonium sulphate levels. The induction of OsPTR9 expression by NH4+ occurred later than that of the ammonium transporter (OsAMT1;2).

==Labs working on this gene==
1. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
2. University of Chinese Academy of Sciences, Beijing, China
3. Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
4. Institute of Plant Sciences, University of Bern, Bern, Switzerland
5. Wuhan Bioengineering Institute, Wuhan, China

==References==
<references>
<ref name="ref1">Fang, Z., Xia, K., Yang, X., Grotemeyer, M.S., Meier, S., Rentsch, D., Xu, X., Zhang, M. (2012) Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. Plant Biotechnol. J doi: 10.1111/pbi.12031 </ref>
<ref name="ref2">Weichert, A., Brinkmann, C., Komarova, N.Y., Dietrich, D., Thor, K., Meier, S., Grotemeyer, M.S. and Rentsch, D. (2012) AtPTR4 and AtPTR6 are differentially expressed, tonoplast-localized members of the peptide transporter/nitrate transporter 1 (PTR/NRT1) family. Planta, 235, 311–323. </ref>
<ref name="ref3">Chiang, C.S., Stacey, G. and Tsay, Y.F. (2004) Mechanisms and functional properties of two peptide transporters, AtPTR2 and fPTR2. J. Biol. Chem. 279, 30150–30157. </ref>
<ref name="ref4">Kanno, Y., Hanada, A., Chiba, Y., Ichikawa, T., Nakazawa, M., Matsui, M., Koshiba, T., Kamiya, Y. and Seo, M. (2012) Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor. Proc. Natl Acad. Sci. USA, 109, 9653–9658. </ref>
<ref name="ref5">Krouk, G., Lacombe, B. and Bielach, A. (2010) Nitrate-regulated auxin transport by NRT1. 1 defines a mechanism for nutrient sensing in plants. Dev. Cell, 18, 927–937. </ref>
<ref name="ref6">Nour-Eldin, H.H., Andersen, T.G., Burow, M., Madsen, S.R., Jorgensen, M.E., Olsen, C.E., Dreyer, I., Hedrich, R., Geiger, D. and Halkier, B.A. (2012) NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds. Nature, 488, 531–534. </ref>
<ref name="ref7">Tsay, Y.F., Chiu, C.C., Tsai, C.B., Ho, C.H. and Hsu, P.K. (2007) Nitrate transporters and peptide transporters. FEBS Lett. 581, 2290–2300. </ref>
<ref name="ref8">Delhon, P., Gojon, A., Tillard, P. and Passama, L. (1995) Diurnal regulation of NO3− uptake in soybean plants I. Changes in NO3− influx, efflux, and N utilization in the plant during the day/night cycle. J. Exp. Bot. 46, 1585–1594. </ref>
<ref name="ref9">Gazzarrini, S., Lejay, L., Gojon, A., Ninnemann, O., Frommer, W.B. and von Wirén, N. (1999) Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots. Plant Cell, 11, 937–948. </ref>
<ref name="ref10">Lam, H.M., Coschigano, K., Schultz, C., Melo-Oliveira, R., Tjaden, G., Oliveira, I., Ngai, N., Hsieh, M.H. and Coruzzi, G. (1995) Use of Arabidopsis mutants and genes to study amide amino acid biosynthesis. Plant Cell, 7, 887–898. </ref>
<ref name="ref11">Lima, J.E., Kojima, S., Takahashi, H. and Wirén, N.V. (2010) Ammonium triggers lateral root branching in Arabidopsis in an ammonium transporter 1;3-dependent manner. Plant Cell, 22, 3621–3633. </ref>
<ref name="ref12">Sonoda, Y., Ikeda, A., Saiki, S., von Wirén, N., Yamaya, T. and Yamaguchi, J. (2003) Distinct expression and function of three ammonium transporter Genes (OsAMT1;1-1;3) in rice. Plant Cell Physiol. 44, 726–734. </ref>
<ref name="ref13">Gazzarrini, S., Lejay, L., Gojon, A., Ninnemann, O., Frommer, W.B. and von Wirén, N. (1999) Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots. Plant Cell, 11, 937–948. </ref>
<ref name="ref14">Girin, T., Lejay, L., Wirth, J., Widiez, T., Palenchar, P.M., Nazoa, P., Touraine, B., Gojon, A. and Lepetit, M. (2007) Identification of a 150 bp cis-acting element of the AtNRT2.1 promoter involved in the regulation of gene expression by the N and C status of the plant. Plant Cell Env. 30, 1366–1380. </ref>
<ref name="ref15">Sasakawa, H. and Yamamoto, Y. (1978) Comparison of the uptake of nitrate and ammonium by rice seedlings. Plant Physiol. 62, 665–669. </ref>
<ref name="ref16">Bucio, J.L., Ramirez, A.C. and Estrella, L.H. (2003) The role of nutrient availability in regulating root architecture. Curr. Opin. Plant Biol. 6, 280–287. </ref>
<ref name="ref17">Forde, B. and Lorenzo, H. (2001) The nutritional control of root development. Plant Soil, 232, 51–68. </ref>
<ref name="ref18">Barlow, P.W. (1978) Cell displacement through the columella of the root cap of Zea mays L. Ann. Bot. 42, 783–790. </ref>
<ref name="ref19">Williams, L. and Miller, A. (2001) Transporters responsible for the uptake and partitioning of nitrogenous solutes. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52, 659–688.</ref>
<ref name="ref20">Zhang, L.Z., Tan, Q.M., Lee, R., Trethewy, A., Lee, Y.H. and Tegeder, M. (2010) Altered xylem-phloem transfer of amino acids affects metabolism and leads to increased seed yield and oil content in Arabidopsis. Plant Cell, 22, 3603–3620. </ref>
<ref name="ref21">Kichey, T., Hirel, B., Heumez, E., Dubois, F. and Le Gouis, J. (2007) In winter wheat (Triticum aestivum L.), post-anthesis nitrogen uptake and remobilisation to the grain correlates with agronomic traits and nitrogen physiological markers. Field Crop. Res. 102, 22–32. </ref>
<ref name="ref22">Mae, T. and Ohira, K. (1981) The remobilization of nitrogen related to leaf growth and senescence in rice plants (Oryza sativa L.). Plant Cell Physiol. 22, 1067–1074. </ref>
<ref name="ref23">Tabuchi, M., Abiko, T. and Yamaya, T. (2007) Assimilation of ammonium ions an reutilization of nitrogen in rice (Oryza sativa L.). J. Exp. Bot. 58, 2319–2327. </ref>
<ref name="ref24">Wang, Z., Chen, C.B., Xu, Y.Y., Jiang, R.X., Han, Y., Xu, Z.H. and Chong, K. (2004) A practical vector for efficient knockdown of gene expression in rice (Oryza sativa L.). Plant Mol. Biol. Rep. 22, 409–417. </ref>
<ref name="ref25">Zhang, W., McElroy, D. and Wu, R. (1991) Analysis of rice Act1 5[prime] region activity in transgenic rice plants. Plant Cell, 3, 1155–1165. </ref>
<ref name="ref26">Dietrich, D., Hammes, U., Thor, K., Suter-Grotemeyer, M., Fluckiger, R., Slusarenko, A.J., Ward, J.M. and Rentsch, D. (2004) AtPTR1, a plasma membrane peptide transporter expressed during seed germination and in vascular tissue of Arabidopsis. Plant J. 40, 488–499. </ref>
<ref name="ref27">Fei, Y.J., Ganapathy, V. and Leibach, F.H. (1998) Molecular and structural features of the proton-coupled oligopeptide transporter superfamily. Prog. Nucleic Acid Res. Mol. Biol. 58, 239–261. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0706400|
Description = Similar to Peptide transporter PTR2-B (Histidine transporting protein)|
Version = NM_001188057.1 GI:297725244 GeneID:9268091|
Length = 2951 bp|
Definition = Oryza sativa Japonica Group Os06g0706400, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:30715316..30718266|
CDS = 30715362..30715418,30715623..30715722,30715952..30716253|
GCID = <gbrowseImage1>
name=NC_008399:30715316..30718266
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:30715316..30718266
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgtccacggacactgagcagcaggaacacgcagtggcgctgctacaacccgaggttgaagaagcatacaccactgatgggtctcttggcgtcgatggcaacccggcgctgaagcatcgcacaggcggatggatggcatgccgcccgattcttggcaccgagttctgctactgcctggcctactacggcatcacgttcaacctcgtcacctacctcaccgccgagctgcaccagagcaacgtcgccgccgccaacaacgtgtcgacgtggcaggccacctgcttcctcacgccgctggccggagccgtcgccgccgattcctactggggaaggtaccgcaccatggtcgtcagctgctgcatcggcgtcgctgttagtcccctccatttcattcgatccgggttgtgtttagttccaaattttttttttcaaacttctaactttccatcacattaa</cdnaseq>|
AA = <aaseq>MASTDTEQQEHAVALLQPEVEEAYTTDGSLGVDGNPALKHRTGG WMACRPILGTEFCYCLAYYGITFNLVTYLTAELHQSNVAAANNVSTWQATCFLTPLAG AVAADSYWGRYRTMVVSCCIGVAVSPLHFIRSGLCLVPNFFFQTSNFPSH</aaseq>|
DNA = <dnaseqindica>47..103#308..407#637..938#gattagcttgtacagtttgtcctcgagctctcgaccggctccggcaatggcgtccacggacactgagcagcaggaacacgcagtggcgctgctacaacccgaggtaattaattaatcgctgttcataatctccttactgctagccttatgccgatttccacgatgcagtttgtttaatttctcatcagtttccctgcagaaaaatattgattgagccttgcctgaactagctactcctagttaatttgaagcagccgctcatggatacgttcagtgctaactaggctggggattttggttgctgcaggttgaagaagcatacaccactgatgggtctcttggcgtcgatggcaacccggcgctgaagcatcgcacaggcggatggatggcatgccgcccgattcttggtaataaacttcattagatatccctgcagctctattaattatttcctaaccttttttacttgccaattttttgatgattaatgtgtctctcactttgtgtgttcttgttccaaaaaagaaaaaaatgaaaaaaaaaataaatgaggaacttctttgttgatgtggttatctgagctatgacaacactgaggagagatgcttattctgcttgctttgtgattgtggataggcaccgagttctgctactgcctggcctactacggcatcacgttcaacctcgtcacctacctcaccgccgagctgcaccagagcaacgtcgccgccgccaacaacgtgtcgacgtggcaggccacctgcttcctcacgccgctggccggagccgtcgccgccgattcctactggggaaggtaccgcaccatggtcgtcagctgctgcatcggcgtcgctgttagtcccctccatttcattcgatccgggttgtgtttagttccaaattttttttttcaaacttctaactttccatcacattaaatttttcatacacacaatttttttcagtcacgtcgtcttcaatttcaaccaaaatctaaactttataccaatctaaacacagccttaattagaattagtcactgtgtccttcctgccgtgaatttatggctgatggcaagtaatcagtcactgtgtgggatgtggatttttatcccttgagagaacatttaattttatattaatattaatttatgttaatttatgttgtcatttaattttatattttatattaatttatgttgtccattttttttaatttttttatgactaattagttggcatggatgaaacgagggatatttcctggagggatgaaatcactttccccactgtgtgctgccatgaatgcaaatccaatcagcttcatggctgtacgtacctaatctgtggtgcagggcatgctcatggcggctctgtcggcgcttctgccgctgctgatcaaggacacgtcgtccatggcttcagctcaagtgatcatcctgtttcttggcctgtacatgatcgcatttggggtgggtggtctccggccgtgcctgatgtccttcggcgccgaccagttcgacgacggcgacacgtcggagcgcatcagcaagggctcctacttcaactggtacatcttcaccatgaactgcgcgtccgtgatatccaccaccgccatggtgtgggtgcaagaccactacgggtgggcattggggttggggattccggcgatggtcctcgccgtcgggctctcctgccttgtcgccgcgtctcgggcgtacaggtttcagacaacccgcggtagcccgctcaccagagtctgccaggtcgtcgtcgccgccgtccgcaagttcaacgtcgcgccgccggccgacatggcccttctctacgacctatcggaggatgcctcctccatgaagggagttcagaggatcgagcacaccgccgatctccggtcagttcatgtctctcgttgcatctggtgtttgtgatgctgtaggtgtaatgtaattggctaattcttgagatgcaactgctcgatcagattcttcgacaaggccgccgtcgtgacggcgtcggacgaggaggcggagggcgccgcgccgcgcaatccatggaggctttgcgtggtgacgcaggtggaggagctcaagattctcgtcaggatgctgcccctgtgggcgtgcgtcgccttctactacaccgcgacggcgcaggccaattcgacgttcgtcgagcagggcatggcgatggacacgcgcgtcggctccttccacgtcccgccggcatccctggccaccttccagatcatcaccacgatcgtgttgatcccgctgtacgaccgcgcgttcgtgccggcggcgaggaggctgacggggagagagaagggcatctccgaccttctcaggatcggcggcggcctcgccatggccgcgctcgccatggccgcggcggcgctggtcgagacgaggcgcgcccgcgcggcgcacgccgggatggagccgacgagcatcctgtggcaggcgccgcagtacgtgctggtgggcgtcggcgagctgctcgccaccgtggggcagctggacttcttctacagccaggcgccgccggccatgaagacggtgtgcacggcgctcgggttcatctccgtcgcggcgggggagtacctgagctcgctcgtcgtgacggccgtgtcgtgggcgacggcgaccggcggccggccggggtggatccccgacgacctcaacgaggggcacctgatcgcttcttctggatgatggctgggctcggttgcctcaatcttgtggtgtttacgagctgtgccatgaggtacaaatccaggaaggcctgttgatacttctgggcttgtttggtaggctcgaaattccggcccatgcactctgacgggccattatgtatgggaataagtccatccgacctccctcatctcttgcacttggtcgaatcgcatccctcagccgcaaaaaactgggtaaaacgcctcctgaatctccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188057.1 RefSeq:Os06g0706400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0706400

2014-12-30T16:49:33Z

Shijc:

OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os06g0706400-Fig1.png|right|thumb|200px|'' The effect of OsPTR9 on the formation of roots. (from reference <ref name="ref1" />).'']]
'''OsPTR9 expression is regulated by light and N source'''
OsPTR9 is closely related to the functional di/tripeptide transporters <ref name="ref2" /> and is localized at the plasma membrane. Members of the PTR/NRT1 family transport a wide range of substrates, including di/tripeptides, nitrate, histidine, carboxylates, other N-containing compounds such as IAA-amino acid conjugates, ABA, glutathione, and even the defence compound glucosinolate, and other substrate compounds might be identified <ref name="ref3" /><ref name="ref4" /><ref name="ref5" /><ref name="ref6" /><ref name="ref7" /><ref name="ref2" />.
OsPTR9 was found to be expressed in all organs analysed, but expression levels varied. The expression of OsPTR9 was high at night and low during the light period, which is different than the expression patterns of many ammonium and nitrate transporter genes <ref name="ref8" /><ref name="ref9" />. Inorganic N is usually used for metabolic synthesis in Arabidopsis under light, but organic N is usually used for long-distance transport and substance storage under dark conditions <ref name="ref10" />. Therefore, OsPTR9 might also be an organic N transporter. Similar to AMT1;3 <ref name="ref11" />, but different from other inorganic N transporters, OsPTR9 expression also affected root growth. The expression of OsPTR9 was repressed during N starvation and induced by ammonium, similar to the expression induction of the ammonium transporter OsAMT1;2 <ref name="ref12" />. The regulation of OsPTR9-expression by N sources and light/dark changes shows that there are common feedback regulatory pathways for C/N balance in rice, similar to reports from studies of Arabidopsis <ref name="ref13" /><ref name="ref14" />.
[[File: Shijc-Os06g0706400-Fig2.png|right|thumb|200px|'' Root architecture is affected by altered expression of OsPTR9. (from reference <ref name="ref1" />).'']]
'''The effect of OsPTR9 on the development of roots and stems may contribute to nutrient uptake and allocation'''
Biomass and photosynthesis rate differed most between altered-OsPTR9 expressing plants and the wild type, when ammonium or nitrate was the sole N source other than nitrate. Ammonium is the preferred N species taken up by rice <ref name="ref15" />. Root development is strongly affected by the plant's nutritional status and by the external availability of nutrients <ref name="ref16" /><ref name="ref17" />. Ammonium is complementary to nitrate in shaping lateral root development and, in Arabidopsis, the stimulation of lateral root branching by ammonium occurs in an AMT1;3-dependent manner <ref name="ref11" />. Increased expression of OsPTR9 promoted the growth of lateral roots, while a lower number of lateral roots were found in the osptr9 mutant and the OsPTR9-RNAi lines, suggesting that OsPTR9 contributes to ammonium-stimulated lateral root branching. In maize seedlings, the time required for the entire cap to be displaced by a new set of cells ranges from 24 h to 7 days, depending on growth conditions <ref name="ref18" />. Abnormal cell displacement of the root cap in the osptr9 mutant and the OsPTR9-RNAi lines might block root growth into soil, while the thickened cell wall of the osptr9 mutant and the OsPTR9-RNAi lines may hinder lateral root formation leading to reduced root surface area for N uptake. Dense cytoplasm accumulated in the cortical fibre cells of the OsPTR9-RNAi lines and the osptr9 mutant, which might suggest a transportation obstacle due to the down-expression of OsPTR9 leading to cytoplasm accumulation in cells on the outside of the cortex.
Rice roots in paddy soil prefer ammonium as the N source <ref name="ref15" />, and the major N forms in the xylem sap of rice plants are Gln and Asn <ref name="ref19" />. Down-regulation of OsPTR9 expression caused decreased concentrations of some amino acids in roots and leaves, while many amino acids accumulated in stems. These might be caused by the abnormal development of the stem, which resulted in short and slim plants, and a reduced and disordered arrangement of the outer vascular bundle. These may, finally, block N translocation from source organs (leaves and roots) to sink (seed) resulting in nutrient accumulation in the stems and a reduced number of filled seeds. Generally, N partitioning to leaves positively regulates photosynthesis and consequently improves allocation of carbohydrates to sink tissues for vegetative and reproductive growth <ref name="ref20" />. The changed levels and partitioning of amino acids and proteins might lead to the observed growth effects and reduced N translocation to seeds.

'''N recycling from leaves is important for increased grain yields in OsPTR9-over-expressing plants'''
The leaves are sinks for N during the vegetative stage; subsequently, this N is remobilized to the developing seeds. Up to 80% of grain N contents are derived from leaves in rice and wheat <ref name="ref21" /> <ref name="ref22" /> <ref name="ref23" />. The high transport rate of amino acids is an essential prerequisite for seed development. Down-regulation of OsPTR9 resulted in higher concentrations of amino acids in the stems, suggesting that OsPTR9 directly or indirectly affected the transport of amino acids to seeds. Over-expression of OsPTR9 also promoted ammonium uptake, which might be the reason for the up-regulation of OsAMT1;2 expression in the OsPTR9-over-expressing lines, as OsAMT1;2 expression was shown to be induced by ammonium <ref name="ref12" />.

===Mutation===
[[File: Shijc-Os06g0706400-Fig3.png|right|thumb|200px|'' Phenotypes of rice plants with altered expression of OsPTR9. (from reference <ref name="ref1" />).'']]
An OsPTR9 T-DNA insertion mutant (04Z11AH79, osptr9) was obtained from the Rice Mutant Database at Huazhong Agricultural University, China (http://rmd.ncpgr.cn/). One T-DNA copy was inserted in the first exon of OsPTR9, that is, 521 nucleotides downstream of the start codon of the OsPTR9 gene, as verified by sequencing the flanking region. The homozygous mutant (osptr9) was screened and used for analysis. RT-PCR analysis revealed that OsPTR9 mRNA is absent in the osptr9 at both day and night. OsPTR9-RNAi transgenic rice plants (RNAi) were generated under control of the rice Ubi-1 promoter <ref name="ref24" />. Nine independent OsPTR9-RNAi lines were obtained, 3 of which showed very low OsPTR9 transcript levels in panicles. To address the effect of increased OsPTR9 expression, OsPTR9 over-expressing (OE) rice was constructed under the control of the 35S promoter <ref name="ref25" />. Three of 11 independent OE lines were obtained that accumulated large amounts of OsPTR9 transcripts.

===Expression===
[[File: Shijc-Os06g0706400-Fig4.png|right|thumb|200px|'' Subcellular localization of OsPTR9-eGFP fusion protein. (from reference <ref name="ref1" />).'']]
OsPTR9 (LOC_06g49250) is most closely related to the members of subgroup II of the PTR/NRT1 family, containing the Arabidopsis di/tripeptide transporter AtPTR2 (At2g02040) <ref name="ref7" />. The OsPTR9 mRNA (AK064899) encodes a protein with the domain (LGTGGIKPXV) characteristic of the PTR proteins <ref name="ref26" /> <ref name="ref27" />. Transient expression of 35S:OsPTR9-eGFP in onion epidermal cells resulted in green fluorescence at the periphery of the cells, outside of the nucleus. In addition, stable expression of 35S:OsPTR9-eGFP in plasmolysed root cells of tobacco and roots of rice showed OsPTR9-eGFP localized to the plasma membrane.
[[File: Shijc-Os06g0706400-Fig5.png|right|thumb|200px|'' Expression analysis of OsPTR9. (from reference <ref name="ref1" />).'']]
In roots, GUS staining was mainly observed in young main root tips and in the cortical fibre cells of lateral roots. Furthermore, OsPTR9 expression was higher in leaves and panicles than in roots and stems.
[[File: Shijc-Os06g0706400-Fig6.png|right|thumb|200px|'' OsPTR9 expression is regulated by light and N source. (from reference <ref name="ref1" />).'']]
Higher transcript levels of OsPTR9 were observed where inorganic N (NO3−, NH4+ or NH4NO3) was the sole N source, compared with organic or mixed N sources (peptone or NH4NO3 + peptone). Preliminary experiments showed that the osptr9 mutant was more seriously affected by growth on ammonium than on nitrate (data not shown), and OsPTR9 expression was induced by both low (0.5 mm) and high (5 mm) ammonium sulphate levels. The induction of OsPTR9 expression by NH4+ occurred later than that of the ammonium transporter (OsAMT1;2).

==Labs working on this gene==
1. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
2. University of Chinese Academy of Sciences, Beijing, China
3. Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
4. Institute of Plant Sciences, University of Bern, Bern, Switzerland
5. Wuhan Bioengineering Institute, Wuhan, China

==References==
<references>
<ref name="ref1">Fang, Z., Xia, K., Yang, X., Grotemeyer, M.S., Meier, S., Rentsch, D., Xu, X., Zhang, M. (2012) Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. Plant Biotechnol. J doi: 10.1111/pbi.12031 </ref>
<ref name="ref2">Weichert, A., Brinkmann, C., Komarova, N.Y., Dietrich, D., Thor, K., Meier, S., Grotemeyer, M.S. and Rentsch, D. (2012) AtPTR4 and AtPTR6 are differentially expressed, tonoplast-localized members of the peptide transporter/nitrate transporter 1 (PTR/NRT1) family. Planta, 235, 311–323. </ref>
<ref name="ref3">Chiang, C.S., Stacey, G. and Tsay, Y.F. (2004) Mechanisms and functional properties of two peptide transporters, AtPTR2 and fPTR2. J. Biol. Chem. 279, 30150–30157. </ref>
<ref name="ref4">Kanno, Y., Hanada, A., Chiba, Y., Ichikawa, T., Nakazawa, M., Matsui, M., Koshiba, T., Kamiya, Y. and Seo, M. (2012) Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor. Proc. Natl Acad. Sci. USA, 109, 9653–9658. </ref>
<ref name="ref5">Krouk, G., Lacombe, B. and Bielach, A. (2010) Nitrate-regulated auxin transport by NRT1. 1 defines a mechanism for nutrient sensing in plants. Dev. Cell, 18, 927–937. </ref>
<ref name="ref6">Nour-Eldin, H.H., Andersen, T.G., Burow, M., Madsen, S.R., Jorgensen, M.E., Olsen, C.E., Dreyer, I., Hedrich, R., Geiger, D. and Halkier, B.A. (2012) NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds. Nature, 488, 531–534. </ref>
<ref name="ref7">Tsay, Y.F., Chiu, C.C., Tsai, C.B., Ho, C.H. and Hsu, P.K. (2007) Nitrate transporters and peptide transporters. FEBS Lett. 581, 2290–2300. </ref>
<ref name="ref8">Delhon, P., Gojon, A., Tillard, P. and Passama, L. (1995) Diurnal regulation of NO3− uptake in soybean plants I. Changes in NO3− influx, efflux, and N utilization in the plant during the day/night cycle. J. Exp. Bot. 46, 1585–1594. </ref>
<ref name="ref9">Gazzarrini, S., Lejay, L., Gojon, A., Ninnemann, O., Frommer, W.B. and von Wirén, N. (1999) Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots. Plant Cell, 11, 937–948. </ref>
<ref name="ref10">Lam, H.M., Coschigano, K., Schultz, C., Melo-Oliveira, R., Tjaden, G., Oliveira, I., Ngai, N., Hsieh, M.H. and Coruzzi, G. (1995) Use of Arabidopsis mutants and genes to study amide amino acid biosynthesis. Plant Cell, 7, 887–898. </ref>
<ref name="ref11">Lima, J.E., Kojima, S., Takahashi, H. and Wirén, N.V. (2010) Ammonium triggers lateral root branching in Arabidopsis in an ammonium transporter 1;3-dependent manner. Plant Cell, 22, 3621–3633. </ref>
<ref name="ref12">Sonoda, Y., Ikeda, A., Saiki, S., von Wirén, N., Yamaya, T. and Yamaguchi, J. (2003) Distinct expression and function of three ammonium transporter Genes (OsAMT1;1-1;3) in rice. Plant Cell Physiol. 44, 726–734. </ref>
<ref name="ref13">Gazzarrini, S., Lejay, L., Gojon, A., Ninnemann, O., Frommer, W.B. and von Wirén, N. (1999) Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots. Plant Cell, 11, 937–948. </ref>
<ref name="ref14">Girin, T., Lejay, L., Wirth, J., Widiez, T., Palenchar, P.M., Nazoa, P., Touraine, B., Gojon, A. and Lepetit, M. (2007) Identification of a 150 bp cis-acting element of the AtNRT2.1 promoter involved in the regulation of gene expression by the N and C status of the plant. Plant Cell Env. 30, 1366–1380. </ref>
<ref name="ref15">Sasakawa, H. and Yamamoto, Y. (1978) Comparison of the uptake of nitrate and ammonium by rice seedlings. Plant Physiol. 62, 665–669. </ref>
<ref name="ref16">Bucio, J.L., Ramirez, A.C. and Estrella, L.H. (2003) The role of nutrient availability in regulating root architecture. Curr. Opin. Plant Biol. 6, 280–287. </ref>
<ref name="ref17">Forde, B. and Lorenzo, H. (2001) The nutritional control of root development. Plant Soil, 232, 51–68. </ref>
<ref name="ref18">Barlow, P.W. (1978) Cell displacement through the columella of the root cap of Zea mays L. Ann. Bot. 42, 783–790. </ref>
<ref name="ref19">Williams, L. and Miller, A. (2001) Transporters responsible for the uptake and partitioning of nitrogenous solutes. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52, 659–688.</ref>
<ref name="ref20">Zhang, L.Z., Tan, Q.M., Lee, R., Trethewy, A., Lee, Y.H. and Tegeder, M. (2010) Altered xylem-phloem transfer of amino acids affects metabolism and leads to increased seed yield and oil content in Arabidopsis. Plant Cell, 22, 3603–3620. </ref>
<ref name="ref21">Kichey, T., Hirel, B., Heumez, E., Dubois, F. and Le Gouis, J. (2007) In winter wheat (Triticum aestivum L.), post-anthesis nitrogen uptake and remobilisation to the grain correlates with agronomic traits and nitrogen physiological markers. Field Crop. Res. 102, 22–32. </ref>
<ref name="ref22">Mae, T. and Ohira, K. (1981) The remobilization of nitrogen related to leaf growth and senescence in rice plants (Oryza sativa L.). Plant Cell Physiol. 22, 1067–1074. </ref>
<ref name="ref23">Tabuchi, M., Abiko, T. and Yamaya, T. (2007) Assimilation of ammonium ions an reutilization of nitrogen in rice (Oryza sativa L.). J. Exp. Bot. 58, 2319–2327. </ref>
<ref name="ref24">Wang, Z., Chen, C.B., Xu, Y.Y., Jiang, R.X., Han, Y., Xu, Z.H. and Chong, K. (2004) A practical vector for efficient knockdown of gene expression in rice (Oryza sativa L.). Plant Mol. Biol. Rep. 22, 409–417. </ref>
<ref name="ref25">Zhang, W., McElroy, D. and Wu, R. (1991) Analysis of rice Act1 5[prime] region activity in transgenic rice plants. Plant Cell, 3, 1155–1165. </ref>
<ref name="ref26">Dietrich, D., Hammes, U., Thor, K., Suter-Grotemeyer, M., Fluckiger, R., Slusarenko, A.J., Ward, J.M. and Rentsch, D. (2004) AtPTR1, a plasma membrane peptide transporter expressed during seed germination and in vascular tissue of Arabidopsis. Plant J. 40, 488–499. </ref>
<ref name="ref27">Fei, Y.J., Ganapathy, V. and Leibach, F.H. (1998) Molecular and structural features of the proton-coupled oligopeptide transporter superfamily. Prog. Nucleic Acid Res. Mol. Biol. 58, 239–261. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0706400|
Description = Similar to Peptide transporter PTR2-B (Histidine transporting protein)|
Version = NM_001188057.1 GI:297725244 GeneID:9268091|
Length = 2951 bp|
Definition = Oryza sativa Japonica Group Os06g0706400, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:30715316..30718266|
CDS = 30715362..30715418,30715623..30715722,30715952..30716253|
GCID = <gbrowseImage1>
name=NC_008399:30715316..30718266
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:30715316..30718266
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgtccacggacactgagcagcaggaacacgcagtggcgctgctacaacccgaggttgaagaagcatacaccactgatgggtctcttggcgtcgatggcaacccggcgctgaagcatcgcacaggcggatggatggcatgccgcccgattcttggcaccgagttctgctactgcctggcctactacggcatcacgttcaacctcgtcacctacctcaccgccgagctgcaccagagcaacgtcgccgccgccaacaacgtgtcgacgtggcaggccacctgcttcctcacgccgctggccggagccgtcgccgccgattcctactggggaaggtaccgcaccatggtcgtcagctgctgcatcggcgtcgctgttagtcccctccatttcattcgatccgggttgtgtttagttccaaattttttttttcaaacttctaactttccatcacattaa</cdnaseq>|
AA = <aaseq>MASTDTEQQEHAVALLQPEVEEAYTTDGSLGVDGNPALKHRTGG WMACRPILGTEFCYCLAYYGITFNLVTYLTAELHQSNVAAANNVSTWQATCFLTPLAG AVAADSYWGRYRTMVVSCCIGVAVSPLHFIRSGLCLVPNFFFQTSNFPSH</aaseq>|
DNA = <dnaseqindica>47..103#308..407#637..938#gattagcttgtacagtttgtcctcgagctctcgaccggctccggcaatggcgtccacggacactgagcagcaggaacacgcagtggcgctgctacaacccgaggtaattaattaatcgctgttcataatctccttactgctagccttatgccgatttccacgatgcagtttgtttaatttctcatcagtttccctgcagaaaaatattgattgagccttgcctgaactagctactcctagttaatttgaagcagccgctcatggatacgttcagtgctaactaggctggggattttggttgctgcaggttgaagaagcatacaccactgatgggtctcttggcgtcgatggcaacccggcgctgaagcatcgcacaggcggatggatggcatgccgcccgattcttggtaataaacttcattagatatccctgcagctctattaattatttcctaaccttttttacttgccaattttttgatgattaatgtgtctctcactttgtgtgttcttgttccaaaaaagaaaaaaatgaaaaaaaaaataaatgaggaacttctttgttgatgtggttatctgagctatgacaacactgaggagagatgcttattctgcttgctttgtgattgtggataggcaccgagttctgctactgcctggcctactacggcatcacgttcaacctcgtcacctacctcaccgccgagctgcaccagagcaacgtcgccgccgccaacaacgtgtcgacgtggcaggccacctgcttcctcacgccgctggccggagccgtcgccgccgattcctactggggaaggtaccgcaccatggtcgtcagctgctgcatcggcgtcgctgttagtcccctccatttcattcgatccgggttgtgtttagttccaaattttttttttcaaacttctaactttccatcacattaaatttttcatacacacaatttttttcagtcacgtcgtcttcaatttcaaccaaaatctaaactttataccaatctaaacacagccttaattagaattagtcactgtgtccttcctgccgtgaatttatggctgatggcaagtaatcagtcactgtgtgggatgtggatttttatcccttgagagaacatttaattttatattaatattaatttatgttaatttatgttgtcatttaattttatattttatattaatttatgttgtccattttttttaatttttttatgactaattagttggcatggatgaaacgagggatatttcctggagggatgaaatcactttccccactgtgtgctgccatgaatgcaaatccaatcagcttcatggctgtacgtacctaatctgtggtgcagggcatgctcatggcggctctgtcggcgcttctgccgctgctgatcaaggacacgtcgtccatggcttcagctcaagtgatcatcctgtttcttggcctgtacatgatcgcatttggggtgggtggtctccggccgtgcctgatgtccttcggcgccgaccagttcgacgacggcgacacgtcggagcgcatcagcaagggctcctacttcaactggtacatcttcaccatgaactgcgcgtccgtgatatccaccaccgccatggtgtgggtgcaagaccactacgggtgggcattggggttggggattccggcgatggtcctcgccgtcgggctctcctgccttgtcgccgcgtctcgggcgtacaggtttcagacaacccgcggtagcccgctcaccagagtctgccaggtcgtcgtcgccgccgtccgcaagttcaacgtcgcgccgccggccgacatggcccttctctacgacctatcggaggatgcctcctccatgaagggagttcagaggatcgagcacaccgccgatctccggtcagttcatgtctctcgttgcatctggtgtttgtgatgctgtaggtgtaatgtaattggctaattcttgagatgcaactgctcgatcagattcttcgacaaggccgccgtcgtgacggcgtcggacgaggaggcggagggcgccgcgccgcgcaatccatggaggctttgcgtggtgacgcaggtggaggagctcaagattctcgtcaggatgctgcccctgtgggcgtgcgtcgccttctactacaccgcgacggcgcaggccaattcgacgttcgtcgagcagggcatggcgatggacacgcgcgtcggctccttccacgtcccgccggcatccctggccaccttccagatcatcaccacgatcgtgttgatcccgctgtacgaccgcgcgttcgtgccggcggcgaggaggctgacggggagagagaagggcatctccgaccttctcaggatcggcggcggcctcgccatggccgcgctcgccatggccgcggcggcgctggtcgagacgaggcgcgcccgcgcggcgcacgccgggatggagccgacgagcatcctgtggcaggcgccgcagtacgtgctggtgggcgtcggcgagctgctcgccaccgtggggcagctggacttcttctacagccaggcgccgccggccatgaagacggtgtgcacggcgctcgggttcatctccgtcgcggcgggggagtacctgagctcgctcgtcgtgacggccgtgtcgtgggcgacggcgaccggcggccggccggggtggatccccgacgacctcaacgaggggcacctgatcgcttcttctggatgatggctgggctcggttgcctcaatcttgtggtgtttacgagctgtgccatgaggtacaaatccaggaaggcctgttgatacttctgggcttgtttggtaggctcgaaattccggcccatgcactctgacgggccattatgtatgggaataagtccatccgacctccctcatctcttgcacttggtcgaatcgcatccctcagccgcaaaaaactgggtaaaacgcctcctgaatctccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188057.1 RefSeq:Os06g0706400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os07g0150700

2014-12-27T15:21:14Z

Shijc:

Os-AKT1, an inward K+ channel, is critical for K+ uptake in rice roots and is modulated by the rice CBL1-CIPK23 Complex. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os07g0150700-Fig1.jpg|right|thumb|200px|'' Functional Characterization of Os-AKT1 in Yeast and Arabidopsis. (from reference <ref name="ref1" />).'']]
AKT1 is an important K+ channel and plays crucial roles in K+ uptake in Arabidopsis roots. The Arabidopsis akt1 mutant plants exhibit low-K+-sensitive phenotypes and a significant decrease in K+ content after growth on low-K+ medium <ref name="ref2" /><ref name="ref3" /> <ref name="ref4" />. To examine the possible function of Os-AKT1, the coding sequence of Os-AKT1 was cloned and transformed into Arabidopsis akt1 mutant (ecotype Columbia [Col]) and two transgenic lines were obtained. The phenotype tests showed that the low-K+-sensitive phenotype of akt1 mutant was rescued in these two transgenic lines (akt1/Os-AKT1), which displayed a similar phenotype as wild-type (Col) plants. The K+ contents in these two transgenic lines were also rescued. Moreover, the root K+ content in these two lines were even higher than that in wild-type plants under low-K+ conditions. These results demonstrate that Os-AKT1 has similar function in K+ uptake as AKT1 in Arabidopsis.
To measure the Os-AKT1-mediated K+ currents in Arabidopsis root cells, patch-clamp whole-cell recording was conducted using root cell protoplasts. Inward K+ currents were observed in root cell protoplasts of wild-type plants, but not in those of the akt1 mutant, suggesting that the inward K+ currents in wild-type root cells were contributed by AKT1 channel <ref name="ref2" /><ref name="ref5" /><ref name="ref4" />. However, the akt1/Os-AKT1 transgenic line showed obvious inward K+ currents, suggesting that Os-AKT1 could mediate K+ uptake in Arabidopsis root cells. It should be noted that the Os-AKT1-mediated K+ currents were different from the currents conducted by Arabidopsis AKT1 channel. The half-activation voltage of Os-AKT1 (V1/2 = −173 ± 5 mV) was more negative than that of At-AKT1 (V1/2 = −133 ± 4 mV), suggesting that Os-AKT1 requires a more negative membrane potential to be activated.

===Mutation===
[[File: Shijc-Os07g0150700-Fig2.jpg|right|thumb|200px|'' Phenotype of Rice Os-akt1 Mutant. (from reference <ref name="ref1" />).'']]
The T-DNA insertion mutant line of Os-AKT1 from RiceGE (Rice Functional Genomic Express Database, http://signal.salk.edu/cgi-bin/RiceGE) was used to validate the physiological function of Os-AKT1 in rice. In this Os-akt1 mutant, the T-DNA fragment is inserted into the 5′-untranslated region of Os-AKT1, 303 bp upstream of the start codon. The insertion leads to the knockdown of Os-AKT1 in the mutant plants compared with wild-type (O. sativa ssp japonica cv Dongjin) plants. The results of DNA gel blot assays indicated that there is only one copy of the T-DNA fragment inserting into the mutant plants.
[[File: Shijc-Os07g0150700-Fig3.jpg|right|thumb|200px|'' Phenotype of Rice Os-akt1 Complementation Plants. (from reference <ref name="ref1" />).'']]
Using hydroponic culture, the phenotype of Os-akt1 mutant and wild-type (Dongjin) plants was tested. The 14-d-old rice seedlings were transferred into normal (1 mM K+) and low K+ (100 μM K+) medium. After growth for 7 d, the Os-akt1 mutant seedlings showed overall growth inhibition compared with wild-type plants in both normal and low K+ conditions. In addition, the Os-akt1 mutant displayed the brown spots on old leaves, which was a typical K+-deficient symptom of rice. This symptom in Os-akt1 mutant became more remarkable under low K+ conditions. The K+ content of the Os-akt1 mutant was significantly reduced in both root and shoot compared with wild-type plants. Since Os-AKT1 is an inward K+ channel, this K+ deficiency in Os-akt1 might be due to the defect of Os-AKT1-mediated K+ uptake. The results of K+ depletion experiments <ref name="ref6" /> showed that the K+ uptake in Os-akt1 was obviously slower than that in the wild type. These results demonstrated that the loss of function of Os-AKT1 led to the reduction of K+ uptake in Os-akt1 mutants, which caused growth inhibition and K+-deficient symptoms in mutant plants. The function of Os-AKT1 was further confirmed using two complementation lines for the Os-akt1 mutant. The expression of Os-AKT1 in these two transgenic lines was recovered and the growth inhibition and K+-deficient symptoms were relieved.
[[File: Shijc-Os07g0150700-Fig4.jpg|right|thumb|200px|'' Lesion of Os-AKT1 Inhibits Plant Growth and Impairs Grain Yield. (from reference <ref name="ref1" />).'']]
The growth of Os-akt1 mutant plants was inhibited throughout development. The heading and grain-filling stages were delayed in Os-akt1. In addition, the lesion of Os-AKT1 also impaired grain yield. The grain number, seed set percentage, and 100-grain weight of the main panicle were all significantly reduced in Os-akt1.

===Expression===
[[File: Shijc-Os07g0150700-Fig5.jpg|right|thumb|200px|'' Phylogenetic Analysis of AKT1-Like K+ Channels from Different Plant Species. (from reference <ref name="ref1" />).'']]
To determine the expression profiles of Os-AKT1 in rice, transgenic rice plants carrying a GUS gene under control of an Os-AKT1 promoter fragment (1010 bp; O. sativa ssp japonica cv Nipponbare) were generated. The β-glucuronidase (GUS) activity assays showed that the Os-AKT1 promoter drives strong expression in roots and slight expression in shoots. In root tissues, GUS activity was observed in all cell types. The expression of Os-AKT1 in the epidermis and root hairs suggests a physiological role for Os-AKT1 in root K+ uptake from soil. Furthermore, GUS activity was also detected in cortex, endodermis, and vascular bundles, which indicates Os-AKT1 may also participate in K+ translocation in roots. In shoot tissues, Os-AKT1 promoter activity was mainly found in epidermis and vascular bundles.

===Evolution===
[[File: Shijc-Os07g0150700-Fig6.png|right|thumb|200px|'' Subcellular Localization and Expression Pattern of Os-AKT1. (from reference <ref name="ref1" />).'']]
Os-AKT1 shares high similarity with other Shaker K+ channels from plant species, such as At-AKT1, Sl-LKT1, St-SKT1, Zm-ZMK1, Ta-AKT1, and Hv-AKT1 (58, 60, 60, 73, 76, and 75% identities, respectively). Phylogenetic analysis classified the K+ channels from monocots and dicots separatel. The Os-AKT1 P-loop domain contains a typical TxxTxGYG motif, a hallmark of K+-selective channels <ref name="ref7" />, suggesting that Os-AKT1 is likely to exhibit high ion selectivity for K+. The high degree of similarity of these Shaker K+ channels indicates that they likely have similar physiological functions in the different plant species.

==Labs working on this gene==
1. State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, National Plant Gene Research Centre (Beijing), China Agricultural University, Beijing 100193, China

==References==
<references>
<ref name="ref1">Juan Li;Yu Long;Guo-Ning Qi;Juan Li;Zi-Jian Xu;Wei-Hua Wu;Yi Wang. (2014) The Os-AKT1 Channel Is Critical for K+ Uptake in Rice Roots and Is Modulated by the Rice CBL1-CIPK23 Complex. The Plant Cell, 26(8): 3387-3402. </ref>
<ref name="ref2">Hirsch R.E., Lewis B.D., Spalding E.P., Sussman M.R. (1998). A role for the AKT1 potassium channel in plant nutrition. Science 280: 918–921. </ref>
<ref name="ref3">Spalding E.P., Hirsch R.E., Lewis D.R., Qi Z., Sussman M.R., Lewis B.D. (1999). Potassium uptake supporting plant growth in the absence of AKT1 channel activity: Inhibition by ammonium and stimulation by sodium. J. Gen. Physiol. 113: 909–918. </ref>
<ref name="ref4">Xu J., Li H.D., Chen L.Q., Wang Y., Liu L.L., He L., Wu W.H. (2006). A protein kinase, interacting with two calcineurin B-like proteins, regulates K+ transporter AKT1 in Arabidopsis. Cell 125: 1347–1360. </ref>
<ref name="ref5">Reintanz B., Szyroki A., Ivashikina N., Ache P., Godde M., Becker D., Palme K., Hedrich R. (2002). AtKC1, a silent Arabidopsis potassium channel α-subunit modulates root hair K+ influx. Proc. Natl. Acad. Sci. USA 99: 4079–4084. </ref>
<ref name="ref6"> Drew M.C., Saker L.R., Barber S.A., Jenkins W. (1984). Changes in the kinetics of phosphate and potassium absorption in nutrient-deficient barley roots measured by a solution-depletion technique. Planta 160: 490–499. </ref>
<ref name="ref7"> Doyle D.A., Morais Cabral J., Pfuetzner R.A., Kuo A., Gulbis J.M., Cohen S.L., Chait B.T., MacKinnon R. (1998). The structure of the potassium channel: molecular basis of K+ conduction and selectivity. Science 280: 69–77.</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os07g0150700|
Description = Similar to Serine/threonine kinase|
Version = NM_001065436.1 GI:115470604 GeneID:4342410|
Length = 4234 bp|
Definition = Oryza sativa Japonica Group Os07g0150700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 7|Chromosome 7]]|
AP = Chromosome 7:2675692..2679925|
CDS = 2675951..2676049,2676146..2676220,2676339..2676395,2676485..2676604,2676720..2676836 ,2676924..2677043,2677129..2677218,2677313..2677438,2677566..2677619 ,2677856..2677936,2678025..2678132,2678218..2678289,2678885..2678947 ,2679476..2679646|
GCID = <gbrowseImage1>
name=NC_008400:2675692..2679925
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008400:2675692..2679925
source=RiceChromosome07
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgagcgtgtcgggcgggaggacgcgggtggggaggtacgagctcgggaggacgctcggcgagggcaccttcgccaaggtcaagttcgcccgcaacgcggactccggcgagaatgtcgccatcaagatcctcgacaaggacaaggtcctcaagcacaagatgatcgcccagataaagcgcgagatctccaccatgaagctcatcaggcaccccaacgtcatccggatgcatgaggtgatggccagcaagaccaaaatatacatagtgatggagcttgtcaccggtggtgaacttttcgacaagattgcttcgcgtgggaggctgaaagaggatgatgcaaggaagtattttcagcagctgatcaacgctgtcgattactgtcatagcagaggagtctatcaccgggatctcaagcccgaaaatcttctgcttgatgctagtggcactctcaaagtatcagattttgggctgagtgcactgtctcaacaagtcagagaggatggtctgttgcacactacctgtggaactcctaattatgttgctcccgaggttatcaacaacaaaggatatgatggagccaaggctgatctgtggtcatgtggagtgattctctttgtcctcatggcaggctaccttccatttgaagactcaaacctcatgtcactttacaagaagatcttcaaagcagacttcagttgcccgtcttggttctctacaagtgcgaagaagctcatcaagaaaatactagatcctaatcctagcaccaggattaccatcgcagagcttatcaacaatgagtggttcaagaagggatatcagcctccaaggtttgagacagcagatgttaacctggatgatatcaactctatttttaatgaatctggggaccaaacacagcttgttgtcgagaggcgagaagagaggccatcagtgatgaatgcttttgagttgatctctacatctcagggtctcaatcttggcacactctttgaaaagcaatcgcagggttctgtgaagcgagaaacaagatttgcatcaaggctgcctgcaaacgagatattgtcgaaaattgaagcagctgctggacccatgggctttaatgtacagaagcgcaactacaagctgaagttgcaaggagagaatccaggaaggaaaggtcagcttgcaattgcaacagaggtttttgaagtcacgccctcgctgtacatggttgagctccgcaaatctaacggcgacactcttgaattccataagttctaccacaacatctccaatggcctgaaagatgtgatgtggaagccggagagtagcataatcgcaggcgatgagatccagcatcggaggtcaccgtga</cdnaseq>|
AA = <aaseq>MSVSGGRTRVGRYELGRTLGEGTFAKVKFARNADSGENVAIKIL DKDKVLKHKMIAQIKREISTMKLIRHPNVIRMHEVMASKTKIYIVMELVTGGELFDKI ASRGRLKEDDARKYFQQLINAVDYCHSRGVYHRDLKPENLLLDASGTLKVSDFGLSAL SQQVREDGLLHTTCGTPNYVAPEVINNKGYDGAKADLWSCGVILFVLMAGYLPFEDSN LMSLYKKIFKADFSCPSWFSTSAKKLIKKILDPNPSTRITIAELINNEWFKKGYQPPR FETADVNLDDINSIFNESGDQTQLVVERREERPSVMNAFELISTSQGLNLGTLFEKQS QGSVKRETRFASRLPANEILSKIEAAAGPMGFNVQKRNYKLKLQGENPGRKGQLAIAT EVFEVTPSLYMVELRKSNGDTLEFHKFYHNISNGLKDVMWKPESSIIAGDEIQHRRSP </aaseq>|
DNA = <dnaseqindica>3877..3975#3706..3780#3531..3587#3322..3441#3090..3206#2883..3002#2708..2797#2488..2613#2307..2360#1990..2070#1794..1901#1637..1708#979..1041#280..450#aagttgcaacctcccgcctcacccgccgccattgacgaccaccgcgctcgtcccatcccatgcctgcggccgtgaccgcgaggttgtgaggagaagagagtcccaagagaggaggatcgatgcggcagcggcaggccggcgagcaggaggcggagctgttcgtccagtggaggccctgcgacaagaagcggtcctagtcgcccgccgccgctcgcccactcgccggcgtcgtcgatctgagagggacaggggaagaggaagaagcagaggaggaggaggatgagcgtgtcgggcgggaggacgcgggtggggaggtacgagctcgggaggacgctcggcgagggcaccttcgccaaggtcaagttcgcccgcaacgcggactccggcgagaatgtcgccatcaagatcctcgacaaggacaaggtcctcaagcacaagatgatcgcccaggtcagctcacccatactattttctatccccccaatcgattctcgatttggagaggtctccatggatttcttcccatgatgatagtactgttcgaatttctcgccttcttgtttttttttaatcatatcatacgctgttcttgagtgaatttcgtggacaatttcaattcctatacgtacgagtcccaaatcatgaacagtttgtactactgctgttttgtttcctctcacgacaagacgtgatgattttgttttaaccagaaacagtaaacattactaattactactagcgttcttgctgcaaaaaaaaaaaggtttggtatcgttccaaaattgcgttcttacttccaaaattgcaacagcctagactttgacgtgaggttagcacgggcgcctcgtgcagtgttcgttggaacttgtgctgagttagttattattaatgtgcatcaactttggcttagcttctgactttttgtgggggagttctgactttgatgtgtgtttgtggtttgtgtggtggtgtttgcagataaagcgcgagatctccaccatgaagctcatcaggcaccccaacgtcatccggatgcatgaggtttactaatctccaatcattaatctcagctcatcttgcccatggaaaaattttgtaactgatgataagtccaccaatgaaatcgactaatcataagcagagctcgtgattttggttcgaaattttcgaaatttcgggtctaccagtgggtcctggttggatgtgattcccagtcttgaattgtggattttttttttaattttgtaaaatttgttcgaattcagctagagcctgttcaaaattcattttttttctggtttgaaacttctgaaaaattttggtcccccccagattttttttttctaggccgagattgtgaaccctgctaattaagttaagatatggttctcaaggctttgagcaatctgaaattatgaaaaaccagggtaaattaaattggtcaaggatgacataatgaacaagttgttccttcacatgaaaagttgcaattagagatcgttctggaaggaaattcctgtgacactaaactatgtgttatctgaaactttcctagctcttgctttctgatattttccttttgttgtcttggctttatgtcgatctccacttagtggttttgttttcttctctgaaggtgatggccagcaagaccaaaatatacatagtgatggagcttgtcaccggtggtgaacttttcgacaagattgtgagtgcttggccttttctatcgacatctgaattactctttatgctatgcacacatgttcaatttgtcataattcctgttataggcttcgcgtgggaggctgaaagaggatgatgcaaggaagtattttcagcagctgatcaacgctgtcgattactgtcatagcagaggagtctatcaccgggatctcaaggttagcggcgtttaactgtttgcggtgtttactactgctatgcaagagagccgagaagcagtgaattgatacacaaattcaatttcagcccgaaaatcttctgcttgatgctagtggcactctcaaagtatcagattttgggctgagtgcactgtctcaacaagtcagagtaagtaatttgactcttcctatttattcttttattatctttttgtggagagtttccttttattcaaagtgatgaaaagccgagagttgttagtcgtaaaaaaattagcatttcaattgctttctgtagattccatttgttttctacatcttttcacatggtaatacagatagtttcagatccatctgaataaagttcttacattagtgctgcatatctttctgtttactctgcaggaggatggtctgttgcacactacctgtggaactcctaattatgttgctcccgaggtaccttcttacactcatacattaaactagtatatagttattatcatcgttggattgaatatttgttttcatgttacttatctaaaaaaatatttgttctcatgtttcaataatattgtctgtgcaggttatcaacaacaaaggatatgatggagccaaggctgatctgtggtcatgtggagtgattctctttgtcctcatggcaggctaccttccatttgaagactcaaacctcatgtcactttacaagaaggttggtccctcttaaccatgtcaaaggattgttggtttatgaaccctaaacaaagtttttgtttggaagattaatgtgattattgctcatccagatcttcaaagcagacttcagttgcccgtcttggttctctacaagtgcgaagaagctcatcaagaaaatactagatcctaatcctagcaccgtatgttttgcagcattttaaccttcatttctttggagcattcttatacataagtagcttatcccatcgttatctccttgtgcagaggattaccatcgcagagcttatcaacaatgagtggttcaagaagggatatcagcctccaaggtttgagacagcagatgttaacctggatgatatcaactctatttttaatgaatctggggtaagctctcacaccattcagctcatagcattacattcttcataatgcactggatgggcttggtaacatctattctaactaacgcaggaccaaacacagcttgttgtcgagaggcgagaagagaggccatcagtgatgaatgcttttgagttgatctctacatctcagggtctcaatcttggcacactctttgaaaagcaatcggtacgatcacattcttaaattggtcattctgaagtctgaactaaacatgttcaagtacacttacagtcatgagttataatctaaaatgctaaaccaattttctttctacttttagcagggttctgtgaagcgagaaacaagatttgcatcaaggctgcctgcaaacgagatattgtcgaaaattgaagcagctgctggacccatgggctttaatgtacagaagcgcaactacaaggtaactaatccaaaattccacaacttgtttctaccatttttatctgaaacaattaacattctgatgacacttttatggattggaatcagctgaagttgcaaggagagaatccaggaaggaaaggtcagcttgcaattgcaacagaggtacaccaatgatacaacatcactatttactatgttctgtcattctatatgctgtgcagcttgtgctactactctttcctgggtttatagactgaaatcagttcatccatttctaaaggtttttgaagtcacgccctcgctgtacatggttgagctccgcaaatctaacggcgacactcttgaattccataaggtacacataacagtaaaattactgcaggacctcacagttcatacttcagactgggattcggctaactcatggtgtaattttttacgcgtttcgcagttctaccacaacatctccaatggcctgaaagatgtgatgtggaagccggagagtagcataatcgcaggcgatgagatccagcatcggaggtcaccgtgattggcagtttggcaccaaaagttcagtgatagtataaagtagataaccagccaggaaaacctactaaggaatggcctgtggctgtttttttttttttggttctttttaccttttaagttgagttactatctaatctagacatggttgtaaacaaagtttgtatggagatggaatgtgaatgaagaatgtgcatagttttgcttccttgacttattttaaaagcagtaacctgtgaaatccgatgaatgaaattgaaatc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001065436.1 RefSeq:Os07g0150700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 7]]
[[Category:Chromosome 7]]

File:Shijc-Os07g0150700-Fig6.png

2014-12-27T15:16:30Z

Shijc: Phylogenetic Analysis of AKT1-Like K+ Channels from Different Plant Species.

Phylogenetic Analysis of AKT1-Like K+ Channels from Different Plant Species.

File:Shijc-Os07g0150700-Fig5.jpg

2014-12-27T15:16:15Z

Shijc: Subcellular Localization and Expression Pattern of Os-AKT1.

Subcellular Localization and Expression Pattern of Os-AKT1.

File:Shijc-Os07g0150700-Fig4.jpg

2014-12-27T15:15:59Z

Shijc: Lesion of Os-AKT1 Inhibits Plant Growth and Impairs Grain Yield.

Lesion of Os-AKT1 Inhibits Plant Growth and Impairs Grain Yield.

File:Shijc-Os07g0150700-Fig3.jpg

2014-12-27T15:15:38Z

Shijc: Phenotype of Rice Os-akt1 Complementation Plants.

Phenotype of Rice Os-akt1 Complementation Plants.

File:Shijc-Os07g0150700-Fig2.jpg

2014-12-27T15:15:16Z

Shijc: Phenotype of Rice Os-akt1 Mutant.

Phenotype of Rice Os-akt1 Mutant.

File:Shijc-Os07g0150700-Fig1.jpg

2014-12-27T15:14:57Z

Shijc: Functional Characterization of Os-AKT1 in Yeast and Arabidopsis.

Functional Characterization of Os-AKT1 in Yeast and Arabidopsis.

Os09g0104200

2014-12-27T14:08:57Z

Shijc:

OsRAD51D plays a critical role in reproductive growth in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os09g0104200-Fig1.png|right|thumb|200px|'' Phenotypic characterization of vegetative and reproductive organs of osrad51d mutant and Ubi:RNAi-OsRAD51D transgenic rice plants. (from reference <ref name="ref1" />).'']]
Osrad51d knock-out and RNAi-mediated knock-down transgenic (Ubi:RNAi-OsRAD51D) plants revealed that suppression of OsRAD51D exerted negligible effects on the vegetative growth of rice plants. In contrast, loss of OsRAD51D caused defects in reproductive growth. Homozygous mutant flowers displayed impaired development of pollen, lemma and palea, stamen, and carpel, which resulted in sterile flowers. The abnormalities of heterozygous mutant and Ubi:RNAi-OsRAD51D plants were intermediate between wild type and homozygous mutant plants.
[[File: Shijc-Os09g0104200-Fig2.png|right|thumb|200px|'' Cytogenetic analysis of root tips, PMCs, and pollen cells from wild type (WT) andosrad51d mutant rice plants. (from reference <ref name="ref1" />).'']]
Furthermore, previous studies in Arabidopsis indicate that AtRAD51B, AtRAD51D, and AtXRCC2 are not essential for meiosis <ref name="ref2" /><ref name="ref3" /><ref name="ref4" />. Triple, as well as single/double, mutations of AtRAD51B, AtRAD51D, and AtXRCC2 result in normal growth and fertility <ref name="ref5" />. These results are in sharp contrast with our results in that loss of OsRAD51D function caused severe errors in floral development and infertility. Cytogenetic analysis showed that osrad51d PMCs were unable to form normal homologous chromosome pairings and most mutant chromosomes were fragmented and scattered throughout the cells during meiosis I. Due to these meiotic anomalies, homozygous osrad51d pollen cells contained numerous micro-nuclei and formed atypical tetrads, resulting in malfunctioning pollen. Taken together, our results are consistent with the view that, unlike Arabidopsis AtRAD51D, OsRAD51D is critically involved in meiosis and is an essential factor for reproductive growth in rice plants. Nevertheless, it is still possible that absence of OsRAD51D could be affecting cellular stability of other OsRAD51 paralogs and thus producing an indirect effect on meiosis and floral development. A previous study of RAD51 in moss Physcomitrella patens suggested that there are fundamental differences in the use of the HR pathway in different plant species, and that an essential role of RAD51 in viability does not correlate with organism taxonomic complexity<ref name="ref6" />.

===Mutation===
[[File: Shijc-Os09g0104200-Fig3.png|right|thumb|200px|'' Molecular characterization of T-DNA osrad51d knock-out mutant and Ubi:RNAi-OsRAD51D knock-down transgenic rice plants. (from reference <ref name="ref1" />).'']]
A single loss-of-function rice mutant line that contained a T-DNA insertion in the OsRAD51D gene was obtained (Yi and An, 2013; http://signal.salk.edu/cgi-bin/RiceGE). This mutant was named osrad51d. The T-DNA insertion was mapped to the third exon in OsRAD51D located on chromosome 9 (line PFG_4A-00300.R). A homozygous line for the T-DNA insertion was identified by genomic PCR with FW2/RV3 and RB/RV3 primer sets. Disruption of OsRAD51D by T-DNA insertion was further verified by RT-PCR. The results showed that the homozygous osrad51d mutant leaves contained undetectable amounts of all three OsRAD51D isoform transcripts under the experimental conditions, whereas the heterozygous osrad51d line possessed reduced levels (approximately 50%) of the transcripts. Genomic Southern blot analysis indicated that the osrad51d mutant progeny contained a single T-DNA integration into the OsRAD51D gene. Because only one allele of the osrad51d loss-of-function mutant plant was obtained, RNAi-mediated knock-down transgenic rice lines (Ubi:RNAi-OsRAD51D) were generated. RT-PCR revealed that the mRNA levels of OsRAD51D.1/OsRAD51D.3 and OsRAD51D.2 significantly decreased in the independent T2 Ubi:RNAi-OsRAD51D lines #1 and #2. Genomic Southern blotting demonstrated that these two RNAi-transgenic plants were independent lines .

===Expression===
[[File: Shijc-Os09g0104200-Fig4.png|right|thumb|200px|'' Identification and expression of OsRAD51D in rice. (from reference <ref name="ref1" />).'']]
OsRAD51D.1/OsRAD51D.3 and OsRAD51D.2 isoforms were expressed in all tissues examined in rice plants. A FW1/RV1 primer set detected both OsRAD51D.1 and OsRAD51D.3 mRNAs due to their similar structure. Yeast two-hybrid assay showed that human RAD51B and RAD51D interacted in the presence of RAD51C. In vivo immuno-precipitation results indicated that human AD51 paralogs form the RAD51B-RAD51C-RAD51D-XRCC2 complex. Arabidopsis AtRAD51B and AtRAD51C also interact in yeast cells <ref name="ref7" />. Yeast two-hybrid studies showed that rice OsRAD51D.1 interacted with OsRAD51B and OsRAD51C, whereas OsRAD51D.2 and OsRAD51D.3 were unable to associate with other OsRAD51 paralogs. In vitro pull-down assays also indicated that bacterially expressed OsRAD51D.1, but not OsRAD51D.2 and OsRAD51D.3, was associated with OsRAD51B and OsRAD51C. These results raise the possibility that the OsRAD51D.1 isoform is the major OsRAD51D protein in rice plants.

===Splicing Variants===
There are five RAD51 paralogs, OsRAD51B, OsRAD51C, OsRAD51D, OsXRCC2, and OsXRCC3, in rice. The rice OsRAD51D gene is 5804 bp in length and composed of nine exons and eight introns. Three splicing variants of OsRAD51D were predicted and termed OsRAD51D.1 (GenBank accession no. KJ472480), OsRAD51D.2 (GenBank accession no. KJ472481), and OsRAD51D.3 (GenBank accession no. KJ472482). The coding regions of OsRAD51D.1, OsRAD51D.2, and OsRAD51D.3 are 849 bp encoding 283 amino acids (30.3 kDa), 552 bp encoding 184 amino acids (19.8 kDa), and 768 bp encoding 256 amino acids (27.4 kDa), respectively All three deduced OsRAD51D proteins contained Walker A and Walker B motifs and a RecA domain in their central regions. Walker A and Walker B motifs function as nucleotide binding domains <ref name="ref8" />, whereas the RecA motif is an ATP hydrolysis domain <ref name="ref9" />. Both Walker A and Walker B motifs are highly conserved in plant (rice, wheat, maize, and Arabidopsis) and human RAD51D homologs. The RecA domain in OsRAD51D is 45–76% and 29% identical to those in plant and human RAD51D proteins, respectively.

==Labs working on this gene==
1. Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea

==References==
<references>
<ref name="ref1"> Byun, M. Y. and Kim, W. T. (2014), Suppression of OsRAD51D results in defects in reproductive development in rice (Oryza sativa L.). The Plant Journal, 79: 256–269. doi: 10.1111/tpj.12558 </ref>
<ref name="ref2">Bleuyard, J.Y., Gallego, M.E., Savigny, F. and White, C.I. (2005) Differing requirements for the Arabidopsis Rad51 paralogs in meiosis and DNA repair. Plant J. 41, 533–545. </ref>
<ref name="ref3">Durrant, W.E., Wang, S. and Dong, X. (2007) Arabidopsis SNI1 and RAD51D regulate both gene transcription and DNA recombination during the defense response. Proc. Natl Acad. Sci. USA, 104, 4223–4227. </ref>
<ref name="ref4">Da Ines, O., Degroote, F., Amiard, S., Goubely, C., Gallego, M.E. and White, C.I. (2013) Effects of XRCC2 and RAD51B mutations on somatic and meiotic recombination in Arabidopsis thaliana. Plant J. 74, 959–970. </ref>
<ref name="ref5">Wang, Y., Xiao, R., Wang, H., Cheng, Z., Li, W., Zhu, G., Wang, Y. and Ma, H. (2013) The Arabidopsis RAD51 paralogs RAD51B, RAD51D and XRCC2 play partially redundant roles in somatic DNA repair and gene regulation. New Phytol. 201, 292–304. </ref>
<ref name="ref6">Markmann-Mulisch, U., Wendeler, E., Zobell, O., Schween, G., Steinbiss, H.H. and Reissa, B. (2007) Differential requirements for RAD51 in Physcomitrella patens and Arabidopsis thaliana development and DNA damage repair. Plant Cell, 19, 3080–3089. </ref>
<ref name="ref7">Osakabe, K., Abe, K., Yamanouchi, H. et al. (2005) Arabidopsis Rad51B is important for double-strand DNA breaks repair in somatic cells. Plant Mol. Biol. 57, 819–833. </ref>
<ref name="ref8">Hanson, P.I. and Whiteheart, S.W. (2005) AAA+ proteins: have engine, will work. Nat. Rev. Mol. Cell Biol. 6, 519–529.</ref>
<ref name="ref9">Cox, M.M. (2007) Motoring along with the bacterial RecA protein. Nat. Rev. Mol. Cell Biol. 8, 127–138. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0104200|
Description = RecA bacterial DNA recombination family protein|
Version = NM_001069094.2 GI:297609026 GeneID:4346376|
Length = 5790 bp|
Definition = Oryza sativa Japonica Group Os09g0104200, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:431724..437513|
CDS = 432061..432099,434262..434408,435614..435676|
GCID = <gbrowseImage1>
name=NC_008402:431724..437513
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:431724..437513
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgatgatatcagtggctatgattctaaagaagctagcatatgagcataatctatctgttctggttactaaccatatggttgctgggaatggagctcccaagcctgctcttggtgagagctggaaaactgttccacatgtccgcttggtgatatctcgtgagcgtggtagcaaaatctgcgcagcaactgtgctgaagcacacactactggcttcgggccgtgttatgaaatttgccgtaccaagctga</cdnaseq>|
AA = <aaseq>MMISVAMILKKLAYEHNLSVLVTNHMVAGNGAPKPALGESWKTV PHVRLVISRERGSKICAATVLKHTLLASGRVMKFAVPS</aaseq>|
DNA = <dnaseqindica>5415..5453#3106..3252#1838..1900#ttccccttctggctgtaatggcgatggcggcgacgtcggcgagcggcggcgccggctgcttccccaggcctcctccctccggcggcgaggttagtcctccgtcctcggctgcttgacggccatttcagttcatccccagcttttttattcctgcttcgaaatctcagcttaatcgggaacggaatgctgcacaaaaaccgtttgctcttgacgagataatgcgcatgcgattcacccgcagttggtttcacggcttcatactactgatcaatcgtattttctgtgtgtatgtggcatggatttgtgcttggggtacaggagaagaagcaagatgaggaggggcaatgctttctggatggaatggacttgctcaaggatgcgacggagaacaagcgcttcctccccacgggccttcaagggtactcctatcttcaatgtaccaatcatttcctttccctctctatctattgctattggccctcccccaacttgtttggatcataggattcccctaactgccttgctttagtttttttagtttttgggtaatttcactaccaaattgcagattttgacttcatcatgtcctcaattttccagcgtcgacgcgcttcttggaggcggcctgcgccaaggtcagctcactgaaataaccggccaatcgtcctccggtaaaacacaggtgaaaatgttaaccacttctatctttcttaacttattagacgcaatagatagatatacattttatatgcttactcctccggacaagattggcttgccaaaaacagtaggattttaaggtatacatcacaattcacaagcggcactgttgtttattctgtctatgtaactgcaggtctgtctttgttctgcttcacatgtggcagccaggcagttgggtgttgttatgtacttggatactagcaattccttttcccctagccgcattgctcgaatagttgatggattccccatctctttggtcagagaggtaggtaatcatacttgtacacatatttgaatactgctcctaccctgttacttggacttacctgaattgcttcctttgctgtggtgtcactaaatatagttgaagacatgtttctgctattagattactctaactagtaacacttgtttaacaacttgctatactacttgcttttttctaattaccacatttgacttgcagccaaagaatgtgcgactcgagagggtcatgagcagcatcatttgtaagtcagtctttgatatattcgatttgtttgaagtgctacatcaacttgaattgtcactgaagagcaaggtgagtgtgaagtgattgttcaatttgtgccttgaaaaactctgatgtgccacgtgctttttaggtaaacaatgggggtaacaagatatgcttgcttatcattgactcaatatcgtctatacttgctcccatcaacggtgggaagtatccacgaggtacttgcatagtctttgtgccctacttttattattcatagcataagttgcaccttgctattgaacaagtaaatcagtctcgataagcagggacgtcataagtggctgagatatactagatccgattagcaagttagaaatagcagaaaattagttcagtgagcacttaacctgcaattatacagcgagatattgatactttgatctggtcataaattcaatgtgcttctgttaattgttgaagttccaaaaatcatttattttctcacacaattacttcctgagagggtccttattaatttttaaagtttattatgaagtaaatttgttgtttccttttgtctctgcatgtcttattaacctaacagggcgatcgatgatgatatcagtggctatgattctaaagaagctagcatatgagcataatctatctgttctggtaattctactttagtctaatttgtgtgctaataatttttggcatttgcactgcacgctttgggttgagcatatctgcacaaggctttctaaaatattattctgactcatcaagctattgtatgcattatacttcttttaacacatcggttgtgcaataacacctttgacaatggtgtggctaagatcacattactacagcgttcacccctttcgattgaatttagattctcatcatcctttctcgtttaaccccactcaatccccatcctgtgaattacataactgtggcccccgcaccctcatggttaaggtcatgcaatgtcctgaactcctgattgtgcctactcctggtaggatgtatgctggccagagttgctttggtctccacaattttatattgcttgcacttccttacatacagagaggtgacccttaacctccaggttgcttcacatgaaataggcagataggaacaggtggggatacatttcaagatagaatctctagaggtcaggcgtttgagtactaaagaagaactgctgtggtcacgtgccctcactgacattttttacatgttggagctagttgtcagtccacgttatcacttaaggttatgatgggcaggttaaggatcttgtgtgaatcacttaatgcacattataccgttgtgcagattttcagtttggtcacctaaatatgccacttaaactaatgtagtaacccctagtgcaatttgctctaattaattgctgtacaaattcacttattcagcatgccatctttctcatgaacagattgggacatgtatctggaaatgcttcatttcctgctttacttctaagataagctattaaagtaaattgatcatgtactgttagttttagtgggtttgctcatgtccatctctgttattctgtggaaattttaacttctctatcttgagcacatattccctctactttctctagtttagttttcctggtttggaaaaaggcaccaaagcctctattacttggagcaacttttctttagttagttaccttgaagactgactaccaagtttcagaaggcttgctaaattagagaagtcaccataaggcttgctaacttgggcactatgcctgttgtgcttaaaatgtatgctgaaacaaaaatatggtcatcattttcatttatcggtttgcccccttgcattgactccaggttactaaccatatggttgctgggaatggagctcccaagcctgctcttggtgagagctggaaaactgttccacatgtccgcttggtgatatctcgtgagcgtggtagcaaaatctgcgcagcaactgtgctgaagcacacactactggtatttgcttaaacaattagattataagtttaaatgtcataatcatagcagcattgcttattgtctttctagaaattgcattaataatgtgttagctatcattttgttgaaaataagtggtgaagatattggcatgaggagaacaaaagtagtatactccctccatccataagtctaaggcatatttcatttctagtttttccaaataagatggcatatttgtagtcttcatgcatctaagacttaaatgaaggggttatcttttcgttttacggtgctaaattaaattgttgaccggaacccgagcaatcatcttaataatcattggttgcatgcatgcatatagttccttggtgtttgttatatgtgggatgagttaatttctccttggtcttgttgacaaaagaaatacccccttgttccacaaaatttacacctattacttttgtcaccaagaccaaggagaaattaactcatcttgcatgtaacaaagatcaagctgtgtacgcacacgtgcaaccaataagtattaagatgactcctcgggttccgatcaaacatttagtttacctctccatttaagtcttggatgcatagagactacaaatagaaacaacttatttggaaaaactcaaatatgaaataggtctaattcttgtggatggagggagtatgccttagacttttggatggagggagtaaacaattatatggtgccagtgcatacctctatatcctaatcctacatgttgcgtgttgttttcatgctatgctgcatttatatatttttgtatcatctttttttttctcactttttgtgcttttgaattgggctgtgaaaacaatagtggtaggtagatgccagatacatttttctcctatataaaaatttgagctggtagtgatggccatcagtcatcagtcatcccaagtcccctctaactcaagacaaactctgtaggatcctcatggaaaatttgcaaaagccacaaactcctttagactcttatttgtttgtaggaaatatgggtataccaccagtgtacctagccaatgaagctgcacatttaatgagtatttctatgttagatctgtcttatgatgaaatggaatggtctagtacctggcaatcctgcataaacgttctgagtactgcagagaggagactgagactaaagattatgttaattcattgcttaaagaaattacatggatcgattgcttctaatgtgggtggccctaaaaatctctaaaaataacttggtaactattaaaaaaagatacttgataactggaagataacttatctcttgactctcaagtctcaacatctgcatttgccgctcgctgtgtgtgtggccatcgcattcaaatcccatagcatctgaattgtgctggcgtctgagaatccatttgcctctggccacagtagacagttgtgacatgtaagaaaaaagtgatcatgtaaatgctatgccgctgagctcaaaattaatatgcaatatccatcataatttgttttagaaatacgcacttcaaaaataaattgttttcagttgacactttatatgagatggatgttgttctttcttagttttcttttcgttgtttttcttttatttattttgtaagcagacgcctgaggctcaaattccctttcttgggtgttcgaatttagggataaaggggtggaatatgggttagaatatcaggtggggagatgctaaccttccatctctttctaatgagttaggactgtctggccttattcatactccaatcctacttctttttgcacaaatacaaatctattggcatttctttgctctctaagaatcatgcaaggaaaagacggccattttgaatgatatgctgccctgccataaattaatctgcattatatcactgcaaaggaagttttttttaatctatttgcttcttttttgcagtaatgctcacaattgatgttttacactaaattacacccacttgacaagtttgtgcactaaattagacccactaaatgacacaagacgatgctaagtaccgtcatttcttccaatgtctggtagcaaaataaattgcatgattcttggtatcatctgtacatgcccaaaaacaaaaaagtgcgggcatgtcatctttgtttttcttcattgcaggcttcgggccgtgttatgaaatttgccgtaccaagctgaattcagcaacttgatgcttcatatataaccagaagggaactgatctttgtagttcaagctatagaaagaacttcacccgtaagggtaaccttttgatttaccttggctttatgttccaggccatttgtatattaatccaatggtttttgcatgttgcctgcgtccgtggtatcacgcttaactgatccatatatatagtttcttggtaaactgaatgtatcagaaacattcagttttcaagtttttgtttcttcaattattcactgtgaatactggaaaatggtagtttcccatcagtggataaaattgaatgaaattatatttgttccttgttttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069094.2 RefSeq:Os09g0104200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os09g0104200

2014-12-27T14:01:25Z

Shijc:

OsRAD51D plays a critical role in reproductive growth in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os09g0104200-Fig1.png|right|thumb|200px|'' Phenotypic characterization of vegetative and reproductive organs of osrad51d mutant and Ubi:RNAi-OsRAD51D transgenic rice plants. (from reference <ref name="ref1" />).'']]
Osrad51d knock-out and RNAi-mediated knock-down transgenic (Ubi:RNAi-OsRAD51D) plants revealed that suppression of OsRAD51D exerted negligible effects on the vegetative growth of rice plants. In contrast, loss of OsRAD51D caused defects in reproductive growth. Homozygous mutant flowers displayed impaired development of pollen, lemma and palea, stamen, and carpel, which resulted in sterile flowers. The abnormalities of heterozygous mutant and Ubi:RNAi-OsRAD51D plants were intermediate between wild type and homozygous mutant plants.
[[File: Shijc-Os09g0104200-Fig2.png|right|thumb|200px|'' Cytogenetic analysis of root tips, PMCs, and pollen cells from wild type (WT) andosrad51d mutant rice plants. (from reference <ref name="ref1" />).'']]
Furthermore, previous studies in Arabidopsis indicate that AtRAD51B, AtRAD51D, and AtXRCC2 are not essential for meiosis. Triple, as well as single/double, mutations of AtRAD51B, AtRAD51D, and AtXRCC2 result in normal growth and fertility <ref name="ref5" />. These results are in sharp contrast with our results in that loss of OsRAD51D function caused severe errors in floral development and infertility. Cytogenetic analysis showed that osrad51d PMCs were unable to form normal homologous chromosome pairings and most mutant chromosomes were fragmented and scattered throughout the cells during meiosis I. Due to these meiotic anomalies, homozygous osrad51d pollen cells contained numerous micro-nuclei and formed atypical tetrads, resulting in malfunctioning pollen. Taken together, our results are consistent with the view that, unlike Arabidopsis AtRAD51D, OsRAD51D is critically involved in meiosis and is an essential factor for reproductive growth in rice plants. Nevertheless, it is still possible that absence of OsRAD51D could be affecting cellular stability of other OsRAD51 paralogs and thus producing an indirect effect on meiosis and floral development. A previous study of RAD51 in moss Physcomitrella patens suggested that there are fundamental differences in the use of the HR pathway in different plant species, and that an essential role of RAD51 in viability does not correlate with organism taxonomic complexity<ref name="ref6" />.

===Mutation===
[[File: Shijc-Os09g0104200-Fig3.png|right|thumb|200px|'' Molecular characterization of T-DNA osrad51d knock-out mutant and Ubi:RNAi-OsRAD51D knock-down transgenic rice plants. (from reference <ref name="ref1" />).'']]
A single loss-of-function rice mutant line that contained a T-DNA insertion in the OsRAD51D gene was obtained (Yi and An, 2013; http://signal.salk.edu/cgi-bin/RiceGE). This mutant was named osrad51d. The T-DNA insertion was mapped to the third exon in OsRAD51D located on chromosome 9 (line PFG_4A-00300.R). A homozygous line for the T-DNA insertion was identified by genomic PCR with FW2/RV3 and RB/RV3 primer sets. Disruption of OsRAD51D by T-DNA insertion was further verified by RT-PCR. The results showed that the homozygous osrad51d mutant leaves contained undetectable amounts of all three OsRAD51D isoform transcripts under the experimental conditions, whereas the heterozygous osrad51d line possessed reduced levels (approximately 50%) of the transcripts. Genomic Southern blot analysis indicated that the osrad51d mutant progeny contained a single T-DNA integration into the OsRAD51D gene. Because only one allele of the osrad51d loss-of-function mutant plant was obtained, RNAi-mediated knock-down transgenic rice lines (Ubi:RNAi-OsRAD51D) were generated. RT-PCR revealed that the mRNA levels of OsRAD51D.1/OsRAD51D.3 and OsRAD51D.2 significantly decreased in the independent T2 Ubi:RNAi-OsRAD51D lines #1 and #2. Genomic Southern blotting demonstrated that these two RNAi-transgenic plants were independent lines .

===Expression===
[[File: Shijc-Os09g0104200-Fig4.png|right|thumb|200px|'' Identification and expression of OsRAD51D in rice. (from reference <ref name="ref1" />).'']]
OsRAD51D.1/OsRAD51D.3 and OsRAD51D.2 isoforms were expressed in all tissues examined in rice plants. A FW1/RV1 primer set detected both OsRAD51D.1 and OsRAD51D.3 mRNAs due to their similar structure. Yeast two-hybrid assay showed that human RAD51B and RAD51D interacted in the presence of RAD51C. In vivo immuno-precipitation results indicated that human AD51 paralogs form the RAD51B-RAD51C-RAD51D-XRCC2 complex. Arabidopsis AtRAD51B and AtRAD51C also interact in yeast cells <ref name="ref7" />. Yeast two-hybrid studies showed that rice OsRAD51D.1 interacted with OsRAD51B and OsRAD51C, whereas OsRAD51D.2 and OsRAD51D.3 were unable to associate with other OsRAD51 paralogs. In vitro pull-down assays also indicated that bacterially expressed OsRAD51D.1, but not OsRAD51D.2 and OsRAD51D.3, was associated with OsRAD51B and OsRAD51C. These results raise the possibility that the OsRAD51D.1 isoform is the major OsRAD51D protein in rice plants.

===Splicing Variants===
There are five RAD51 paralogs, OsRAD51B, OsRAD51C, OsRAD51D, OsXRCC2, and OsXRCC3, in rice. The rice OsRAD51D gene is 5804 bp in length and composed of nine exons and eight introns. Three splicing variants of OsRAD51D were predicted and termed OsRAD51D.1 (GenBank accession no. KJ472480), OsRAD51D.2 (GenBank accession no. KJ472481), and OsRAD51D.3 (GenBank accession no. KJ472482). The coding regions of OsRAD51D.1, OsRAD51D.2, and OsRAD51D.3 are 849 bp encoding 283 amino acids (30.3 kDa), 552 bp encoding 184 amino acids (19.8 kDa), and 768 bp encoding 256 amino acids (27.4 kDa), respectively All three deduced OsRAD51D proteins contained Walker A and Walker B motifs and a RecA domain in their central regions. Walker A and Walker B motifs function as nucleotide binding domains <ref name="ref8" />, whereas the RecA motif is an ATP hydrolysis domain <ref name="ref9" />. Both Walker A and Walker B motifs are highly conserved in plant (rice, wheat, maize, and Arabidopsis) and human RAD51D homologs. The RecA domain in OsRAD51D is 45–76% and 29% identical to those in plant and human RAD51D proteins, respectively.

==Labs working on this gene==
1. Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea

==References==
<references>
<ref name="ref1"> Byun, M. Y. and Kim, W. T. (2014), Suppression of OsRAD51D results in defects in reproductive development in rice (Oryza sativa L.). The Plant Journal, 79: 256–269. doi: 10.1111/tpj.12558 </ref>
<ref name="ref2">Bleuyard, J.Y., Gallego, M.E., Savigny, F. and White, C.I. (2005) Differing requirements for the Arabidopsis Rad51 paralogs in meiosis and DNA repair. Plant J. 41, 533–545. </ref>
<ref name="ref3">Durrant, W.E., Wang, S. and Dong, X. (2007) Arabidopsis SNI1 and RAD51D regulate both gene transcription and DNA recombination during the defense response. Proc. Natl Acad. Sci. USA, 104, 4223–4227. </ref>
<ref name="ref4">Da Ines, O., Degroote, F., Amiard, S., Goubely, C., Gallego, M.E. and White, C.I. (2013) Effects of XRCC2 and RAD51B mutations on somatic and meiotic recombination in Arabidopsis thaliana. Plant J. 74, 959–970. </ref>
<ref name="ref5">Wang, Y., Xiao, R., Wang, H., Cheng, Z., Li, W., Zhu, G., Wang, Y. and Ma, H. (2013) The Arabidopsis RAD51 paralogs RAD51B, RAD51D and XRCC2 play partially redundant roles in somatic DNA repair and gene regulation. New Phytol. 201, 292–304. </ref>
<ref name="ref6">Markmann-Mulisch, U., Wendeler, E., Zobell, O., Schween, G., Steinbiss, H.H. and Reissa, B. (2007) Differential requirements for RAD51 in Physcomitrella patens and Arabidopsis thaliana development and DNA damage repair. Plant Cell, 19, 3080–3089. </ref>
<ref name="ref7">Osakabe, K., Abe, K., Yamanouchi, H. et al. (2005) Arabidopsis Rad51B is important for double-strand DNA breaks repair in somatic cells. Plant Mol. Biol. 57, 819–833. </ref>
<ref name="ref8">Hanson, P.I. and Whiteheart, S.W. (2005) AAA+ proteins: have engine, will work. Nat. Rev. Mol. Cell Biol. 6, 519–529.</ref>
<ref name="ref9">Cox, M.M. (2007) Motoring along with the bacterial RecA protein. Nat. Rev. Mol. Cell Biol. 8, 127–138. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0104200|
Description = RecA bacterial DNA recombination family protein|
Version = NM_001069094.2 GI:297609026 GeneID:4346376|
Length = 5790 bp|
Definition = Oryza sativa Japonica Group Os09g0104200, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:431724..437513|
CDS = 432061..432099,434262..434408,435614..435676|
GCID = <gbrowseImage1>
name=NC_008402:431724..437513
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:431724..437513
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgatgatatcagtggctatgattctaaagaagctagcatatgagcataatctatctgttctggttactaaccatatggttgctgggaatggagctcccaagcctgctcttggtgagagctggaaaactgttccacatgtccgcttggtgatatctcgtgagcgtggtagcaaaatctgcgcagcaactgtgctgaagcacacactactggcttcgggccgtgttatgaaatttgccgtaccaagctga</cdnaseq>|
AA = <aaseq>MMISVAMILKKLAYEHNLSVLVTNHMVAGNGAPKPALGESWKTV PHVRLVISRERGSKICAATVLKHTLLASGRVMKFAVPS</aaseq>|
DNA = 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Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069094.2 RefSeq:Os09g0104200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os10g0513200

2014-12-27T13:52:07Z

Shijc:

OsNIP3;1, a rice boric acid channel, regulates boron distribution and is essential for growth under boron-deficient conditions. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os10g0513200-Fig1.png|right|thumb|200px|'' Altered boron distribution in shoots of OsNIP3;1 RNAi plants. (from reference <ref name="ref1" />).'']]
OsNIP3;1 is the boric acid channel gene, with similarities to both AtNIP5;1 and AtNIP6;1. This suggests that OsNIP3;1 functions both in roots and shoots for boron homeostasis, whereas AtNIP5;1 and AtNIP6;1 mediate boron transport in roots and shoots, respectively. The promoter–GUS staining analysis is indicative of a role for OsNIP3;1 in the vascular bundles of leaf sheaths and blades, as well as in root exodermis and stele.
OsNIP3;1 regulates boron distribution among leaf tissues, similar to AtNIP6;1 in A. thaliana <ref name="ref2" />. The RNAi plants of OsNIP3;1 showed significant disturbance in boron distribution between leaf blades and leaf sheaths and among leaf blades. Because boron transport in shoots is primarily transpiration-dependent, boron tends to accumulate in large, mature leaves with higher transpiration rates <ref name="ref3" />. Boron is distributed to larger leaf blades rather than the leaf sheath in OsNIP3;1 RNAi plants. This suggests that OsNIP3;1 plays a role in regulating boron distribution against transpirational flow. Preferential boron distribution to young tissues is essential for their development under boron-deficient conditions, and AtNIP6;1 plays a central role in this process in A. thaliana <ref name="ref2" />. Imbalance of boron distribution in RNAi plants was more apparent under boron-deficient conditions, which may result in growth defects in RNAi plants under boron-deficient conditions. In addition, OsNIP3;1 functions in boron distribution among leaves under boron-sufficient conditions. Rice has efficient boron transport and utilization mechanisms, such as boron translocation from mature leaves <ref name="ref4" /> and endosperm <ref name="ref5" />. In broccoli (Brassica oleracea) and lupin (Lupinus albus), boron remobilization is mediated through the phloem <ref name="ref6" />. OsNIP3;1 expression in the phloem tissues of leaf sheaths suggests that OsNIP3;1 plays a role in boron remobilization.
Disruption of AtNIP5;1 impaired the growth of A. thaliana by resulting in insufficient boron uptake under boron-deficient conditions <ref name="ref7" />. In rice, RNAi-mediated suppression of OsNIP3;1 expression also caused a severe growth deficit under the boron-deficient conditions, suggesting that OsNIP3;1 is involved in root boron uptake, similar to AtNIP5;1. Boron-dependent mRNA accumulation and enhanced expression of OsNIP3;1 in the exodermis under boron-deficient conditions supports this hypothesis, and similar results have been reported for AtNIP5;1 <ref name="ref7" />. One of the two Casparian strips in rice roots is located in the exodermis, and a transporter expressed in this cell type in rice roots plays a major role in nutrient uptake <ref name="ref8" /><ref name="ref9" /><ref name="ref10" />. Under boron-deficient conditions, OsBOR1 expression is induced in the exodermis, which is thought to enhance boron transport into shoots <ref name="ref9" />. OsNIP3;1 expressed in the exodermis is likely to transport boron coordinately with OsBOR1, similar to AtBOR1 and AtNIP5;1 <ref name="ref11" /><ref name="ref12" />. However, unlike nip5;1 mutants <ref name="ref7" />, disruption of OsNIP3;1 does not affect the total boron concentration or the boron distribution between shoots and roots, although boron contents in shoots were significantly lower in RNAi plants under boron-deficient conditions. These results suggest that OsNIP3;1 plays a role in facilitating boron uptake in roots, similar to AtNIP5;1, but the contribution of OsBOR1 and other transporters in boron uptake may be greater. In support of this hypothesis, the growth defect phenotype of osbor1 plants under boron-deficient conditions is considerably more severe <ref name="ref9" /> than that of OsNIP3;1 RNAi plants. OsBOR1 and OsNIP3;1 are expressed in the exodermis and endodermis under boron-deficient conditions <ref name="ref9" />. The silicon uptake channel OsNIP2;1 (Lsi1), which is also expressed in the exodermis and endodermis <ref name="ref8" />, may mediate root boron uptake (Schnurbusch et al., 2010). In A. thaliana, AtNIP5;1 and AtBOR1 are expressed mainly in the epidermis and endodermis, respectively <ref name="ref12" />. The distinct cell-type specificity of AtNIP5;1 compared with AtBOR1 highlights the major contribution of AtNIP5;1 to boron uptake by A. thaliana roots <ref name="ref7" />, whereas the redundant function and cell type-specific expression of OsNIP3;1 and other transporters in rice roots may have abrogated the effect of OsNIP3;1 disruption on boron uptake. It should be noted that the rice endosperm supplies sufficient boron to developing seedlings under boron-starved conditions <ref name="ref5" />. This compensatory boron delivery to rice seedlings under boron-deficient conditions may also mask the reduction of boron uptake as the result of OsNIP3;1 repression.
The paradox between unchanged boron uptake and significant growth inhibition of the OsNIP3;1 RNAi plants may also be explained by insufficient boron availability and/or improper distribution in the cells, similar to the ‘iron (Fe) deficiency paradox’ <ref name="ref13" />. The Fe concentration in Fe-deficient leaves showing chlorosis is often comparable to that of Fe-sufficient leaves, and despite similar concentration to Fe-requiring enzymes in cells is believed to cause this phenomenon. Similar phenotypes have been observed in the mutants AtBOR2 and OsBOR4 <ref name="ref14" /><ref name="ref15" />. These studies suggest that the lack of functional boron transporters impairs proper boron distribution in the cells and results in boron deficiency symptoms without affecting tissue boron concentrations. Given the cell type-specific expression patterns of OsNIP3;1, it is possible that disruption of OsNIP3;1 alters boron distribution to cells and/or cellular compartments with high boron demands, which may impair whole plant growth through homeostatic regulation.

===Mutation===
[[File: Shijc-Os10g0513200-Fig2.png|right|thumb|200px|'' Growth defect of OsNIP3;1 RNAi plants under boron-deficient conditions. (from reference <ref name="ref1" />).'']]
RNAi-mediated OsNIP3;1 knockdown plants were established. The target sequence was selected from the C–terminal and 3′ UTR regions of OsNIP3;1 to avoid non-specific down-regulation of other OsNIP3 genes. The accumulation of OsNIP3;1 transcript was quantified in roots by RT-mediated real-time PCR. RNA samples were prepared from plants subjected to 1 day of −B treatment. Two independent lines of T2 progeny (L9 and L13) showed reduced OsNIP3;1 expression in both shoots and roots. In roots, the expression levels of OsNIP3;1 in lines L9 and L13 decreased to 3 and 30%, respectively, of the levels in the wild-type plants.

===Expression===
[[File: Shijc-Os10g0513200-Fig3.png|right|thumb|200px|'' Subcellular localization of GFP–OsNIP3;1. (from reference <ref name="ref1" />).'']]
To investigate the subcellular localization of OsNIP3;1, GFP fused N–terminally to OsNIP3;1 (GFP–OsNIP3;1) was expressed transiently under the control of the CaMV 35S RNA promoter in tobacco (Nicotiana tabacum) BY2 cells. Fluorescence was observed mainly at the cell periphery, indicative of plasma membrane localization of the fusion protein, whereas free GFP localized to the cytoplasm and nucleus. This suggests that OsNIP3;1 is a plasma membrane-localized protein.

===Evolution===
[[File: Shijc-Os10g0513200-Fig4.png|right|thumb|200px|'' Rooted phylogenetic tree of sub-group II NIP proteins and their close relatives inA. thaliana (At), Lotus japonicus (Lj), grape (Vv), rice (Os), sorghum (Sb) and maize (Zm). (from reference <ref name="ref1" />).'']]
Among 38 rice MIP genes listed in GenBank, 12 are known to belong to the OsNIP sub-family <ref name="ref16" />. Based on phylogenetic analysis, the OsNIP sub-family may be divided into four groups: OsNIP1, OsNIP2, OsNIP3 and OsNIP4 <ref name="ref17" />. Among 10 rice NIP genes and nine A. thaliana NIP genes, OsNIP3;1 (accession number AAG13499) is most similar to A. thaliana AtNIP5;1 <ref name="ref18" />. Specific PCR primers were designed based on the predicted ORF of OsNIP3;1. Using cDNA prepared from plants grown under boron-deficient conditions as a template, a fragment corresponding to OsNIP3;1 ORF was isolated. The nucleotide sequence of the OsNIP3;1 cDNA was identical to the transcript sequence of LOC_Os10g36924.1. Phylogenetic analysis of the predicted amino acid sequences of all NIP genes in rice and A. thaliana revealed that OsNIP3;1 has high similarity to AtNIP5;1 (71.1% identity and 86.2% similarity) and AtNIP6;1 (60.7% identity and 80.0% similarity). There is no other paralog of OsNIP3;1 that is similar to AtNIP6;1, and OsNIP3;2–3;5 were more distantly related to OsNIP3;1.
The substrate selectivity of aquaglycerol porins is determined based on the amino acid composition of the pore filter <ref name="ref18" />. As mentioned above, NIPs may be classified into three sub-groups (NIP I, II and III) based on the sequences forming the pore <ref name="ref18" /><ref name="ref19" />. OsNIP3;1 belongs to NIP sub-group II. All three A. thaliana NIPs from this group (AtNIP5;1, AtNIP6;1 and AtNIP7;1) possess transport activity for boric acid <ref name="ref7" /><ref name="ref11" /><ref name="ref20" />, suggesting that members of sub-group II have functions in boric acid transport. NIPs belonging to sub-group II were identified from the representative eudicots A. thaliana, Lotus japonicus and Vitis vinifera (grape) and the monocots rice, maize (Zea mays) and sorghum (Sorghum bicolor) based on genomic database analysis. Orthologs of AtNIP5;1 were identified from all tested plant species, including rice OsNIP3;1; however, orthologs of AtNIP6;1 were identified only in eudicots. OsNIP3;2–3;5 and their orthologs were unique to monocots, and were more distantly related to OsNIP3;1/AtNIP5;1 and AtNIP6;1.

==Labs working on this gene==
1. Biotechnology Research Center, University of Tokyo, Tokyo, Japan
2. Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
3. Division of Applied Bioscience, Graduate School of Agriculture, Hokkaido University, Sapporo, Japan

==References==
<references>
<ref name="ref1">Hanaoka, H., Uraguchi, S., Takano, J., Tanaka, M. and Fujiwara, T. (2014), OsNIP3;1, a rice boric acid channel, regulates boron distribution and is essential for growth under boron-deficient conditions. The Plant Journal, 78: 890–902. </ref>
<ref name="ref2">Tanaka, M., Wallace, I.S., Takano, J., Roberts, D.M. and Fujiwara, T. (2008) NIP6;1 is a boric acid channel for preferential transport of boron to growing shoot tissues in Arabidopsis. Plant Cell, 20, 2860–2875. </ref>
<ref name="ref3">Brown, P.H. and Shelp, B.J. (1997) Boron mobility in plants. Plant Soil, 193, 85–101. </ref>
<ref name="ref4">Bellaloui, N., Yadavc, R.C., Chern, M.S., Hu, H., Gillen, A.M., Greve, C., Dandekar, A.M., Ronald, P.C. and Brown, P.H. (2003) Transgenically enhanced sorbitol synthesis facilitates phloem-boron mobility in rice. Physiol. Plant. 117, 79–84. </ref>
<ref name="ref5">Uraguchi, S. and Fujiwara, T. (2011) Significant contribution of boron stored in seeds to initial growth of rice seedlings. Plant Soil, 340, 435–442. </ref>
<ref name="ref6">Shelp, B.J., Kitheka, A.M., Vanderpool, R.A., Van Cauwenberghe, O.R. and Spiers, G.A. (1998) Xylem-to-phloem transfer of boron in broccoli and lupin during early reproductive growth. Physiol. Plant. 104, 533–540. </ref>
<ref name="ref7">Takano, J., Wada, M., Ludewig, U., Schaaf, G., von Wiren, N. and Fujiwara, T. (2006) The Arabidopsis major intrinsic protein NIP5;1 is essential for efficient boron uptake and plant development under boron limitation. Plant Cell, 18, 1498–1509. </ref>
<ref name="ref8">Ma, J.F., Tamai, K., Yamaji, N., Mitani, N., Konishi, S., Katsuhara, M., Ishiguro, M., Murata, Y. and Yano, M. (2006) A silicon transporter in rice. Nature, 440, 688–691. </ref>
<ref name="ref9">Nakagawa, Y., Hanaoka, H., Kobayashi, M., Miyoshi, K., Miwa, K. and Fujiwara, T. (2007) Cell-type specificity of the expression of OsBOR1, a rice efflux boron transporter gene, is regulated in response to boron availability for efficient boron uptake and xylem loading. Plant Cell, 19, 2624–2635. </ref>
<ref name="ref10">Sasaki, A., Yamaji, N., Yokosho, K. and Ma, J.F. (2012) Nramp5 is a major transporter responsible for manganese and cadmium uptake in rice. Plant Cell, 24, 2155–2167. </ref>
<ref name="ref11">Takano, J., Miwa, K. and Fujiwara, T. (2008) Boron transport mechanisms: collaboration of channels and transporters. Trends Plant Sci. 13, 451–457. </ref>
<ref name="ref12">Takano, J., Tanaka, M., Toyoda, A., Miwa, K., Kasai, K., Fuji, K., Onouchi, H., Naito, S. and Fujiwara, T. (2010) Polar localization and degradation of Arabidopsis boron transporters through distinct trafficking pathways. Proc. Natl Acad. Sci. USA, 107, 5220–5225. </ref>
<ref name="ref13">Römheld, V. (2000) The chlorosis paradox: Fe inactivation as a secondary event in chlorotic leaves of grapevine. J. Plant Nutr. 23, 1629–1643. </ref>
<ref name="ref14">Miwa, K., Wakuta, S., Takada, S., Ide, K., Takano, J., Naito, S., Omori, H., Matsunaga, T. and Fujiwara, T. (2013) Roles of BOR2, a boron exporter, in cross linking of rhamnogalacturonan II and root elongation under boron limitation in Arabidopsis. Plant Physiol. 163, 1699–1709. </ref>
<ref name="ref15">Tanaka, N., Uraguchi, S., Saito, A., Kajikawa, M., Kasai, K., Sato, Y., Nagamura, Y. and Fujiwara, T. (2013) Roles of pollen-specific boron efflux transporter, OsBOR4, in the rice fertilization process. Plant Cell Physiol. 54, 2011–2019. </ref>
<ref name="ref16">Bansal, A. and Sankararamakrishnan, R. (2007) Homology modeling of major intrinsic proteins in rice, maize and A. thaliana: comparative analysis of transmembrane helix association and aromatic/arginine selectivity filters. BMC Struct. Biol. 7, 27. </ref>
<ref name="ref17">Sakurai, J., Ishikawa, F., Yamaguchi, T., Uemura, M. and Maeshima, M. (2005) Identification of 33 rice aquaporin genes and analysis of their expression and function. Plant Cell Physiol. 46, 1568–1577. </ref>
<ref name="ref18">Wallace, I.S., Choi, W.G. and Roberts, D.M. (2006) The structure, function and regulation of the nodulin 26-like intrinsic protein family of plant aquaglyceroporins. Biochim. Biophys. Acta, 1758, 1165–1175. </ref>
<ref name="ref19">Mitani-Ueno, N., Yamaji, N., Zhao, F.-J. and Ma, J.F. (2011) The aromatic/arginine selectivity filter of NIP aquaporins plays a critical role in substrate selectivity for silicon, boron, and arsenic. J. Exp. Bot. 62, 4391–4398. </ref>
<ref name="ref20">Li, T., Choi, W.-G., Wallace, I.S., Baudry, J. and Roberts, D.M. (2011) Arabidopsis thaliana NIP7;1: an anther-specific boric acid transporter of the aquaporin superfamily regulated by an unusual tyrosine in helix 2 of the transport pore. Biochemistry, 50, 6633–6641. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os10g0513200|
Description = Similar to Nodulin-26 (N-26)|
Version = NM_001071583.2 GI:297610777 GeneID:4349102|
Length = 1570 bp|
Definition = Oryza sativa Japonica Group Os10g0513200, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 10|Chromosome 10]]|
AP = Chromosome 10:20233381..20234950|
CDS = 20233841..20234036,20234687..20234949|
GCID = <gbrowseImage1>
name=NC_008403:20233381..20234950
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008403:20233381..20234950
source=RiceChromosome10
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>gtcccggcgtacgtcgccgtccaggtgctcggctccatctgcgccggcttcgccctcaagggcgtcttccaccccttcctctccggcggcgtcaccgtccccgaccccaccatctccaccgcccaggccttcttcaccgagttcatcatcaccttcaacctcctcttcgtcgtcaccgccgtcgccaccgacacccgcgccgtcggcgagctcgccggcatcgccgtcggcgccgccgtcaccctcaacatcctcatcgccgggccgacgacaggagggtcgatgaacccggtgaggacgctggggccggcggtggcggcgggcaactaccggcagctgtggatatacctgatcgcgccgacgctgggcgcggtcgccggcgccggcgtgtacacggcggtgaagctccgcgacgagaacggcgagaccccgcgcccccagcgcagcttccgccgctga</cdnaseq>|
AA = <aaseq>VPAYVAVQVLGSICAGFALKGVFHPFLSGGVTVPDPTISTAQAF FTEFIITFNLLFVVTAVATDTRAVGELAGIAVGAAVTLNILIAGPTTGGSMNPVRTLG PAVAAGNYRQLWIYLIAPTLGAVAGAGVYTAVKLRDENGETPRPQRSFRR</aaseq>|
DNA = <dnaseqindica>915..1110#2..264#ggtcccggcgtacgtcgccgtccaggtgctcggctccatctgcgccggcttcgccctcaagggcgtcttccaccccttcctctccggcggcgtcaccgtccccgaccccaccatctccaccgcccaggccttcttcaccgagttcatcatcaccttcaacctcctcttcgtcgtcaccgccgtcgccaccgacacccgcgccgtcggcgagctcgccggcatcgccgtcggcgccgccgtcaccctcaacatcctcatcgccgggtacgtataatcctcttcctcctccttgtagccaggttttaatctttcagtttgaatgtttctatcggaacgtgtcgatataccgaaatttggatcaaattttagtcaaattaagcaaattattaccaaaataaaaaaaattggccgaaataatcacataggggatccaaaataaccaaaattttggaaatttcatttcagaatttttgaaccctgctcgtagcacgttactgcctctgtgttatattgcaagtttattaaatttatataagaatatagtaacatttctaacataaataaacatattaaaagttagttttattaaaaactattttctataaatttggaaaaggaaattttgaaaaaaaaataaaacgacctataatatgaaacaatgagcactaaaaatggatggatttccaaaaaaaaaagaaaatttgaaccatgccacacaaattttataaattttgtaaaatttgtgatatgacaccctgacccacatgacattaacttatgtggttcctacgtgtcattgagatacgggtggcatattttaaattttacaaaattagggtgtcatggttccaacaaacaaaaaaaaaatggatggatttgatctccggctaaccggcggcgtgggtgcggtgcaggccgacgacaggagggtcgatgaacccggtgaggacgctggggccggcggtggcggcgggcaactaccggcagctgtggatatacctgatcgcgccgacgctgggcgcggtcgccggcgccggcgtgtacacggcggtgaagctccgcgacgagaacggcgagaccccgcgcccccagcgcagcttccgccgctgatccaaatcatatccaaatccatatccataaaaacaaattattatacacgacgtagttaacctgaacaaattatatggcttccaattaaaaaaaaatcagtcgtgtcatccttgggccttgttccacatgggccgaacaccaagagaaatccgcgtgaatatgggccgtgattttggttgaaaattttcggtccattcacgtagatgggccgggtttgaggccttttcaaatgagaccttgggggcgtgtaataaaccccgttttgcttcgtccagaacggcagagtataatagttcgagttgtgtgtgatgtgtcagaactcagaataaaaatgcacgccgatgcaccggggtgatgggcatcttgctgtgcgaatggtgtaaggttttatttaatttcctatttgacaaattgtgtaattttccctgttccgacattgataattgagaaaaattgtccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001071583.2 RefSeq:Os10g0513200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 10]]
[[Category:Chromosome 10]]

Os09g0104200

2014-12-27T13:51:19Z

Shijc:

OsRAD51D plays a critical role in reproductive growth in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os09g0104200-Fig1.png|right|thumb|200px|'' Phenotypic characterization of vegetative and reproductive organs of osrad51d mutant and Ubi:RNAi-OsRAD51D transgenic rice plants. (from reference <ref name="ref1" />).'']]
Osrad51d knock-out and RNAi-mediated knock-down transgenic (Ubi:RNAi-OsRAD51D) plants (Figure 2) revealed that suppression of OsRAD51D exerted negligible effects on the vegetative growth of rice plants (Figure 3a). In contrast, loss of OsRAD51D caused defects in reproductive growth. Homozygous mutant flowers displayed impaired development of pollen (Figure 3b–d) and Table 1), lemma and palea (Figure 4a,b), stamen, and carpel (Figure 4c and Table 2), which resulted in sterile flowers (Figure 4d). The abnormalities of heterozygous mutant and Ubi:RNAi-OsRAD51D plants were intermediate between wild type and homozygous mutant plants.
[[File: Shijc-Os09g0104200-Fig2.png|right|thumb|200px|'' Cytogenetic analysis of root tips, PMCs, and pollen cells from wild type (WT) andosrad51d mutant rice plants. (from reference <ref name="ref1" />).'']]
Furthermore, previous studies in Arabidopsis indicate that AtRAD51B, AtRAD51D, and AtXRCC2 are not essential for meiosis <ref name="ref2" /><ref name="ref3" /><ref name="ref4" />(Bleuyard et al., 2005; Durrant et al., 2007; Da Ines et al., 2013). Triple, as well as single/double, mutations of AtRAD51B, AtRAD51D, and AtXRCC2 result in normal growth and fertility <ref name="ref5" />(Wang et al., 2013). These results are in sharp contrast with our results in that loss of OsRAD51D function caused severe errors in floral development and infertility (Figures 3 and 4). Cytogenetic analysis showed that osrad51d PMCs were unable to form normal homologous chromosome pairings and most mutant chromosomes were fragmented and scattered throughout the cells during meiosis I (Figure 5b). Due to these meiotic anomalies, homozygous osrad51d pollen cells contained numerous micro-nuclei and formed atypical tetrads, resulting in malfunctioning pollen (Figure 5c). Taken together, our results are consistent with the view that, unlike Arabidopsis AtRAD51D, OsRAD51D is critically involved in meiosis and is an essential factor for reproductive growth in rice plants. Nevertheless, it is still possible that absence of OsRAD51D could be affecting cellular stability of other OsRAD51 paralogs and thus producing an indirect effect on meiosis and floral development. A previous study of RAD51 in moss Physcomitrella patens suggested that there are fundamental differences in the use of the HR pathway in different plant species, and that an essential role of RAD51 in viability does not correlate with organism taxonomic complexity<ref name="ref6" />(Markmann-Mulisch et al., 2007).

===Mutation===
[[File: Shijc-Os09g0104200-Fig3.png|right|thumb|200px|'' Molecular characterization of T-DNA osrad51d knock-out mutant and Ubi:RNAi-OsRAD51D knock-down transgenic rice plants. (from reference <ref name="ref1" />).'']]
A single loss-of-function rice mutant line that contained a T-DNA insertion in the OsRAD51D gene was obtained (Yi and An, 2013; http://signal.salk.edu/cgi-bin/RiceGE). This mutant was named osrad51d. The T-DNA insertion was mapped to the third exon in OsRAD51D located on chromosome 9 (line PFG_4A-00300.R; Figure 2a). A homozygous line for the T-DNA insertion was identified by genomic PCR with FW2/RV3 and RB/RV3 primer sets (Figure 2b). Disruption of OsRAD51D by T-DNA insertion was further verified by RT-PCR. The results showed that the homozygous osrad51d mutant leaves contained undetectable amounts of all three OsRAD51D isoform transcripts under the experimental conditions, whereas the heterozygous osrad51d line possessed reduced levels (approximately 50%) of the transcripts (Figure 2c). Genomic Southern blot analysis indicated that the osrad51d mutant progeny contained a single T-DNA integration into the OsRAD51D gene (Figure 2d). Because only one allele of the osrad51d loss-of-function mutant plant was obtained, RNAi-mediated knock-down transgenic rice lines (Ubi:RNAi-OsRAD51D) were generated. RT-PCR revealed that the mRNA levels of OsRAD51D.1/OsRAD51D.3 and OsRAD51D.2 significantly decreased in the independent T2 Ubi:RNAi-OsRAD51D lines #1 and #2 (Figure 2c). Genomic Southern blotting demonstrated that these two RNAi-transgenic plants were independent lines (Figure 2d).

===Expression===
[[File: Shijc-Os09g0104200-Fig4.png|right|thumb|200px|'' Identification and expression of OsRAD51D in rice. (from reference <ref name="ref1" />).'']]
OsRAD51D.1/OsRAD51D.3 and OsRAD51D.2 isoforms were expressed in all tissues examined in rice plants (Figure 1d). A FW1/RV1 primer set detected both OsRAD51D.1 and OsRAD51D.3 mRNAs due to their similar structure. Yeast two-hybrid assay showed that human RAD51B and RAD51D interacted in the presence of RAD51C (Schild et al., 2000). In vivo immuno-precipitation results indicated that human AD51 paralogs form the RAD51B-RAD51C-RAD51D-XRCC2 complex (Masson et al., 2001; Liu et al., 2002). Arabidopsis AtRAD51B and AtRAD51C also interact in yeast cells <ref name="ref7" />(Osakabe et al., 2005). Yeast two-hybrid studies showed that rice OsRAD51D.1 interacted with OsRAD51B and OsRAD51C, whereas OsRAD51D.2 and OsRAD51D.3 were unable to associate with other OsRAD51 paralogs (Figure 1e). In vitro pull-down assays also indicated that bacterially expressed OsRAD51D.1, but not OsRAD51D.2 and OsRAD51D.3, was associated with OsRAD51B and OsRAD51C (Figures 1f and S3). These results raise the possibility that the OsRAD51D.1 isoform is the major OsRAD51D protein in rice plants.

===Splicing Variants===
There are five RAD51 paralogs, OsRAD51B, OsRAD51C, OsRAD51D, OsXRCC2, and OsXRCC3, in rice (Figure S1). The rice OsRAD51D gene is 5804 bp in length and composed of nine exons and eight introns (Figure 1a). Three splicing variants of OsRAD51D were predicted and termed OsRAD51D.1 (GenBank accession no. KJ472480), OsRAD51D.2 (GenBank accession no. KJ472481), and OsRAD51D.3 (GenBank accession no. KJ472482) (Figure 1b). The coding regions of OsRAD51D.1, OsRAD51D.2, and OsRAD51D.3 are 849 bp encoding 283 amino acids (30.3 kDa), 552 bp encoding 184 amino acids (19.8 kDa), and 768 bp encoding 256 amino acids (27.4 kDa), respectively (Figure 1c). All three deduced OsRAD51D proteins contained Walker A and Walker B motifs and a RecA domain in their central regions (Figure 1c). Walker A and Walker B motifs function as nucleotide binding domains <ref name="ref8" />(Hanson and Whiteheart, 2005), whereas the RecA motif is an ATP hydrolysis domain <ref name="ref9" />(Cox, 2007). Both Walker A and Walker B motifs are highly conserved in plant (rice, wheat, maize, and Arabidopsis) and human RAD51D homologs (Figure S2a,b). The RecA domain in OsRAD51D is 45–76% and 29% identical to those in plant and human RAD51D proteins, respectively.

==Labs working on this gene==
1. Department of Systems Biology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea

==References==
<references>
<ref name="ref1"> Byun, M. Y. and Kim, W. T. (2014), Suppression of OsRAD51D results in defects in reproductive development in rice (Oryza sativa L.). The Plant Journal, 79: 256–269. doi: 10.1111/tpj.12558 </ref>
<ref name="ref2">Bleuyard, J.Y., Gallego, M.E., Savigny, F. and White, C.I. (2005) Differing requirements for the Arabidopsis Rad51 paralogs in meiosis and DNA repair. Plant J. 41, 533–545. </ref>
<ref name="ref3">Durrant, W.E., Wang, S. and Dong, X. (2007) Arabidopsis SNI1 and RAD51D regulate both gene transcription and DNA recombination during the defense response. Proc. Natl Acad. Sci. USA, 104, 4223–4227. </ref>
<ref name="ref4">Da Ines, O., Degroote, F., Amiard, S., Goubely, C., Gallego, M.E. and White, C.I. (2013) Effects of XRCC2 and RAD51B mutations on somatic and meiotic recombination in Arabidopsis thaliana. Plant J. 74, 959–970. </ref>
<ref name="ref5">Wang, Y., Xiao, R., Wang, H., Cheng, Z., Li, W., Zhu, G., Wang, Y. and Ma, H. (2013) The Arabidopsis RAD51 paralogs RAD51B, RAD51D and XRCC2 play partially redundant roles in somatic DNA repair and gene regulation. New Phytol. 201, 292–304. </ref>
<ref name="ref6">Markmann-Mulisch, U., Wendeler, E., Zobell, O., Schween, G., Steinbiss, H.H. and Reissa, B. (2007) Differential requirements for RAD51 in Physcomitrella patens and Arabidopsis thaliana development and DNA damage repair. Plant Cell, 19, 3080–3089. </ref>
<ref name="ref7">Osakabe, K., Abe, K., Yamanouchi, H. et al. (2005) Arabidopsis Rad51B is important for double-strand DNA breaks repair in somatic cells. Plant Mol. Biol. 57, 819–833. </ref>
<ref name="ref8">Hanson, P.I. and Whiteheart, S.W. (2005) AAA+ proteins: have engine, will work. Nat. Rev. Mol. Cell Biol. 6, 519–529.</ref>
<ref name="ref9">Cox, M.M. (2007) Motoring along with the bacterial RecA protein. Nat. Rev. Mol. Cell Biol. 8, 127–138. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os09g0104200|
Description = RecA bacterial DNA recombination family protein|
Version = NM_001069094.2 GI:297609026 GeneID:4346376|
Length = 5790 bp|
Definition = Oryza sativa Japonica Group Os09g0104200, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 9|Chromosome 9]]|
AP = Chromosome 9:431724..437513|
CDS = 432061..432099,434262..434408,435614..435676|
GCID = <gbrowseImage1>
name=NC_008402:431724..437513
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008402:431724..437513
source=RiceChromosome09
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgatgatatcagtggctatgattctaaagaagctagcatatgagcataatctatctgttctggttactaaccatatggttgctgggaatggagctcccaagcctgctcttggtgagagctggaaaactgttccacatgtccgcttggtgatatctcgtgagcgtggtagcaaaatctgcgcagcaactgtgctgaagcacacactactggcttcgggccgtgttatgaaatttgccgtaccaagctga</cdnaseq>|
AA = <aaseq>MMISVAMILKKLAYEHNLSVLVTNHMVAGNGAPKPALGESWKTV PHVRLVISRERGSKICAATVLKHTLLASGRVMKFAVPS</aaseq>|
DNA = <dnaseqindica>5415..5453#3106..3252#1838..1900#ttccccttctggctgtaatggcgatggcggcgacgtcggcgagcggcggcgccggctgcttccccaggcctcctccctccggcggcgaggttagtcctccgtcctcggctgcttgacggccatttcagttcatccccagcttttttattcctgcttcgaaatctcagcttaatcgggaacggaatgctgcacaaaaaccgtttgctcttgacgagataatgcgcatgcgattcacccgcagttggtttcacggcttcatactactgatcaatcgtattttctgtgtgtatgtggcatggatttgtgcttggggtacaggagaagaagcaagatgaggaggggcaatgctttctggatggaatggacttgctcaaggatgcgacggagaacaagcgcttcctccccacgggccttcaagggtactcctatcttcaatgtaccaatcatttcctttccctctctatctattgctattggccctcccccaacttgtttggatcataggattcccctaactgccttgctttagtttttttagtttttgggtaatttcactaccaaattgcagattttgacttcatcatgtcctcaattttccagcgtcgacgcgcttcttggaggcggcctgcgccaaggtcagctcactgaaataaccggccaatcgtcctccggtaaaacacaggtgaaaatgttaaccacttctatctttcttaacttattagacgcaatagatagatatacattttatatgcttactcctccggacaagattggcttgccaaaaacagtaggattttaaggtatacatcacaattcacaagcggcactgttgtttattctgtctatgtaactgcaggtctgtctttgttctgcttcacatgtggcagccaggcagttgggtgttgttatgtacttggatactagcaattccttttcccctagccgcattgctcgaatagttgatggattccccatctctttggtcagagaggtaggtaatcatacttgtacacatatttgaatactgctcctaccctgttacttggacttacctgaattgcttcctttgctgtggtgtcactaaatatagttgaagacatgtttctgctattagattactctaactagtaacacttgtttaacaacttgctatactacttgcttttttctaattaccacatttgacttgcagccaaagaatgtgcgactcgagagggtcatgagcagcatcatttgtaagtcagtctttgatatattcgatttgtttgaagtgctacatcaacttgaattgtcactgaagagcaaggtgagtgtgaagtgattgttcaatttgtgccttgaaaaactctgatgtgccacgtgctttttaggtaaacaatgggggtaacaagatatgcttgcttatcattgactcaatatcgtctatacttgctcccatcaacggtgggaagtatccacgaggtacttgcatagtctttgtgccctacttttattattcatagcataagttgcaccttgctattgaacaagtaaatcagtctcgataagcagggacgtcataagtggctgagatatactagatccgattagcaagttagaaatagcagaaaattagttcagtgagcacttaacctgcaattatacagcgagatattgatactttgatctggtcataaattcaatgtgcttctgttaattgttgaagttccaaaaatcatttattttctcacacaattacttcctgagagggtccttattaatttttaaagtttattatgaagtaaatttgttgtttccttttgtctctgcatgtcttattaacctaacagggcgatcgatgatgatatcagtggctatgattctaaagaagctagcatatgagcataatctatctgttctggtaattctactttagtctaatttgtgtgctaataatttttggcatttgcactgcacgctttgggttgagcatatctgcacaaggctttctaaaatattattctgactcatcaagctattgtatgcattatacttcttttaacacatcggttgtgcaataacacctttgacaatggtgtggctaagatcacattactacagcgttcacccctttcgattgaatttagattctcatcatcctttctcgtttaaccccactcaatccccatcctgtgaattacataactgtggcccccgcaccctcatggttaaggtcatgcaatgtcctgaactcctgattgtgcctactcctggtaggatgtatgctggccagagttgctttggtctccacaattttatattgcttgcacttccttacatacagagaggtgacccttaacctccaggttgcttcacatgaaataggcagataggaacaggtggggatacatttcaagatagaatctctagaggtcaggcgtttgagtactaaagaagaactgctgtggtcacgtgccctcactgacattttttacatgttggagctagttgtcagtccacgttatcacttaaggttatgatgggcaggttaaggatcttgtgtgaatcacttaatgcacattataccgttgtgcagattttcagtttggtcacctaaatatgccacttaaactaatgtagtaacccctagtgcaatttgctctaattaattgctgtacaaattcacttattcagcatgccatctttctcatgaacagattgggacatgtatctggaaatgcttcatttcctgctttacttctaagataagctattaaagtaaattgatcatgtactgttagttttagtgggtttgctcatgtccatctctgttattctgtggaaattttaacttctctatcttgagcacatattccctctactttctctagtttagttttcctggtttggaaaaaggcaccaaagcctctattacttggagcaacttttctttagttagttaccttgaagactgactaccaagtttcagaaggcttgctaaattagagaagtcaccataaggcttgctaacttgggcactatgcctgttgtgcttaaaatgtatgctgaaacaaaaatatggtcatcattttcatttatcggtttgcccccttgcattgactccaggttactaaccatatggttgctgggaatggagctcccaagcctgctcttggtgagagctggaaaactgttccacatgtccgcttggtgatatctcgtgagcgtggtagcaaaatctgcgcagcaactgtgctgaagcacacactactggtatttgcttaaacaattagattataagtttaaatgtcataatcatagcagcattgcttattgtctttctagaaattgcattaataatgtgttagctatcattttgttgaaaataagtggtgaagatattggcatgaggagaacaaaagtagtatactccctccatccataagtctaaggcatatttcatttctagtttttccaaataagatggcatatttgtagtcttcatgcatctaagacttaaatgaaggggttatcttttcgttttacggtgctaaattaaattgttgaccggaacccgagcaatcatcttaataatcattggttgcatgcatgcatatagttccttggtgtttgttatatgtgggatgagttaatttctccttggtcttgttgacaaaagaaatacccccttgttccacaaaatttacacctattacttttgtcaccaagaccaaggagaaattaactcatcttgcatgtaacaaagatcaagctgtgtacgcacacgtgcaaccaataagtattaagatgactcctcgggttccgatcaaacatttagtttacctctccatttaagtcttggatgcatagagactacaaatagaaacaacttatttggaaaaactcaaatatgaaataggtctaattcttgtggatggagggagtatgccttagacttttggatggagggagtaaacaattatatggtgccagtgcatacctctatatcctaatcctacatgttgcgtgttgttttcatgctatgctgcatttatatatttttgtatcatctttttttttctcactttttgtgcttttgaattgggctgtgaaaacaatagtggtaggtagatgccagatacatttttctcctatataaaaatttgagctggtagtgatggccatcagtcatcagtcatcccaagtcccctctaactcaagacaaactctgtaggatcctcatggaaaatttgcaaaagccacaaactcctttagactcttatttgtttgtaggaaatatgggtataccaccagtgtacctagccaatgaagctgcacatttaatgagtatttctatgttagatctgtcttatgatgaaatggaatggtctagtacctggcaatcctgcataaacgttctgagtactgcagagaggagactgagactaaagattatgttaattcattgcttaaagaaattacatggatcgattgcttctaatgtgggtggccctaaaaatctctaaaaataacttggtaactattaaaaaaagatacttgataactggaagataacttatctcttgactctcaagtctcaacatctgcatttgccgctcgctgtgtgtgtggccatcgcattcaaatcccatagcatctgaattgtgctggcgtctgagaatccatttgcctctggccacagtagacagttgtgacatgtaagaaaaaagtgatcatgtaaatgctatgccgctgagctcaaaattaatatgcaatatccatcataatttgttttagaaatacgcacttcaaaaataaattgttttcagttgacactttatatgagatggatgttgttctttcttagttttcttttcgttgtttttcttttatttattttgtaagcagacgcctgaggctcaaattccctttcttgggtgttcgaatttagggataaaggggtggaatatgggttagaatatcaggtggggagatgctaaccttccatctctttctaatgagttaggactgtctggccttattcatactccaatcctacttctttttgcacaaatacaaatctattggcatttctttgctctctaagaatcatgcaaggaaaagacggccattttgaatgatatgctgccctgccataaattaatctgcattatatcactgcaaaggaagttttttttaatctatttgcttcttttttgcagtaatgctcacaattgatgttttacactaaattacacccacttgacaagtttgtgcactaaattagacccactaaatgacacaagacgatgctaagtaccgtcatttcttccaatgtctggtagcaaaataaattgcatgattcttggtatcatctgtacatgcccaaaaacaaaaaagtgcgggcatgtcatctttgtttttcttcattgcaggcttcgggccgtgttatgaaatttgccgtaccaagctgaattcagcaacttgatgcttcatatataaccagaagggaactgatctttgtagttcaagctatagaaagaacttcacccgtaagggtaaccttttgatttaccttggctttatgttccaggccatttgtatattaatccaatggtttttgcatgttgcctgcgtccgtggtatcacgcttaactgatccatatatatagtttcttggtaaactgaatgtatcagaaacattcagttttcaagtttttgtttcttcaattattcactgtgaatactggaaaatggtagtttcccatcagtggataaaattgaatgaaattatatttgttccttgttttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001069094.2 RefSeq:Os09g0104200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 9]]
[[Category:Chromosome 9]]

Os06g0706400

2014-12-27T13:50:36Z

Shijc:

OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os06g0706400-Fig1.png|right|thumb|200px|'' The effect of OsPTR9 on the formation of roots. (from reference <ref name="ref1" />).'']]
‘’’OsPTR9 expression is regulated by light and N source’’’
OsPTR9 is closely related to the functional di/tripeptide transporters <ref name="ref2" /> and is localized at the plasma membrane. Members of the PTR/NRT1 family transport a wide range of substrates, including di/tripeptides, nitrate, histidine, carboxylates, other N-containing compounds such as IAA-amino acid conjugates, ABA, glutathione, and even the defence compound glucosinolate, and other substrate compounds might be identified <ref name="ref3" /><ref name="ref4" /><ref name="ref5" /><ref name="ref6" /><ref name="ref7" /><ref name="ref2" />.
OsPTR9 was found to be expressed in all organs analysed, but expression levels varied. The expression of OsPTR9 was high at night and low during the light period, which is different than the expression patterns of many ammonium and nitrate transporter genes <ref name="ref8" /><ref name="ref9" />. Inorganic N is usually used for metabolic synthesis in Arabidopsis under light, but organic N is usually used for long-distance transport and substance storage under dark conditions <ref name="ref10" />. Therefore, OsPTR9 might also be an organic N transporter. Similar to AMT1;3 <ref name="ref11" />, but different from other inorganic N transporters, OsPTR9 expression also affected root growth. The expression of OsPTR9 was repressed during N starvation and induced by ammonium, similar to the expression induction of the ammonium transporter OsAMT1;2 <ref name="ref12" />. The regulation of OsPTR9-expression by N sources and light/dark changes shows that there are common feedback regulatory pathways for C/N balance in rice, similar to reports from studies of Arabidopsis <ref name="ref13" /><ref name="ref14" />.
[[File: Shijc-Os06g0706400-Fig2.png|right|thumb|200px|'' Root architecture is affected by altered expression of OsPTR9. (from reference <ref name="ref1" />).'']]
‘’’The effect of OsPTR9 on the development of roots and stems may contribute to nutrient uptake and allocation’’’
Biomass and photosynthesis rate differed most between altered-OsPTR9 expressing plants and the wild type, when ammonium or nitrate was the sole N source other than nitrate. Ammonium is the preferred N species taken up by rice <ref name="ref15" />. Root development is strongly affected by the plant's nutritional status and by the external availability of nutrients <ref name="ref16" /><ref name="ref17" />. Ammonium is complementary to nitrate in shaping lateral root development and, in Arabidopsis, the stimulation of lateral root branching by ammonium occurs in an AMT1;3-dependent manner <ref name="ref11" />. Increased expression of OsPTR9 promoted the growth of lateral roots, while a lower number of lateral roots were found in the osptr9 mutant and the OsPTR9-RNAi lines, suggesting that OsPTR9 contributes to ammonium-stimulated lateral root branching. In maize seedlings, the time required for the entire cap to be displaced by a new set of cells ranges from 24 h to 7 days, depending on growth conditions <ref name="ref18" />. Abnormal cell displacement of the root cap in the osptr9 mutant and the OsPTR9-RNAi lines might block root growth into soil, while the thickened cell wall of the osptr9 mutant and the OsPTR9-RNAi lines may hinder lateral root formation leading to reduced root surface area for N uptake. Dense cytoplasm accumulated in the cortical fibre cells of the OsPTR9-RNAi lines and the osptr9 mutant, which might suggest a transportation obstacle due to the down-expression of OsPTR9 leading to cytoplasm accumulation in cells on the outside of the cortex.
Rice roots in paddy soil prefer ammonium as the N source <ref name="ref15" />, and the major N forms in the xylem sap of rice plants are Gln and Asn <ref name="ref19" />. Down-regulation of OsPTR9 expression caused decreased concentrations of some amino acids in roots and leaves, while many amino acids accumulated in stems. These might be caused by the abnormal development of the stem, which resulted in short and slim plants, and a reduced and disordered arrangement of the outer vascular bundle. These may, finally, block N translocation from source organs (leaves and roots) to sink (seed) resulting in nutrient accumulation in the stems and a reduced number of filled seeds. Generally, N partitioning to leaves positively regulates photosynthesis and consequently improves allocation of carbohydrates to sink tissues for vegetative and reproductive growth <ref name="ref20" />. The changed levels and partitioning of amino acids and proteins might lead to the observed growth effects and reduced N translocation to seeds.

‘’’N recycling from leaves is important for increased grain yields in OsPTR9-over-expressing plants’’’
The leaves are sinks for N during the vegetative stage; subsequently, this N is remobilized to the developing seeds. Up to 80% of grain N contents are derived from leaves in rice and wheat <ref name="ref21" /> <ref name="ref22" /> <ref name="ref23" />. The high transport rate of amino acids is an essential prerequisite for seed development. Down-regulation of OsPTR9 resulted in higher concentrations of amino acids in the stems, suggesting that OsPTR9 directly or indirectly affected the transport of amino acids to seeds. Over-expression of OsPTR9 also promoted ammonium uptake, which might be the reason for the up-regulation of OsAMT1;2 expression in the OsPTR9-over-expressing lines, as OsAMT1;2 expression was shown to be induced by ammonium <ref name="ref12" />.

===Mutation===
[[File: Shijc-Os06g0706400-Fig3.png|right|thumb|200px|'' Phenotypes of rice plants with altered expression of OsPTR9. (from reference <ref name="ref1" />).'']]
An OsPTR9 T-DNA insertion mutant (04Z11AH79, osptr9) was obtained from the Rice Mutant Database at Huazhong Agricultural University, China (http://rmd.ncpgr.cn/). One T-DNA copy was inserted in the first exon of OsPTR9, that is, 521 nucleotides downstream of the start codon of the OsPTR9 gene, as verified by sequencing the flanking region. The homozygous mutant (osptr9) was screened and used for analysis. RT-PCR analysis revealed that OsPTR9 mRNA is absent in the osptr9 at both day and night. OsPTR9-RNAi transgenic rice plants (RNAi) were generated under control of the rice Ubi-1 promoter <ref name="ref24" />. Nine independent OsPTR9-RNAi lines were obtained, 3 of which showed very low OsPTR9 transcript levels in panicles. To address the effect of increased OsPTR9 expression, OsPTR9 over-expressing (OE) rice was constructed under the control of the 35S promoter <ref name="ref25" />. Three of 11 independent OE lines were obtained that accumulated large amounts of OsPTR9 transcripts.

===Expression===
[[File: Shijc-Os06g0706400-Fig4.png|right|thumb|200px|'' Subcellular localization of OsPTR9-eGFP fusion protein. (from reference <ref name="ref1" />).'']]
OsPTR9 (LOC_06g49250) is most closely related to the members of subgroup II of the PTR/NRT1 family, containing the Arabidopsis di/tripeptide transporter AtPTR2 (At2g02040) <ref name="ref7" />. The OsPTR9 mRNA (AK064899) encodes a protein with the domain (LGTGGIKPXV) characteristic of the PTR proteins <ref name="ref26" /> <ref name="ref27" />. Transient expression of 35S:OsPTR9-eGFP in onion epidermal cells resulted in green fluorescence at the periphery of the cells, outside of the nucleus. In addition, stable expression of 35S:OsPTR9-eGFP in plasmolysed root cells of tobacco and roots of rice showed OsPTR9-eGFP localized to the plasma membrane.
[[File: Shijc-Os06g0706400-Fig5.png|right|thumb|200px|'' Expression analysis of OsPTR9. (from reference <ref name="ref1" />).'']]
In roots, GUS staining was mainly observed in young main root tips and in the cortical fibre cells of lateral roots. Furthermore, OsPTR9 expression was higher in leaves and panicles than in roots and stems.
[[File: Shijc-Os06g0706400-Fig6.png|right|thumb|200px|'' OsPTR9 expression is regulated by light and N source. (from reference <ref name="ref1" />).'']]
Higher transcript levels of OsPTR9 were observed where inorganic N (NO3−, NH4+ or NH4NO3) was the sole N source, compared with organic or mixed N sources (peptone or NH4NO3 + peptone). Preliminary experiments showed that the osptr9 mutant was more seriously affected by growth on ammonium than on nitrate (data not shown), and OsPTR9 expression was induced by both low (0.5 mm) and high (5 mm) ammonium sulphate levels. The induction of OsPTR9 expression by NH4+ occurred later than that of the ammonium transporter (OsAMT1;2).

==Labs working on this gene==
1. Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
2. University of Chinese Academy of Sciences, Beijing, China
3. Key Laboratory of South China Agricultural Plant Genetics and Breeding, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
4. Institute of Plant Sciences, University of Bern, Bern, Switzerland
5. Wuhan Bioengineering Institute, Wuhan, China

==References==
<references>
<ref name="ref1">Fang, Z., Xia, K., Yang, X., Grotemeyer, M.S., Meier, S., Rentsch, D., Xu, X., Zhang, M. (2012) Altered expression of the PTR/NRT1 homologue OsPTR9 affects nitrogen utilization efficiency, growth and grain yield in rice. Plant Biotechnol. J doi: 10.1111/pbi.12031 </ref>
<ref name="ref2">Weichert, A., Brinkmann, C., Komarova, N.Y., Dietrich, D., Thor, K., Meier, S., Grotemeyer, M.S. and Rentsch, D. (2012) AtPTR4 and AtPTR6 are differentially expressed, tonoplast-localized members of the peptide transporter/nitrate transporter 1 (PTR/NRT1) family. Planta, 235, 311–323. </ref>
<ref name="ref3">Chiang, C.S., Stacey, G. and Tsay, Y.F. (2004) Mechanisms and functional properties of two peptide transporters, AtPTR2 and fPTR2. J. Biol. Chem. 279, 30150–30157. </ref>
<ref name="ref4">Kanno, Y., Hanada, A., Chiba, Y., Ichikawa, T., Nakazawa, M., Matsui, M., Koshiba, T., Kamiya, Y. and Seo, M. (2012) Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor. Proc. Natl Acad. Sci. USA, 109, 9653–9658. </ref>
<ref name="ref5">Krouk, G., Lacombe, B. and Bielach, A. (2010) Nitrate-regulated auxin transport by NRT1. 1 defines a mechanism for nutrient sensing in plants. Dev. Cell, 18, 927–937. </ref>
<ref name="ref6">Nour-Eldin, H.H., Andersen, T.G., Burow, M., Madsen, S.R., Jorgensen, M.E., Olsen, C.E., Dreyer, I., Hedrich, R., Geiger, D. and Halkier, B.A. (2012) NRT/PTR transporters are essential for translocation of glucosinolate defence compounds to seeds. Nature, 488, 531–534. </ref>
<ref name="ref7">Tsay, Y.F., Chiu, C.C., Tsai, C.B., Ho, C.H. and Hsu, P.K. (2007) Nitrate transporters and peptide transporters. FEBS Lett. 581, 2290–2300. </ref>
<ref name="ref8">Delhon, P., Gojon, A., Tillard, P. and Passama, L. (1995) Diurnal regulation of NO3− uptake in soybean plants I. Changes in NO3− influx, efflux, and N utilization in the plant during the day/night cycle. J. Exp. Bot. 46, 1585–1594. </ref>
<ref name="ref9">Gazzarrini, S., Lejay, L., Gojon, A., Ninnemann, O., Frommer, W.B. and von Wirén, N. (1999) Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots. Plant Cell, 11, 937–948. </ref>
<ref name="ref10">Lam, H.M., Coschigano, K., Schultz, C., Melo-Oliveira, R., Tjaden, G., Oliveira, I., Ngai, N., Hsieh, M.H. and Coruzzi, G. (1995) Use of Arabidopsis mutants and genes to study amide amino acid biosynthesis. Plant Cell, 7, 887–898. </ref>
<ref name="ref11">Lima, J.E., Kojima, S., Takahashi, H. and Wirén, N.V. (2010) Ammonium triggers lateral root branching in Arabidopsis in an ammonium transporter 1;3-dependent manner. Plant Cell, 22, 3621–3633. </ref>
<ref name="ref12">Sonoda, Y., Ikeda, A., Saiki, S., von Wirén, N., Yamaya, T. and Yamaguchi, J. (2003) Distinct expression and function of three ammonium transporter Genes (OsAMT1;1-1;3) in rice. Plant Cell Physiol. 44, 726–734. </ref>
<ref name="ref13">Gazzarrini, S., Lejay, L., Gojon, A., Ninnemann, O., Frommer, W.B. and von Wirén, N. (1999) Three functional transporters for constitutive, diurnally regulated, and starvation-induced uptake of ammonium into Arabidopsis roots. Plant Cell, 11, 937–948. </ref>
<ref name="ref14">Girin, T., Lejay, L., Wirth, J., Widiez, T., Palenchar, P.M., Nazoa, P., Touraine, B., Gojon, A. and Lepetit, M. (2007) Identification of a 150 bp cis-acting element of the AtNRT2.1 promoter involved in the regulation of gene expression by the N and C status of the plant. Plant Cell Env. 30, 1366–1380. </ref>
<ref name="ref15">Sasakawa, H. and Yamamoto, Y. (1978) Comparison of the uptake of nitrate and ammonium by rice seedlings. Plant Physiol. 62, 665–669. </ref>
<ref name="ref16">Bucio, J.L., Ramirez, A.C. and Estrella, L.H. (2003) The role of nutrient availability in regulating root architecture. Curr. Opin. Plant Biol. 6, 280–287. </ref>
<ref name="ref17">Forde, B. and Lorenzo, H. (2001) The nutritional control of root development. Plant Soil, 232, 51–68. </ref>
<ref name="ref18">Barlow, P.W. (1978) Cell displacement through the columella of the root cap of Zea mays L. Ann. Bot. 42, 783–790. </ref>
<ref name="ref19">Williams, L. and Miller, A. (2001) Transporters responsible for the uptake and partitioning of nitrogenous solutes. Annu. Rev. Plant Physiol. Plant Mol. Biol. 52, 659–688.</ref>
<ref name="ref20">Zhang, L.Z., Tan, Q.M., Lee, R., Trethewy, A., Lee, Y.H. and Tegeder, M. (2010) Altered xylem-phloem transfer of amino acids affects metabolism and leads to increased seed yield and oil content in Arabidopsis. Plant Cell, 22, 3603–3620. </ref>
<ref name="ref21">Kichey, T., Hirel, B., Heumez, E., Dubois, F. and Le Gouis, J. (2007) In winter wheat (Triticum aestivum L.), post-anthesis nitrogen uptake and remobilisation to the grain correlates with agronomic traits and nitrogen physiological markers. Field Crop. Res. 102, 22–32. </ref>
<ref name="ref22">Mae, T. and Ohira, K. (1981) The remobilization of nitrogen related to leaf growth and senescence in rice plants (Oryza sativa L.). Plant Cell Physiol. 22, 1067–1074. </ref>
<ref name="ref23">Tabuchi, M., Abiko, T. and Yamaya, T. (2007) Assimilation of ammonium ions an reutilization of nitrogen in rice (Oryza sativa L.). J. Exp. Bot. 58, 2319–2327. </ref>
<ref name="ref24">Wang, Z., Chen, C.B., Xu, Y.Y., Jiang, R.X., Han, Y., Xu, Z.H. and Chong, K. (2004) A practical vector for efficient knockdown of gene expression in rice (Oryza sativa L.). Plant Mol. Biol. Rep. 22, 409–417. </ref>
<ref name="ref25">Zhang, W., McElroy, D. and Wu, R. (1991) Analysis of rice Act1 5[prime] region activity in transgenic rice plants. Plant Cell, 3, 1155–1165. </ref>
<ref name="ref26">Dietrich, D., Hammes, U., Thor, K., Suter-Grotemeyer, M., Fluckiger, R., Slusarenko, A.J., Ward, J.M. and Rentsch, D. (2004) AtPTR1, a plasma membrane peptide transporter expressed during seed germination and in vascular tissue of Arabidopsis. Plant J. 40, 488–499. </ref>
<ref name="ref27">Fei, Y.J., Ganapathy, V. and Leibach, F.H. (1998) Molecular and structural features of the proton-coupled oligopeptide transporter superfamily. Prog. Nucleic Acid Res. Mol. Biol. 58, 239–261. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0706400|
Description = Similar to Peptide transporter PTR2-B (Histidine transporting protein)|
Version = NM_001188057.1 GI:297725244 GeneID:9268091|
Length = 2951 bp|
Definition = Oryza sativa Japonica Group Os06g0706400, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:30715316..30718266|
CDS = 30715362..30715418,30715623..30715722,30715952..30716253|
GCID = <gbrowseImage1>
name=NC_008399:30715316..30718266
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:30715316..30718266
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgtccacggacactgagcagcaggaacacgcagtggcgctgctacaacccgaggttgaagaagcatacaccactgatgggtctcttggcgtcgatggcaacccggcgctgaagcatcgcacaggcggatggatggcatgccgcccgattcttggcaccgagttctgctactgcctggcctactacggcatcacgttcaacctcgtcacctacctcaccgccgagctgcaccagagcaacgtcgccgccgccaacaacgtgtcgacgtggcaggccacctgcttcctcacgccgctggccggagccgtcgccgccgattcctactggggaaggtaccgcaccatggtcgtcagctgctgcatcggcgtcgctgttagtcccctccatttcattcgatccgggttgtgtttagttccaaattttttttttcaaacttctaactttccatcacattaa</cdnaseq>|
AA = <aaseq>MASTDTEQQEHAVALLQPEVEEAYTTDGSLGVDGNPALKHRTGG WMACRPILGTEFCYCLAYYGITFNLVTYLTAELHQSNVAAANNVSTWQATCFLTPLAG AVAADSYWGRYRTMVVSCCIGVAVSPLHFIRSGLCLVPNFFFQTSNFPSH</aaseq>|
DNA = <dnaseqindica>47..103#308..407#637..938#gattagcttgtacagtttgtcctcgagctctcgaccggctccggcaatggcgtccacggacactgagcagcaggaacacgcagtggcgctgctacaacccgaggtaattaattaatcgctgttcataatctccttactgctagccttatgccgatttccacgatgcagtttgtttaatttctcatcagtttccctgcagaaaaatattgattgagccttgcctgaactagctactcctagttaatttgaagcagccgctcatggatacgttcagtgctaactaggctggggattttggttgctgcaggttgaagaagcatacaccactgatgggtctcttggcgtcgatggcaacccggcgctgaagcatcgcacaggcggatggatggcatgccgcccgattcttggtaataaacttcattagatatccctgcagctctattaattatttcctaaccttttttacttgccaattttttgatgattaatgtgtctctcactttgtgtgttcttgttccaaaaaagaaaaaaatgaaaaaaaaaataaatgaggaacttctttgttgatgtggttatctgagctatgacaacactgaggagagatgcttattctgcttgctttgtgattgtggataggcaccgagttctgctactgcctggcctactacggcatcacgttcaacctcgtcacctacctcaccgccgagctgcaccagagcaacgtcgccgccgccaacaacgtgtcgacgtggcaggccacctgcttcctcacgccgctggccggagccgtcgccgccgattcctactggggaaggtaccgcaccatggtcgtcagctgctgcatcggcgtcgctgttagtcccctccatttcattcgatccgggttgtgtttagttccaaattttttttttcaaacttctaactttccatcacattaaatttttcatacacacaatttttttcagtcacgtcgtcttcaatttcaaccaaaatctaaactttataccaatctaaacacagccttaattagaattagtcactgtgtccttcctgccgtgaatttatggctgatggcaagtaatcagtcactgtgtgggatgtggatttttatcccttgagagaacatttaattttatattaatattaatttatgttaatttatgttgtcatttaattttatattttatattaatttatgttgtccattttttttaatttttttatgactaattagttggcatggatgaaacgagggatatttcctggagggatgaaatcactttccccactgtgtgctgccatgaatgcaaatccaatcagcttcatggctgtacgtacctaatctgtggtgcagggcatgctcatggcggctctgtcggcgcttctgccgctgctgatcaaggacacgtcgtccatggcttcagctcaagtgatcatcctgtttcttggcctgtacatgatcgcatttggggtgggtggtctccggccgtgcctgatgtccttcggcgccgaccagttcgacgacggcgacacgtcggagcgcatcagcaagggctcctacttcaactggtacatcttcaccatgaactgcgcgtccgtgatatccaccaccgccatggtgtgggtgcaagaccactacgggtgggcattggggttggggattccggcgatggtcctcgccgtcgggctctcctgccttgtcgccgcgtctcgggcgtacaggtttcagacaacccgcggtagcccgctcaccagagtctgccaggtcgtcgtcgccgccgtccgcaagttcaacgtcgcgccgccggccgacatggcccttctctacgacctatcggaggatgcctcctccatgaagggagttcagaggatcgagcacaccgccgatctccggtcagttcatgtctctcgttgcatctggtgtttgtgatgctgtaggtgtaatgtaattggctaattcttgagatgcaactgctcgatcagattcttcgacaaggccgccgtcgtgacggcgtcggacgaggaggcggagggcgccgcgccgcgcaatccatggaggctttgcgtggtgacgcaggtggaggagctcaagattctcgtcaggatgctgcccctgtgggcgtgcgtcgccttctactacaccgcgacggcgcaggccaattcgacgttcgtcgagcagggcatggcgatggacacgcgcgtcggctccttccacgtcccgccggcatccctggccaccttccagatcatcaccacgatcgtgttgatcccgctgtacgaccgcgcgttcgtgccggcggcgaggaggctgacggggagagagaagggcatctccgaccttctcaggatcggcggcggcctcgccatggccgcgctcgccatggccgcggcggcgctggtcgagacgaggcgcgcccgcgcggcgcacgccgggatggagccgacgagcatcctgtggcaggcgccgcagtacgtgctggtgggcgtcggcgagctgctcgccaccgtggggcagctggacttcttctacagccaggcgccgccggccatgaagacggtgtgcacggcgctcgggttcatctccgtcgcggcgggggagtacctgagctcgctcgtcgtgacggccgtgtcgtgggcgacggcgaccggcggccggccggggtggatccccgacgacctcaacgaggggcacctgatcgcttcttctggatgatggctgggctcggttgcctcaatcttgtggtgtttacgagctgtgccatgaggtacaaatccaggaaggcctgttgatacttctgggcttgtttggtaggctcgaaattccggcccatgcactctgacgggccattatgtatgggaataagtccatccgacctccctcatctcttgcacttggtcgaatcgcatccctcagccgcaaaaaactgggtaaaacgcctcctgaatctccc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001188057.1 RefSeq:Os06g0706400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0196700

2014-12-27T13:49:12Z

Shijc:

OsARF16, an auxin response factor, functions in both auxin and −Pi responses in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os06g0196700-Fig1.gif|right|thumb|200px|'' Indole acetic acid (IAA) content, and expressions of auxin biosynthesis genes and auxin transporters in Nipponbare (NIP) and osarf16 under normal nutritional solution (CK), IAA and −Pi treatments. (from reference <ref name="ref1" />).'']]
'''OsARF16 effects on the −Pi signalling were correlated with auxin distribution'''
To elucidate the function of ARF in rice, the structures of OsARF genes and OsARF12 features were investigated in our previous study <ref name="ref2" /><ref name="ref3" /> . Further identified and characterized the biological function of OsARF16 with TOS17 insertion in greater detail in rice. osarf16 mutant or Ov16 scarcely showed phenotypic differences in their roots, suggesting that OsARF16, one member of the ARF gene family might have functional redundancy with another member. However, the PR, LR, and RH of osarf16 showed auxin insensitivity, suggesting that OsARF16 plays a role on auxin response in root development. OsARF16 was mainly expressed in the stele and root tip of PR, AR and LR, which further supported that it was implicated in root development. And, OsARF16 expression in PR and LR was induced by auxin and −Pi treatments, and the expression of most OsLAX and OsPINs in osarf16 was markedly lower than in NIP under exogenous IAA treatment – this demonstrated that absence of OsARF16 might affect auxin polar transport. The temporal and spatial distribution of auxin mainly depends on the dynamic expression and subcellular localization of auxin efflux proteins, PINs <ref name="ref4" />. The genomic sequencing of these auxin transporter genes, OsLAX and OsPINs, in rice was recently published in our study where it was compared to Arabidopsis <ref name="ref5" />, but their individual functions remain unknown. However, the expression pattern of OsARF16 in PR was the same as OsPIN1b, OsPIN4 and OsPIN9 <ref name="ref6" />, suggesting that OsARF16 may affect auxin transport mainly via these three genes. In addition, in osarf16 under −Pi, the expression of the four OsYUCCAs was highly induced, and most OsLAXs and OsPINs showed a similar trend with IAA treatment, indicating that an auxin transporter was also involved in −Pi response. The results indicated that −Pi response may alter auxin distribution or auxin polar transport via the regulation of OsARF16. In NIP, the auxin content was increased by −Pi condition while in osarf16 mutant, it was not affected. These results suggested that the impact of −Pi signalling on auxin distribution depends on OsARF16. On the other hand, in NIP, applying exogenous auxin enhanced Pi absorption, but in the OsARF16 knockout mutant, the Pi content was not increased. Therefore, the improvement of Pi absorption caused by changes of auxin distribution also depends on OsARF16. Taken together, results further confirmed that the effects of OsARF16 on −Pi signalling were correlated with auxin distribution.
[[File: Shijc-Os06g0196700-Fig2.gif|right|thumb|200px|'' Interaction between auxin distribution and −Pi signalling in Nipponbare (NIP) andosarf16. Indole acetic acid (IAA) contents from lateral roots (LR) initiation to maturation in NIP and osarf16 under CK and −Pi conditions. (from reference <ref name="ref1" />).'']]
Furthermore, microarray data <ref name="ref7" /><ref name="ref8" /> showed that auxin signalling takes part in differences responses to Pi deficiency in the shoot and root. Most of the auxin-induced genes in the rice root were also up-regulated by Pi deficiency. These data further confirmed that a number of genes co-participate in auxin and −Pi response, and not only OsARF16.

'''RH and LR development under P deficiency in rice depends on OsARF16-mediated −Pi signalling'''
The phenotype of a plant under auxin treatment is similar to that for Pi starvation <ref name="ref9" /><ref name="ref10" /><ref name="ref11" />. Our study found that osarf16 had auxin insensitivity and was also insensitive to Pi deficiency, especially in terms of RH and LR development. In NIP, but not in osarf16, the RH length was extended by −Pi, and OsARF16::GUS staining was also induced in RH by −Pi. RH development in −Pi has been infrequently reported <ref name="ref12" /><ref name="ref13" /><ref name="ref14" />. The present study was the first to demonstrate that OsARF16 was a key regulator in RH expansion under −Pi in rice. Moreover, the LR number in osarf16 showed a small increase under −Pi, consistent with an arf19 mutant in Arabidopsis <ref name="ref15" />. OsARF16 is highly homologous to ARF19, which is implicated in responses to Pi deficiency <ref name="ref16" />. The data indicated that OsARF16 also acted in LR development under −Pi as well as ARF19. Plants respond to Pi deficiency by allocating more carbon to their roots, thereby increasing their root-to-shoot ratio <ref name="ref17" /><ref name="ref18" />. The root-to-shoot ratio in osarf16 was only slightly increased compared with NIP, which further suggested that osarf16 was insensitive to Pi deficiency. It is worth mentioning that Fe accumulation in osarf16 under −Pi was lower than in NIP. A previous report showed that −Pi induced Fe acquisition and increased the Fe content of rice <ref name="ref19" />. Our results suggested that the knockout of OsARF16 may indirectly affect the Fe signal via the −Pi response.

'''OsARF16 is an essential regulator in −Pi response'''
[[File: Shijc-Os06g0196700-Fig2.gif|right|thumb|200px|'' Indole acetic acid (IAA) content, and expressions of auxin biosynthesis genes and auxin transporters in Nipponbare (NIP) and osarf16 under normal nutritional solution (CK), IAA and −Pi treatments. (from reference <ref name="ref1" />).'']]
Under −Pi conditions, a plant enhances P absorption efficiency by regulating the expression of genes induced by phosphate starvation (PSIs) to maintain normal growth and development <ref name="ref20" /><ref name="ref21" />. In Arabidopsis, the complete regulatory network for the P signal is important for plant responses to −Pi. Thus, the absence of AtPHR1 located in the centre of the P signal network resulted in the expression of numerous downstream genes that were inhibited under −Pi, and with an impaired P signal <ref name="ref22" /><ref name="ref23" /><ref name="ref24" />. In rice, the knockdown of OsPHR2 led to a series of PSIs genes that were not distinctly induced by −Pi <ref name="ref25" />. The genetic effect of OsARF16 knockout was similar to the absence of AtPHR1 and OsPHR2. The knockout of OsARF16 greatly weakened the transmission of the P signal, leading PSIs genes to lose their correct response. The P deficiency response still was impaired in the osarf16 mutant, even if OsPHR2 was normally expressed. Thus, the P deficiency response via OsPHR2 was dependent on OsARF16-mediated −Pi signalling. The effect of the OsPHR2 function was based on the normal expression of the OsARF16 gene, which maintained P signal transmission and allowed rice to respond to P deficiency in time.

In Arabidopsis, the modulation of auxin sensitivity by Pi depends on the auxin receptor transport inhibitor response1 (TIR1) and ARF19. Auxin sensitivity is enhanced in Pi-deprived plants by an increased expression of TIR1, which accelerates the degradation of AUX/IAA proteins. This indicated that ARF transcription factors activate/repress genes that are related to auxin signalling <ref name="ref26" />. In rice, OsTIR1 in osarf16 was also less up-regulated by −Pi compared with NIP. Taken together, the results indicate that OsARF16 may be an essential regulator in −Pi response.

===Mutation===
[[File: Shijc-Os06g0196700-Fig3.gif|right|thumb|200px|'' Identification of mutant osarf16-Tos17 (osarf16) and phenotypic analysis. (from reference <ref name="ref1" />).'']]
Rice endogenous retrotransposon (TOS17) was integrated into the seventh exon of OsARF16 genes using analysis of the Rice Genome Resource Center (RGRC) database (http://www.rgrc.dna.affrc.go.jp) and sequencing. PCR analysis confirmed that the TOS17 fragment had been inserted into OsARF16 genes and the homozygous line was harvested. RT-PCR result demonstrated that OsARF16 was expressed in NIP and overexpressed in Ov16 and Ov16/mutant (Ov16/MT), but not the mutant osarf16. The phenotypes of NIP, osarf16, Ov16 and Ov16/MT were approximately the same under control (CK) conditions. However, the mutant osarf16 showed longer PR than the other three lines under IAA treatments, indicating it was insensitive to auxin. These results confirmed that OsARF16 was knocked out in osarf16, and that it rescued the function of OsARF16 in Ov16/MT. Exogenous auxin can decrease PR length <ref name="ref27" /> and induce LR formation <ref name="ref28" /> and RH elongation <ref name="ref29" /><ref name="ref30" />. However, under IAA treatment, the PR length with 2,4-D and IBA treatments and the LR number in osarf16 were greater than NIP and Ov16, whereas the RH length in osaf16 was lower compared with both lines. Ov16 was more sensitive to IAA or NPA than NIP in terms of lateral root number. In addition, Ov16 was also more sensitive to IAA than NIP in terms of RH length, although the RH length in Ov16 under NPA treatment was similar to that of NIP. These results further confirmed that osarf16 is actually insensitive to auxin. Under IAA treatment, there was no difference in the adventitious root (AR) number between osarf16 and NIP, or Ov16, although more AR was produced in osarf16 than the other lines with an auxin influx transport inhibitor, that is, NOA treatment. To know the phenotype of osarf16 when blocking auxin transport, the PR length was measured under PATIs. The PR length in osarf16 was longer than NIP and Ov16 with TIBA, NPA and 1-NOA treatments, which indicated that osarf16 was also insensitive to PATIs. These results showed that OsARF16 was required for auxin responses in roots.

===Expression===
[[File: Shijc-Os06g0196700-Fig4.gif|right|thumb|200px|'' OsARF16 expression patterns. (from reference <ref name="ref1" />).'']]
The expression patterns of OsARF16 in various organs was evaluated using the GUS reporter gene. The 2641 bp of the OsARF16 sequence upstream of its ATG (predicted by the annotated rice genome (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/#search) was fused to GUS and the transgene was introduced into rice NIP. Ten positive transgenic lines were obtained and three lines were used for further investigation. GUS staining was found to be prominent in the stele and root tip of PR and AR (equal to PR). In LR, OsARF16 was weakly expressed in the stele, root tip and primordia. OsARF16 was expressed at a lower level in the leaf relative to the leaf tip. It was not expressed in RH and it was highly expressed in the vascular tissue of the stem. OsARF16 expression was also observed in the anther, the stigma of the flower and the glume. Semi-quantitative RT-PCR (sqRT-PCR) further confirmed that OsARF16 was expressed at different levels in various tissues, consistent with the GUS staining results. Therefore, OsARF16 was expressed in different organs and tissues, with the highest expression being in roots and vasculature.
The effects of auxin and −Pi treatments on the expression of OsARF16 was tested using the OsARF16::GUS reporter line. OsARF16 expression in the stele was completely inhibited by IAA, whereas that in the PR tip was highly induced by about 10-fold. OsARF16 expression in the stele, epidermis and tip of PR was highly induced (about 12-fold) by −Pi treatment. Interestingly, under the −Pi/+IAA treatment, the OsARF16 expression was highly increased in tip of PR than with only −Pi or IAA treatment (about 15-fold) while it was impaired in epidermis. This data provide an evidence for that auxin controls OsARF16 expression at a higher degree than −Pi. qRT-PCR analysis of PR further confirmed these trends. OsARF16::GUS staining was observed at the LR primordia, and induced by auxin and −Pi treatments. The above results suggest that the function of OsARF16 may be related to auxin and −Pi response.
[[File: Shijc-Os06g0196700-Fig5.gif|right|thumb|200px|'' OsARF16 expression pattern in root of Nipponbare (NIP; 7-day-old) under auxin and −Pi treatments. (from reference <ref name="ref1" />).'']]

==Labs working on this gene==
1. State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058
2. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 359 Tiyuchang Road, Hangzhou, China

==References==
<references>
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<ref name="ref2">Shen C., Wang S., Bai Y., Wu Y., Zhang S., Chen M., Guilfoyle T.J., Wu P. & Qi Y. (2010a) Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L. Journal of Experimental Botany 61, 3971–3981. </ref>
<ref name="ref3">Qi Y., Wang S., Shen C., Zhang S., Chen Y., Xu Y., Liu Y., Wu Y. & Jiang D. (2012) OsARF12, a transcription activator on auxin response gene, regulates root elongation and affects iron accumulation in rice (Oryza sativa). New Phytologist 193, 109–120. </ref>
<ref name="ref4">Bureau M., Rast M.I., Illmer J. & Simon R. (2010) JAGGED LATERAL ORGAN (JLO) controls auxin dependent patterning during development of the Arabidopsis embryo and root. Plant Molecular Biology 74, 479–491. </ref>
<ref name="ref5">Shen C., Bai Y., Wang S., Zhang S., Wu Y., Chen M., Jiang D. & Qi Y. (2010b) Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress. FEBS Journal 277, 2954–2969. </ref>
<ref name="ref6">Wang J.R., Hu H., Wang G.H., Li J., Chen J.Y. & Wu P. (2009b) Expression of PIN genes in rice (Oryza sativa L.): tissue specificity and regulation by hormones. Molecular Plant 2, 823–831. </ref>
<ref name="ref7">Jain M. & Khurana J.P. (2009) Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS Journal 276, 3148–3162. </ref>
<ref name="ref8">Zheng L., Huang F., Narsai R., et al. (2009) Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiology 151, 262–274. </ref>
<ref name="ref9">López-Bucio J., Cruz-Ramı'rez A. & Herrera-Estrella L. (2003) The role of nutrient availability in regulating root architecture. Current Opinion in Plant Biology 6, 280–287. </ref>
<ref name="ref10">Nacry P., Canivenc G., Muller B., Azmi A., Van O.H., Rossignol M. & Doumas P. (2005) A role for auxin redistribution in the responses of the root system architecture to phosphate starvation in Arabidopsis. Plant Physiology 138, 2061–2074. </ref>
<ref name="ref11">Vanneste S. & Friml J. (2009) Auxin: a trigger for change in plant development. Cell 136, 1005–1016. </ref>
<ref name="ref12">Sánchez-Calderón L., López-Bucio J., Chacón-López A., Gutiérrez-Ortega A., Hernández-Abreu E. & Herrera-Estrella L. (2006) Characterization of low phosphorus insensitive mutants reveals a crosstalk between low phosphorus-induced determinate root development and the activation of genes involved in the adaptation of Arabidopsis to phosphorus deficiency. Plant Physiology 140, 879–889. </ref>
<ref name="ref13">Bustos R., Castrillo G., Linhares F., Puga M.I., Rubio V., Pérez-Pérez J., Solano R., Leyva A. & Paz-Ares J. (2010) A central regulatory system largely controls transcriptional activation and repression responses to phosphate starvation in Arabidopsis. PLoS Genetics 9, pii: e1001102. </ref>
<ref name="ref14">Wang X., Du G., Wang X., Meng Y., Li Y., Wu P. & Yi K. (2010b) The function of LPR1 is controlled by an element in the promoter and is independent of SUMO E3 Ligase SIZ1 in response to low Pi stress in Arabidopsis thaliana. Plant Cell and Physiology 51, 380–394. </ref>
<ref name="ref15">Pérez-Torres C.A., Lo'pez-Bucio J., Cruz-Ramı'rez A., Ibarra-Laclette E., Dharmasiri S., Estelle M. & Herrera-Estrella L. (2008) Phosphate availability alters lateral root development in Arabidopsis by modulating auxin sensitivity via a mechanism involving the TIR1 auxin receptor. The Plant Cell 20, 3258–3272. </ref>
<ref name="ref16">Wang D., Pei K., Fu Y., Sun Z., Li S., Liu H., Tang K., Han B. & Tao Y. (2007) Genome-wide analysis of the auxin response factor (ARF) gene family in rice (Oryza sativa). Gene 394, 13–24. </ref>
<ref name="ref17">López-Bucio J., Cruz-Ramı'rez A. & Herrera-Estrella L. (2003) The role of nutrient availability in regulating root architecture. Current Opinion in Plant Biology 6, 280–287. </ref>
<ref name="ref18">Hermans C., Hammond J.P., White P.J. & Verbruggen N. (2006) How do plants respond to nutrient shortage by biomass allocation? Trends in Plant Science 11, 610–617. </ref>
<ref name="ref19">Zheng L., Huang F., Narsai R., et al. (2009) Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiology 151, 262–274. </ref>
<ref name="ref20">Martín A.C., del Pozo J.C., Iglesias J., Rubio V., Solano R., de LaPeña A., Leyva A. & Paz-Ares J. (2000) Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. The Plant Journal 24, 559–567. </ref>
<ref name="ref21">Schachtman D.P. & Shin R. (2007) Nutrient sensing and signaling: NPKS. Annual Review of Plant Biology 58, 47–69. </ref>
<ref name="ref22">Rubio V., Linhares F., Solano R., Martín A.C., Iglesias J., Leyva A. & Paz-Ares J. (2001) A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes & Development 15, 2122–2133. </ref>
<ref name="ref23">Nilsson L., Müller R. & Nielsen T.H. (2007) Increased expression of the MYB-related transcription factor, PHR1, leads to enhanced phosphate uptake in Arabidopsis thaliana. Plant, Cell & Environment 30, 1499–1512. </ref>
<ref name="ref24">Panigrahy M., Rao D.N. & Sarla N. (2009) Molecular mechanisms in response to phosphate starvation in rice. Biotechnology Advances 27, 389–397. </ref>
<ref name="ref25">Zhou J., Jiao F., Wu Z., Li Y., Wang X., He X., Zhong W. & Wu P. (2008) OsPHR2 is involved in phosphate-starvation signaling and excessive phosphate accumulation in shoots of plants. Plant Physiology 146, 1673–1686. </ref>
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</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0196700|
Description = Similar to Auxin response factor 1|
Version = NM_001187722.1 GI:297724574 GeneID:9270361|
Length = 6594 bp|
Definition = Oryza sativa Japonica Group Os06g0196700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:4925020..4931613|
CDS = 4925493..4925538,4925790..4925902,4925994..4926089,4926187..4926243,4926329..4926484 ,4926586..4926670,4926911..4927001,4927080..4927365|
GCID = <gbrowseImage1>
name=NC_008399:4925020..4931613
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:4925020..4931613
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaaggatcagggatcatccggtgtgtctcccgccccaggggaaggggagaagaaagccatcaattcggagctatggcatgcttgtgccgggcctcttgtgtcgctgccgccggtgggcagtctcgtcgtgtacttccctcagggtcatagcgagcaggttgctgcttccatgcacaaggagctggacaacatccctggttatccctctcttccgtctaagctgatctgcaaacttctgagtctcaccttacatgcagattctgaaactgatgaagtttatgctcagatgacacttcaaccagtcaataaatatgatcgagatgcaatgctggcatctgaactgggcctgaagcaaaacaagcaaccagcggagttcttttgcaaaacgctgacggcgagcgacacaagtacccatggtggattttcagtgccacgtcgtgcggcggagaagatatttccaccactagactttaccatgcaaccaccagcacaagagctcatcgccaaggatctgcatgatatttcatggaaatttcgacacatttaccgaggtcaaccaaagaggcaccttctgacaactggttggagcgtctttgtcagcacaaaaaggcttctagctggtgattcagttctgtttataagggatgagaaatctcagcttctattaggcatacgtcgtgctaccagaccccaaccagctctatcgtcatcagttctatcaagtgatagcatgcacattgggattctagctgctgcagcacatgctgctgcaaacagtagcccatttactattttctacaatccaaggtattatagttcttacttgatatcccattatcccaatgcactctctgctaccctttgggactatgaactcattgttgttattctgatagggcaagtccatcagaatttgtcattcctttag</cdnaseq>|
AA = <aaseq>MKDQGSSGVSPAPGEGEKKAINSELWHACAGPLVSLPPVGSLVV YFPQGHSEQVAASMHKELDNIPGYPSLPSKLICKLLSLTLHADSETDEVYAQMTLQPV NKYDRDAMLASELGLKQNKQPAEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDFTM QPPAQELIAKDLHDISWKFRHIYRGQPKRHLLTTGWSVFVSTKRLLAGDSVLFIRDEK SQLLLGIRRATRPQPALSSSVLSSDSMHIGILAAAAHAAANSSPFTIFYNPRYYSSYL ISHYPNALSATLWDYELIVVILIGQVHQNLSFL</aaseq>|
DNA = <dnaseqindica>474..519#771..883#975..1070#1168..1224#1310..1465#1567..1651#1892..1982#2061..2346#ggcttcctcctccacttgcttcgtcgtcgtcgtcctcctcctcctctctctactctctctctccgaaccatccttcccacccggcacgccgccgcgcgctgttcccgacggcggccggtggccggagtgagaggctgggtgtactgtccgctgatgctcgtgggaggcggcggcggcggcggcggcgtgtgatgagcggaggccgcgtgggcgagaacctgtcgcgtcggcacggcggcggcggcggtggcgagggctcgtcaggcttggccacgctttgctcccttcgcagtggcgctcccctggtgccgaatattatactcgccgccgcctcgtgccgcctactttaggcggaaagggggagagctctcctatcctagctgctgctgctgccactggctaagttggtaaaaggtggaggaggcggatattcgtgtatccggaggagagatttggatcgggatctcgccgggatgaaggatcagggatcatccggtgtgtctcccgccccaggggaaggtgagaagaatccttttgctctttgctcatgtgcttgcttcctttgcattgttcagaaaaattcaggtcgttttgcttgagcatttgccgaattcatggccatcatcgttgccgcagcgcacatttgcagtgaaaccttgctcatggcctcctcctcctcctccctatgaatcttatcgcattagcgtgtgctgtgtagtgtgaggttggatacactgctgtaacaactgagcatgggttttgcaaagcaggggagaagaaagccatcaattcggagctatggcatgcttgtgccgggcctcttgtgtcgctgccgccggtgggcagtctcgtcgtgtacttccctcagggtcatagcgagcaggtgaacaattttgtcatcttactgtctgaaatgtgctgaatcgtgacaagtttctgaaaattttcttgttttctggtatgcctttgtttaggttgctgcttccatgcacaaggagctggacaacatccctggttatccctctcttccgtctaagctgatctgcaaacttctgagtctcaccttacatgtatgtgcatagtactttccactttgatgctatagttgtgtttttcctttttcatctttgctaattgggtgcgcgcaacatgttttttattgttcaggcagattctgaaactgatgaagtttatgctcagatgacacttcaaccagtcaataaagtatgtaagatgatgatctatttgattatgggaacacactatttatctccgtgaaattgaaatatgttttctggatgtgttttagtatgatcgagatgcaatgctggcatctgaactgggcctgaagcaaaacaagcaaccagcggagttcttttgcaaaacgctgacggcgagcgacacaagtacccatggtggattttcagtgccacgtcgtgcggcggagaagatatttccaccactagtatgcagagtttcttcataacccttgcagtaattttgatggaactatgcatttatcagatgcagtgaatacctgccttaccaggataacatgttcgataggactttaccatgcaaccaccagcacaagagctcatcgccaaggatctgcatgatatttcatggaaatttcgacacatttaccgaggtatgccaaactgctaactgctcagagaatatctgtacattgacttggttttatatttatttcattgccacattttttttgacagacccattacttacacttagttagcactttgcatctagttttcctgctttttctttgaactgctaaggatgtctctgtcctgggacatggtggccgatcaatcaattgcattctgtacttacctgtatactactgtaccttcacatggacacgcaggtcaaccaaagaggcaccttctgacaactggttggagcgtctttgtcagcacaaaaaggcttctagctggtgattcagttctgtttataaggtagcacactgaaattcaagtgcatcgatttgtctaaatcgtttcaagaaatattgattctacatcttttgtttgcagggatgagaaatctcagcttctattaggcatacgtcgtgctaccagaccccaaccagctctatcgtcatcagttctatcaagtgatagcatgcacattgggattctagctgctgcagcacatgctgctgcaaacagtagcccatttactattttctacaatccaaggtattatagttcttacttgatatcccattatcccaatgcactctctgctaccctttgggactatgaactcattgttgttattctgatagggcaagtccatcagaatttgtcattcctttagcgaaatataacaaggctttgtatacacaagtatctcttggaatgcggttcagaatgctgtttgagacagaggattcaggggttcgaagatatatgggaacaatcacaggtattggtgacttggatccagtgcgctggaagaactctcattggcgaaaccttcaggtgtgctactcttttcttcttttagttctgcaatgtgtcacattcatacatctcattctcatctatgatctgtaagaaataacaaaatatctggattaattatttgtattaaattagaaaattcaacctcattttgaagaaatctttgaaataagattgcctaacaccctatagaattgttgtttgcaagtttgtttagcatattatacaaaaccttccctgacttcacctcctctttctaagttaggttggttgggatgaatcaacagcatctgagaggcgcactcgtgtttcaatatgggagattgaaccagtcgcgacacctttttatatttgtccaccaccatttttcaggccaaaacttcctaagcagccaggaatgccaggtacagatacttccactcaacattatatatatattagctagtattactatttagggaatagtgtaatatgcagatcattttgatctttgggaattagtgcttcaatcatacagtcattctcttcttgctgaactcattaagcttgtaaagaacactgcaacctaattttcaccaacgtgcatacgcattatactaaaaatggtttgcttcttgcatgcatatgaacttgatgcatctgttaacagcaagaggttctagccaaagcacataaacacacttcaattctcttaaatgtagttgcttcttgattgtgtataaacttgaaatattaataatcagcaagaactgtggatttgttgtttgttacctgtgtacaagttaacttccttgcaaattttgcttgcattttcttaagattagtttgggcctcatatgaaaattgctaaaacttgcagatgatgaaaatgaagttgagagtgctttcaaaagagccatgccatggcttgctgatgactttgccctgaaagatgtgcaaagtgcattatttccaggtctgagcctagtccaatggatggctatgcaacagaatcctcagatgctaacagctgcgtcccaaacagtgcaatcaccgtacttgaactccaatgcattggctatgcaggatgtgatgggtagtagcaacgaggacccaacaaaaagattgaacacacaggcacaaaatatggttttacctaatttacaggttggctcaaaagtggatcaccctgtaatgtctcaacatcaacagcagccacaccaactatcacaacagcagcaggtccagccatcgcagcaaagttctgtggttttacagcaacatcaagcccagttgctgcagcagaacgccattcacttgcagcagcagcaagaacatctccagcggcagcagtcacaaccggcacagcagttgaaggctgcttcaagtctgcattcagtggaacagcacaagctgaaagaacagacttcaggtgggcaggttgcctcacaagcacaaatgttaaaccagattttcccaccatcttcatcgcagctacaacagttaggtttacccaagtcacctactcatcgccaagggttgacaggattaccaattgcaggttctttgcagcagcccacactaactcagacatctcaagtccagcaagcagccgaatatcagcaggccctcctacagagtcagcaacagcaacagcaactgcaactgcaacaactatcacaaccagaagtacagctgcagctgcttcaaaagattcaacaacaaaacatgctatctcagctgaacccacaacatcagtcccagttgattcaacaattgtctcagaaaagccaggaaattctacagcaacaaattttgcaacatcaatttggtgggtctgattctattggtcaactcaagcaatcaccatcgcagcaagctcctttaaaccacatgacaggatctttgacgccccagcaacttgtcagatcacattcggcacttgctgagagtggggatccatccagttcaactgctccatccaccagccgtatttctccaataaattcgctgagtagggcaaaccaaggaagcagaaatttaactgacatggtggcaacaccacaaattgacaacttacttcaggaaattcaaagcaagccagataatcgaattaagaatgacatacagagcaaagaaacagtccctatacataaccgacatccagtttctgatcaacttgatgcatcatctgctacctccttttgtttagacgagagcccacgagaaggtttttccttccctccagtttgtttggataacaatgttcaagttgatccaagagataactttcttattgcggaaaatgtggacgcattgatgccagatgccctgttgtcaagaggtatggcttcaggaaagggcatgtgcactctgacttctggacaaagggatcacagggatgtcgagaatgagctatcatctgctgcatt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Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001187722.1 RefSeq:Os06g0196700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os06g0196700

2014-12-27T13:48:31Z

Shijc:

OsARF16, an auxin response factor, functions in both auxin and −Pi responses in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os06g0196700-Fig1.gif|right|thumb|200px|'' Indole acetic acid (IAA) content, and expressions of auxin biosynthesis genes and auxin transporters in Nipponbare (NIP) and osarf16 under normal nutritional solution (CK), IAA and −Pi treatments. (from reference <ref name="ref1" />).'']]
‘’’OsARF16 effects on the −Pi signalling were correlated with auxin distribution’’’
To elucidate the function of ARF in rice, the structures of OsARF genes and OsARF12 features were investigated in our previous study <ref name="ref2" /><ref name="ref3" /> . Further identified and characterized the biological function of OsARF16 with TOS17 insertion in greater detail in rice. osarf16 mutant or Ov16 scarcely showed phenotypic differences in their roots, suggesting that OsARF16, one member of the ARF gene family might have functional redundancy with another member. However, the PR, LR, and RH of osarf16 showed auxin insensitivity, suggesting that OsARF16 plays a role on auxin response in root development. OsARF16 was mainly expressed in the stele and root tip of PR, AR and LR, which further supported that it was implicated in root development. And, OsARF16 expression in PR and LR was induced by auxin and −Pi treatments, and the expression of most OsLAX and OsPINs in osarf16 was markedly lower than in NIP under exogenous IAA treatment – this demonstrated that absence of OsARF16 might affect auxin polar transport. The temporal and spatial distribution of auxin mainly depends on the dynamic expression and subcellular localization of auxin efflux proteins, PINs <ref name="ref4" />. The genomic sequencing of these auxin transporter genes, OsLAX and OsPINs, in rice was recently published in our study where it was compared to Arabidopsis <ref name="ref5" />, but their individual functions remain unknown. However, the expression pattern of OsARF16 in PR was the same as OsPIN1b, OsPIN4 and OsPIN9 <ref name="ref6" />, suggesting that OsARF16 may affect auxin transport mainly via these three genes. In addition, in osarf16 under −Pi, the expression of the four OsYUCCAs was highly induced, and most OsLAXs and OsPINs showed a similar trend with IAA treatment, indicating that an auxin transporter was also involved in −Pi response. The results indicated that −Pi response may alter auxin distribution or auxin polar transport via the regulation of OsARF16. In NIP, the auxin content was increased by −Pi condition while in osarf16 mutant, it was not affected. These results suggested that the impact of −Pi signalling on auxin distribution depends on OsARF16. On the other hand, in NIP, applying exogenous auxin enhanced Pi absorption, but in the OsARF16 knockout mutant, the Pi content was not increased. Therefore, the improvement of Pi absorption caused by changes of auxin distribution also depends on OsARF16. Taken together, results further confirmed that the effects of OsARF16 on −Pi signalling were correlated with auxin distribution.
[[File: Shijc-Os06g0196700-Fig2.gif|right|thumb|200px|'' Interaction between auxin distribution and −Pi signalling in Nipponbare (NIP) andosarf16. Indole acetic acid (IAA) contents from lateral roots (LR) initiation to maturation in NIP and osarf16 under CK and −Pi conditions. (from reference <ref name="ref1" />).'']]
Furthermore, microarray data <ref name="ref7" /><ref name="ref8" /> showed that auxin signalling takes part in differences responses to Pi deficiency in the shoot and root. Most of the auxin-induced genes in the rice root were also up-regulated by Pi deficiency. These data further confirmed that a number of genes co-participate in auxin and −Pi response, and not only OsARF16.

‘’’RH and LR development under P deficiency in rice depends on OsARF16-mediated −Pi signalling’’’
The phenotype of a plant under auxin treatment is similar to that for Pi starvation <ref name="ref9" /><ref name="ref10" /><ref name="ref11" />. Our study found that osarf16 had auxin insensitivity and was also insensitive to Pi deficiency, especially in terms of RH and LR development. In NIP, but not in osarf16, the RH length was extended by −Pi, and OsARF16::GUS staining was also induced in RH by −Pi. RH development in −Pi has been infrequently reported <ref name="ref12" /><ref name="ref13" /><ref name="ref14" />. The present study was the first to demonstrate that OsARF16 was a key regulator in RH expansion under −Pi in rice. Moreover, the LR number in osarf16 showed a small increase under −Pi, consistent with an arf19 mutant in Arabidopsis <ref name="ref15" />. OsARF16 is highly homologous to ARF19, which is implicated in responses to Pi deficiency <ref name="ref16" />. The data indicated that OsARF16 also acted in LR development under −Pi as well as ARF19. Plants respond to Pi deficiency by allocating more carbon to their roots, thereby increasing their root-to-shoot ratio <ref name="ref17" /><ref name="ref18" />. The root-to-shoot ratio in osarf16 was only slightly increased compared with NIP, which further suggested that osarf16 was insensitive to Pi deficiency. It is worth mentioning that Fe accumulation in osarf16 under −Pi was lower than in NIP. A previous report showed that −Pi induced Fe acquisition and increased the Fe content of rice <ref name="ref19" />. Our results suggested that the knockout of OsARF16 may indirectly affect the Fe signal via the −Pi response.

‘’’OsARF16 is an essential regulator in −Pi response’’’
[[File: Shijc-Os06g0196700-Fig2.gif|right|thumb|200px|'' Indole acetic acid (IAA) content, and expressions of auxin biosynthesis genes and auxin transporters in Nipponbare (NIP) and osarf16 under normal nutritional solution (CK), IAA and −Pi treatments. (from reference <ref name="ref1" />).'']]
Under −Pi conditions, a plant enhances P absorption efficiency by regulating the expression of genes induced by phosphate starvation (PSIs) to maintain normal growth and development <ref name="ref20" /><ref name="ref21" />. In Arabidopsis, the complete regulatory network for the P signal is important for plant responses to −Pi. Thus, the absence of AtPHR1 located in the centre of the P signal network resulted in the expression of numerous downstream genes that were inhibited under −Pi, and with an impaired P signal <ref name="ref22" /><ref name="ref23" /><ref name="ref24" />. In rice, the knockdown of OsPHR2 led to a series of PSIs genes that were not distinctly induced by −Pi <ref name="ref25" />. The genetic effect of OsARF16 knockout was similar to the absence of AtPHR1 and OsPHR2. The knockout of OsARF16 greatly weakened the transmission of the P signal, leading PSIs genes to lose their correct response. The P deficiency response still was impaired in the osarf16 mutant, even if OsPHR2 was normally expressed. Thus, the P deficiency response via OsPHR2 was dependent on OsARF16-mediated −Pi signalling. The effect of the OsPHR2 function was based on the normal expression of the OsARF16 gene, which maintained P signal transmission and allowed rice to respond to P deficiency in time.

In Arabidopsis, the modulation of auxin sensitivity by Pi depends on the auxin receptor transport inhibitor response1 (TIR1) and ARF19. Auxin sensitivity is enhanced in Pi-deprived plants by an increased expression of TIR1, which accelerates the degradation of AUX/IAA proteins. This indicated that ARF transcription factors activate/repress genes that are related to auxin signalling <ref name="ref26" />. In rice, OsTIR1 in osarf16 was also less up-regulated by −Pi compared with NIP. Taken together, the results indicate that OsARF16 may be an essential regulator in −Pi response.

===Mutation===
[[File: Shijc-Os06g0196700-Fig3.gif|right|thumb|200px|'' Identification of mutant osarf16-Tos17 (osarf16) and phenotypic analysis. (from reference <ref name="ref1" />).'']]
Rice endogenous retrotransposon (TOS17) was integrated into the seventh exon of OsARF16 genes using analysis of the Rice Genome Resource Center (RGRC) database (http://www.rgrc.dna.affrc.go.jp) and sequencing. PCR analysis confirmed that the TOS17 fragment had been inserted into OsARF16 genes and the homozygous line was harvested. RT-PCR result demonstrated that OsARF16 was expressed in NIP and overexpressed in Ov16 and Ov16/mutant (Ov16/MT), but not the mutant osarf16. The phenotypes of NIP, osarf16, Ov16 and Ov16/MT were approximately the same under control (CK) conditions. However, the mutant osarf16 showed longer PR than the other three lines under IAA treatments, indicating it was insensitive to auxin. These results confirmed that OsARF16 was knocked out in osarf16, and that it rescued the function of OsARF16 in Ov16/MT. Exogenous auxin can decrease PR length <ref name="ref27" /> and induce LR formation <ref name="ref28" /> and RH elongation <ref name="ref29" /><ref name="ref30" />. However, under IAA treatment, the PR length with 2,4-D and IBA treatments and the LR number in osarf16 were greater than NIP and Ov16, whereas the RH length in osaf16 was lower compared with both lines. Ov16 was more sensitive to IAA or NPA than NIP in terms of lateral root number. In addition, Ov16 was also more sensitive to IAA than NIP in terms of RH length, although the RH length in Ov16 under NPA treatment was similar to that of NIP. These results further confirmed that osarf16 is actually insensitive to auxin. Under IAA treatment, there was no difference in the adventitious root (AR) number between osarf16 and NIP, or Ov16, although more AR was produced in osarf16 than the other lines with an auxin influx transport inhibitor, that is, NOA treatment. To know the phenotype of osarf16 when blocking auxin transport, the PR length was measured under PATIs. The PR length in osarf16 was longer than NIP and Ov16 with TIBA, NPA and 1-NOA treatments, which indicated that osarf16 was also insensitive to PATIs. These results showed that OsARF16 was required for auxin responses in roots.

===Expression===
[[File: Shijc-Os06g0196700-Fig4.gif|right|thumb|200px|'' OsARF16 expression patterns. (from reference <ref name="ref1" />).'']]
The expression patterns of OsARF16 in various organs was evaluated using the GUS reporter gene. The 2641 bp of the OsARF16 sequence upstream of its ATG (predicted by the annotated rice genome (http://rice.plantbiology.msu.edu/cgi-bin/gbrowse/rice/#search) was fused to GUS and the transgene was introduced into rice NIP. Ten positive transgenic lines were obtained and three lines were used for further investigation. GUS staining was found to be prominent in the stele and root tip of PR and AR (equal to PR). In LR, OsARF16 was weakly expressed in the stele, root tip and primordia. OsARF16 was expressed at a lower level in the leaf relative to the leaf tip. It was not expressed in RH and it was highly expressed in the vascular tissue of the stem. OsARF16 expression was also observed in the anther, the stigma of the flower and the glume. Semi-quantitative RT-PCR (sqRT-PCR) further confirmed that OsARF16 was expressed at different levels in various tissues, consistent with the GUS staining results. Therefore, OsARF16 was expressed in different organs and tissues, with the highest expression being in roots and vasculature.
The effects of auxin and −Pi treatments on the expression of OsARF16 was tested using the OsARF16::GUS reporter line. OsARF16 expression in the stele was completely inhibited by IAA, whereas that in the PR tip was highly induced by about 10-fold. OsARF16 expression in the stele, epidermis and tip of PR was highly induced (about 12-fold) by −Pi treatment. Interestingly, under the −Pi/+IAA treatment, the OsARF16 expression was highly increased in tip of PR than with only −Pi or IAA treatment (about 15-fold) while it was impaired in epidermis. This data provide an evidence for that auxin controls OsARF16 expression at a higher degree than −Pi. qRT-PCR analysis of PR further confirmed these trends. OsARF16::GUS staining was observed at the LR primordia, and induced by auxin and −Pi treatments. The above results suggest that the function of OsARF16 may be related to auxin and −Pi response.
[[File: Shijc-Os06g0196700-Fig5.gif|right|thumb|200px|'' OsARF16 expression pattern in root of Nipponbare (NIP; 7-day-old) under auxin and −Pi treatments. (from reference <ref name="ref1" />).'']]

==Labs working on this gene==
1. State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou 310058
2. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, 359 Tiyuchang Road, Hangzhou, China

==References==
<references>
<ref name="ref1">SHEN, C., WANG, S., ZHANG, S., XU, Y., QIAN, Q., QI, Y. and JIANG, D. A. (2013), OsARF16, a transcription factor, is required for auxin and phosphate starvation response in rice (Oryza sativa L.). Plant, Cell & Environment, 36: 607–620. doi: 10.1111/pce.12001 </ref>
<ref name="ref2">Shen C., Wang S., Bai Y., Wu Y., Zhang S., Chen M., Guilfoyle T.J., Wu P. & Qi Y. (2010a) Functional analysis of the structural domain of ARF proteins in rice (Oryza sativa L. Journal of Experimental Botany 61, 3971–3981. </ref>
<ref name="ref3">Qi Y., Wang S., Shen C., Zhang S., Chen Y., Xu Y., Liu Y., Wu Y. & Jiang D. (2012) OsARF12, a transcription activator on auxin response gene, regulates root elongation and affects iron accumulation in rice (Oryza sativa). New Phytologist 193, 109–120. </ref>
<ref name="ref4">Bureau M., Rast M.I., Illmer J. & Simon R. (2010) JAGGED LATERAL ORGAN (JLO) controls auxin dependent patterning during development of the Arabidopsis embryo and root. Plant Molecular Biology 74, 479–491. </ref>
<ref name="ref5">Shen C., Bai Y., Wang S., Zhang S., Wu Y., Chen M., Jiang D. & Qi Y. (2010b) Expression profile of PIN, AUX/LAX and PGP auxin transporter gene families in Sorghum bicolor under phytohormone and abiotic stress. FEBS Journal 277, 2954–2969. </ref>
<ref name="ref6">Wang J.R., Hu H., Wang G.H., Li J., Chen J.Y. & Wu P. (2009b) Expression of PIN genes in rice (Oryza sativa L.): tissue specificity and regulation by hormones. Molecular Plant 2, 823–831. </ref>
<ref name="ref7">Jain M. & Khurana J.P. (2009) Transcript profiling reveals diverse roles of auxin-responsive genes during reproductive development and abiotic stress in rice. FEBS Journal 276, 3148–3162. </ref>
<ref name="ref8">Zheng L., Huang F., Narsai R., et al. (2009) Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiology 151, 262–274. </ref>
<ref name="ref9">López-Bucio J., Cruz-Ramı'rez A. & Herrera-Estrella L. (2003) The role of nutrient availability in regulating root architecture. Current Opinion in Plant Biology 6, 280–287. </ref>
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<ref name="ref11">Vanneste S. & Friml J. (2009) Auxin: a trigger for change in plant development. Cell 136, 1005–1016. </ref>
<ref name="ref12">Sánchez-Calderón L., López-Bucio J., Chacón-López A., Gutiérrez-Ortega A., Hernández-Abreu E. & Herrera-Estrella L. (2006) Characterization of low phosphorus insensitive mutants reveals a crosstalk between low phosphorus-induced determinate root development and the activation of genes involved in the adaptation of Arabidopsis to phosphorus deficiency. Plant Physiology 140, 879–889. </ref>
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<ref name="ref14">Wang X., Du G., Wang X., Meng Y., Li Y., Wu P. & Yi K. (2010b) The function of LPR1 is controlled by an element in the promoter and is independent of SUMO E3 Ligase SIZ1 in response to low Pi stress in Arabidopsis thaliana. Plant Cell and Physiology 51, 380–394. </ref>
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<ref name="ref17">López-Bucio J., Cruz-Ramı'rez A. & Herrera-Estrella L. (2003) The role of nutrient availability in regulating root architecture. Current Opinion in Plant Biology 6, 280–287. </ref>
<ref name="ref18">Hermans C., Hammond J.P., White P.J. & Verbruggen N. (2006) How do plants respond to nutrient shortage by biomass allocation? Trends in Plant Science 11, 610–617. </ref>
<ref name="ref19">Zheng L., Huang F., Narsai R., et al. (2009) Physiological and transcriptome analysis of iron and phosphorus interaction in rice seedlings. Plant Physiology 151, 262–274. </ref>
<ref name="ref20">Martín A.C., del Pozo J.C., Iglesias J., Rubio V., Solano R., de LaPeña A., Leyva A. & Paz-Ares J. (2000) Influence of cytokinins on the expression of phosphate starvation responsive genes in Arabidopsis. The Plant Journal 24, 559–567. </ref>
<ref name="ref21">Schachtman D.P. & Shin R. (2007) Nutrient sensing and signaling: NPKS. Annual Review of Plant Biology 58, 47–69. </ref>
<ref name="ref22">Rubio V., Linhares F., Solano R., Martín A.C., Iglesias J., Leyva A. & Paz-Ares J. (2001) A conserved MYB transcription factor involved in phosphate starvation signaling both in vascular plants and in unicellular algae. Genes & Development 15, 2122–2133. </ref>
<ref name="ref23">Nilsson L., Müller R. & Nielsen T.H. (2007) Increased expression of the MYB-related transcription factor, PHR1, leads to enhanced phosphate uptake in Arabidopsis thaliana. Plant, Cell & Environment 30, 1499–1512. </ref>
<ref name="ref24">Panigrahy M., Rao D.N. & Sarla N. (2009) Molecular mechanisms in response to phosphate starvation in rice. Biotechnology Advances 27, 389–397. </ref>
<ref name="ref25">Zhou J., Jiao F., Wu Z., Li Y., Wang X., He X., Zhong W. & Wu P. (2008) OsPHR2 is involved in phosphate-starvation signaling and excessive phosphate accumulation in shoots of plants. Plant Physiology 146, 1673–1686. </ref>
<ref name="ref26">Pérez-Torres C.A., Lo'pez-Bucio J., Cruz-Ramı'rez A., Ibarra-Laclette E., Dharmasiri S., Estelle M. & Herrera-Estrella L. (2008) Phosphate availability alters lateral root development in Arabidopsis by modulating auxin sensitivity via a mechanism involving the TIR1 auxin receptor. The Plant Cell 20, 3258–3272. </ref>
<ref name="ref27">Woodward A.W. & Bartel B. (2005) Auxin: regulation, action, and interaction. Annals of Botany 95, 707–735. </ref>
<ref name="ref28">Dong L., Wang L., Zhang Y., Zhang Y., Deng X. & Xue Y. (2006) An auxin-inducible F-box protein CEGENDUO negatively regulates auxin-mediated lateral root formation in Arabidopsis. Plant Molecular Biology 60, 599–615. </ref>
<ref name="ref29">Lee S.H. & Cho H.T. (2006) PINOID positively regulates auxin efflux in Arabidopsis root hair cells and tobacco cells. The Plant Cell 18, 1604–1616. </ref>
<ref name="ref30">Duan Q.H., Kita D., Li C., Cheung A.Y. & Wu H.M. (2010) FERONIA receptor-like kinase regulates RHO GTPase signaling of root hair development. Proceedings of the National Academy of Sciences of the United States of America 107, 17821–11782. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os06g0196700|
Description = Similar to Auxin response factor 1|
Version = NM_001187722.1 GI:297724574 GeneID:9270361|
Length = 6594 bp|
Definition = Oryza sativa Japonica Group Os06g0196700, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 6|Chromosome 6]]|
AP = Chromosome 6:4925020..4931613|
CDS = 4925493..4925538,4925790..4925902,4925994..4926089,4926187..4926243,4926329..4926484 ,4926586..4926670,4926911..4927001,4927080..4927365|
GCID = <gbrowseImage1>
name=NC_008399:4925020..4931613
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008399:4925020..4931613
source=RiceChromosome06
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaaggatcagggatcatccggtgtgtctcccgccccaggggaaggggagaagaaagccatcaattcggagctatggcatgcttgtgccgggcctcttgtgtcgctgccgccggtgggcagtctcgtcgtgtacttccctcagggtcatagcgagcaggttgctgcttccatgcacaaggagctggacaacatccctggttatccctctcttccgtctaagctgatctgcaaacttctgagtctcaccttacatgcagattctgaaactgatgaagtttatgctcagatgacacttcaaccagtcaataaatatgatcgagatgcaatgctggcatctgaactgggcctgaagcaaaacaagcaaccagcggagttcttttgcaaaacgctgacggcgagcgacacaagtacccatggtggattttcagtgccacgtcgtgcggcggagaagatatttccaccactagactttaccatgcaaccaccagcacaagagctcatcgccaaggatctgcatgatatttcatggaaatttcgacacatttaccgaggtcaaccaaagaggcaccttctgacaactggttggagcgtctttgtcagcacaaaaaggcttctagctggtgattcagttctgtttataagggatgagaaatctcagcttctattaggcatacgtcgtgctaccagaccccaaccagctctatcgtcatcagttctatcaagtgatagcatgcacattgggattctagctgctgcagcacatgctgctgcaaacagtagcccatttactattttctacaatccaaggtattatagttcttacttgatatcccattatcccaatgcactctctgctaccctttgggactatgaactcattgttgttattctgatagggcaagtccatcagaatttgtcattcctttag</cdnaseq>|
AA = <aaseq>MKDQGSSGVSPAPGEGEKKAINSELWHACAGPLVSLPPVGSLVV YFPQGHSEQVAASMHKELDNIPGYPSLPSKLICKLLSLTLHADSETDEVYAQMTLQPV NKYDRDAMLASELGLKQNKQPAEFFCKTLTASDTSTHGGFSVPRRAAEKIFPPLDFTM QPPAQELIAKDLHDISWKFRHIYRGQPKRHLLTTGWSVFVSTKRLLAGDSVLFIRDEK SQLLLGIRRATRPQPALSSSVLSSDSMHIGILAAAAHAAANSSPFTIFYNPRYYSSYL ISHYPNALSATLWDYELIVVILIGQVHQNLSFL</aaseq>|
DNA = <dnaseqindica>474..519#771..883#975..1070#1168..1224#1310..1465#1567..1651#1892..1982#2061..2346#ggcttcctcctccacttgcttcgtcgtcgtcgtcctcctcctcctctctctactctctctctccgaaccatccttcccacccggcacgccgccgcgcgctgttcccgacggcggccggtggccggagtgagaggctgggtgtactgtccgctgatgctcgtgggaggcggcggcggcggcggcggcgtgtgatgagcggaggccgcgtgggcgagaacctgtcgcgtcggcacggcggcggcggcggtggcgagggctcgtcaggcttggccacgctttgctcccttcgcagtggcgctcccctggtgccgaatattatactcgccgccgcctcgtgccgcctactttaggcggaaagggggagagctctcctatcctagctgctgctgctgccactggctaagttggtaaaaggtggaggaggcggatattcgtgtatccggaggagagatttggatcgggatctcgccgggatgaaggatcagggatcatccggtgtgtctcccgccccaggggaaggtgagaagaatccttttgctctttgctcatgtgcttgcttcctttgcattgttcagaaaaattcaggtcgttttgcttgagcatttgccgaattcatggccatcatcgttgccgcagcgcacatttgcagtgaaaccttgctcatggcctcctcctcctcctccctatgaatcttatcgcattagcgtgtgctgtgtagtgtgaggttggatacactgctgtaacaactgagcatgggttttgcaaagcaggggagaagaaagccatcaattcggagctatggcatgcttgtgccgggcctcttgtgtcgctgccgccggtgggcagtctcgtcgtgtacttccctcagggtcatagcgagcaggtgaacaattttgtcatcttactgtctgaaatgtgctgaatcgtgacaagtttctgaaaattttcttgttttctggtatgcctttgtttaggttgctgcttccatgcacaaggagctggacaacatccctggttatccctctcttccgtctaagctgatctgcaaacttctgagtctcaccttacatgtatgtgcatagtactttccactttgatgctatagttgtgtttttcctttttcatctttgctaattgggtgcgcgcaacatgttttttattgttcaggcagattctgaaactgatgaagtttatgctcagatgacacttcaaccagtcaataaagtatgtaagatgatgatctatttgattatgggaacacactatttatctccgtgaaattgaaatatgttttctggatgtgttttagtatgatcgagatgcaatgctggcatctgaactgggcctgaagcaaaacaagcaaccagcggagttcttttgcaaaacgctgacggcgagcgacacaagtacccatggtggattttcagtgccacgtcgtgcggcggagaagatatttccaccactagtatgcagagtttcttcataacccttgcagtaattttgatggaactatgcatttatcagatgcagtgaatacctgccttaccaggataacatgttcgataggactttaccatgcaaccaccagcacaagagctcatcgccaaggatctgcatgatatttcatggaaatttcgacacatttaccgaggtatgccaaactgctaactgctcagagaatatctgtacattgacttggttttatatttatttcattgccacattttttttgacagacccattacttacacttagttagcactttgcatctagttttcctgctttttctttgaactgctaaggatgtctctgtcctgggacatggtggccgatcaatcaattgcattctgtacttacctgtatactactgtaccttcacatggacacgcaggtcaaccaaagaggcaccttctgacaactggttggagcgtctttgtcagcacaaaaaggcttctagctggtgattcagttctgtttataaggtagcacactgaaattcaagtgcatcgatttgtctaaatcgtttcaagaaatattgattctacatcttttgtttgcagggatgagaaatctcagcttctattaggcatacgtcgtgctaccagaccccaaccagctctatcgtcatcagttctatcaagtgatagcatgcacattgggattctagctgctgcagcacatgctgctgcaaacagtagcccatttactattttctacaatccaaggtattatagttcttacttgatatcccattatcccaatgcactctctgctaccctttgggactatgaactcattgttgttattctgatagggcaagtccatcagaatttgtcattcctttagcgaaatataacaaggctttgtatacacaagtatctcttggaatgcggttcagaatgctgtttgagacagaggattcaggggttcgaagatatatgggaacaatcacaggtattggtgacttggatccagtgcgctggaagaactctcattggcgaaaccttcaggtgtgctactcttttcttcttttagttctgcaatgtgtcacattcatacatctcattctcatctatgatctgtaagaaataacaaaatatctggattaattatttgtattaaattagaaaattcaacctcattttgaagaaatctttgaaataagattgcctaacaccctatagaattgttgtttgcaagtttgtttagcatattatacaaaaccttccctgacttcacctcctctttctaagttaggttggttgggatgaatcaacagcatctgagaggcgcactcgtgtttcaatatgggagattgaaccagtcgcgacacctttttatatttgtccaccaccatttttcaggccaaaacttcctaagcagccaggaatgccaggtacagatacttccactcaacattatatatatattagctagtattactatttagggaatagtgtaatatgcagatcattttgatctttgggaattagtgcttcaatcatacagtcattctcttcttgctgaactcattaagcttgtaaagaacactgcaacctaattttcaccaacgtgcatacgcattatactaaaaatggtttgcttcttgcatgcatatgaacttgatgcatctgttaacagcaagaggttctagccaaagcacataaacacacttcaattctcttaaatgtagttgcttcttgattgtgtataaacttgaaatattaataatcagcaagaactgtggatttgttgtttgttacctgtgtacaagttaacttccttgcaaattttgcttgcattttcttaagattagtttgggcctcatatgaaaattgctaaaacttgcagatgatgaaaatgaagttgagagtgctttcaaaagagccatgccatggcttgctgatgactttgccctgaaagatgtgcaaagtgcattatttccaggtctgagcctagtccaatggatggctatgcaacagaatcctcagatgctaacagctgcgtcccaaacagtgcaatcaccgtacttgaactccaatgcattggctatgcaggatgtgatgggtagtagcaacgaggacccaacaaaaagattgaacacacaggcacaaaatatggttttacctaatttacaggttggctcaaaagtggatcaccctgtaatgtctcaacatcaacagcagccacaccaactatcacaacagcagcaggtccagccatcgcagcaaagttctgtggttttacagcaacatcaagcccagttgctgcagcagaacgccattcacttgcagcagcagcaagaacatctccagcggcagcagtcacaaccggcacagcagttgaaggctgcttcaagtctgcattcagtggaacagcacaagctgaaagaacagacttcaggtgggcaggttgcctcacaagcacaaatgttaaaccagattttcccaccatcttcatcgcagctacaacagttaggtttacccaagtcacctactcatcgccaagggttgacaggattaccaattgcaggttctttgcagcagcccacactaactcagacatctcaagtccagcaagcagccgaatatcagcaggccctcctacagagtcagcaacagcaacagcaactgcaactgcaacaactatcacaaccagaagtacagctgcagctgcttcaaaagattcaacaacaaaacatgctatctcagctgaacccacaacatcagtcccagttgattcaacaattgtctcagaaaagccaggaaattctacagcaacaaattttgcaacatcaatttggtgggtctgattctattggtcaactcaagcaatcaccatcgcagcaagctcctttaaaccacatgacaggatctttgacgccccagcaacttgtcagatcacattcggcacttgctgagagtggggatccatccagttcaactgctccatccaccagccgtatttctccaataaattcgctgagtagggcaaaccaaggaagcagaaatttaactgacatggtggcaacaccacaaattgacaacttacttcaggaaattcaaagcaagccagataatcgaattaagaatgacatacagagcaaagaaacagtccctatacataaccgacatccagtttctgatcaacttgatgcatcatctgctacctccttttgtttagacgagagcccacgagaaggtttttccttccctccagtttgtttggataacaatgttcaagttgatccaagagataactttcttattgcggaaaatgtggacgcattgatgccagatgccctgttgtcaagaggtatggcttcaggaaagggcatgtgcactctgacttctggacaaagggatcacagggatgtcgagaatgagctatcatctgctgcatt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Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001187722.1 RefSeq:Os06g0196700]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 6]]
[[Category:Chromosome 6]]

Os04g0612000

2014-12-27T13:47:40Z

Shijc:

OsKS2 gene is a chromosome 4-located ent-kaurene synthase (KS), encoding the enzyme that catalyses an early step of the GA biosynthesis pathway. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os04g0612000-Fig1.png|right|thumb|200px|'' The GA biosynthesis pathway and RT-PCR analysis of the 22 candidate GA metabolic pathway genes in Dongjin and dwarf2. (from reference <ref name="ref1" />).'']]
Gibberellins play a fundamental role in regulating several developmental processes, e.g. seed germination <ref name="ref2" /> and flowering <ref name="ref3" />. During germination, GA promotes embryo growth, concurrent with a reduction in the physical restraint imposed by the endosperm and testa, allowing radical protrusion <ref name="ref2" />. During flowering, GA is fundamental to development of stamens and petals <ref name="ref4" />.
Brassinosteroids (BRs), a class of steroidal plant hormone, are widely distributed in both lower and higher plants <ref name="ref5" />. BRs are integrated in a complex signalling network, and numerous BR effects appear to be mediated via modulation of levels and sensitivities of other phytohormones. In previous reports, BR activity was demonstrated in almost all auxin and in selected GA bioassays <ref name="ref6" /><ref name="ref7" />(.
he inductions of α-amylase and shoot elongation by GA, both of which are GA-mediated physiological processes, are classical model systems for studying how GAs act <ref name="ref8" /><ref name="ref9" />. For detection of α-amylase activity, halved seeds are used, and only seeds secreting α-amylase form transparent halos around the seed, resulting from the digestion of starch by α-amylase <ref name="ref10" />.
The dwarf2 mutant has a defective OsKS2 gene, which is an early step in the GA biosynthesis pathway in rice. The mutant phenotype was restored similar the wild type after exogenous application of bioactive GA3 2 weeks later. Previously, Margis-Pinheiro et al. <ref name="ref11" /> suggested that mutant seedlings respond similar to the wild type when treated with exogenous GA3. The mutant exhibits multiple abnormal phenotypes: dwarfism, short, wide and dark green leaf blades, reduced tiller number, short roots and early reduction in shoot growth at the seedling stage. In the wild type the internal structures, such as motor cells, large and small vascular bundles and phloem, presented a regular pattern and normal development of leaf blades and elongated stems, whereas in the dwarf mutant there was dramatic modification, including large lacunae, loss of small vascular bundles and submerged lacunae instead of normal, small and large vascular bundles and air spaces in the elongated stem.
In rice, GA signalling pathway genes have been reported to regulate fertilisation. Chhun et al. <ref name="ref12" /> blocked the expression of OsCPS upstream of the GA pathway, which directly affected rice fertilisation and pollen development. However, when the OsKAO gene downstream of the GA pathway was blocked, the resulting mutant exhibited a severe dwarf phenotype and barely developed floral organs. One of the best-known functions of GAs in plants is promotion of stem elongation <ref name="ref2" />. Although the number of naturally occurring GAs is large, the number of biologically active GAs is quite small (e.g. GA1, GA3, GA4, GA7 and a few others). Other GAs are either intermediates in the biosynthetic pathway or exist in inactivate forms. Most dicots and some monocots respond by growing faster when treated with GAs, but several species in the Pinaceae show few or no elongation responses to GA3 <ref name="ref13" />. However, they do respond well to a mixture of GA4 and GA7 <ref name="ref14" />. Short bush beans become climbing pole beans, and dwarf genetic mutants of rice, maize and peas phenotypically exhibit the tall characteristics of normal varieties when treated with GA3 <ref name="ref15" />.
Terpenes, or terpenoids, are a large class of plant secondary products with a major role in defence against plant-feeding insects and herbivores <ref name="ref16" />. However, not all terpenoids act as secondary products, e.g. those involved in photosynthesis, stability of cell membranes, signalling and in biosynthesis of several plant hormones. OsKSL1, OsKSL3 and OsKS2 interact with each other and are involved in the catalytic reactions of GA biosynthesis. The differences between vascular bundles of leaf blade tips in osks2 and Dongjin might cause the curly phenotype of leaf blades, because motor cells play an important role in leaf rolling <ref name="ref17" />. The difference of plant growth between Dongjin and osks2 was caused by differences in the shape and cell size of xylem, phloem, motor and mesophyll cells. The abnormal osks2 cell shapes and disorganised cell arrangements may be caused by a defect in their synchronous division and elongation <ref name="ref18" />. The OsKS2 mRNA transcripts of Dongjin encoded a putative KS after treatment with UV, salinity, drought or wounding. In particular, expression was higher in salinity- and drought-treated samples than in UV-treated and wounded samples. Moreover, the OsKS2 gene was predominantly expressed under environmental stress.

===Mutation===
[[File: Shijc-Os04g0612000-Fig2.png|right|thumb|200px|'' Morphological variations in Dongjin and the dwarf mutant. (from reference <ref name="ref1" />).'']]
Among the dwarf mutants whose leaves and stems are externally treated with 50 μm GA3 for 2 weeks, three dwarf mutant lines (dwarf1, dwarf2 and dwarf3) have a restored phenotype similar to the wild type, Dongjin. These dwarf mutants went through a normal vegetative growth stage and exhibited relatively smaller organs compared to Dongjin at various growth stages. The dwarf mutant showed reduced shoot growth, less crown roots and reduced growth of branch roots compared to Dongjin. Additionally, the dwarf mutants showed abnormal leaf blade morphology, with dark-green leaves, shorter and wider edges and leaf tips more rounded than in the wild-type Dongjin. The dwarf mutant has almost sterile seeds, and rapid stem elongation occurred about 2 weeks later.
To confirm identification of Ac/Ds inserted dwarfs, Ac/Ds genotype PCR is performed using Ac/Ds gene-specific primers, while the DNA blot analysis of Ds elements is performed using a gene-trap Ds in three dwarf lines. The gene-trap Ds construct contained the 1.2 kb GUS coding region as a reporter <ref name="ref19" />, and DNA from this region is used as a probe <ref name="ref20" />.

===Expression===
[[File: Shijc-Os04g0612000-Fig3.png|right|thumb|200px|'' mRNA expression of OsKS2. (from reference <ref name="ref1" />).'']]
The CPS-like and KS-like genes are considered likely to be involved in diterpene phytoalexin biosynthesis in response to pathogen infection and UV irradiation <ref name="ref21" />. Since OsKSL genes are usually induced by environmental stresses, The mRNA expression pattern of OsKS2 in response to various environmental stresses. Northern blot analysis showed that mRNA expression of OsKS2 is induced by salinity (twofold) and drought (four-fold). However, there is no significant increase in mRNA levels after UV treatment and mechanical wounding. OsKS2 transcripts are strongly expressed in salinity and drought compared to the untreated control.
An OsKS2 transcript of about 1.8 kb is detected in Dongjin leaves. An 800-bp fragment of the OsKS2 transcript is used as a probe. A total of 15 μg RNA is isolated from different plant parts (i.e. leaf, stem or root) during growth for 30 and 60 days in the wild type. During investigation of the time-course pattern of OsKS2 gene expression, a 2.7-kb transcript of OsKS2 is more strongly detected in leaves, stems and roots of 30-day-old Dongjin than in 60-day-old Dongjin. Generally, the expression of OsKS2 is higher in 30-day-old than 60-day-old plants when probed with 800 bp OsKS2 cDNA at high stringency.
The mRNA expression pattern of OsKS2 in various organs of 30-day-old wild-type Dongjin and found it is expressed in all organs – leaf blades, stem, root, callus, flowers and panicles at flowering stage. The OsKS2 mRNA indicated significantly higher expression in the stem, followed by flowers and panicles, whereas expression in leaf, root and callus is similar. These variations in OsKS2 expression at different stages clearly indicate its involvement in regulating the growth period of the plants, which warrants further investigation.

===Evolution===
[[File: Shijc-Os04g0612000-Fig4.png|right|thumb|200px|'' Terpene cyclase domain of OsKSL1, OsKS2 and OsKSL3 proteins. (from reference <ref name="ref1" />).'']]
The OsKS family genes are not broadly conserved by function. Especially OsKSL1, OsKSL3, OsKSL7 and OsKS2 proteins are more closely related than other proteins. All of the OsKSL family proteins shared significant homology (29–47%) to the OsKS2 protein. The OsKS2 protein has high homology with OsKSL1, sharing 47% identity at the amino acid level. However, relatively lower homology is found between OsKSL3 and OsKS2, with only 29% amino acid sequence identity.

==Labs working on this gene==
1. Department of Molecular Biotechnology, Konkuk University, Seoul, Korea
2. Subtropical Horticulture Research Institute, Faculty of Biotechnology, Jeju National University, Jeju, Korea
3. Smart Bio Lab Co., Ltd., Suwon, Korea
4. National Academy of Agricultural Science, RDA, Suwon, Korea

==References==
<references>
<ref name="ref1"> i, S. H., Gururani, M. A., Lee, J. W., Ahn, B.-O., Chun, S.-C. (2014), Isolation and characterisation of a dwarf rice mutant exhibiting defective gibberellins biosynthesis. Plant Biology, 16: 428–439. doi: 10.1111/plb.12069 </ref>
<ref name="ref2"> Debeaujon I., Koornneef M. (2000) Gibberellin requirement for Arabidopsis seed germination is determined both by testa characterization and embryonic abscisic acid. Plant Physiology, 122, 415–424. </ref>
<ref name="ref3">King R.W., Evans L.T. (2003) Gibberellins and flowering of grasses and cereals: prizing open the lid of the “Florigen” black box. Annual Review of Plant Biology, 54, 307–328.</ref>
<ref name="ref4">Olszewski N., Sun T.P., Gubler F. (2002) Gibberellin signaling: Biosynthesis, catabolism, and response pathways. The Plant Cell, 14, 61–80.</ref>
<ref name="ref5">Grove M.D., Spencer G.F., Rohwedder W.K., Mandava N.B., Worley J.F., Warthen J.D., Steffens G.L., Flippen-Anderson J.L., Cook J.C. (1979) Brassinolide, a plant growth-promoting steroid isolated from Brassica napus pollen. Nature, 281, 216–217. </ref>
<ref name="ref6">Yopp J.H., Colclasure G.C., Mandava N. (1979) Effects of brassin-complex on auxin and gibberellin mediated events in the morphogenesis of the etiolated bean hypocotyl. Physiologia Plantarum, 46, 247–254. </ref>
<ref name="ref7">Mandava N.B., Sasse J.M., Yopp J.H. (1981) Brassinolide, a growth-promoting steroidal lactone. II. Activity in selected gibberellin and cytokinin bioassays. Physiologia Plantarum, 53, 453–461. </ref>
<ref name="ref8"> Lanahan M.B., Ho T.D.H., Rogers S.W., Rogers J.C. (1992) A gibberellin response complex in cereal alpha-amylase gene promoters. The Plant Cell, 4, 203–211. </ref>
<ref name="ref9">Matsukura C., Itoh S., Nemoto K., Tanimoto E., Yamaguchi J. (1998) Promotion of leaf sheath growth by gibberellic acid in a dwarf mutant of rice. Planta, 205, 145–152. </ref>
<ref name="ref10"> Lanahan M.B., Ho T.D.H. (1988) Slender barley: a constitutive gibberellin-response mutant. Planta, 175, 107–114. </ref>
<ref name="ref11">Margis-Pinheiro M., Zhou X.R., Zhu Q.H., Dennis E.S., Upadhyaya N.M. (2005) Isolation and characterization of a Ds-tagged rice (Oryza sativa L.) GA-responsive dwarf mutant defective in an early step of the gibberellin biosynthesis pathway. Plant Cell Reports, 23, 819–833. </ref>
<ref name="ref12">Chhun T., Aya K., Asano K., Yamamoto E., Morinaka Y., Watanabe M., Kitano H., Ashikari M., Matsuoka M., Ueguchi-Tanaka M. (2007) Gibberellin regulates pollen viability and pollen tube growth in rice. The Plant Cell, 19, 3876–3888. </ref>
<ref name="ref13">Pharisr P., Kuo C.G. (1977) Physiology of gibberellins in conifers. Canadian Journal of Forest Research, 7, 299–325. </ref>
<ref name="ref14">Pharis R.P., Evans L.T., King R.W., Mander L.N. (1989) Gibberellins and Flowering in Higher Plants – Differing structures yield highly specific effects. In: Lord E., Bernier G. (Eds), Plant reproduction: from floral induction to pollination, 1. Symposium of the American Society of Plant Physiology, 29–41. </ref>
<ref name="ref15">Nishijima T., Katsuma N. (1989) A modified micro-drop bioassay using dwarf rice for detection of femtomol quantities of gibberellins. Plant & Cell Physiology, 30, 623–627. </ref>
<ref name="ref16">Yamaguchi S., Sun T., Kawaide H., Kamiya Y. (1998) The GA2 locus of Arabidopsis thaliana encodes ent-kaurene synthase of gibberellin biosynthesis. Plant Physiology, 116, 1271–1278. </ref>
<ref name="ref17">Hoshikawa K. (1989) The growing rice plant—an anatomical monograph. Nobunkyo Press, Tokyo, Japan.</ref>
<ref name="ref18">Komorisono M., Ueguchi-Tanaka M., Aichi I., Hasegawa Y., Ashikari M., Kitano H., Matsuoka M., Sazuka T. (2005) Analysis of rice mutant dwarf and gladius leaf 1. Aberrant katanin-mediated microtubule organization genes independently of gibberellin signaling. Plant Physiology, 138, 1982–1993. </ref>
<ref name="ref19">Chin H.G., Choe M.S., Lee S.H., Park S.H., Koo J.C., Kim N.Y., Lee J.J., Oh B.G., Yi G.H., Kim S.C., Choi H.C., Cho M.J., Han C.D. (1999) Molecular analysis of rice plants harboring an Ac/Ds transposable element-mediated gene trapping system. The Plant Journal, 19, 615–623. </ref>
<ref name="ref20">Park S.H., Jun N.S., Kim C.M., Oh T.Y., Huang J., Xuan Y.H., Park S.J., Je B.I., Piao H.L., Park S.H., Cha Y.S., Ahn B.O., Ji H.S., Lee M.C., Suh S.C., Nam M.H., Eun M.Y., Yi G.H., Yun D.W., Han C.D. (2007) Analysis of gene-trap DS rice populations in Korea. Plant Molecular Biology, 65, 373–384. </ref>
<ref name="ref21">Sakamoto T., Miura K., Itoh H., Tatsumi T., Ueguchi-Tanaka M., Ishiyama K., Kobayashi M., Agrawal G.K., Takeda S., Abe K., Miyao A., Hirochika H., Kitano H., Ashihikara M., Matsuoka M. (2004) An overview of gibberellin metabolism enzyme genes and their related mutants in rice. Plant Physiology, 134, 1642–1653. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os04g0612000|
Description = Similar to Ent-kaurene synthase-like protein 1|
Version = NM_001060377.2 GI:297603338 GeneID:4336962|
Length = 6239 bp|
Definition = Oryza sativa Japonica Group Os04g0612000, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 4|Chromosome 4]]|
AP = Chromosome 4:31433420..31439658|
CDS = 31433420..31433801,31434412..31434568,31436716..31436936,31437022..31437142,31437233..31437330 ,31437521..31437642,31437816..31437928,31438087..31438182,31438272..31438487 ,31438589..31438701,31438774..31438877,31438976..31439071,31439350..31439658 |
GCID = <gbrowseImage1>
name=NC_008397:31433420..31439658
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008397:31433420..31439658
source=RiceChromosome04
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgatcgaggccatgcggcactgcagcagcagcagcagcagcgaggaaggaggagcggcggcgacgacggcggccagatcagcagtacgggagcgcctccaattagcgccgccgtcgccgtcgccgtcgccgtacgacacggcgtgggtggccatggtgccggccctccgccgtggcggcggcggcccgcggttcccgcagtgcgtcgcgtggatccagcggaaccagcggggcgacgggtcatggcgccacgcggcggcggcgcaccagcagctcggctcctcgccggagatcgtcaccgagcgcgacctctcgtccaccctcgcctgcgtcctcgcgctcgcgcgatgggacgccggcagtgagcacgtcaggagagggctgcagtttatcgggaggaacatgtcggtcgccatggacgatcagacggctgctccggcgtctggttccgtcgtcagtttcgcagcgatgctccggatggcgatggagatgggtttggaggttcctgccgtcagccaagctgacgtccgcgacagagatgctggggtgatctgccacggtggaagaacagaatatacggcttatgtctcagaaggattaggcaatattcagaactggaatgaagtgatgaaattccaaagaaagaatggctcactgttcaactccccttacacaactgcagctgcattagtccacaactatgatgccaaagctctccagtacttagacatgcttctggacaaatttggaagtgcagtgccagcggcctatcctgcaaatattcagtctcagctctacatggtggatgtgcttgaaaagatgggaatatctaggcattttgttggtgagataaagagcatactggacatgacctacagttgctggaaacagagggatgaggaaattgtgcttgacatgcaaacatgtgggatggcatttcgtatgttgcgtatgaatggatatgatgtttcttcagatgagctatctcatttttctgaaccttcaagtttccacaattcacttcaaggatatctgaatgatacaagatctttattagaattacataaggcttcaaaagtcagtatcgcagaaaaggaggttgaatatgctcttgaatttcccttctataccatcttggatcgtctagaccataaaagaaatatcgaacattttgacattacaagcagtcagatgctagaaacagcgtacttgccatgtcattccaatgaagaaatcatggccttgggtgtgagagattttagtagctctcagtttattttccaagaagagctgcagcaactcaacagctgggtgaaagagagcaggttggatcagctgcaattcgcacggcagaagttggactacttctatttctctgctgctgctaccattttcactcctgaactgtcagatgttcgcattttgtgggccaaaaatggcgtgctgacaacggtcgtcgacgacttcttcgacgttggaggatcaaaagaagaactggaaaacctcgtcgcattagttgagaagtgggacaagaatgacaaaactgagtactactctgaacaagtagagattgtgttctctgcaatttatacttcaactaaccagcttggatcaatggcctctgtagtacaaggccaagtgagaactgacaagctaaatatagtggcctctgttaatctgtgtatagtggcaagaattgctgaggtctatgatgacagaggtagagtggaggcagagccgatgcctgattctgtcataagaagccaagaatgcagcgagttgttccggctaatgagcaaatgtggccgtctcctgaatgatgtccaatcctacgagagagagggcagccagggcaagctgaacagcgtctctctgcttgccctccacagtggaggctctgtctccatggaagaggctgtgaagcagattcagagacccatcgagaaatgcaggagagagttgctgaagctggtcgtcagcagaggaggcgccgttccaaggccatgcagggagctgttctggagcatgtgcaaggtctgccacttcttctactccggcggcgacgggttcagctcgccgacggcgaaggccggcgcgttggacgcggtgatccacgagccgctgaatctgtcttgttctgtgtga</cdnaseq>|
AA = <aaseq>MAIEAMRHCSSSSSSEEGGAAATTAARSAVRERLQLAPPSPSPS PYDTAWVAMVPALRRGGGGPRFPQCVAWIQRNQRGDGSWRHAAAAHQQLGSSPEIVTE RDLSSTLACVLALARWDAGSEHVRRGLQFIGRNMSVAMDDQTAAPASGSVVSFAAMLR MAMEMGLEVPAVSQADVRDRDAGVICHGGRTEYTAYVSEGLGNIQNWNEVMKFQRKNG SLFNSPYTTAAALVHNYDAKALQYLDMLLDKFGSAVPAAYPANIQSQLYMVDVLEKMG ISRHFVGEIKSILDMTYSCWKQRDEEIVLDMQTCGMAFRMLRMNGYDVSSDELSHFSE PSSFHNSLQGYLNDTRSLLELHKASKVSIAEKEVEYALEFPFYTILDRLDHKRNIEHF DITSSQMLETAYLPCHSNEEIMALGVRDFSSSQFIFQEELQQLNSWVKESRLDQLQFA RQKLDYFYFSAAATIFTPELSDVRILWAKNGVLTTVVDDFFDVGGSKEELENLVALVE KWDKNDKTEYYSEQVEIVFSAIYTSTNQLGSMASVVQGQVRTDKLNIVASVNLCIVAR IAEVYDDRGRVEAEPMPDSVIRSQECSELFRLMSKCGRLLNDVQSYEREGSQGKLNSV SLLALHSGGSVSMEEAVKQIQRPIEKCRRELLKLVVSRGGAVPRPCRELFWSMCKVCH FFYSGGDGFSSPTAKAGALDAVIHEPLNLSCSV</aaseq>|
DNA = <dnaseqindica>1..382#993..1149#3297..3517#3603..3723#3814..3911#4102..4223#4397..4509#4668..4763#4853..5068#5170..5282#5355..5458#5557..5652#5931..6239#atggcgatcgaggccatgcggcactgcagcagcagcagcagcagcgaggaaggaggagcggcggcgacgacggcggccagatcagcagtacgggagcgcctccaattagcgccgccgtcgccgtcgccgtcgccgtacgacacggcgtgggtggccatggtgccggccctccgccgtggcggcggcggcccgcggttcccgcagtgcgtcgcgtggatccagcggaaccagcggggcgacgggtcatggcgccacgcggcggcggcgcaccagcagctcggctcctcgccggagatcgtcaccgagcgcgacctctcgtccaccctcgcctgcgtcctcgcgctcgcgcgatgggacgccggcagtgagcacgtcaggagaggtatagtagtagctcgttgaattctcagtcatctgatcgaccaatctctgatcagatctatcgatgatcgcaaatgatcagtgactgattgagctgctgctgggatcgcatatactcccttcatcccataaaaaataaatctaagaccgattcgtagtattaggatgtgtcgcatctgatactaggttgtttttttatgggacggagggagtacacatgtattgatgctcggttaaaatggagaatggattcttagagcctgtttgaagctgaagctcaaccaaacagtttcagcttcacctaaaataggagcgaagctaggtagagcactctcataaaatgctgattttagctaggctactccacaaccacactctagacctaactcctaaaggtaaattttagaagttggaaactctaccaaacagacccataattcatgagcggatgtctcctatgtcctatctttgtttttttttcacatcatctaaatatgtataatttttttataggatagattaatatgtgtgatatatcactccgcaagcatattaacctagctatatcttatcaaatttagataacatacatagtttgctggtaaatgcagggctgcagtttatcgggaggaacatgtcggtcgccatggacgatcagacggctgctccggcgtctggttccgtcgtcagtttcgcagcgatgctccggatggcgatggagatgggtttggaggttcctgccgtcagccaagctgacgtccgcgacaggttaattgatttgcatgtgaaagaacagcatttcgttcccgcgttactgtttgtatttttcagggtaacgtacggtacggtcgagcttcagaaacaagttgattaaattgtttaatttgctacctatcgaagatggattctgattcttgattggagagggtgtcacacatattacacgtttttactgttttcaaattcaatttaaaaagcgaattgagcatctctctctaatcagctcctaagctaagttcatcgttatgtgggggtgagtaagtgtttggtgatgtgagggtgagtatacgcaaggcgcctgcgtttatattttgtgtttcgagaaaaaaatatcaatttaaaaagttaaactgcgttgtatacgagcgcttacaatatttgtactttgtattttgagaaaaaaaatcaatttaaaggttaaaaattttataatataattaagcacgacatacacatatgacccgttagaataattaaatcaacttgaatttgtattttagtgatccatgcatattgtgagttgtgaggaatatcctcactagtgaagaaaaaacactttcggtacactggcaagctcctgcatttttcgttgggctggtctggctctagatgttcttgaagaagaaaccgtgttatttattttttttattactctctctaactaccaatatttggtgtttagggcgagataccatcgaactaattctatattaaattaagtttatggaatctaataaacttgtgtgttactacttttcaaagcaaacattatttgagaaattgttttagttaaagtttttaaattttttaaactactagtaagtcttattataaatgttatttttttatgatgggagggaatacttatttatctccttcaacttcatgagtcaggacaaggatctcaacagattaatttacacgtgagagaactacatttcggtccccatttttttaattttctggtacgatgtatggagcttgctagctaccttccaaagatgggctctaatacttcgagaagacgtccttttaaacacttttattttccaaatgcagtaaaaaggctataataaactatgataatataggtgtgtatgctatatatgttctgtgacagtgacatccaccagctcatgcatgctctgggggaaaaaatacattgacgacatggtagactatttattaatatcaagattaaaaaaagtagccgtcaaagtcacatttcccaaattaattaagaggtcaaaaaccatatagagaaaaggaaaacgcagtagtttgagaaaggggagataaagaagattgggaagatacgcaaaacaaggtgagccattagcgtatgattaattgagtattaactattttaaattttaaaaatggactaatatgattttttaaagcaactttcctataattttttttgaaaaaaacacaccgtttattagtttgggaagcgtgcgcgcggaaaacgagtcacaatcttcccaatctcctttgaaagaacgcagccgtcaagtcgcatcttcgaaattaattaagaggtcaaaatcatctacagaaaaagaaaactactataagtactccttccactttatattgctttgattttttttttctaaatcattactccatccgttctattttaagtgcagtcgtgtatttctgtgttcaacatttgatcatctgtcttatttgaaatgtttttatgattaatatttttattgttattagatgataaaatataattagtactttatgcgcgactttttttttagttttttcatagtttttttaaataagatagacgatgaaacgttggacacagaaacccacaactacacttaaaatagaacgagggagtattttaaattttgattaaatctataaaaaagtacagtacaaaataagtatagtatcaaaatatatatattaaatgttagatttaatgaaactaatttgatttagtgttatagatgttgttatgttttctataaatatgattaaattaaacttaagaaaatttggcttagaaaaaaaatcgaaacttcttataatatgaaaggggggaggagtatcaaaactatatcaacttgatcattacaataacaatcttgctgtgtaaattaattcagagatgctggggtgatctgccacggtggaagaacagaatatacggcttatgtctcagaaggattaggcaatattcagaactggaatgaagtgatgaaattccaaagaaagaatggctcactgttcaactccccttacacaactgcagctgcattagtccacaactatgatgccaaagctctccagtacttagacatgcttctggacaaatttggaagtgcaggtaactgcactttgtcaatggtttaataggatacgaaatataaacatttgctgaatgcctaattaatgtcagttaaaatttgcagtgccagcggcctatcctgcaaatattcagtctcagctctacatggtggatgtgcttgaaaagatgggaatatctaggcattttgttggtgagataaagagcatactggacatgacctacaggtactaagtactaccttaagataataagattagttgtttggagaccgtggttaattagcagttcaggtaaatgactaaatttggttgcagttgctggaaacagagggatgaggaaattgtgcttgacatgcaaacatgtgggatggcatttcgtatgttgcgtatgaatggatatgatgtttcttcaggtactttattctgctagaacctaaaaggataactcggtactttcttttacctacttaagaatcataaaaaaaatcaattgctagctcgattttatgattcttgagaagataacgggaggtagccctttgatctttagtttcagttccttgtaccaagctaatgtattgcattttaaaaaatgtggtgcagatgagctatctcatttttctgaaccttcaagtttccacaattcacttcaaggatatctgaatgatacaagatctttattagaattacataaggcttcaaaagtcagtatcgcagaaaaggaggtgatcctagataatataggctcctggacaggttgcttattgaaggaacaattgttatccagtgcaatgaaaagaaatccactctctgaagaggcaagttgtcaagtgtgaatttctcatctccattatttatccataacgatattattataattattattttgtattttcaggttgaatatgctcttgaatttcccttctataccatcttggatcgtctagaccataaaagaaatatcgaacattttgacattacaagcagtcagatgctagaaacagcgtacttgtaagtttttttcctttgatgaaacaagccagttccatcaaacctgacctattcagacaccagaaatcaatatatatttttttgccgggtcggccgaaaaatcgaccaaccagaaatcaatttgtcatgaataattaaatatttctgaaactaaacaggccatgtcattccaatgaagaaatcatggccttgggtgtgagagattttagtagctctcagtttattttccaagaagagctgcagcaactcaacaggtatgtacatctgacatttattgctcttttttatttcctatgtaaaccaacaaacttgcagataatttcgttacaattttttgctgcagctgggtgaaagagagcaggttggatcagctgcaattcgcacggcagaagttggactacttctatttctctgctgctgctaccattttcactcctgaactgtcagatgttcgcattttgtgggccaaaaatggcgtgctgacaacggtcgtcgacgacttcttcgacgttggaggatcaaaagaagaactggaaaacctcgtcgcattagttgagaagtaaaactaatccttaaaacaaattaatgtcttaaccaattctagttcctcaggctaacaaaaatttcagccctgataacgcttgtgatattcatatctaggtgggacaagaatgacaaaactgagtactactctgaacaagtagagattgtgttctctgcaatttatacttcaactaaccagcttggatcaatggcctctgtagtacaaggccgtgatgtcaccaaacaccttgtagaaatagtaagcatcatctctgacatactttggaattattttttttcagaagtgagaactgacaagctaaatatagtggcctctgttaatctgtgtatagtggcaagaattgctgaggtctatgatgacagaggtagagtggaggcagagccggtatgtgccaacagcagaggaatacatggaaaatgcagttgtgacatttgcactgggacccgttgtgctcccagcattgtatcttgttgggaccaaagatgcctgattctgtcataagaagccaagaatgcagcgagttgttccggctaatgagcaaatgtggccgtctcctgaatgatgtccaatcctacgaggtacagactacagaactactagctgttctgtcgagtttctaagccactgccaaattttaaattttaaattttaactttgtagtttattttaaaggtttttctccgaagcttgttttttcagcattgatttttaaacaatgaaaacagtgtctttctgaagagttgtgcactttctgaagtttgtactagaacttctgaacttgtgcgtcaattcgatctttctgaattctgaagttcccacgatgaatttgagtgtttcacactgtctcatgctgcagagagagggcagccagggcaagctgaacagcgtctctctgcttgccctccacagtggaggctctgtctccatggaagaggctgtgaagcagattcagagacccatcgagaaatgcaggagagagttgctgaagctggtcgtcagcagaggaggcgccgttccaaggccatgcagggagctgttctggagcatgtgcaaggtctgccacttcttctactccggcggcgacgggttcagctcgccgacggcgaaggccggcgcgttggacgcggtgatccacgagccgctgaatctgtcttgttctgtgtga</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001060377.2 RefSeq:Os04g0612000]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 4]]
[[Category:Chromosome 4]]

Os03g0395000

2014-12-27T13:46:59Z

Shijc:

OsHO2 has a potential regulatory role for tetrapyrrole biosynthesis in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os03g0395000-Fig1.gif|right|thumb|200px|'' Tetrapyrrole biosynthesis pathway in plants. The carbon skeleton of tetrapyrroles is derived from glutamate. (from reference <ref name="ref1" />).'']]
In higher plants, a major regulatory mechanism for tetrapyrrole metabolism has been attributed to the feedback inhibition of HEMA (glutamyl tRNA reductase) by heme <ref name="ref2" />(Beale 1999). HEMA catalyzes the first committed step of tetrapyrrole biosynthesis by generating the immediate precursor (i.e. glutamate 1-semialdehyde) of ALA. Disruption of HO1 or PΦB synthase genes is believed to cause over-accumulation of heme which in turn represses HEMA activities and ALA formation <ref name="ref3" />(Tanaka et al. 2011). However, our Osho2 mutants showed decreased levels of heme but increased levels of ALA, indicating that the Chl deficiency was not a consequence of heme-induced HEMA inhibition. In addition, the levels of Proto IX (the last common precursor of Chl and PΦB), Pchlide and Chlide (Chl precursors), and BV (PΦB precursor) were all diminished in the mutant seedlings, presumably reflecting the overall reduction of metabolic flux toward Chl and PΦB production. Interestingly, the Osho2 mutants were found to accumulate elevated levels of Mg-Proto IX, which is the first committed Chl precursor. Meanwhile, the accumulation of transcripts encoding different tetrapyrrole enzymes was consistent with the corresponding metabolite changes. Thus, the expression levels of PPOX (for Proto IX), MgCY (for Pchlide), POR (for Chlide), FeCh (for Heme), and HO1/YGL2 (for BV) were down-regulated while the expression levels of HEMA (for ALA) and CHLI, CHLD, and CHLH (for Mg-Proto IX) were up-regulated in the mutant seedlings.
The biosynthesis of different tetrapyrrole-derived biomolecules is under sophisticated controls to meet specific cellular demands and to prevent excessive accumulation of photosensitizing intermediates <ref name="ref3" />(Tanaka et al. 2011). For example, chlorophyll biosynthesis is often subject to coordinated transcriptional regulation of genes encoding key enzymes like HEMA1, CHLH, MgMT, MgCy, POR, and CAO <ref name="ref4" /> (Waters et al. 2009). Interestingly, the expression of HEMA1 and MgCH genes (CHLI, CHLD, and CHLH) appears to be regulated independently from other tetrapyrrole biosynthesis genes in our Osho2 mutants which accumulated higher levels of ALA and Mg-Proto IX. These unique changes in metabolite and transcript levels suggest the existence of a novel regulatory mechanism, potentially involving OsHO2, for tetrapyrrole biosynthesis, especially during early developmental stages in rice. Instead of binding to heme, the synthetic AtHO2 recombinant protein binds Proto IX with high affinity in vitro, implicating a regulatory role on substrate flow through binding of tetrapyrrole intermediates <ref name="ref5" />(Gisk et al. 2010). On the other hand, Arabidopsis GUN4 stimulates MgCH activities by binding to the CHLH subunit as well as the enzyme substrate (Proto IX) and product (Mg-Proto IX) <ref name="ref6" />(Adhikari et al. 2011). Meanwhile, OsHO2 may regulate tetrapyrrole biosynthesis through interaction with tetrapyrrole metabolites and/or enzymes inside chloroplasts. Further investigations involving metabolite binding and protein–protein interaction analyses will be necessary to elucidate the biochemical activities of OsHO2.

===Mutation===
[[File: Shijc-Os03g0395000-Fig2.gif|right|thumb|200px|'' Phenotypes of the ylc2 mutant. (from reference <ref name="ref1" />).'']]
The ylc2 mutant was identified by screening of a population of rice 60Coγ-irradiated mutants in our laboratory. The chlorosis phenotype was most prominent during the seedling stage (Fig. 2a). In field-grown mutant plants, the mature leaves showed darker green pigmentation but newly emerged leaves were still pale in color (Fig. 2b). Chl contents of WT and ylc2 mutant seedlings (1-week-old) were then measured to characterize the chlorosis mutant phenotype. As shown in Fig. 2c, the contents of Chl a, Chl b, and total Chl in mutant seedlings were 18, 27, and 23 % of those measured in WT Nipponbare plants. The amount of total carotenoids was also reduced by more than 65 % in the ylc2 seedlings. The ultrastructure of chloroplasts was then examined using transmission electron microscopy (TEM). In WT plants, the chloroplasts showed well-developed thylakoid membrane with stacks of grana (Fig. 2d). However, the thylakoid membrane system in the mutant chloroplasts is poorly organized with larger numbers of plastoglobules, indicating that chloroplast development is defective in the ylc2 seedlings.

===Expression===
[[File: Shijc-Os03g0395000-Fig3.gif|right|thumb|200px|'' Subcellular localization of the YLC2 (OsHO2)-EYFP fusion protein transiently expressed in N. benthamiana leaves by Agrobacterium infiltration. (from reference <ref name="ref1" />).'']]
To elucidate the subcellular localization of the OsHO2 protein, a translational fusion with enhanced yellow fluorescent protein (EYFP) at the C-terminus driven by the CaMV 35S promoter was constructed for Agrobacterium-mediated transient expression in N. benthamiana. As revealed by confocal microscopy analysis, the OsHO2-EYFP fluorescent signals were detected in organelles of mesophyll cells consistent with the sizes and chlorophyll autofluorescence of chloroplasts (Fig. 4a). The sub-organelle location of OsHO2-EYFP was further examined by immunoblot analyses of stromal and membrane fractions from Percoll-purified chloroplasts of infiltrated N. benthamiana leaves. As shown in Fig. 4c, the OsHO2-EYFP fusion protein was only detected in the stromal fraction. Therefore, the above analyses suggested that OsHO2 is a chloroplast protein residing inside the stroma.
[[File: Shijc-Os03g0395000-Fig4.gif|right|thumb|200px|''Gene expression analysis of OsHO2. (from reference <ref name="ref1" />).'']]
Gene expression of OsHO2 in different tissues was first examined in the publicly available Affymetrix GeneChip microarray data. YLC2 expression was detected in almost all tissues of rice with highest levels detected in leaves and shoot apical meristem (Fig. 5a). Levels of OsHO2 expression were then compared in ylc2 mutant and WT seedlings using RT-PCR. Results indicated that the gene expression was not affected by the 8-bp deletion in ylc2 mutant (Fig. 5b). On the other hand, OsHO2 transcript accumulation in WT plants was reduced by approximately 50–60 % in mature leaves (third leaf) of 12-week-old plants in comparison to newly emerged leaves or young seedlings (Fig. 5c), further suggesting that the rice gene plays a more important role during early development.

===Evolution===
[[File: Shijc-Os03g0395000-Fig5.png|right|thumb|200px|'' Phylogenetic relationships of OsHO1, OsHO2 and their closely related homologs. (from reference <ref name="ref1" />).'']]

BLAST search in the rice genome revealed that Os03g27770 is a single-copy gene with an ORF of 993 bp. The coding region contains 4 exons (3 introns) and encodes a protein of 330 amino acids with a molecular weight of approximately 36.5 kDa. The 8-bp deletion in ylc2 generated a frame-shift mutation, resulting in premature translational termination. Consequently, the ylc2 mutant protein is identical to the WT sequence up to the 244th position, followed by a short stretch of 15 amino acid residues (Fig. S2). The WT protein harbors a predicted N-terminal chloroplast-targeted sequence of 47 amino acids (www.cbs.dtu.dk/service/TargetP). The rice protein is annotated as heme oxygenase 2 (HO2) which contains a heme oxygenase (HO) domain (Pfam 01126) in the second half of the protein (176th–325th residues). Pairwise 3D structural alignment <ref name="ref7" /> (Gelly et al. 2011) demonstrated the tight superimposition of the mutant protein with OsHO2 except for the absence of three C-terminal α-helices (Fig. S3) which may be important for OsHO2 functions.
The HO signature sequence which includes the His residue required for protein stability <ref name="ref8" /> (Matera et al. 1997) is conserved in OsHO2 (His-246). The His residue involved in HO-ascorbic acid binding <ref name="ref8" /> (Matera et al. 1997) can also be identified (His-254). However, the His residue essential for heme binding in HO is replaced by Arg-102 in OsHO2. Phylogeny analysis of plant HO homologous sequences clearly revealed the separation of the HO1 and HO2 subfamilies (Fig. S4). OsHO2 is clustered with two highly conserved sequences from maize and sorghum in the HO2 family. These cereal sequences share more than 75 % identity but are only weakly homologous to the dicot HO2 sequences with less than 50 % identity. By contrast, the HO1 sequences are highly homologous between monocot and dicot species. For example, OsHO1 shares 70 % sequence identity to the Arabidopsis HO1.

==Labs working on this gene==
1. State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Crops and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
2. School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong, China
3. College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
4. Department of Biology, Concordia University, Montreal, QC, H4B 1R6, Canada

==References==
<references>
<ref name="ref1"> Qingzhu Li, Fu-Yuan Zhu, Xiaoli Gao, Yi Sun, Sujuan Li, Yuezhi Tao, Clive Lo, Hongjia Liu (2014) Young Leaf Chlorosis 2 encodes the stroma-localized heme oxygenase 2 which is required for normal tetrapyrrole biosynthesis in rice. Planta 10.1007/s00425-014-2116-0 </ref>
<ref name="ref2">Beale SI (1999) Enzymes of chlorophyll biosynthesis. Photosynth Res 60:43–73 </ref>
<ref name="ref3">Tanaka R, Kobayashi K, Masuda T (2011) Tetrapyrrole metabolism in Arabidopsis thaliana. The Arabidopsis Book 9:e0145</ref>
<ref name="ref4"> Waters MT, Wang P, Korkaric M, Capper RG, Saunders NJ, Langdale JA (2009) GLK transcription factors coordinate expression of the photosynthetic apparatus in Arabidopsis. Plant Cell 21:1109–1128 </ref>
<ref name="ref5"> Gisk B, Yasui Y, Kohchi T, Frankenberg-Dinkel N (2010) Characterization of the haem oxygenase protein family in Arabidopsis thaliana reveals a diversity of functions. Biochem J 425:425–434 </ref>
<ref name="ref6"> Adhikari ND, Froehlich JE, Strand DD, Buck SM, Kramer DM, Larkin RM (2011) GUN4-porphyrin complexes bind the ChlH/GUN5 subunit of Mg-Chelatase and promote chlorophyll biosynthesis in Arabidopsis. Plant Cell 23:1449–1467
</ref>
<ref name="ref7">Gelly JC, Joseph AP, Srinivasan N, De Brevern AG (2011) iPBA: a tool for protein structure comparison using sequence alignment strategies. Nucleic Acids Res 39:18–23 </ref>
<ref name="ref8">Matera KM, Zhou H, Migita CT, Hobert SE, Ishikawa K, Katakura K, Maeshima H, Yoshida T, Ikeda-Saito M (1997) Histidine-132 does not stabilize a distal water ligand and is not an important residue for the enzyme activity in heme oxygenase-1. Biochemistry 36:4909–4915</ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0395000|
Description = Similar to Heme oxygenase 2 (Fragment)|
Version = NM_001056825.1 GI:115453378 GeneID:4333033|
Length = 3360 bp|
Definition = Oryza sativa Japonica Group Os03g0395000, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:16475031..16478390|
CDS = 16475569..16475661,16475774..16475881,16476725..16476948,16477781..16478348|
GCID = <gbrowseImage1>
name=NC_008396:16475031..16478390
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:16475031..16478390
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgccgctcgccgccgccgtcgccgcctcggcggtcgtgccgccgcggccgcctcctccgccgccgcggagagcgcggcccttgcgctcctttactggactaatactaacgagggacctagcagccctaacggtggcccgctgcgctccctcccctcctgcccccgcggcggaggcggaggcggaggcggtggcggtggatgaggcgccgccagcgaagccgcggccgcggcggtacccgaggcagtaccccggcgaggcggtgggcgtcgccgaggagatgcggttcgtcgccatgcgcctccggaaccccaagcggaccaccctcaagatggacgatacgggggccgaggaggaggtgggcgatggcgtcagtgaggatgcgtcggcgtcagaggaggaggaggaggaggaggacgacgacgacgtggttgaggaggaggaggagggagcggggttggagggggagtggatgccgagcatggaggggttcgtcaagtacctggtggacagcaagctcgtcttcgacaccgtcgagcggatcgtagccgagtccaccgacgtcgcctatgtttacttcaggaaaagtggtctggaacgctcagctagaattacaaaagatttggagtggtttggagggcaaggaattgcagtaccagagccaagtactgctggatcaacatatgcaacttatctgactgaacttgctgagagcaatgccccagccttcctttcccactattacaatatttattttgcacatacaactggaggggtggctataggtaacaagatatccaagaaaattttggaaggaagggagctagagttttacaaatgggattctgatgtagaacttttgctaaaagataccagggagaagcttaacgaacttagcaagcattggtctcggaaggacaggaacttgtgcttgaaagaagctgcaaaatgtttccagcatttggggcggattgttcgcttaatcatcttatag</cdnaseq>|
AA = <aaseq>MPLAAAVAASAVVPPRPPPPPPRRARPLRSFTGLILTRDLAALT VARCAPSPPAPAAEAEAEAVAVDEAPPAKPRPRRYPRQYPGEAVGVAEEMRFVAMRLR NPKRTTLKMDDTGAEEEVGDGVSEDASASEEEEEEEDDDDVVEEEEEGAGLEGEWMPS MEGFVKYLVDSKLVFDTVERIVAESTDVAYVYFRKSGLERSARITKDLEWFGGQGIAV PEPSTAGSTYATYLTELAESNAPAFLSHYYNIYFAHTTGGVAIGNKISKKILEGRELE FYKWDSDVELLLKDTREKLNELSKHWSRKDRNLCLKEAAKCFQHLGRIVRLIIL</aaseq>|
DNA = <dnaseqindica>2730..2822#2510..2617#1443..1666#43..610#gccgtgcaggatgcccgagtggataacccgttaaaccccccgatgccgctcgccgccgccgtcgccgcctcggcggtcgtgccgccgcggccgcctcctccgccgccgcggagagcgcggcccttgcgctcctttactggactaatactaacgagggacctagcagccctaacggtggcccgctgcgctccctcccctcctgcccccgcggcggaggcggaggcggaggcggtggcggtggatgaggcgccgccagcgaagccgcggccgcggcggtacccgaggcagtaccccggcgaggcggtgggcgtcgccgaggagatgcggttcgtcgccatgcgcctccggaaccccaagcggaccaccctcaagatggacgatacgggggccgaggaggaggtgggcgatggcgtcagtgaggatgcgtcggcgtcagaggaggaggaggaggaggaggacgacgacgacgtggttgaggaggaggaggagggagcggggttggagggggagtggatgccgagcatggaggggttcgtcaagtacctggtggacagcaagctcgtcttcgacaccgtcgagcggatcgtagccgagtccaccgacgtcgcctgtgagttgcgattcctactctccaaatccccgccttcccaatgcaattagaatatcctaattcaatgttgttccttaatcagcttagtcttcagtttccaatgcaattggaatctcctaatttttcaggaattatagatttagaatatgacatattgacttgttggtaggatggtaaaatgtgtcggtaagaacatgtttgggggatacaagctaggtggtaggaattccatttttagtgctcacttgggtatgcggcgaaggttgcaattattttggcaatatgcaaggttgaaatttaaggttgtgattattttgatggaacttgatgcatggtgtgaagtcgtggcgtgaaatgaaaattgtatggattacaattttggaaggcatttactgccaaatggtggaagatgcactttagcacaatacatgttctgcgtgtgcagcaatcatcctacggctgaatctcctttagtggtgcaccgtgaaagaaatgatcttttgggatgttctggagtatagatggcagaccatattggtaatgaagcacattgctggcatcatgcatcatagtgtacttgagcatctccgcgaagatctccgcatcgatttttgtcagtgatattgttttctgacaacttaattagtgtgagacaccaaccatgttgcctagaatgcttgccaaattgaattgttcagcactcggtagtatatgctacatacttttacgtatggctctttaggggcattcagtacctctgtttggaactttgttcaatcactgcaacagaaactgcagttacttacatatcatttatgcaattttcattcagatgtttacttcaggaaaagtggtctggaacgctcagctagaattacaaaagatttggagtggtttggagggcaaggaattgcagtaccagagccaagtactgctggatcaacatatgcaacttatctgactgaacttgctgagagcaatgccccagccttcctttcccactattacaatatttattttgcacatacaactggaggggtggctataggtaacaaggtaatgctattcccatattggatttaagtccccattaagttgtgtaatgaactgttgatatatatactcatgtttcatacctaacctgattaaatatccattatatgtctattaaactataaacaaaatataaaccagcagatttaaatgaaatactgagttcaacgctactttcttatcagatgagatgatacattgtgatttcattgtttcatgtctcaacatgtttctcattaaatggattggcagcacggagctttttgtatggagttgacaaaagagtgtaaagctgaatatctagactgatacatttctattctgggtatcagatattcatatataaagttcctctgttagctggtgatacagggctatttaaacatttggtttctattttcctttgatgtagcagcttgtggccaaaattgctaccaaatccaccaaaatatggcattgccaaagtttagtgatggatttgcgaatcaacattttggctagacattgacatccattggctccaaccaaacagccttataatagcaaagaatcttcttaaacaagaatagagagatagttgctttgttctccccatctcttttgtgattttgagctcacctgcatgccctcttaacctttttgagcgaaatacaagttctgtttaagctttcatatttcccctaaattctcttcacacttgcaccatcataataatgatgctagataatttgttcagtataaaggcaagtttactttgtagtttgtattattacaactctgtaagttctttgaaaacaaaatttatttaattgctctctgaagaagtattagtttgaaacgtaacagatatccaagaaaattttggaaggaagggagctagagttttacaaatgggattctgatgtagaacttttgctaaaagataccagggagaagcttaacgaacttagcaaggtaaccgcctcaagatcactttcttttattttcttgtaagctcgaaactggaatttgccacagaagttatatgcttatgtaacctgattagtctatctgtcatgctgtccagcattggtctcggaaggacaggaacttgtgcttgaaagaagctgcaaaatgtttccagcatttggggcggattgttcgcttaatcatcttatagttcctcatagatgagcaactgatcaaatcaacctataatctattcctgaagacaggaaagctagagatatattaaacttgaggcttagtgcagtcatttttgtcgaagactacacgtcttaactatgttgaagtctggtacagaaggatcttctggtgtgagactgaagctgatcagcgagcactatcctggagattgaaaacaccaggccacaacaatagcctcttttctggcttgcatggtggagctgctcgttggagtgagctcttgctttcagcaacttcgaactgtgcaaagttgaagatgcttgctgctgtcgatcaggatctcacgcgttcaatcgcaatgatgccagcctgacacaattcacttagcagcagaacaccatgctagccagccaggatccccccatgcctgccaaagcttcgtctcctcttgtacctcaccacattatccatttatccttgcaatgaattcgctttgcttgtaccaatcctagctactactactactaccatcttacattatccttgcaatc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001056825.1 RefSeq:Os03g0395000]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0332400

2014-12-27T13:46:19Z

Shijc:

OsGLYII-2, a glutathione responsive rice glyoxalase II, functions in salinity adaptation by maintaining better photosynthesis efficiency and anti-oxidant pool. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os03g0332400-Fig1.png|right|thumb|200px|'' Transgenic plants ectopically expressing OsGLYII-2 maintained physiological balance under salinity stress. (from reference <ref name="ref1" />).'']]
Glyoxalase II is the second enzyme of the glyoxalase pathway that converts SLG (product of the GLY I enzyme) to d-lactate with recycling of one molecule of reduced glutathione. Both GLY I and GLY II transcripts and proteins have been reported to be induced in response to various abiotic stresses in plants <ref name="ref2" /><ref name="ref3" />. The plant genome contains multiple GLY II members, three in the case of rice and five in the case of Arabidopsis, based on their common Pfam ID (PF00753;)<ref name="ref3" />. Moreover, it was observed that AtGlx2-1 and OsGLYII-1 show activity other than GLY II <ref name="ref4" /> <ref name="ref5" />. Functional complementation of the yeast GLY II mutant by OsGLYII-2 indicated that OsGLYII-2 is an active GLY II enzyme. Moreover, expression of the OsGLYII-2 transcript has been reported to be up-regulated in response to salinity <ref name="ref3" />.

Various kinetic parameters of OsGLYII-2 were measured and compared with other reported GLY II from diverse species. The Km and kcat/Km values for OsGLYII-2 were found to be 254 μm and 2.00 × 106 m−1 sec−1 respectively, that is higher than prokaryotic and lower than eukaryotic GLY II, and quite comparable with higher eukaryotes. Activity of the enzymes is affected by their products or substrates for a prompt response on cellular need <ref name="ref6" />. Since one of the product of GLY II i.e. GSH, is a signalling molecule <ref name="ref7" /> and plays a vital role in maintaining cellular redox status, it might influence GLY II activity also. Under normal physiological conditions, total GLY I activity is much higher than GLY II and occupies one molecule of GSH to form SLG. Additionally, the total glutathione in plants (~4.8 μmol g−1) is relatively lower as compared with animals (16–25 μmol g−1) <ref name="ref8" />. In this context, the product inhibition of OsGLYII-2 gains importance and a tight correlation between OsGLYII-2 activity and cellular GSH level eventually leads to maintenance of redox status. As the level of MG increases during stress, more GSH will bind to MG to form SLG. Lower levels of GSH would increase the activity of OsGLYII-2 that will regenerate GSH from SLG and also fully detoxify MG to d-lactate.

Glyoxalase II is a member of the metallo-β-lactamase superfamily and requires a divalent cation for its activity <ref name="ref9" />. Most members of this family appear to contain a binuclear metal centre, especially zinc or iron <ref name="ref10" />. But the metal ion content might vary depending upon the composition of growth media, purification column and buffer composition <ref name="ref11" />. Based on a metal content study of OsGLYII-2 using ICP-AES, OsGLYII-2 may contain a binuclear Zn/Fe centre, like the one in its Arabidopsis counterpart, AtGLYII-2 <ref name="ref12" />. Some of the other Zn/Fe binuclear proteins have already been reported from different sources, such as kidney bean purple acid phosphatases and protein phosphatases I, 2A and 2B. Interestingly, none of Zn and/or Fe could reactivate the activity when added externally in the metal chelated form. A similar pattern of metal inhibition was observed in the case of the Zn-containing UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase (LpxC) enzyme <ref name="ref13" />. The inability of Zn2+ to reactivate chelated OsGLYII-2, may be due to the presence of eight cysteine residues in the OsGLYII-2 protein that could form mis-metallation by thiolate ligation as observed previously <ref name="ref14" />. Moreover, the activity of chelated OsGLYII-2 protein could be reactivated by incubation with Co2+ or Mn2+ because of their facile nature to insert into the active site cavity. Similar observations have been shown in the case of E. coli GLY II <ref name="ref14" />.

Methylglyoxal accumulates inside the cell under stress conditions <ref name="ref15" /> and glyoxalase enzymes protects the cells from the deleterious effects of MG. Since total GLY I activity is higher than GLY II, overexpression of GLY II provides better tolerance as compared with GLY I transgenic <ref name="ref16" />. Previously, it has been shown that overexpression of OsGLYII-3 in tobacco, rice and Brassica enhanced tolerance against salinity <ref name="ref16" /><ref name="ref17" /><ref name="ref18" />. These studies indicated towards the significant role of GLY II during stress that prompted us to investigate further the role of OsGLYII-2 in plants. Overexpression of GLY I leads to an increase in the enzyme activity of GLY II also <ref name="ref16" />, whereas the reverse was not observed in the case of OsGLYII-2-overexpressing tobacco transgenic plants, a finding which needs to be explored further. Transgenic plants showed significant tolerance towards dicarbonyl and salinity stresses, by resisting the accumulation of excess MG in the system.

Apart from the accumulation of MG, stress can disturb a number of other cellular processes, such as growth, photosynthesis, water balance and ion homeostasis etc. All these processes ultimately lead to a decrease in the total productivity and yield of plants. Photosynthesis machinery plays a central role to deal with the adverse conditions and was found to be affected first by stress <ref name="ref19" />. During stress conditions, plants try to minimize water loss by closing their stomata. A low stomatal conductance leads to lower transpiration and sub-stomatal CO2 concentration that ultimately leads to a decrease in the rate of photosynthesis. Although the plants’ capability to capture light energy remains intact, this extra energy leads to the generation of excess ROS. GSH along with other components, played an important role to fight against the ROS <ref name="ref15" />. OsGLYII-2-expressing transgenic tobacco plants can maintain physiologically favourable levels of all the important components of the photosynthesis machinery and thus are able to produce a yield with a minimum loss (~20%) under salinity stress. Transgenic plants could maintain a balance between osmotic loss and photosynthesis capability by fine tuning the stomatal conductance, transpiration rate, chlorophyll content, RWC and photosynthesis rate. However, WT plants were not able to maintain the balance that ultimately drives them towards senescence and death. Moreover, transgenic plants were able to maintain the anti-oxidant pool, by maintaining a GSH level that has been considered as an adaptation strategy for plants under stress <ref name="ref20" />.

===Mutation===
[[File: Shijc-Os03g0332400-Fig2.png|right|thumb|200px|'' Comparison of various growth and yield parameters of wild-type (WT) and OsGLYII-2 ectopically expressing tobacco plants, continuously grown under saline conditions. (from reference <ref name="ref1" />).'']]
As OsGLYII-2 transgenic plants showed better performance in dicarbonyl stress than WT, tolerance of these plants was further tested under salinity stress. For this, one set of 60-day-old transgenic plants (L1, L2, L4 and L5) along with WT were irrigated with saline water (150 mm NaCl) and another set of the same plants were irrigated with normal water (experimental control) in earthen pots until maturity. It was observed that transgenic plants were able to grow normally, flowered and produced seeds under salinity stress. However, WT plants showed stunted growth with only a few flowers and seeds. For the assessment of plant stress tolerance potential, different parameters such as plant height, fresh weight, number of pods and average weight of pods from all the plants grown under stress and control conditions were measured and compared. The transgenic plants were found to maintain higher biomass and yield than WT grown under saline conditions as well as control conditions. The number of pods in WT plants showed a 90% reduction under salinity stress while transgenic plants showed only a 30% decline in pod number under similar conditions as compared with their respective control counterparts.

===Expression===
[[File: Shijc-Os03g0332400-Fig3.png|right|thumb|200px|'' Expression analysis and subcellular localization of OsGLYII-2. (from reference <ref name="ref1" />).'']]
The presence of multiple members of a family raises the question of their significance under various stages of plant development and tissues. To unravel the role of OsGLYII-2, its detailed expression pattern was analyzed based on publicly available microarray databases. OsGLYII-2 expression was checked at nine distinct developmental stages of rice; namely germination, seedling, tillering, stem elongation, booting, heading, flowering, and two stages of seed development (milk and dough) and data were analyzed. High transcript abundance of OsGLYII-2 was observed at all the developmental stages with slight upregulation during the late vegetative phase and a slight downregulation during the early reproductive stage. Moreover, OsGLYII-2 showed a medium to high level of expression in various tissues such as callus, seedling, leaf, flag leaf, shoot, root, inflorescence, panicle, anther, stigma, ovary, embryo and endosperm, except pollen, where its expression levels were relatively low.
Apart from expression, localization of various members of the same family may also vary to perform the same job in different subcellular compartments. To check the in planta localization of the OsGLYII-2 protein, the corresponding cDNA was cloned into the pMBPII vector to make a OsGLYII-2:GFP (green fluorescent protein) fusion construct. This chimeric protein (OsGLYII-2–GFP) was expressed transiently in onion epidermal cells through particle bombardment and OsGLYII-2 was found to be localized in the cytosol as indicated through GFP visualization.

===Structure===
[[File: Shijc-Os03g0332400-Fig4.png|right|thumb|200px|'' A binuclear metal centre is essential for OsGLYII-2 activity. (from reference <ref name="ref1" />).'']]
Previous studies have indicated the presence of varying amounts of metals bound to the active site of GLY II enzymes <ref name="ref21" />. Thus, to know the active site residues and its coordination with metals, a homology-based structure of OsGLYII-2 was built based on the available crystal structure of human GLY II. According to the model, OsGLYII-2 is a monomeric protein consisting of two structural domains, a N-terminal domain (residues 1–171) with a two βββαβ topology and a C-terminal domain (172–258) with five folded α-helices. The structure is predominantly α-helical. Superimposition of the modelled and template structure indicated that the metal coordination residues are conserved between them and the residues of OsGLYII-2 that could form two metal-binding sites are His 54, His56, Asp58, His59, His112, Asp135 and His174.
To study the exact metal content of OsGLYII-2, His-tag cleaved protein was analyzed by Inductively Coupled Plasma Atomic Emission spectroscopy (ICP-AES). The analysis indicated that there were ~1 mol of zinc, 0.9 mol of iron and 0.2 mol of manganese per mol of protein. Some other metals such as nickel, cadmium, cobalt, and copper were also found to be present in trace amounts. From this analysis, it can be inferred that OsGLYII-2 may contain a zinc/iron binuclear centre, and that is quite consistent with other GLY II. The role of bound metals of OsGLYII-2 was investigated further by measuring the activity after chelation of metals by EDTA. EDTA treatment resulted in a near complete loss of enzyme activity (~95% decrease as compared with the pre-EDTA treated form. After the removal of excess EDTA by dialysis, the metal chelated protein was incubated with different divalent ions to check their potential to reactivate the activity. As OsGLYII-2 has a Zn/Fe binuclear metal centre, GLY II activity of metal chelated OsGLYII-2 was expected to revert back by the addition of either Zn2+ or Fe2+ or both of them together. Interestingly, it was observed that the addition of zinc and/or iron was not able to reactivate the enzyme; whereas reconstitution of the protein with Co2+ resulted in a significant restoration of GLY II activity (73%) compared with the pre-EDTA treated form. These results indicated that Co2+ could reactivate the metal chelated form of a Zn/Fe-containing enzyme.
==Labs working on this gene==
1. Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, India
2. Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India

==References==
<references>
<ref name="ref1">Ghosh, A., Pareek, A., Sopory, S. K. and Singla-Pareek, S. L. (2014), A glutathione responsive rice glyoxalase II, OsGLYII-2, functions in salinity adaptation by maintaining better photosynthesis efficiency and anti-oxidant pool. The Plant Journal, 80: 93–105. </ref>
<ref name="ref2">Hossain, M.A., Hossain, M.Z. and Fujita, M. (2009) Stress-induced changes of methylglyoxal level and glyoxalase I activity in pumpkin seedlings and cDNA cloning of glyoxalase I gene. Aust. J. Crop Sci. 3, 53–64. </ref>
<ref name="ref3">Mustafiz, A., Singh, A., Pareek, A., Sopory, S.K. and Singla-Pareek, S.L. (2011) Genome-wide analysis of rice and Arabidopsis identifies two glyoxalase genes that are highly expressed in abiotic stresses. Funct. Integr. Genomics, 11, 293–305. </ref>
<ref name="ref4">Limphong, P., McKinney, R.M., Adams, N.E., Bennett, B., Makaroff, C.A., Gunasekera, T. and Crowder, M.W. (2009) Human glyoxalase II contains an Fe(II)Zn(II) center but is active as a mononuclear Zn(II) enzyme. Biochemistry, 48, 5426–5434. </ref>
<ref name="ref5">Kaur, C., Mustafiz, A., Sarkar, A.K., Ariyadasa, T.U., Singla-Pareek, S.L. and Sopory, S.K. (2014c) Expression of abiotic stress inducible ETHE1-like protein from rice is higher in roots and is regulated by calcium. Physiol. Plant. doi: 10.1111/ppl.12147. </ref>
<ref name="ref6">Majumdar, R., Shao, L., Minocha, R., Long, S. and Minocha, S.C. (2013) Ornithine: the overlooked molecule in the regulation of polyamine metabolism3. Plant Cell Physiol. 54, 990–1004. </ref>
<ref name="ref7">Ghanta, S. and Chattopadhyay, S. (2011) Glutathione as a signaling molecule: another challenge to pathogens. Plant Signal. Behav. 6, 783–788. </ref>
<ref name="ref8">Newton, G., Arnold, K., Price, M., Sherrill, C., Delcardayre, S., Aharonowitz, Y., Cohen, G., Davies, J., Fahey, R. and Davis, C. (1996) Distribution of thiols in microorganisms: mycothiol is a major thiol in most actinomycetes. J. Bacteriol. 178, 1990–1995. </ref>
<ref name="ref9">Crowder, M.W., Spencer, J. and Vila, A.J. (2006) Metallo-beta-lactamases: novel weaponry for antibiotic resistance in bacteria. Acc. Chem. Res. 39, 721–728. </ref>
<ref name="ref10">Campos-Bermudez, V.A., Leite, N.R., Krog, R., Costa-Filho, A.J., Soncini, F.C., Oliva, G. and Vila, A.J. (2007) Biochemical and structural characterization of Salmonella typhimurium glyoxalase II: new insights into metal ion selectivity. Biochemistry, 46, 11069–11079. </ref>
<ref name="ref11">Wenzel, N.F., Carenbauer, A.L., Pfiester, M.P., Schilling, O., Meyer-Klaucke, W., Makaroff, C.A. and Crowder, M.W. (2004) The binding of iron and zinc to glyoxalase II occurs exclusively as di-metal centers and is unique within the metallo-beta-lactamase family. J. Biol. Inorg. Chem. 9, 429–438. </ref>
<ref name="ref12">Zang, T.M., Hollman, D.A., Crawford, P.A., Crowder, M.W. and Makaroff, C.A. (2001) Arabidopsis glyoxalase II contains a zinc/iron binuclear metal center that is essential for substrate binding and catalysis. J. Biol. Chem. 276, 4788–4795. </ref>
<ref name="ref13">Jackman, J., Raetz, C. and Fierke, C. (1999) UDP-3-O-(R-3-hydroxymyristoyl)-N-acetylglucosamine deacetylase of Escherichia coli is a zinc metalloenzyme. Biochemistry, 38, 1902–1911. </ref>
<ref name="ref14">O'Young, J., Sukdeo, N. and Honek, J. (2007) Escherichia coli glyoxalase II is a binuclear zinc-dependent metalloenzyme. Arch. Biochem. Biophys. 459, 20–26. </ref>
<ref name="ref15">Yadav, S.K., Singla-Pareek, S.L., Ray, M., Reddy, M.K. and Sopory, S.K. (2005) Methylglyoxal levels in plants under salinity stress are dependent on glyoxalase I and glutathione. Biochem. Biophys. Res. Commun. 337, 61–67. </ref>
<ref name="ref16">Singla-Pareek, S.L., Reddy, M. and Sopory, S.K. (2003) Genetic engineering of the glyoxalase pathway in tobacco leads to enhanced salinity tolerance. Proc. Natl Acad. Sci. USA, 100, 14672–14677. </ref>
<ref name="ref17">Singla-Pareek, S.L., Yadav, S.K., Pareek, A., Reddy, M. and Sopory, S.K. (2008) Enhancing salt tolerance in a crop plant by overexpression of glyoxalase II. Transgenic Res. 17, 171–180. </ref>
<ref name="ref18">Saxena, M., Roy, S.D., Singla-Pareek, S.L., Sopory, S.K. and Bhalla-Sarin, N. (2011) Overexpression of the glyoxalase II gene leads to enhanced salinity tolerance in Brassica juncea. Open Plant Sci. J. 5, 23–28. </ref>
<ref name="ref19">Tezara, W., Mitchell, V.J., Driscoll, S.D. and Lawlor, D.W. (1999) Water stress inhibits plant photosynthesis by decreasing coupling factor and ATP. Nature, 401, 914–917. </ref>
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<ref name="ref21">Sousa Silva, M., Gomes, R.A., Ferreira, A.E., Freire, P.A. and Cordeiro, C. (2013) The glyoxalase pathway: the first hundred years… and beyond. Biochem. J. 453, 1–15. </ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0332400|
Description = Similar to Hydroxyacylglutathione hydrolase cytoplasmic (EC 3.1.2.6) (Glyoxalase II) (Glx II)|
Version = NM_001056551.1 GI:115452830 GeneID:4332736|
Length = 2956 bp|
Definition = Oryza sativa Japonica Group Os03g0332400, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:12314136..12317091|
CDS = 12314481..12314555,12314780..12314956,12315516..12315629,12315703..12315781,12316147..12316308 ,12316732..12316854,12316947..12316993|
GCID = <gbrowseImage1>
name=NC_008396:12314136..12317091
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:12314136..12317091
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgaagatcatcccggtcgcttgcctggaggacaactatgcctacctaatcgtggacgagagcaccaagtcggcggcggccgtcgaccccgtggagccggagaaggtgcttgcggcggccgcggaggtcggcgtccgcatcgactgcgtactcaccacccaccatcactgggatcatgctggtggcaatgaaaagatggcgcagtcagtgccagggattaaggtctatggaggatccctggacaatgtgaaaggatgcactgatcaggtggagaatggaaccaaattgtcccttgggaaggacattgagatactatgcctgcacacaccgtgccacacaaaaggacatatcagctattacgtcactagtaaagaggaggaagatccagcagtgtttactggagacaccttgttcattgctggttgtgggagattttttgagggcactgcagagcaaatgtaccaatccctttgtgtaacactgggctcgctgcctaagccaactcaagtttactgcgggcatgagtacactgtgaagaacctgaaattcatactgacggtcgagccagataacgaaaaagtgaagcagaaactagaatgggctcaaaagcagcgtgaagcaaaccaaccaactattccatcaactataggagaggaatttgagacaaacaccttcatgcgtgttgatctgccagaaatacaggcaaagtttggtgccaagtcgccagttgaggccctgcgagaagttaggaagaccaaggataactggaaaagttaa</cdnaseq>|
AA = <aaseq>MKIIPVACLEDNYAYLIVDESTKSAAAVDPVEPEKVLAAAAEVG VRIDCVLTTHHHWDHAGGNEKMAQSVPGIKVYGGSLDNVKGCTDQVENGTKLSLGKDI EILCLHTPCHTKGHISYYVTSKEEEDPAVFTGDTLFIAGCGRFFEGTAEQMYQSLCVT LGSLPKPTQVYCGHEYTVKNLKFILTVEPDNEKVKQKLEWAQKQREANQPTIPSTIGE EFETNTFMRVDLPEIQAKFGAKSPVEALREVRKTKDNWKS</aaseq>|
DNA = <dnaseqindica>2537..2611#2136..2312#1463..1576#1311..1389#784..945#238..360#99..145#gtttacacctgctcatcttcgtcgcgactcggtgttggctccagaaatctcgccaagagaccataagcccaatccaaatctctccgcgtaggaagcagatgaagatcatcccggtcgcttgcctggaggacaactatgcctacctgtaccctcctgaatccatccttgtcagttgtctgtatgttcggttcttgtttcttggctctttcttgattatccttcgttttgttcttgaagaatcgtggacgagagcaccaagtcggcggcggccgtcgaccccgtggagccggagaaggtgcttgcggcggccgcggaggtcggcgtccgcatcgactgcgtactcaccacccaccatcactggtgagcgtcctagtcctccttctagtttagttatggaaaaattccgcccaaatgttggccttccagagtttcctatgggatgcaatcagtgctgtgccaaaattttccccaatcccaccctcagggaccaatcacctaccaccagaaagtgagtgattttagttagttgcagattgggatttattgcattaggattttataataaattgagaaatacggtgtctgagcatgcggctgaggaagtgctttgcaccatatgataaaataaacacaaatacattaaaaggattgattttttttaggattactctcaggtgcattctatgcatagaatattatttgccagattttgctgaattcattagcaacgatgtagagaagtggtaattgaaaagcccaactaatccgtggttgtggttgtagggatcatgctggtggcaatgaaaagatggcgcagtcagtgccagggattaaggtctatggaggatccctggacaatgtgaaaggatgcactgatcaggtggagaatggaaccaaattgtcccttgggaaggacattgagatactatgcctgcacacaccgtggtatgctgttttctttataagtcacatttcatttatggtatcatcagtgtgattacttcgatggaatcatagaagcactgaagatcaggatttaaacctctacaataacagataggcaaatccaacatgtttccacttgtactcactataataacccatcctgcagatttgccaattgagaagtttatgaaacatttatgttcaaggacttcgcatgcaactaagcgatagttgatagcacaaagacttaaacaatattgctgtagtgcattggttgtacagtctagtcaaccttttatatgtttctgtaacagcttgttgattacttaaatctcatagtcctttcatttcccttcttctaacagccacacaaaaggacatatcagctattacgtcactagtaaagaggaggaagatccagcagtgtttactggagacaccttggttagtatatgcatctgacttacagtgatggctccttttctatttaacatatcgaccttcctttttggtatagttcattgctggttgtgggagattttttgagggcactgcagagcaaatgtaccaatccctttgtgtaacactgggctcgctgcctaagccaactcaagtttactgcgggcatgaggtacattttctatttcccccatttgcttctttgctcttcctccatttttgagggatgtgaatctgtagtgaaatatgtaggatatgtatgctgtgtgccttgccttatttttttccttcttcctcgtgatttgtgttgacaactgatgttttatccctttggcttctacttcatgttccatgctattttcttactttaatttggacctgtccataaacctccattattaaagatgctggaagctttgaatctagattacaaactagatgaggctagtatgtgcagccttaactgaaggataataactaacgtgttcttttctggcaaaaaaaagaatgtggtctggccttctgcattaaggaaaaataagttcatgctgtcagttcttcataaatggaggataacgtgattgccattagtttatgtgtgcaaccaaggaaatttttggttgccctttgttatgtacttctacttatcatggtatggttcttgtcattcaaaagaaaaaaaaaaggtaacagccatactttattcttactagtcttattatgacttacagtacactgtgaagaacctgaaattcatactgacggtcgagccagataacgaaaaagtgaagcagaaactagaatgggctcaaaagcagcgtgaagcaaaccaaccaactattccatcaactataggagaggaatttgagacaaacaccttcatgcgtgttgatctgccagaaatacaggttctaatccacttattagttacatctgttcaacatgatgctatgtttctttgtggctgtgttggaaaaatctttgcgtccatggaggttgacagcaagataaagctaatattgtttagaaacttgcggtcttactgacaagaatcaacaactatcaattcttaatttcgaagatagttcctttgccggtgatgcttatgcagataatgccatcgatcttgcaggcaaagtttggtgccaagtcgccagttgaggccctgcgagaagttaggaagaccaaggataactggaaaagttaataccgatgcaactgttactcttcgtctgatggtccggtctctcgaggttagctaatgcagaaagcttaccctgtaggtggggcttactgccgtgcaacgctttaagagcgatggtgttaggaagagttttaagctataaataagctccatgttaatgttcaaggagacatcatcagatgtgcatgttaatgctggtcttgtctatcactgtactacatgagctacgtatgaattttggagttggtcttgtttaactttgaaaagtcgaaaacgagaggtagtagtcatcctccagtttacatataaacgcataataagggtgaagtgaatcaagattattgtgcc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001056551.1 RefSeq:Os03g0332400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0281900

2014-12-27T13:45:25Z

Shijc:

RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os03g0281900-Fig1.png|right|thumb|200px|'' rcn1-2 mutant (cv. Shiokari background) shows defect in the suberization in the hypodermis but not in the endodermis. (from reference <ref name="ref1" />).'']]
'''Role of hypodermal suberin under waterlogged conditions'''
Rice is well adapted to waterlogged conditions. However, the rice mutant, rcn1 developed a short and shallow root system when growing in a rice paddy field or in deoxygenated stagnant nutrient solution. Waterlogging negatively affects the growth and survival of most plants, because oxygen is limited and phytotoxic compounds can accumulate in waterlogged soils <ref name="ref2" />. The apoplastic barrier in the hypodermis reduces soil and microbial toxins taken up into the roots from waterlogged soils <ref name="ref2" /> <ref name="ref3" />. Furthermore, the suberized barrier in the hypodermis may limit radial oxygen loss (ROL) from the aerenchyma in the roots to anaerobic (i.e. deep) soil <ref name="ref4" /> <ref name="ref5" /> <ref name="ref6" />. The rcn1 mutants had a well lignified sclerenchyma under stagnant deoxygenated conditions, but rcn1 lacked hypodermal suberization under aerated and stagnant deoxygenated conditions. In a wetland plant, Phragmites australis, the penetration of periodic acid is stopped at the suberized hypodermis, but the apoplastic tracer easily penetrated the thickened and lignified cell walls at the sclerenchyma <ref name="ref3" />. In the wild types of rice grown in stagnant deoxygenated conditions, the apoplastic tracers (periodic acid and berberine) were unable to penetrate at the outside of the suberized hypodermis. But, rcn1 could not stop their penetration in the OPR even in the presence of a well lignified sclerenchyma. A sufficient suberized apoplastic transport barrier was not formed in the hypodermis of rcn1. This is one of the reasons why rcn1 could not develop roots longer than about 100 mm length in waterlogged soil or deoxygenated stagnant nutrient solution. Our results suggest that rice needs hypodermal suberization to act as an apoplastic barrier under wetland conditions.
Suberin of the rcn1 mutants and the wild types is composed of five aliphatic substance classes and two aromatic monomers. Suberin forms a barrier against water flow, and the aliphatic domain is thought to be more important than the aromatic domain for establishing the barrier <ref name="ref7" /> <ref name="ref8" />. Our results are consistent with this idea because the rcn1 mutants, which have a high level of aromatic monomers, could not block the penetration of apoplastic tracers.
On the other hand, some of the aliphatic suberin fractions were dramatically reduced in the rcn1 mutants compared with the wild type, especially under stagnant deoxygenated conditions. In rice, the chain lengths of aliphatic suberin monomers ranged from C16 to C30 <ref name="ref9" /><ref name="ref10" />, while the chain length in maize roots ranged only from C16 to C26 in rhizodermal and hypodermal cell walls <ref name="ref9" />. In our results, chain lengths of aliphatic suberin ranged from C16 to C30 and chain lengths of C20 and C22 were less common than other lengths, as was previously reported for rice root suberin <ref name="ref9" /><ref name="ref10" />. The total contents of aliphatic suberin fraction and its monomers were significantly increased in rice (cv. Azucena) roots by stagnant deoxygenated treatments <ref name="ref10" />, which is in agreement with the data for wild types in our results. There was a remarkable increase in the chain length of C28 and C30 monomers of aliphatic suberin (fatty acids and ω-OH fatty acids) in the wild types under stagnant deoxygenated conditions. In the rcn1 mutants, however, monomers with chain lengths of C28 and C30 in the OPR did not greatly increase under stagnant deoxygenated conditions. Chain lengths of C28 and C30 of aliphatic suberin are absent in Arabidopsis <ref name="ref11" /> and maize <ref name="ref9" />, which are non-wetland species. On the other hand, P. australis and Glyceria maxima, which are wetland species, develop a well suberized hypodermis in the roots and were able to form a barrier to ROL. Their roots accumulated significant amounts of monomers with chain lengths between C28 and C30 <ref name="ref3" />. Further studies are needed to understand the correlation between waterlogging tolerance and accumulation of the chain lengths of C28 and C30 of aliphatic suberin.

[[File: Shijc-Os03g0281900-Fig2.png|right|thumb|200px|'' rcn1-2 (cv. Shiokari background) mutant shows reduced aliphatic suberin monomer contents. (from reference <ref name="ref1" />).'']]
'''RCN1/OsABCG5 is involved in hypodermal suberization'''
Suberin monomers are thought to be transported to their extracellular destination in the apoplast by a vesicular pathway and/or export by ABC transporters localized in the plasma membrane <ref name="ref5" /><ref name="ref12" /><ref name="ref13" />. The structure of suberin is close to the structure of cutin, which form a cuticular layer that covers all plant aerial surfaces. Thus, the biosynthesis of suberin may be similar to the biosynthesis of cutin and associated waxes <ref name="ref12" />. So far, two Arabidopsis WBC/WHITE-subgroup ABC transporters, AtABCG11 and AtABCG12, which are localized in the plasma membrane, have been implicated in the formation of cuticular waxes <ref name="ref14" /><ref name="ref15" /><ref name="ref16" /><ref name="ref17" />. In barley, HvABCG31 (a full-size ABCG transporter) is also involved in cutin formation <ref name="ref18" />. Additionally, its rice ortholog OsABCG31 may affect cutin formation, although the cutin contents of osabcg31 have not been reported <ref name="ref18" /> <ref name="ref11" /> reported that an AtABCG11-silenced line (dso-4) has reduced suberin contents in the root as well as reduced cutin and wax (i.e. an ABC transporter affects suberin accumulation in roots). They suggested that the reduced suberin in dso-4 results from the perturbation of cutin and/or wax transport because suberin and cutin share common precursors. dso-4 clearly suppressed the expressions of suberin-related genes, e.g. 3-KETOACYL-COA SYNTHASE2 (KCS2/DAISY) and CYP86A1 <ref name="ref11" />. However, the authors suggested that AtABCG11 does not regulate suberin biosynthesis directly because AtABCG11 was expressed in lateral root primordia, developing lateral roots and root tips, but not in the endodermis in the root <ref name="ref17" />. By contrast, RCN1/OsABCG5 expression was associated with suberized cells in roots (i.e. the endodermis and hypodermis). Furthermore, hypodermal suberization declined in both of the rcn1 mutants. These results support our hypothesis that RCN1/OsABCG5 is directly involved in suberin formation in the hypodermis.
Some suberin components were less abundant in the rcn1 mutants than in the wild types. When a transporter exports a substance to the apoplast, the loss-of-function mutant of its transporter reduced the substance in the apoplast compared with the wild type. In the present study, the OPR in both of rcn1 mutants had significantly reduced amounts of very-long-chain fatty acids (≥C28) of suberin main monomers (i.e. fatty acids and ω-OH fatty acids) and diacids of C16 than the wild types. This suggests that RCN1/OsABCG5 exports very-long-chain fatty acids of suberin monomers and/or diacids to the apoplast in the hypodermis. On the other hand, some suberin components were more abundant in the rcn1 mutants than in the wild types. These accumulations may be secondary effects of the reduction of the contents of very long chains of aliphatic suberin monomers in the hypodermis.
In rice, the endodermis is also well suberized. The RCN1/OsABCG5 gene was expressed not only in the hypodermis but also in the endodermis under stagnant deoxygenated conditions. However, in rcn1, very-long-chain fatty acids (≥C28) of suberin main monomers were reduced in the hypodermis but not in the endodermis. Under waterlogged soil and stagnant deoxygenated conditions, the rcn1 mutants clearly lacked suberization at the hypodermis and had noticeably abnormal root systems. The rcn1 mutants were originally isolated by their smaller number of culms <ref name="ref19" />. However, stagnant deoxygenated treatments did not change the culm (i.e. tiller) number of rcn1 mutants. The reduced number of culms (tillers) in rcn1 mutants may be caused by a mechanism that differs from the mechanism of suberization in the hypodermis. Because RCN1/OsABCG5 belongs to the half-size WBC/WHITE subgroup of ABCG proteins <ref name="ref19" />, it is thought to form a homo-dimer or hetero-dimer to function as a transporter to mediate the movement of substrates across the membrane. Some human ABCG proteins function as homo-dimers, although their substrate and their localization can be altered when they form hetero-dimers with other subfamily members <ref name="ref20" /> <ref name="ref21" /> <ref name="ref22" />. RCN1/OsABCG5 might function with a different partner in the hypodermis and endodermis under waterlogged conditions, and also in developing tillers. Further studies are needed to test this hypothesis.

===Mutation===
[[File: Shijc-Os03g0281900-Fig3.png|right|thumb|200px|'' A rice mutant, reduced culm number1 (rcn1), cannot develop long roots under waterlogged soil conditions or stagnant deoxygenated conditions. (from reference <ref name="ref1" />).'']]
two allelic lines of the rice rcn1 mutants, reduced culm number1-1 (rcn1-1, whose background cultivar is ‘Akamuro’) and rcn1-2 (whose background cultivar is ‘Shiokari’), showed a reduced tillering phenotype <ref name="ref19" />. rcn1-1 and rcn1-2 had single point mutations in the RCN1/OsABCG5 gene (LOC_Os03g17350), causing amino acid substitutions R488C and A684P, respectively <ref name="ref19" />. In waterlogged soil conditions, the roots of rcn1-1 and rcn1-2 were shorter (maximum root length was about 100 mm), and less flexible than those of the wild type (the roots did not droop when the plant was held in the air). This phenotype was more severe in rcn1-2. rcn1-1 and rcn1-2 also developed short and inflexible roots when grown in stagnant deoxygenated nutrient solution, which mimics waterlogged soil conditions. In stagnant deoxygenated conditions, the roots of rcn1 mutants were brownish compared with those of the wild type (white roots). The abnormal root phenotypes were not observed when the mutants were grown under well drained soil conditions or in well-aerated nutrient solution, suggesting that the mutations in the RCN1/OsABCG5 gene affected root morphology under hypoxic conditions, but not under aerobic conditions. The rcn1-1 roots were completely recovered by introduction of a wild-type RCN1/OsABCG5 gene, but not by introduction of empty vector plasmid (without RCN1/OsABCG5 gene). Together, these results suggest that RCN1/OsABCG5 plays an important role in root growth in a hypoxia-specific manner.

===Expression===
[[File: Shijc-Os03g0281900-Fig4.png|right|thumb|200px|'' RCN1/OsABCG5 is expressed in the hypodermis as well as the endodermis in roots. (from reference <ref name="ref1" />).'']]
RCN1/OsABCG5 gene expression was analyzed in the wild type (cv. Shiokari) by quantitative RT-PCR in three different zones (zone I: 0–15 mm behind the root apex, zone II: 15–25 mm behind the root apex, and zone III: 50–70 mm behind the root apex of roots grown in aerated or stagnant deoxygenated nutrient solution. In all of the zones (I, II and III) of wild-type roots, RCN1/OsABCG5 expression was 4- to 187-times greater under stagnant deoxygenated conditions than under aerated conditions. In particular, RCN1/OsABCG5 was highly expressed in zone II under stagnant deoxygenated conditions.
To determine whether RCN1/OsABCG5 expression in roots is specific to a cell type or to a tissue. RCN1/OsABCG5 expression was enhanced by stagnant deoxygenated treatment in all CC, CP and OPR tissues. The transcript levels were especially high in OPR and CC under stagnant deoxygenated conditions.
To confirm these results, GUS activity in RCN1/OsABCG5Pro::GFP:GUS plants was observed. GUS activity was high in zone II of roots grown under stagnant deoxygenated conditions. Moreover, GUS activity was observed in the hypodermis and the endodermis of zone II in RCN1/OsABCG5Pro::GFP:GUS plants grown under stagnant conditions. These results suggest that RCN1/OsABCG5 was expressed specifically in the hypodermis as well as in the endodermis in rice roots under stagnant deoxygenated conditions (waterlogged conditions). Additionally, GFP-tagged RCN1/OsABCG5 was localized in the plasma membrane of hypodermal cells, suggesting that RCN1/OsABCG5 works as an ABC transporter at the plasma membrane.

==Labs working on this gene==
1.Department of Bioscience, Fukui Prefectural University, Eiheiji, Fukui, Japan
2.Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
3.Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
4.Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, Obihiro, Hokkaido, Japan
5.Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
6.Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
7.Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, Kobe, Hyougo, Japan
8.Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
9.Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
10.NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan
11.Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan

==References==
<references>
<ref name="ref1">Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K., Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M., Takanashi, H., Ranathunge, K., Franke, R. B., Shitan, N., Nishizawa, N. K., Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono, M. and Kato, K. (2014), RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). The Plant Journal, 80: 40–51. doi: 10.1111/tpj.12614</ref>
<ref name="ref2">Armstrong, W. (1979) Aeration in higher plants. Adv. Bot. Res. 7, 225–332. </ref>
<ref name="ref3">Soukup, A., Armstrong, W., Schreiber, L., Franke, R. and Votrubová, O. (2007) Apoplastic barriers to radial oxygen loss and solute penetration: a chemical and functional comparison of the exodermis of two wetland species, Phragmites australis and Glyceria maxima. New Phytol. 173, 264–278. </ref>
<ref name="ref4">Kotula, L., Ranathunge, K., Schreiber, L. and Steudle, E. (2009) Functional and chemical comparison of apoplastic barriers to radial oxygen loss in roots of rice (Oryza sativa L.) grown in aerated or deoxygenated solution. J. Exp. Bot. 60, 2155–2167. </ref>
<ref name="ref5">Ranathunge, K., Schreiber, L. and Franke, R. (2011b) Suberin research in the genomics era - new interest for an old polymer. Plant Sci. 180, 399–413. </ref>
<ref name="ref6">Watanabe, K., Nishiuchi, S., Kulichikhin, K. and Nakazono, M. (2013) Does suberin accumulation in plant roots contribute to waterlogging tolerance? Front. Plant Sci. 4, 1–7. </ref>
<ref name="ref7">Schönherr, J. (1982) Resistance of plant surfaces to water loss: transport properties of cutin, suberin and associated lipids. In Physiological Plant Ecology II, Water Relations and Carbon Assimilation, Encyclopedia of Plant Physiology New Series Volume 12B (Lange, O.L., Nobel, P.S., Osmond, C.B. and Ziegler, H., eds). Berlin, Heidelberg, New York: Springer, pp. 154–179. </ref>
<ref name="ref8">Vogt, E., Schönherr, J. and Schmidt, H.W. (1983) Water permeability of periderm membranes isolated enzymatically from potato tubers (Solanum tuberosum L.). Planta, 158, 294–301. </ref>
<ref name="ref9">Schreiber, L., Franke, R., Hartmann, K.D., Ranathunge, K. and Steudle, E. (2005) The chemical composition of suberin in apoplastic barriers affects radial hydraulic conductivity differently in the roots of rice (Oryza sativa L. cv. IR64) and corn (Zea mays L. cv. Helix). J. Exp. Bot. 56, 1427–1436.</ref>
<ref name="ref10">Ranathunge, K., Lin, J., Steudle, E. and Schreiber, L. (2011a) Stagnant deoxygenated growth enhances root suberization and lignifications, but differentially affects water and NaCl permeabilities in rice (Oryza sativa L.) roots. Plant, Cell Environ. 34, 1223–1240. </ref>
<ref name="ref11">Panikashvili, D., Shi, J.X., Bocobza, S., Franke, R.B., Schreiber, L. and Aharoni, A. (2010) The Arabidopsis DSO/ABCG11 transporter affects cutin metabolism in reproductive organs and suberin in roots. Mol. Plant 3, 563–575. </ref>
<ref name="ref12">Franke, R. and Schreiber, L. (2007) Suberin – a biopolyester forming apoplastic plant interfaces. Curr. Opin. Plant Biol. 10, 252–259. </ref>
<ref name="ref13">Beisson, F., Li-Beisson, Y. and Pollard, M. (2012) Solving the puzzles of cutin and suberin polymer biosynthesis. Curr. Opin. Plant Biol. 15, 329–337.</ref>
<ref name="ref14"> Pighin, J.A., Zheng, H., Balakshin, L.J., Goodman, I.P., Western, T.L., Jetter, R., Kunst, L. and Samuels, A.L. (2004) Plant cuticular lipid export requires an ABC transporter. Science, 306, 702–704. </ref>
<ref name="ref15">Bird, D., Beisson, F., Brigham, A., Shin, J., Greer, S., Jetter, R., Kunst, L., Wu, X., Yephremov, A. and Samuels, L. (2007) Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J. 52, 485–498. </ref>
<ref name="ref16">Luo, B., Xue, X., Hu, W., Wang, L. and Chen, X. (2007) An ABC transporter gene of Arabidopsis thaliana, AtWBC11, is involved in cuticle development and prevention of organ fusion. Plant Cell Physiol. 48, 1790–1802. </ref>
<ref name="ref17">Panikashvili, D., Savaldi-Goldstein, S., Mandel, T., Yifhar, T., Franke, R.B., Höfer, R., Schreiber, L., Chory, J. and Aharoni, A. (2007) The Arabidopsis DESPERADO/AtWBC11 transporter is required for cutin and wax secretion. Plant Physiol. 145, 1345–1360. </ref>
<ref name="ref18">Chen, G., Komatsuda, T., Ma, J.F. et al. (2011) An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc. Natl Acad. Sci. USA, 108, 12354–12359. </ref>
<ref name="ref19"> Yasuno, N., Takamure, I., Kidou, S., Tokuji, Y., Ureshi, A., Funabiki, A., Ashikaga, K., Yamanouchi, U., Yano, M. and Kato, K. (2009) Rice shoot branching requires an ATP-binding cassette subfamily G protein. New Phytol. 182, 91–101. </ref>
<ref name="ref20"> Graf, G.A., Li, W., Gerard, R.D., Gelissen, I., White, A., Cohen, J.C. and Hobbs, H.H. (2002) Coexpression of ATP-binding cassette proteins ABCG5 and ABCG8 permits their transport to the apical surface. J. Clin. Invest. 110, 659–669. </ref>
<ref name="ref21">Graf, G.A., Yu, L., Li, W., Gerard, R., Tuma, P.L., Cohen, J.C. and Hobbs, H.H. (2003) ABCG5 and ABCG8 are obligate heterodimers for protein trafficking and biliary cholesterol excretion. J. Biol. Chem. 278, 48275–48282. </ref>
<ref name="ref22">Hirata, T., Okabe, M., Kobayashi, A., Ueda, K. and Matsuo, M. (2009) Molecular mechanisms of subcellular localization of ABCG5 and ABCG8. Biosci. Biotechnol. Biochem. 73, 619–626. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0281900|
Description = ABC transporter related domain containing protein|
Version = NM_001056281.1 GI:115452290 GeneID:4332449|
Length = 2692 bp|
Definition = Oryza sativa Japonica Group Os03g0281900, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:9704996..9707687|
CDS = 9705038..9707401|
GCID = <gbrowseImage1>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtag</cdnaseq>|
AA = <aaseq>MSRFVDKLPLFDRRPSPMEEAEGLPRSGYLGQLHHHQYYQPHSN MLPLEQSPPTSTKHTSVTLAQLLKRVNDARSGSSTPISSPRYTIELGGSKPESVSSES DDHHSDDGGSEGQPRALVLKFTDLTYSVKQRRKGSCLPFRRAAADEPELPAMRTLLDG ISGEARDGEIMAVLGASGSGKSTLIDALANRIAKESLHGSVTINGESIDSNLLKVISA YVRQEDLLYPMLTVEETLMFAAEFRLPRSLPTREKKKRVKELIDQLGLKRAANTIIGD EGHRGVSGGERRRVSIGVDIIHNPIMLFLDEPTSGLDSTSAFMVVTVLKAIAQSGSVV VMSIHQPSYRILGLLDRLLFLSRGKTVYYGPPSELPPFFLDFGKPIPDNENPTEFALD LIKEMETETEGTKRLAEHNAAWQLKHHGEGRGYGGKPGMSLKEAISASISRGKLVSGA TDGTVSVAASDHSAPPPSSSSVSKFVNPFWIEMGVLTRRAFINTKRTPEVFIIRLAAV LVTGFILATIFWRLDESPKGVQERLGFFAIAMSTMYYTCSDALPVFLSERYIFLRETA YNAYRRSSYVLSHTIVGFPSLVVLSFAFALTTFFSVGLAGGVNGFFYFVAIVLASFWA GSGFATFLSGVVTHVMLGFPVVLSTLAYFLLFSGFFINRDRIPRYWLWFHYISLVKYP YEAVMQNEFGDPTRCFVRGVQMFDNTPLAALPAAVKVRVLQSMSASLGVNIGTGTCIT TGPDFLKQQAITDFGKWECLWITVAWGFLFRILFYISLLLGSRNKRR</aaseq>|
DNA = <dnaseqindica>43..2406#tacttgtattggtaagagactaagagagtgagcttgccggagatgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtagacgacgacgacgaccaccttgctgatcgatcagtagctcgtacgtgatagcgatcgtcacctcgtctcaccgcagcggcggcgtggaccggccggcttcgttggagcaagcgacgcgtgggacaccattggttgcatggtttcccttgttttttttttcacttgttaaacatttcgatgttttttgattaaccgcctgtgattaacatgggacgggagttgtttgtaaaatttgtgtgcaagttgcaagtcgaaattgtatctggatgatatgacatttttttttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001056281.1 RefSeq:Os03g0281900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0281900

2014-12-27T13:43:30Z

Shijc:

RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os03g0281900-Fig1.png|right|thumb|200px|'' rcn1-2 mutant (cv. Shiokari background) shows defect in the suberization in the hypodermis but not in the endodermis. (from reference <ref name="ref1" />).'']]
'''Role of hypodermal suberin under waterlogged conditions'''
Rice is well adapted to waterlogged conditions. However, the rice mutant, rcn1 developed a short and shallow root system when growing in a rice paddy field or in deoxygenated stagnant nutrient solution. Waterlogging negatively affects the growth and survival of most plants, because oxygen is limited and phytotoxic compounds can accumulate in waterlogged soils <ref name="ref2" />. The apoplastic barrier in the hypodermis reduces soil and microbial toxins taken up into the roots from waterlogged soils <ref name="ref2" /> <ref name="ref3" />. Furthermore, the suberized barrier in the hypodermis may limit radial oxygen loss (ROL) from the aerenchyma in the roots to anaerobic (i.e. deep) soil <ref name="ref4" /> <ref name="ref5" /> <ref name="ref6" />. The rcn1 mutants had a well lignified sclerenchyma under stagnant deoxygenated conditions, but rcn1 lacked hypodermal suberization under aerated and stagnant deoxygenated conditions. In a wetland plant, Phragmites australis, the penetration of periodic acid is stopped at the suberized hypodermis, but the apoplastic tracer easily penetrated the thickened and lignified cell walls at the sclerenchyma <ref name="ref3"≈. In the wild types of rice grown in stagnant deoxygenated conditions, the apoplastic tracers (periodic acid and berberine) were unable to penetrate at the outside of the suberized hypodermis. But, rcn1 could not stop their penetration in the OPR even in the presence of a well lignified sclerenchyma. A sufficient suberized apoplastic transport barrier was not formed in the hypodermis of rcn1. This is one of the reasons why rcn1 could not develop roots longer than about 100 mm length in waterlogged soil or deoxygenated stagnant nutrient solution. Our results suggest that rice needs hypodermal suberization to act as an apoplastic barrier under wetland conditions.
Suberin of the rcn1 mutants and the wild types is composed of five aliphatic substance classes and two aromatic monomers. Suberin forms a barrier against water flow, and the aliphatic domain is thought to be more important than the aromatic domain for establishing the barrier <ref name="ref7" /> <ref name="ref8" />. Our results are consistent with this idea because the rcn1 mutants, which have a high level of aromatic monomers, could not block the penetration of apoplastic tracers.
On the other hand, some of the aliphatic suberin fractions were dramatically reduced in the rcn1 mutants compared with the wild type, especially under stagnant deoxygenated conditions. In rice, the chain lengths of aliphatic suberin monomers ranged from C16 to C30 <ref name="ref9" /><ref name="ref10" />, while the chain length in maize roots ranged only from C16 to C26 in rhizodermal and hypodermal cell walls <ref name="ref9" />. In our results, chain lengths of aliphatic suberin ranged from C16 to C30 and chain lengths of C20 and C22 were less common than other lengths, as was previously reported for rice root suberin <ref name="ref9" /><ref name="ref10" />. The total contents of aliphatic suberin fraction and its monomers were significantly increased in rice (cv. Azucena) roots by stagnant deoxygenated treatments <ref name="ref10" />, which is in agreement with the data for wild types in our results. There was a remarkable increase in the chain length of C28 and C30 monomers of aliphatic suberin (fatty acids and ω-OH fatty acids) in the wild types under stagnant deoxygenated conditions. In the rcn1 mutants, however, monomers with chain lengths of C28 and C30 in the OPR did not greatly increase under stagnant deoxygenated conditions. Chain lengths of C28 and C30 of aliphatic suberin are absent in Arabidopsis <ref name="ref11" /> and maize <ref name="ref9" />, which are non-wetland species. On the other hand, P. australis and Glyceria maxima, which are wetland species, develop a well suberized hypodermis in the roots and were able to form a barrier to ROL. Their roots accumulated significant amounts of monomers with chain lengths between C28 and C30 <ref name="ref3" />. Further studies are needed to understand the correlation between waterlogging tolerance and accumulation of the chain lengths of C28 and C30 of aliphatic suberin.

[[File: Shijc-Os03g0281900-Fig2.png|right|thumb|200px|'' rcn1-2 (cv. Shiokari background) mutant shows reduced aliphatic suberin monomer contents. (from reference <ref name="ref1" />).'']]
'''RCN1/OsABCG5 is involved in hypodermal suberization'''
Suberin monomers are thought to be transported to their extracellular destination in the apoplast by a vesicular pathway and/or export by ABC transporters localized in the plasma membrane <ref name="ref5" /><ref name="ref12" /><ref name="ref13" />. The structure of suberin is close to the structure of cutin, which form a cuticular layer that covers all plant aerial surfaces. Thus, the biosynthesis of suberin may be similar to the biosynthesis of cutin and associated waxes <ref name="ref12" />. So far, two Arabidopsis WBC/WHITE-subgroup ABC transporters, AtABCG11 and AtABCG12, which are localized in the plasma membrane, have been implicated in the formation of cuticular waxes <ref name="ref14" /><ref name="ref15" /><ref name="ref16" /><ref name="ref17" />. In barley, HvABCG31 (a full-size ABCG transporter) is also involved in cutin formation <ref name="ref18" />. Additionally, its rice ortholog OsABCG31 may affect cutin formation, although the cutin contents of osabcg31 have not been reported <ref name="ref18" /> <ref name="ref11"> reported that an AtABCG11-silenced line (dso-4) has reduced suberin contents in the root as well as reduced cutin and wax (i.e. an ABC transporter affects suberin accumulation in roots). They suggested that the reduced suberin in dso-4 results from the perturbation of cutin and/or wax transport because suberin and cutin share common precursors. dso-4 clearly suppressed the expressions of suberin-related genes, e.g. 3-KETOACYL-COA SYNTHASE2 (KCS2/DAISY) and CYP86A1 <ref name="ref11">. However, the authors suggested that AtABCG11 does not regulate suberin biosynthesis directly because AtABCG11 was expressed in lateral root primordia, developing lateral roots and root tips, but not in the endodermis in the root <ref name="ref17" />. By contrast, RCN1/OsABCG5 expression was associated with suberized cells in roots (i.e. the endodermis and hypodermis). Furthermore, hypodermal suberization declined in both of the rcn1 mutants. These results support our hypothesis that RCN1/OsABCG5 is directly involved in suberin formation in the hypodermis.
Some suberin components were less abundant in the rcn1 mutants than in the wild types. When a transporter exports a substance to the apoplast, the loss-of-function mutant of its transporter reduced the substance in the apoplast compared with the wild type. In the present study, the OPR in both of rcn1 mutants had significantly reduced amounts of very-long-chain fatty acids (≥C28) of suberin main monomers (i.e. fatty acids and ω-OH fatty acids) and diacids of C16 than the wild types. This suggests that RCN1/OsABCG5 exports very-long-chain fatty acids of suberin monomers and/or diacids to the apoplast in the hypodermis. On the other hand, some suberin components were more abundant in the rcn1 mutants than in the wild types. These accumulations may be secondary effects of the reduction of the contents of very long chains of aliphatic suberin monomers in the hypodermis.
In rice, the endodermis is also well suberized. The RCN1/OsABCG5 gene was expressed not only in the hypodermis but also in the endodermis under stagnant deoxygenated conditions. However, in rcn1, very-long-chain fatty acids (≥C28) of suberin main monomers were reduced in the hypodermis but not in the endodermis. Under waterlogged soil and stagnant deoxygenated conditions, the rcn1 mutants clearly lacked suberization at the hypodermis and had noticeably abnormal root systems. The rcn1 mutants were originally isolated by their smaller number of culms <ref name="ref19" />. However, stagnant deoxygenated treatments did not change the culm (i.e. tiller) number of rcn1 mutants. The reduced number of culms (tillers) in rcn1 mutants may be caused by a mechanism that differs from the mechanism of suberization in the hypodermis. Because RCN1/OsABCG5 belongs to the half-size WBC/WHITE subgroup of ABCG proteins <ref name="ref19" />, it is thought to form a homo-dimer or hetero-dimer to function as a transporter to mediate the movement of substrates across the membrane. Some human ABCG proteins function as homo-dimers, although their substrate and their localization can be altered when they form hetero-dimers with other subfamily members <ref name="ref20" /> <ref name="ref21" /> <ref name="ref22" />. RCN1/OsABCG5 might function with a different partner in the hypodermis and endodermis under waterlogged conditions, and also in developing tillers. Further studies are needed to test this hypothesis.

===Mutation===
[[File: Shijc-Os03g0281900-Fig3.png|right|thumb|200px|'' A rice mutant, reduced culm number1 (rcn1), cannot develop long roots under waterlogged soil conditions or stagnant deoxygenated conditions. (from reference <ref name="ref1" />).'']]
two allelic lines of the rice rcn1 mutants, reduced culm number1-1 (rcn1-1, whose background cultivar is ‘Akamuro’) and rcn1-2 (whose background cultivar is ‘Shiokari’), showed a reduced tillering phenotype <ref name="ref19" />. rcn1-1 and rcn1-2 had single point mutations in the RCN1/OsABCG5 gene (LOC_Os03g17350), causing amino acid substitutions R488C and A684P, respectively <ref name="ref19" />. In waterlogged soil conditions, the roots of rcn1-1 and rcn1-2 were shorter (maximum root length was about 100 mm), and less flexible than those of the wild type (the roots did not droop when the plant was held in the air). This phenotype was more severe in rcn1-2. rcn1-1 and rcn1-2 also developed short and inflexible roots when grown in stagnant deoxygenated nutrient solution, which mimics waterlogged soil conditions. In stagnant deoxygenated conditions, the roots of rcn1 mutants were brownish compared with those of the wild type (white roots). The abnormal root phenotypes were not observed when the mutants were grown under well drained soil conditions or in well-aerated nutrient solution, suggesting that the mutations in the RCN1/OsABCG5 gene affected root morphology under hypoxic conditions, but not under aerobic conditions. The rcn1-1 roots were completely recovered by introduction of a wild-type RCN1/OsABCG5 gene, but not by introduction of empty vector plasmid (without RCN1/OsABCG5 gene). Together, these results suggest that RCN1/OsABCG5 plays an important role in root growth in a hypoxia-specific manner.

===Expression===
[[File: Shijc-Os03g0281900-Fig4.png|right|thumb|200px|'' RCN1/OsABCG5 is expressed in the hypodermis as well as the endodermis in roots. (from reference <ref name="ref1" />).'']]
RCN1/OsABCG5 gene expression was analyzed in the wild type (cv. Shiokari) by quantitative RT-PCR in three different zones (zone I: 0–15 mm behind the root apex, zone II: 15–25 mm behind the root apex, and zone III: 50–70 mm behind the root apex of roots grown in aerated or stagnant deoxygenated nutrient solution. In all of the zones (I, II and III) of wild-type roots, RCN1/OsABCG5 expression was 4- to 187-times greater under stagnant deoxygenated conditions than under aerated conditions. In particular, RCN1/OsABCG5 was highly expressed in zone II under stagnant deoxygenated conditions.
To determine whether RCN1/OsABCG5 expression in roots is specific to a cell type or to a tissue. RCN1/OsABCG5 expression was enhanced by stagnant deoxygenated treatment in all CC, CP and OPR tissues. The transcript levels were especially high in OPR and CC under stagnant deoxygenated conditions.
To confirm these results, GUS activity in RCN1/OsABCG5Pro::GFP:GUS plants was observed. GUS activity was high in zone II of roots grown under stagnant deoxygenated conditions. Moreover, GUS activity was observed in the hypodermis and the endodermis of zone II in RCN1/OsABCG5Pro::GFP:GUS plants grown under stagnant conditions. These results suggest that RCN1/OsABCG5 was expressed specifically in the hypodermis as well as in the endodermis in rice roots under stagnant deoxygenated conditions (waterlogged conditions). Additionally, GFP-tagged RCN1/OsABCG5 was localized in the plasma membrane of hypodermal cells, suggesting that RCN1/OsABCG5 works as an ABC transporter at the plasma membrane.

==Labs working on this gene==
1.Department of Bioscience, Fukui Prefectural University, Eiheiji, Fukui, Japan
2.Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
3.Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
4.Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, Obihiro, Hokkaido, Japan
5.Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
6.Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
7.Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, Kobe, Hyougo, Japan
8.Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
9.Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
10.NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan
11.Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan

==References==
<references>
<ref name="ref1">Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K., Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M., Takanashi, H., Ranathunge, K., Franke, R. B., Shitan, N., Nishizawa, N. K., Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono, M. and Kato, K. (2014), RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). The Plant Journal, 80: 40–51. doi: 10.1111/tpj.12614</ref>
<ref name="ref2">Armstrong, W. (1979) Aeration in higher plants. Adv. Bot. Res. 7, 225–332. </ref>
<ref name="ref3">Soukup, A., Armstrong, W., Schreiber, L., Franke, R. and Votrubová, O. (2007) Apoplastic barriers to radial oxygen loss and solute penetration: a chemical and functional comparison of the exodermis of two wetland species, Phragmites australis and Glyceria maxima. New Phytol. 173, 264–278. </ref>
<ref name="ref4">Kotula, L., Ranathunge, K., Schreiber, L. and Steudle, E. (2009) Functional and chemical comparison of apoplastic barriers to radial oxygen loss in roots of rice (Oryza sativa L.) grown in aerated or deoxygenated solution. J. Exp. Bot. 60, 2155–2167. </ref>
<ref name="ref5">Ranathunge, K., Schreiber, L. and Franke, R. (2011b) Suberin research in the genomics era - new interest for an old polymer. Plant Sci. 180, 399–413. </ref>
<ref name="ref6">Watanabe, K., Nishiuchi, S., Kulichikhin, K. and Nakazono, M. (2013) Does suberin accumulation in plant roots contribute to waterlogging tolerance? Front. Plant Sci. 4, 1–7. </ref>
<ref name="ref7">Schönherr, J. (1982) Resistance of plant surfaces to water loss: transport properties of cutin, suberin and associated lipids. In Physiological Plant Ecology II, Water Relations and Carbon Assimilation, Encyclopedia of Plant Physiology New Series Volume 12B (Lange, O.L., Nobel, P.S., Osmond, C.B. and Ziegler, H., eds). Berlin, Heidelberg, New York: Springer, pp. 154–179. </ref>
<ref name="ref8">Vogt, E., Schönherr, J. and Schmidt, H.W. (1983) Water permeability of periderm membranes isolated enzymatically from potato tubers (Solanum tuberosum L.). Planta, 158, 294–301. </ref>
<ref name="ref9">Schreiber, L., Franke, R., Hartmann, K.D., Ranathunge, K. and Steudle, E. (2005) The chemical composition of suberin in apoplastic barriers affects radial hydraulic conductivity differently in the roots of rice (Oryza sativa L. cv. IR64) and corn (Zea mays L. cv. Helix). J. Exp. Bot. 56, 1427–1436.</ref>
<ref name="ref10">Ranathunge, K., Lin, J., Steudle, E. and Schreiber, L. (2011a) Stagnant deoxygenated growth enhances root suberization and lignifications, but differentially affects water and NaCl permeabilities in rice (Oryza sativa L.) roots. Plant, Cell Environ. 34, 1223–1240. </ref>
<ref name="ref11">Panikashvili, D., Shi, J.X., Bocobza, S., Franke, R.B., Schreiber, L. and Aharoni, A. (2010) The Arabidopsis DSO/ABCG11 transporter affects cutin metabolism in reproductive organs and suberin in roots. Mol. Plant 3, 563–575. </ref>
<ref name="ref12">Franke, R. and Schreiber, L. (2007) Suberin – a biopolyester forming apoplastic plant interfaces. Curr. Opin. Plant Biol. 10, 252–259. </ref>
<ref name="ref13">Beisson, F., Li-Beisson, Y. and Pollard, M. (2012) Solving the puzzles of cutin and suberin polymer biosynthesis. Curr. Opin. Plant Biol. 15, 329–337.</ref>
<ref name="ref14"> Pighin, J.A., Zheng, H., Balakshin, L.J., Goodman, I.P., Western, T.L., Jetter, R., Kunst, L. and Samuels, A.L. (2004) Plant cuticular lipid export requires an ABC transporter. Science, 306, 702–704. </ref>
<ref name="ref15">Bird, D., Beisson, F., Brigham, A., Shin, J., Greer, S., Jetter, R., Kunst, L., Wu, X., Yephremov, A. and Samuels, L. (2007) Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J. 52, 485–498. </ref>
<ref name="ref16">Luo, B., Xue, X., Hu, W., Wang, L. and Chen, X. (2007) An ABC transporter gene of Arabidopsis thaliana, AtWBC11, is involved in cuticle development and prevention of organ fusion. Plant Cell Physiol. 48, 1790–1802. </ref>
<ref name="ref17">Panikashvili, D., Savaldi-Goldstein, S., Mandel, T., Yifhar, T., Franke, R.B., Höfer, R., Schreiber, L., Chory, J. and Aharoni, A. (2007) The Arabidopsis DESPERADO/AtWBC11 transporter is required for cutin and wax secretion. Plant Physiol. 145, 1345–1360. </ref>
<ref name="ref18">Chen, G., Komatsuda, T., Ma, J.F. et al. (2011) An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc. Natl Acad. Sci. USA, 108, 12354–12359. </ref>
<ref name="ref19"> Yasuno, N., Takamure, I., Kidou, S., Tokuji, Y., Ureshi, A., Funabiki, A., Ashikaga, K., Yamanouchi, U., Yano, M. and Kato, K. (2009) Rice shoot branching requires an ATP-binding cassette subfamily G protein. New Phytol. 182, 91–101. </ref>
<ref name="ref20"> Graf, G.A., Li, W., Gerard, R.D., Gelissen, I., White, A., Cohen, J.C. and Hobbs, H.H. (2002) Coexpression of ATP-binding cassette proteins ABCG5 and ABCG8 permits their transport to the apical surface. J. Clin. Invest. 110, 659–669. </ref>
<ref name="ref21">Graf, G.A., Yu, L., Li, W., Gerard, R., Tuma, P.L., Cohen, J.C. and Hobbs, H.H. (2003) ABCG5 and ABCG8 are obligate heterodimers for protein trafficking and biliary cholesterol excretion. J. Biol. Chem. 278, 48275–48282. </ref>
<ref name="ref22">Hirata, T., Okabe, M., Kobayashi, A., Ueda, K. and Matsuo, M. (2009) Molecular mechanisms of subcellular localization of ABCG5 and ABCG8. Biosci. Biotechnol. Biochem. 73, 619–626. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0281900|
Description = ABC transporter related domain containing protein|
Version = NM_001056281.1 GI:115452290 GeneID:4332449|
Length = 2692 bp|
Definition = Oryza sativa Japonica Group Os03g0281900, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:9704996..9707687|
CDS = 9705038..9707401|
GCID = <gbrowseImage1>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtag</cdnaseq>|
AA = <aaseq>MSRFVDKLPLFDRRPSPMEEAEGLPRSGYLGQLHHHQYYQPHSN MLPLEQSPPTSTKHTSVTLAQLLKRVNDARSGSSTPISSPRYTIELGGSKPESVSSES DDHHSDDGGSEGQPRALVLKFTDLTYSVKQRRKGSCLPFRRAAADEPELPAMRTLLDG ISGEARDGEIMAVLGASGSGKSTLIDALANRIAKESLHGSVTINGESIDSNLLKVISA YVRQEDLLYPMLTVEETLMFAAEFRLPRSLPTREKKKRVKELIDQLGLKRAANTIIGD EGHRGVSGGERRRVSIGVDIIHNPIMLFLDEPTSGLDSTSAFMVVTVLKAIAQSGSVV VMSIHQPSYRILGLLDRLLFLSRGKTVYYGPPSELPPFFLDFGKPIPDNENPTEFALD LIKEMETETEGTKRLAEHNAAWQLKHHGEGRGYGGKPGMSLKEAISASISRGKLVSGA TDGTVSVAASDHSAPPPSSSSVSKFVNPFWIEMGVLTRRAFINTKRTPEVFIIRLAAV LVTGFILATIFWRLDESPKGVQERLGFFAIAMSTMYYTCSDALPVFLSERYIFLRETA YNAYRRSSYVLSHTIVGFPSLVVLSFAFALTTFFSVGLAGGVNGFFYFVAIVLASFWA GSGFATFLSGVVTHVMLGFPVVLSTLAYFLLFSGFFINRDRIPRYWLWFHYISLVKYP YEAVMQNEFGDPTRCFVRGVQMFDNTPLAALPAAVKVRVLQSMSASLGVNIGTGTCIT TGPDFLKQQAITDFGKWECLWITVAWGFLFRILFYISLLLGSRNKRR</aaseq>|
DNA = <dnaseqindica>43..2406#tacttgtattggtaagagactaagagagtgagcttgccggagatgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtagacgacgacgacgaccaccttgctgatcgatcagtagctcgtacgtgatagcgatcgtcacctcgtctcaccgcagcggcggcgtggaccggccggcttcgttggagcaagcgacgcgtgggacaccattggttgcatggtttcccttgttttttttttcacttgttaaacatttcgatgttttttgattaaccgcctgtgattaacatgggacgggagttgtttgtaaaatttgtgtgcaagttgcaagtcgaaattgtatctggatgatatgacatttttttttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001056281.1 RefSeq:Os03g0281900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0281900

2014-12-27T13:40:04Z

Shijc:

RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os03g0281900-Fig1.png|right|thumb|200px|'' rcn1-2 mutant (cv. Shiokari background) shows defect in the suberization in the hypodermis but not in the endodermis. (from reference <ref name="ref1" />).'']]
'''Role of hypodermal suberin under waterlogged conditions'''
Rice is well adapted to waterlogged conditions. However, the rice mutant, rcn1 developed a short and shallow root system when growing in a rice paddy field or in deoxygenated stagnant nutrient solution. Waterlogging negatively affects the growth and survival of most plants, because oxygen is limited and phytotoxic compounds can accumulate in waterlogged soils <ref name="ref2" />. The apoplastic barrier in the hypodermis reduces soil and microbial toxins taken up into the roots from waterlogged soils <ref name="ref2" /> <ref name="ref3" />. Furthermore, the suberized barrier in the hypodermis may limit radial oxygen loss (ROL) from the aerenchyma in the roots to anaerobic (i.e. deep) soil <ref name="ref4" /> <ref name="ref5" /> <ref name="ref6" />. The rcn1 mutants had a well lignified sclerenchyma under stagnant deoxygenated conditions, but rcn1 lacked hypodermal suberization under aerated and stagnant deoxygenated conditions. In a wetland plant, Phragmites australis, the penetration of periodic acid is stopped at the suberized hypodermis, but the apoplastic tracer easily penetrated the thickened and lignified cell walls at the sclerenchyma <ref name="ref3" />. In the wild types of rice grown in stagnant deoxygenated conditions, the apoplastic tracers (periodic acid and berberine) were unable to penetrate at the outside of the suberized hypodermis. But, rcn1 could not stop their penetration in the OPR even in the presence of a well lignified sclerenchyma. A sufficient suberized apoplastic transport barrier was not formed in the hypodermis of rcn1. This is one of the reasons why rcn1 could not develop roots longer than about 100 mm length in waterlogged soil or deoxygenated stagnant nutrient solution. Our results suggest that rice needs hypodermal suberization to act as an apoplastic barrier under wetland conditions.
Suberin of the rcn1 mutants and the wild types is composed of five aliphatic substance classes and two aromatic monomers. Suberin forms a barrier against water flow, and the aliphatic domain is thought to be more important than the aromatic domain for establishing the barrier <ref name="ref7"> <ref name="ref8">. Our results are consistent with this idea because the rcn1 mutants, which have a high level of aromatic monomers, could not block the penetration of apoplastic tracers.
On the other hand, some of the aliphatic suberin fractions were dramatically reduced in the rcn1 mutants compared with the wild type, especially under stagnant deoxygenated conditions. In rice, the chain lengths of aliphatic suberin monomers ranged from C16 to C30 <ref name="ref9"><ref name="ref10">, while the chain length in maize roots ranged only from C16 to C26 in rhizodermal and hypodermal cell walls <ref name="ref9">. In our results, chain lengths of aliphatic suberin ranged from C16 to C30 and chain lengths of C20 and C22 were less common than other lengths, as was previously reported for rice root suberin <ref name="ref9"><ref name="ref10">. The total contents of aliphatic suberin fraction and its monomers were significantly increased in rice (cv. Azucena) roots by stagnant deoxygenated treatments <ref name="ref10">, which is in agreement with the data for wild types in our results. There was a remarkable increase in the chain length of C28 and C30 monomers of aliphatic suberin (fatty acids and ω-OH fatty acids) in the wild types under stagnant deoxygenated conditions. In the rcn1 mutants, however, monomers with chain lengths of C28 and C30 in the OPR did not greatly increase under stagnant deoxygenated conditions. Chain lengths of C28 and C30 of aliphatic suberin are absent in Arabidopsis <ref name="ref11"> and maize <ref name="ref9">, which are non-wetland species. On the other hand, P. australis and Glyceria maxima, which are wetland species, develop a well suberized hypodermis in the roots and were able to form a barrier to ROL. Their roots accumulated significant amounts of monomers with chain lengths between C28 and C30 <ref name="ref3" />. Further studies are needed to understand the correlation between waterlogging tolerance and accumulation of the chain lengths of C28 and C30 of aliphatic suberin.

[[File: Shijc-Os03g0281900-Fig2.png|right|thumb|200px|'' rcn1-2 (cv. Shiokari background) mutant shows reduced aliphatic suberin monomer contents. (from reference <ref name="ref1" />).'']]
'''RCN1/OsABCG5 is involved in hypodermal suberization'''
Suberin monomers are thought to be transported to their extracellular destination in the apoplast by a vesicular pathway and/or export by ABC transporters localized in the plasma membrane <ref name="ref5" /><ref name="ref12" /><ref name="ref13" />. The structure of suberin is close to the structure of cutin, which form a cuticular layer that covers all plant aerial surfaces. Thus, the biosynthesis of suberin may be similar to the biosynthesis of cutin and associated waxes <ref name="ref12" />. So far, two Arabidopsis WBC/WHITE-subgroup ABC transporters, AtABCG11 and AtABCG12, which are localized in the plasma membrane, have been implicated in the formation of cuticular waxes <ref name="ref14" /><ref name="ref15" /><ref name="ref16" /><ref name="ref17" />. In barley, HvABCG31 (a full-size ABCG transporter) is also involved in cutin formation <ref name="ref18" />. Additionally, its rice ortholog OsABCG31 may affect cutin formation, although the cutin contents of osabcg31 have not been reported <ref name="ref18" /> <ref name="ref11"> reported that an AtABCG11-silenced line (dso-4) has reduced suberin contents in the root as well as reduced cutin and wax (i.e. an ABC transporter affects suberin accumulation in roots). They suggested that the reduced suberin in dso-4 results from the perturbation of cutin and/or wax transport because suberin and cutin share common precursors. dso-4 clearly suppressed the expressions of suberin-related genes, e.g. 3-KETOACYL-COA SYNTHASE2 (KCS2/DAISY) and CYP86A1 <ref name="ref11">. However, the authors suggested that AtABCG11 does not regulate suberin biosynthesis directly because AtABCG11 was expressed in lateral root primordia, developing lateral roots and root tips, but not in the endodermis in the root <ref name="ref17" />. By contrast, RCN1/OsABCG5 expression was associated with suberized cells in roots (i.e. the endodermis and hypodermis). Furthermore, hypodermal suberization declined in both of the rcn1 mutants. These results support our hypothesis that RCN1/OsABCG5 is directly involved in suberin formation in the hypodermis.
Some suberin components were less abundant in the rcn1 mutants than in the wild types. When a transporter exports a substance to the apoplast, the loss-of-function mutant of its transporter reduced the substance in the apoplast compared with the wild type. In the present study, the OPR in both of rcn1 mutants had significantly reduced amounts of very-long-chain fatty acids (≥C28) of suberin main monomers (i.e. fatty acids and ω-OH fatty acids) and diacids of C16 than the wild types. This suggests that RCN1/OsABCG5 exports very-long-chain fatty acids of suberin monomers and/or diacids to the apoplast in the hypodermis. On the other hand, some suberin components were more abundant in the rcn1 mutants than in the wild types. These accumulations may be secondary effects of the reduction of the contents of very long chains of aliphatic suberin monomers in the hypodermis.
In rice, the endodermis is also well suberized. The RCN1/OsABCG5 gene was expressed not only in the hypodermis but also in the endodermis under stagnant deoxygenated conditions. However, in rcn1, very-long-chain fatty acids (≥C28) of suberin main monomers were reduced in the hypodermis but not in the endodermis. Under waterlogged soil and stagnant deoxygenated conditions, the rcn1 mutants clearly lacked suberization at the hypodermis and had noticeably abnormal root systems. The rcn1 mutants were originally isolated by their smaller number of culms <ref name="ref19" />. However, stagnant deoxygenated treatments did not change the culm (i.e. tiller) number of rcn1 mutants. The reduced number of culms (tillers) in rcn1 mutants may be caused by a mechanism that differs from the mechanism of suberization in the hypodermis. Because RCN1/OsABCG5 belongs to the half-size WBC/WHITE subgroup of ABCG proteins <ref name="ref19" />, it is thought to form a homo-dimer or hetero-dimer to function as a transporter to mediate the movement of substrates across the membrane. Some human ABCG proteins function as homo-dimers, although their substrate and their localization can be altered when they form hetero-dimers with other subfamily members <ref name="ref20" /> <ref name="ref21" /> <ref name="ref22" />. RCN1/OsABCG5 might function with a different partner in the hypodermis and endodermis under waterlogged conditions, and also in developing tillers. Further studies are needed to test this hypothesis.

===Mutation===
[[File: Shijc-Os03g0281900-Fig3.png|right|thumb|200px|'' A rice mutant, reduced culm number1 (rcn1), cannot develop long roots under waterlogged soil conditions or stagnant deoxygenated conditions. (from reference <ref name="ref1" />).'']]
two allelic lines of the rice rcn1 mutants, reduced culm number1-1 (rcn1-1, whose background cultivar is ‘Akamuro’) and rcn1-2 (whose background cultivar is ‘Shiokari’), showed a reduced tillering phenotype <ref name="ref19" />. rcn1-1 and rcn1-2 had single point mutations in the RCN1/OsABCG5 gene (LOC_Os03g17350), causing amino acid substitutions R488C and A684P, respectively <ref name="ref19" />. In waterlogged soil conditions, the roots of rcn1-1 and rcn1-2 were shorter (maximum root length was about 100 mm), and less flexible than those of the wild type (the roots did not droop when the plant was held in the air). This phenotype was more severe in rcn1-2. rcn1-1 and rcn1-2 also developed short and inflexible roots when grown in stagnant deoxygenated nutrient solution, which mimics waterlogged soil conditions. In stagnant deoxygenated conditions, the roots of rcn1 mutants were brownish compared with those of the wild type (white roots). The abnormal root phenotypes were not observed when the mutants were grown under well drained soil conditions or in well-aerated nutrient solution, suggesting that the mutations in the RCN1/OsABCG5 gene affected root morphology under hypoxic conditions, but not under aerobic conditions. The rcn1-1 roots were completely recovered by introduction of a wild-type RCN1/OsABCG5 gene, but not by introduction of empty vector plasmid (without RCN1/OsABCG5 gene). Together, these results suggest that RCN1/OsABCG5 plays an important role in root growth in a hypoxia-specific manner.

===Expression===
[[File: Shijc-Os03g0281900-Fig4.png|right|thumb|200px|'' RCN1/OsABCG5 is expressed in the hypodermis as well as the endodermis in roots. (from reference <ref name="ref1" />).'']]
RCN1/OsABCG5 gene expression was analyzed in the wild type (cv. Shiokari) by quantitative RT-PCR in three different zones (zone I: 0–15 mm behind the root apex, zone II: 15–25 mm behind the root apex, and zone III: 50–70 mm behind the root apex of roots grown in aerated or stagnant deoxygenated nutrient solution. In all of the zones (I, II and III) of wild-type roots, RCN1/OsABCG5 expression was 4- to 187-times greater under stagnant deoxygenated conditions than under aerated conditions. In particular, RCN1/OsABCG5 was highly expressed in zone II under stagnant deoxygenated conditions.
To determine whether RCN1/OsABCG5 expression in roots is specific to a cell type or to a tissue. RCN1/OsABCG5 expression was enhanced by stagnant deoxygenated treatment in all CC, CP and OPR tissues. The transcript levels were especially high in OPR and CC under stagnant deoxygenated conditions.
To confirm these results, GUS activity in RCN1/OsABCG5Pro::GFP:GUS plants was observed. GUS activity was high in zone II of roots grown under stagnant deoxygenated conditions. Moreover, GUS activity was observed in the hypodermis and the endodermis of zone II in RCN1/OsABCG5Pro::GFP:GUS plants grown under stagnant conditions. These results suggest that RCN1/OsABCG5 was expressed specifically in the hypodermis as well as in the endodermis in rice roots under stagnant deoxygenated conditions (waterlogged conditions). Additionally, GFP-tagged RCN1/OsABCG5 was localized in the plasma membrane of hypodermal cells, suggesting that RCN1/OsABCG5 works as an ABC transporter at the plasma membrane.

==Labs working on this gene==
1.Department of Bioscience, Fukui Prefectural University, Eiheiji, Fukui, Japan
2.Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
3.Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
4.Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, Obihiro, Hokkaido, Japan
5.Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
6.Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
7.Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, Kobe, Hyougo, Japan
8.Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
9.Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
10.NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan
11.Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan

==References==
<references>
<ref name="ref1">Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K., Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M., Takanashi, H., Ranathunge, K., Franke, R. B., Shitan, N., Nishizawa, N. K., Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono, M. and Kato, K. (2014), RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). The Plant Journal, 80: 40–51. doi: 10.1111/tpj.12614</ref>
<ref name="ref2">Armstrong, W. (1979) Aeration in higher plants. Adv. Bot. Res. 7, 225–332. </ref>
<ref name="ref3">Soukup, A., Armstrong, W., Schreiber, L., Franke, R. and Votrubová, O. (2007) Apoplastic barriers to radial oxygen loss and solute penetration: a chemical and functional comparison of the exodermis of two wetland species, Phragmites australis and Glyceria maxima. New Phytol. 173, 264–278. </ref>
<ref name="ref4">Kotula, L., Ranathunge, K., Schreiber, L. and Steudle, E. (2009) Functional and chemical comparison of apoplastic barriers to radial oxygen loss in roots of rice (Oryza sativa L.) grown in aerated or deoxygenated solution. J. Exp. Bot. 60, 2155–2167. </ref>
<ref name="ref5">Ranathunge, K., Schreiber, L. and Franke, R. (2011b) Suberin research in the genomics era - new interest for an old polymer. Plant Sci. 180, 399–413. </ref>
<ref name="ref6">Watanabe, K., Nishiuchi, S., Kulichikhin, K. and Nakazono, M. (2013) Does suberin accumulation in plant roots contribute to waterlogging tolerance? Front. Plant Sci. 4, 1–7. </ref>
<ref name="ref7">Schönherr, J. (1982) Resistance of plant surfaces to water loss: transport properties of cutin, suberin and associated lipids. In Physiological Plant Ecology II, Water Relations and Carbon Assimilation, Encyclopedia of Plant Physiology New Series Volume 12B (Lange, O.L., Nobel, P.S., Osmond, C.B. and Ziegler, H., eds). Berlin, Heidelberg, New York: Springer, pp. 154–179. </ref>
<ref name="ref8">Vogt, E., Schönherr, J. and Schmidt, H.W. (1983) Water permeability of periderm membranes isolated enzymatically from potato tubers (Solanum tuberosum L.). Planta, 158, 294–301. </ref>
<ref name="ref9">Schreiber, L., Franke, R., Hartmann, K.D., Ranathunge, K. and Steudle, E. (2005) The chemical composition of suberin in apoplastic barriers affects radial hydraulic conductivity differently in the roots of rice (Oryza sativa L. cv. IR64) and corn (Zea mays L. cv. Helix). J. Exp. Bot. 56, 1427–1436.</ref>
<ref name="ref10">Ranathunge, K., Lin, J., Steudle, E. and Schreiber, L. (2011a) Stagnant deoxygenated growth enhances root suberization and lignifications, but differentially affects water and NaCl permeabilities in rice (Oryza sativa L.) roots. Plant, Cell Environ. 34, 1223–1240. </ref>
<ref name="ref11">Panikashvili, D., Shi, J.X., Bocobza, S., Franke, R.B., Schreiber, L. and Aharoni, A. (2010) The Arabidopsis DSO/ABCG11 transporter affects cutin metabolism in reproductive organs and suberin in roots. Mol. Plant 3, 563–575. </ref>
<ref name="ref12">Franke, R. and Schreiber, L. (2007) Suberin – a biopolyester forming apoplastic plant interfaces. Curr. Opin. Plant Biol. 10, 252–259. </ref>
<ref name="ref13">Beisson, F., Li-Beisson, Y. and Pollard, M. (2012) Solving the puzzles of cutin and suberin polymer biosynthesis. Curr. Opin. Plant Biol. 15, 329–337.</ref>
<ref name="ref14"> Pighin, J.A., Zheng, H., Balakshin, L.J., Goodman, I.P., Western, T.L., Jetter, R., Kunst, L. and Samuels, A.L. (2004) Plant cuticular lipid export requires an ABC transporter. Science, 306, 702–704. </ref>
<ref name="ref15">Bird, D., Beisson, F., Brigham, A., Shin, J., Greer, S., Jetter, R., Kunst, L., Wu, X., Yephremov, A. and Samuels, L. (2007) Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J. 52, 485–498. </ref>
<ref name="ref16">Luo, B., Xue, X., Hu, W., Wang, L. and Chen, X. (2007) An ABC transporter gene of Arabidopsis thaliana, AtWBC11, is involved in cuticle development and prevention of organ fusion. Plant Cell Physiol. 48, 1790–1802. </ref>
<ref name="ref17">Panikashvili, D., Savaldi-Goldstein, S., Mandel, T., Yifhar, T., Franke, R.B., Höfer, R., Schreiber, L., Chory, J. and Aharoni, A. (2007) The Arabidopsis DESPERADO/AtWBC11 transporter is required for cutin and wax secretion. Plant Physiol. 145, 1345–1360. </ref>
<ref name="ref18">Chen, G., Komatsuda, T., Ma, J.F. et al. (2011) An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc. Natl Acad. Sci. USA, 108, 12354–12359. </ref>
<ref name="ref19"> Yasuno, N., Takamure, I., Kidou, S., Tokuji, Y., Ureshi, A., Funabiki, A., Ashikaga, K., Yamanouchi, U., Yano, M. and Kato, K. (2009) Rice shoot branching requires an ATP-binding cassette subfamily G protein. New Phytol. 182, 91–101. </ref>
<ref name="ref20"> Graf, G.A., Li, W., Gerard, R.D., Gelissen, I., White, A., Cohen, J.C. and Hobbs, H.H. (2002) Coexpression of ATP-binding cassette proteins ABCG5 and ABCG8 permits their transport to the apical surface. J. Clin. Invest. 110, 659–669. </ref>
<ref name="ref21">Graf, G.A., Yu, L., Li, W., Gerard, R., Tuma, P.L., Cohen, J.C. and Hobbs, H.H. (2003) ABCG5 and ABCG8 are obligate heterodimers for protein trafficking and biliary cholesterol excretion. J. Biol. Chem. 278, 48275–48282. </ref>
<ref name="ref22">Hirata, T., Okabe, M., Kobayashi, A., Ueda, K. and Matsuo, M. (2009) Molecular mechanisms of subcellular localization of ABCG5 and ABCG8. Biosci. Biotechnol. Biochem. 73, 619–626. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0281900|
Description = ABC transporter related domain containing protein|
Version = NM_001056281.1 GI:115452290 GeneID:4332449|
Length = 2692 bp|
Definition = Oryza sativa Japonica Group Os03g0281900, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:9704996..9707687|
CDS = 9705038..9707401|
GCID = <gbrowseImage1>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtag</cdnaseq>|
AA = <aaseq>MSRFVDKLPLFDRRPSPMEEAEGLPRSGYLGQLHHHQYYQPHSN MLPLEQSPPTSTKHTSVTLAQLLKRVNDARSGSSTPISSPRYTIELGGSKPESVSSES DDHHSDDGGSEGQPRALVLKFTDLTYSVKQRRKGSCLPFRRAAADEPELPAMRTLLDG ISGEARDGEIMAVLGASGSGKSTLIDALANRIAKESLHGSVTINGESIDSNLLKVISA YVRQEDLLYPMLTVEETLMFAAEFRLPRSLPTREKKKRVKELIDQLGLKRAANTIIGD EGHRGVSGGERRRVSIGVDIIHNPIMLFLDEPTSGLDSTSAFMVVTVLKAIAQSGSVV VMSIHQPSYRILGLLDRLLFLSRGKTVYYGPPSELPPFFLDFGKPIPDNENPTEFALD LIKEMETETEGTKRLAEHNAAWQLKHHGEGRGYGGKPGMSLKEAISASISRGKLVSGA TDGTVSVAASDHSAPPPSSSSVSKFVNPFWIEMGVLTRRAFINTKRTPEVFIIRLAAV LVTGFILATIFWRLDESPKGVQERLGFFAIAMSTMYYTCSDALPVFLSERYIFLRETA YNAYRRSSYVLSHTIVGFPSLVVLSFAFALTTFFSVGLAGGVNGFFYFVAIVLASFWA GSGFATFLSGVVTHVMLGFPVVLSTLAYFLLFSGFFINRDRIPRYWLWFHYISLVKYP YEAVMQNEFGDPTRCFVRGVQMFDNTPLAALPAAVKVRVLQSMSASLGVNIGTGTCIT TGPDFLKQQAITDFGKWECLWITVAWGFLFRILFYISLLLGSRNKRR</aaseq>|
DNA = <dnaseqindica>43..2406#tacttgtattggtaagagactaagagagtgagcttgccggagatgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtagacgacgacgacgaccaccttgctgatcgatcagtagctcgtacgtgatagcgatcgtcacctcgtctcaccgcagcggcggcgtggaccggccggcttcgttggagcaagcgacgcgtgggacaccattggttgcatggtttcccttgttttttttttcacttgttaaacatttcgatgttttttgattaaccgcctgtgattaacatgggacgggagttgtttgtaaaatttgtgtgcaagttgcaagtcgaaattgtatctggatgatatgacatttttttttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001056281.1 RefSeq:Os03g0281900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0281900

2014-12-27T13:33:10Z

Shijc:

RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os03g0281900-Fig1.png|right|thumb|200px|'' rcn1-2 mutant (cv. Shiokari background) shows defect in the suberization in the hypodermis but not in the endodermis. (from reference <ref name="ref1" />).'']]
'''Role of hypodermal suberin under waterlogged conditions'''
Rice is well adapted to waterlogged conditions. However, the rice mutant, rcn1 developed a short and shallow root system when growing in a rice paddy field or in deoxygenated stagnant nutrient solution (Figures 1 and S2). Waterlogging negatively affects the growth and survival of most plants, because oxygen is limited and phytotoxic compounds can accumulate in waterlogged soils <ref name="ref2" />. The apoplastic barrier in the hypodermis reduces soil and microbial toxins taken up into the roots from waterlogged soils <ref name="ref2" /> <ref name="ref3" />. Furthermore, the suberized barrier in the hypodermis may limit radial oxygen loss (ROL) from the aerenchyma in the roots to anaerobic (i.e. deep) soil <ref name="ref4" /> <ref name="ref5" /> <ref name="ref6" />. The rcn1 mutants had a well lignified sclerenchyma under stagnant deoxygenated conditions, but rcn1 lacked hypodermal suberization under aerated and stagnant deoxygenated conditions (Figures 3a, S3a and S4a). In a wetland plant, Phragmites australis, the penetration of periodic acid is stopped at the suberized hypodermis, but the apoplastic tracer easily penetrated the thickened and lignified cell walls at the sclerenchyma <ref name="ref3" />. In the wild types of rice grown in stagnant deoxygenated conditions, the apoplastic tracers (periodic acid and berberine) were unable to penetrate at the outside of the suberized hypodermis (Figures 5 and S6). But, rcn1 could not stop their penetration in the OPR even in the presence of a well lignified sclerenchyma (Figures 5 and S6). A sufficient suberized apoplastic transport barrier was not formed in the hypodermis of rcn1. This is one of the reasons why rcn1 could not develop roots longer than about 100 mm length in waterlogged soil or deoxygenated stagnant nutrient solution (Figures 1 and S2). Our results suggest that rice needs hypodermal suberization to act as an apoplastic barrier under wetland conditions.
Suberin of the rcn1 mutants and the wild types is composed of five aliphatic substance classes and two aromatic monomers (Figures 4 and S5). Suberin forms a barrier against water flow, and the aliphatic domain is thought to be more important than the aromatic domain for establishing the barrier <ref name="ref7"> <ref name="ref8">. Our results are consistent with this idea because the rcn1 mutants, which have a high level of aromatic monomers, could not block the penetration of apoplastic tracers (Figures 5 and S6).
On the other hand, some of the aliphatic suberin fractions were dramatically reduced in the rcn1 mutants compared with the wild type, especially under stagnant deoxygenated conditions (Figure 4 and S5). In rice, the chain lengths of aliphatic suberin monomers ranged from C16 to C30 <ref name="ref9"><ref name="ref10">, while the chain length in maize roots ranged only from C16 to C26 in rhizodermal and hypodermal cell walls <ref name="ref9">. In our results, chain lengths of aliphatic suberin ranged from C16 to C30 and chain lengths of C20 and C22 were less common than other lengths (Figure S7), as was previously reported for rice root suberin <ref name="ref9"><ref name="ref10">. The total contents of aliphatic suberin fraction and its monomers were significantly increased in rice (cv. Azucena) roots by stagnant deoxygenated treatments <ref name="ref10">, which is in agreement with the data for wild types in our results. There was a remarkable increase in the chain length of C28 and C30 monomers of aliphatic suberin (fatty acids and ω-OH fatty acids) in the wild types under stagnant deoxygenated conditions (Figures 4 and S5). In the rcn1 mutants, however, monomers with chain lengths of C28 and C30 in the OPR did not greatly increase under stagnant deoxygenated conditions (Figure S7). Chain lengths of C28 and C30 of aliphatic suberin are absent in Arabidopsis <ref name="ref11"> and maize <ref name="ref9">, which are non-wetland species. On the other hand, P. australis and Glyceria maxima, which are wetland species, develop a well suberized hypodermis in the roots and were able to form a barrier to ROL. Their roots accumulated significant amounts of monomers with chain lengths between C28 and C30 <ref name="ref3" />. Further studies are needed to understand the correlation between waterlogging tolerance and accumulation of the chain lengths of C28 and C30 of aliphatic suberin.

[[File: Shijc-Os03g0281900-Fig2.png|right|thumb|200px|'' rcn1-2 (cv. Shiokari background) mutant shows reduced aliphatic suberin monomer contents. (from reference <ref name="ref1" />).'']]
'''RCN1/OsABCG5 is involved in hypodermal suberization'''
Suberin monomers are thought to be transported to their extracellular destination in the apoplast by a vesicular pathway and/or export by ABC transporters localized in the plasma membrane <ref name="ref5" /><ref name="ref12" /><ref name="ref13" />. The structure of suberin is close to the structure of cutin, which form a cuticular layer that covers all plant aerial surfaces. Thus, the biosynthesis of suberin may be similar to the biosynthesis of cutin and associated waxes <ref name="ref12" />. So far, two Arabidopsis WBC/WHITE-subgroup ABC transporters, AtABCG11 and AtABCG12, which are localized in the plasma membrane, have been implicated in the formation of cuticular waxes <ref name="ref14" /><ref name="ref15" /><ref name="ref16" /><ref name="ref17" />. In barley, HvABCG31 (a full-size ABCG transporter) is also involved in cutin formation <ref name="ref18" />. Additionally, its rice ortholog OsABCG31 may affect cutin formation, although the cutin contents of osabcg31 have not been reported <ref name="ref18" /> <ref name="ref11"> reported that an AtABCG11-silenced line (dso-4) has reduced suberin contents in the root as well as reduced cutin and wax (i.e. an ABC transporter affects suberin accumulation in roots). They suggested that the reduced suberin in dso-4 results from the perturbation of cutin and/or wax transport because suberin and cutin share common precursors. dso-4 clearly suppressed the expressions of suberin-related genes, e.g. 3-KETOACYL-COA SYNTHASE2 (KCS2/DAISY) and CYP86A1 <ref name="ref11">. However, the authors suggested that AtABCG11 does not regulate suberin biosynthesis directly because AtABCG11 was expressed in lateral root primordia, developing lateral roots and root tips, but not in the endodermis in the root <ref name="ref17" />. By contrast, RCN1/OsABCG5 expression was associated with suberized cells in roots (i.e. the endodermis and hypodermis) (Figure 2). Furthermore, hypodermal suberization declined in both of the rcn1 mutants (Figures 3, S3 and S4). These results support our hypothesis that RCN1/OsABCG5 is directly involved in suberin formation in the hypodermis.
Some suberin components were less abundant in the rcn1 mutants than in the wild types. When a transporter exports a substance to the apoplast, the loss-of-function mutant of its transporter reduced the substance in the apoplast compared with the wild type. In the present study, the OPR in both of rcn1 mutants had significantly reduced amounts of very-long-chain fatty acids (≥C28) of suberin main monomers (i.e. fatty acids and ω-OH fatty acids) and diacids of C16 than the wild types. This suggests that RCN1/OsABCG5 exports very-long-chain fatty acids of suberin monomers and/or diacids to the apoplast in the hypodermis. On the other hand, some suberin components were more abundant in the rcn1 mutants than in the wild types. These accumulations may be secondary effects of the reduction of the contents of very long chains of aliphatic suberin monomers in the hypodermis.
In rice, the endodermis is also well suberized. The RCN1/OsABCG5 gene was expressed not only in the hypodermis but also in the endodermis under stagnant deoxygenated conditions (Figure 2e,f). However, in rcn1, very-long-chain fatty acids (≥C28) of suberin main monomers were reduced in the hypodermis but not in the endodermis (Figures 4b and S5b). Under waterlogged soil and stagnant deoxygenated conditions, the rcn1 mutants clearly lacked suberization at the hypodermis (Figures 3, S3 and S4) and had noticeably abnormal root systems (Figures 1 and S2). The rcn1 mutants were originally isolated by their smaller number of culms <ref name="ref19" />. However, stagnant deoxygenated treatments did not change the culm (i.e. tiller) number of rcn1 mutants (Figure S8). The reduced number of culms (tillers) in rcn1 mutants may be caused by a mechanism that differs from the mechanism of suberization in the hypodermis. Because RCN1/OsABCG5 belongs to the half-size WBC/WHITE subgroup of ABCG proteins <ref name="ref19" />, it is thought to form a homo-dimer or hetero-dimer to function as a transporter to mediate the movement of substrates across the membrane. Some human ABCG proteins function as homo-dimers, although their substrate and their localization can be altered when they form hetero-dimers with other subfamily members <ref name="ref20" /> <ref name="ref21" /> <ref name="ref22" />. RCN1/OsABCG5 might function with a different partner in the hypodermis and endodermis under waterlogged conditions, and also in developing tillers. Further studies are needed to test this hypothesis.

===Mutation===
[[File: Shijc-Os03g0281900-Fig3.png|right|thumb|200px|'' A rice mutant, reduced culm number1 (rcn1), cannot develop long roots under waterlogged soil conditions or stagnant deoxygenated conditions. (from reference <ref name="ref1" />).'']]
two allelic lines of the rice rcn1 mutants, reduced culm number1-1 (rcn1-1, whose background cultivar is ‘Akamuro’) and rcn1-2 (whose background cultivar is ‘Shiokari’), showed a reduced tillering phenotype <ref name="ref19" />. rcn1-1 and rcn1-2 had single point mutations in the RCN1/OsABCG5 gene (LOC_Os03g17350), causing amino acid substitutions R488C and A684P, respectively (Figure S1) <ref name="ref19" />. In waterlogged soil conditions, the roots of rcn1-1 and rcn1-2 were shorter (maximum root length was about 100 mm), and less flexible than those of the wild type (the roots did not droop when the plant was held in the air) (Figures 1a and S2b). This phenotype was more severe in rcn1-2 (Figure S2). rcn1-1 and rcn1-2 also developed short and inflexible roots when grown in stagnant deoxygenated nutrient solution, which mimics waterlogged soil conditions (Figures 1b and S2d). In stagnant deoxygenated conditions, the roots of rcn1 mutants were brownish compared with those of the wild type (white roots) (Figures 1b and S2d). The abnormal root phenotypes were not observed when the mutants were grown under well drained soil conditions (Figure S2a) or in well-aerated nutrient solution (Figure S2c), suggesting that the mutations in the RCN1/OsABCG5 gene affected root morphology under hypoxic conditions, but not under aerobic conditions. The rcn1-1 roots were completely recovered by introduction of a wild-type RCN1/OsABCG5 gene, but not by introduction of empty vector plasmid (without RCN1/OsABCG5 gene) (Figure 1b). Together, these results suggest that RCN1/OsABCG5 plays an important role in root growth in a hypoxia-specific manner.

===Expression===
[[File: Shijc-Os03g0281900-Fig4.png|right|thumb|200px|'' RCN1/OsABCG5 is expressed in the hypodermis as well as the endodermis in roots. (from reference <ref name="ref1" />).'']]
RCN1/OsABCG5 gene expression was analyzed in the wild type (cv. Shiokari) by quantitative RT-PCR in three different zones (zone I: 0–15 mm behind the root apex, zone II: 15–25 mm behind the root apex, and zone III: 50–70 mm behind the root apex) (Figure 2a) of roots grown in aerated or stagnant deoxygenated nutrient solution. In all of the zones (I, II and III) of wild-type roots, RCN1/OsABCG5 expression was 4- to 187-times greater under stagnant deoxygenated conditions than under aerated conditions (Figure 2b). In particular, RCN1/OsABCG5 was highly expressed in zone II under stagnant deoxygenated conditions (Figure 2b).
To determine whether RCN1/OsABCG5 expression in roots is specific to a cell type or to a tissue. RCN1/OsABCG5 expression was enhanced by stagnant deoxygenated treatment in all CC, CP and OPR tissues (Figure 2c). The transcript levels were especially high in OPR and CC under stagnant deoxygenated conditions (Figure 2c).
To confirm these results, GUS activity in RCN1/OsABCG5Pro::GFP:GUS plants was observed. GUS activity was high in zone II of roots grown under stagnant deoxygenated conditions (Figure 2d). Moreover, GUS activity was observed in the hypodermis (Figure 2e) and the endodermis (Figure 2f) of zone II in RCN1/OsABCG5Pro::GFP:GUS plants grown under stagnant conditions. These results suggest that RCN1/OsABCG5 was expressed specifically in the hypodermis as well as in the endodermis in rice roots under stagnant deoxygenated conditions (waterlogged conditions). Additionally, GFP-tagged RCN1/OsABCG5 was localized in the plasma membrane of hypodermal cells (Figure 2g,h), suggesting that RCN1/OsABCG5 works as an ABC transporter at the plasma membrane.

==Labs working on this gene==
1.Department of Bioscience, Fukui Prefectural University, Eiheiji, Fukui, Japan
2.Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
3.Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
4.Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, Obihiro, Hokkaido, Japan
5.Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
6.Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
7.Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, Kobe, Hyougo, Japan
8.Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
9.Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
10.NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan
11.Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan

==References==
<references>
<ref name="ref1">Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K., Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M., Takanashi, H., Ranathunge, K., Franke, R. B., Shitan, N., Nishizawa, N. K., Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono, M. and Kato, K. (2014), RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). The Plant Journal, 80: 40–51. doi: 10.1111/tpj.12614</ref>
<ref name="ref2">Armstrong, W. (1979) Aeration in higher plants. Adv. Bot. Res. 7, 225–332. </ref>
<ref name="ref3">Soukup, A., Armstrong, W., Schreiber, L., Franke, R. and Votrubová, O. (2007) Apoplastic barriers to radial oxygen loss and solute penetration: a chemical and functional comparison of the exodermis of two wetland species, Phragmites australis and Glyceria maxima. New Phytol. 173, 264–278. </ref>
<ref name="ref4">Kotula, L., Ranathunge, K., Schreiber, L. and Steudle, E. (2009) Functional and chemical comparison of apoplastic barriers to radial oxygen loss in roots of rice (Oryza sativa L.) grown in aerated or deoxygenated solution. J. Exp. Bot. 60, 2155–2167. </ref>
<ref name="ref5">Ranathunge, K., Schreiber, L. and Franke, R. (2011b) Suberin research in the genomics era - new interest for an old polymer. Plant Sci. 180, 399–413. </ref>
<ref name="ref6">Watanabe, K., Nishiuchi, S., Kulichikhin, K. and Nakazono, M. (2013) Does suberin accumulation in plant roots contribute to waterlogging tolerance? Front. Plant Sci. 4, 1–7. </ref>
<ref name="ref7">Schönherr, J. (1982) Resistance of plant surfaces to water loss: transport properties of cutin, suberin and associated lipids. In Physiological Plant Ecology II, Water Relations and Carbon Assimilation, Encyclopedia of Plant Physiology New Series Volume 12B (Lange, O.L., Nobel, P.S., Osmond, C.B. and Ziegler, H., eds). Berlin, Heidelberg, New York: Springer, pp. 154–179. </ref>
<ref name="ref8">Vogt, E., Schönherr, J. and Schmidt, H.W. (1983) Water permeability of periderm membranes isolated enzymatically from potato tubers (Solanum tuberosum L.). Planta, 158, 294–301. </ref>
<ref name="ref9">Schreiber, L., Franke, R., Hartmann, K.D., Ranathunge, K. and Steudle, E. (2005) The chemical composition of suberin in apoplastic barriers affects radial hydraulic conductivity differently in the roots of rice (Oryza sativa L. cv. IR64) and corn (Zea mays L. cv. Helix). J. Exp. Bot. 56, 1427–1436.</ref>
<ref name="ref10">Ranathunge, K., Lin, J., Steudle, E. and Schreiber, L. (2011a) Stagnant deoxygenated growth enhances root suberization and lignifications, but differentially affects water and NaCl permeabilities in rice (Oryza sativa L.) roots. Plant, Cell Environ. 34, 1223–1240. </ref>
<ref name="ref11">Panikashvili, D., Shi, J.X., Bocobza, S., Franke, R.B., Schreiber, L. and Aharoni, A. (2010) The Arabidopsis DSO/ABCG11 transporter affects cutin metabolism in reproductive organs and suberin in roots. Mol. Plant 3, 563–575. </ref>
<ref name="ref12">Franke, R. and Schreiber, L. (2007) Suberin – a biopolyester forming apoplastic plant interfaces. Curr. Opin. Plant Biol. 10, 252–259. </ref>
<ref name="ref13">Beisson, F., Li-Beisson, Y. and Pollard, M. (2012) Solving the puzzles of cutin and suberin polymer biosynthesis. Curr. Opin. Plant Biol. 15, 329–337.</ref>
<ref name="ref14"> Pighin, J.A., Zheng, H., Balakshin, L.J., Goodman, I.P., Western, T.L., Jetter, R., Kunst, L. and Samuels, A.L. (2004) Plant cuticular lipid export requires an ABC transporter. Science, 306, 702–704. </ref>
<ref name="ref15">Bird, D., Beisson, F., Brigham, A., Shin, J., Greer, S., Jetter, R., Kunst, L., Wu, X., Yephremov, A. and Samuels, L. (2007) Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J. 52, 485–498. </ref>
<ref name="ref16">Luo, B., Xue, X., Hu, W., Wang, L. and Chen, X. (2007) An ABC transporter gene of Arabidopsis thaliana, AtWBC11, is involved in cuticle development and prevention of organ fusion. Plant Cell Physiol. 48, 1790–1802. </ref>
<ref name="ref17">Panikashvili, D., Savaldi-Goldstein, S., Mandel, T., Yifhar, T., Franke, R.B., Höfer, R., Schreiber, L., Chory, J. and Aharoni, A. (2007) The Arabidopsis DESPERADO/AtWBC11 transporter is required for cutin and wax secretion. Plant Physiol. 145, 1345–1360. </ref>
<ref name="ref18">Chen, G., Komatsuda, T., Ma, J.F. et al. (2011) An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc. Natl Acad. Sci. USA, 108, 12354–12359. </ref>
<ref name="ref19"> Yasuno, N., Takamure, I., Kidou, S., Tokuji, Y., Ureshi, A., Funabiki, A., Ashikaga, K., Yamanouchi, U., Yano, M. and Kato, K. (2009) Rice shoot branching requires an ATP-binding cassette subfamily G protein. New Phytol. 182, 91–101. </ref>
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</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0281900|
Description = ABC transporter related domain containing protein|
Version = NM_001056281.1 GI:115452290 GeneID:4332449|
Length = 2692 bp|
Definition = Oryza sativa Japonica Group Os03g0281900, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:9704996..9707687|
CDS = 9705038..9707401|
GCID = <gbrowseImage1>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtag</cdnaseq>|
AA = <aaseq>MSRFVDKLPLFDRRPSPMEEAEGLPRSGYLGQLHHHQYYQPHSN MLPLEQSPPTSTKHTSVTLAQLLKRVNDARSGSSTPISSPRYTIELGGSKPESVSSES DDHHSDDGGSEGQPRALVLKFTDLTYSVKQRRKGSCLPFRRAAADEPELPAMRTLLDG ISGEARDGEIMAVLGASGSGKSTLIDALANRIAKESLHGSVTINGESIDSNLLKVISA YVRQEDLLYPMLTVEETLMFAAEFRLPRSLPTREKKKRVKELIDQLGLKRAANTIIGD EGHRGVSGGERRRVSIGVDIIHNPIMLFLDEPTSGLDSTSAFMVVTVLKAIAQSGSVV VMSIHQPSYRILGLLDRLLFLSRGKTVYYGPPSELPPFFLDFGKPIPDNENPTEFALD LIKEMETETEGTKRLAEHNAAWQLKHHGEGRGYGGKPGMSLKEAISASISRGKLVSGA TDGTVSVAASDHSAPPPSSSSVSKFVNPFWIEMGVLTRRAFINTKRTPEVFIIRLAAV LVTGFILATIFWRLDESPKGVQERLGFFAIAMSTMYYTCSDALPVFLSERYIFLRETA YNAYRRSSYVLSHTIVGFPSLVVLSFAFALTTFFSVGLAGGVNGFFYFVAIVLASFWA GSGFATFLSGVVTHVMLGFPVVLSTLAYFLLFSGFFINRDRIPRYWLWFHYISLVKYP YEAVMQNEFGDPTRCFVRGVQMFDNTPLAALPAAVKVRVLQSMSASLGVNIGTGTCIT TGPDFLKQQAITDFGKWECLWITVAWGFLFRILFYISLLLGSRNKRR</aaseq>|
DNA = <dnaseqindica>43..2406#tacttgtattggtaagagactaagagagtgagcttgccggagatgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtagacgacgacgacgaccaccttgctgatcgatcagtagctcgtacgtgatagcgatcgtcacctcgtctcaccgcagcggcggcgtggaccggccggcttcgttggagcaagcgacgcgtgggacaccattggttgcatggtttcccttgttttttttttcacttgttaaacatttcgatgttttttgattaaccgcctgtgattaacatgggacgggagttgtttgtaaaatttgtgtgcaagttgcaagtcgaaattgtatctggatgatatgacatttttttttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001056281.1 RefSeq:Os03g0281900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os03g0281900

2014-12-27T13:26:04Z

Shijc:

RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os03g0281900-Fig1.png|right|thumb|200px|'' rcn1-2 mutant (cv. Shiokari background) shows defect in the suberization in the hypodermis but not in the endodermis. (from reference <ref name="ref1" />).'']]
‘’’Role of hypodermal suberin under waterlogged conditions’’’
Rice is well adapted to waterlogged conditions. However, the rice mutant, rcn1 developed a short and shallow root system when growing in a rice paddy field or in deoxygenated stagnant nutrient solution (Figures 1 and S2). Waterlogging negatively affects the growth and survival of most plants, because oxygen is limited and phytotoxic compounds can accumulate in waterlogged soils <ref name="ref2" />. The apoplastic barrier in the hypodermis reduces soil and microbial toxins taken up into the roots from waterlogged soils <ref name="ref2" /> <ref name="ref3" />. Furthermore, the suberized barrier in the hypodermis may limit radial oxygen loss (ROL) from the aerenchyma in the roots to anaerobic (i.e. deep) soil <ref name="ref4" /> <ref name="ref5" /> <ref name="ref6" />. The rcn1 mutants had a well lignified sclerenchyma under stagnant deoxygenated conditions, but rcn1 lacked hypodermal suberization under aerated and stagnant deoxygenated conditions (Figures 3a, S3a and S4a). In a wetland plant, Phragmites australis, the penetration of periodic acid is stopped at the suberized hypodermis, but the apoplastic tracer easily penetrated the thickened and lignified cell walls at the sclerenchyma <ref name="ref3" />. In the wild types of rice grown in stagnant deoxygenated conditions, the apoplastic tracers (periodic acid and berberine) were unable to penetrate at the outside of the suberized hypodermis (Figures 5 and S6). But, rcn1 could not stop their penetration in the OPR even in the presence of a well lignified sclerenchyma (Figures 5 and S6). A sufficient suberized apoplastic transport barrier was not formed in the hypodermis of rcn1. This is one of the reasons why rcn1 could not develop roots longer than about 100 mm length in waterlogged soil or deoxygenated stagnant nutrient solution (Figures 1 and S2). Our results suggest that rice needs hypodermal suberization to act as an apoplastic barrier under wetland conditions.
Suberin of the rcn1 mutants and the wild types is composed of five aliphatic substance classes and two aromatic monomers (Figures 4 and S5). Suberin forms a barrier against water flow, and the aliphatic domain is thought to be more important than the aromatic domain for establishing the barrier <ref name="ref7"> <ref name="ref8">. Our results are consistent with this idea because the rcn1 mutants, which have a high level of aromatic monomers, could not block the penetration of apoplastic tracers (Figures 5 and S6).
On the other hand, some of the aliphatic suberin fractions were dramatically reduced in the rcn1 mutants compared with the wild type, especially under stagnant deoxygenated conditions (Figure 4 and S5). In rice, the chain lengths of aliphatic suberin monomers ranged from C16 to C30 <ref name="ref9"><ref name="ref10">, while the chain length in maize roots ranged only from C16 to C26 in rhizodermal and hypodermal cell walls <ref name="ref9">. In our results, chain lengths of aliphatic suberin ranged from C16 to C30 and chain lengths of C20 and C22 were less common than other lengths (Figure S7), as was previously reported for rice root suberin <ref name="ref9"><ref name="ref10">. The total contents of aliphatic suberin fraction and its monomers were significantly increased in rice (cv. Azucena) roots by stagnant deoxygenated treatments <ref name="ref10">, which is in agreement with the data for wild types in our results. There was a remarkable increase in the chain length of C28 and C30 monomers of aliphatic suberin (fatty acids and ω-OH fatty acids) in the wild types under stagnant deoxygenated conditions (Figures 4 and S5). In the rcn1 mutants, however, monomers with chain lengths of C28 and C30 in the OPR did not greatly increase under stagnant deoxygenated conditions (Figure S7). Chain lengths of C28 and C30 of aliphatic suberin are absent in Arabidopsis <ref name="ref11"> and maize <ref name="ref9">, which are non-wetland species. On the other hand, P. australis and Glyceria maxima, which are wetland species, develop a well suberized hypodermis in the roots and were able to form a barrier to ROL. Their roots accumulated significant amounts of monomers with chain lengths between C28 and C30 <ref name="ref3" />. Further studies are needed to understand the correlation between waterlogging tolerance and accumulation of the chain lengths of C28 and C30 of aliphatic suberin.

[[File: Shijc-Os03g0281900-Fig2.png|right|thumb|200px|'' rcn1-2 (cv. Shiokari background) mutant shows reduced aliphatic suberin monomer contents. (from reference <ref name="ref1" />).'']]
‘’’RCN1/OsABCG5 is involved in hypodermal suberization’’’
Suberin monomers are thought to be transported to their extracellular destination in the apoplast by a vesicular pathway and/or export by ABC transporters localized in the plasma membrane <ref name="ref5" /><ref name="ref12" /><ref name="ref13" />. The structure of suberin is close to the structure of cutin, which form a cuticular layer that covers all plant aerial surfaces. Thus, the biosynthesis of suberin may be similar to the biosynthesis of cutin and associated waxes <ref name="ref12" />. So far, two Arabidopsis WBC/WHITE-subgroup ABC transporters, AtABCG11 and AtABCG12, which are localized in the plasma membrane, have been implicated in the formation of cuticular waxes <ref name="ref14" /><ref name="ref15" /><ref name="ref16" /><ref name="ref17" />. In barley, HvABCG31 (a full-size ABCG transporter) is also involved in cutin formation <ref name="ref18" />. Additionally, its rice ortholog OsABCG31 may affect cutin formation, although the cutin contents of osabcg31 have not been reported <ref name="ref18" /> <ref name="ref11"> reported that an AtABCG11-silenced line (dso-4) has reduced suberin contents in the root as well as reduced cutin and wax (i.e. an ABC transporter affects suberin accumulation in roots). They suggested that the reduced suberin in dso-4 results from the perturbation of cutin and/or wax transport because suberin and cutin share common precursors. dso-4 clearly suppressed the expressions of suberin-related genes, e.g. 3-KETOACYL-COA SYNTHASE2 (KCS2/DAISY) and CYP86A1 <ref name="ref11">. However, the authors suggested that AtABCG11 does not regulate suberin biosynthesis directly because AtABCG11 was expressed in lateral root primordia, developing lateral roots and root tips, but not in the endodermis in the root <ref name="ref17" />. By contrast, RCN1/OsABCG5 expression was associated with suberized cells in roots (i.e. the endodermis and hypodermis) (Figure 2). Furthermore, hypodermal suberization declined in both of the rcn1 mutants (Figures 3, S3 and S4). These results support our hypothesis that RCN1/OsABCG5 is directly involved in suberin formation in the hypodermis.
Some suberin components were less abundant in the rcn1 mutants than in the wild types. When a transporter exports a substance to the apoplast, the loss-of-function mutant of its transporter reduced the substance in the apoplast compared with the wild type. In the present study, the OPR in both of rcn1 mutants had significantly reduced amounts of very-long-chain fatty acids (≥C28) of suberin main monomers (i.e. fatty acids and ω-OH fatty acids) and diacids of C16 than the wild types. This suggests that RCN1/OsABCG5 exports very-long-chain fatty acids of suberin monomers and/or diacids to the apoplast in the hypodermis. On the other hand, some suberin components were more abundant in the rcn1 mutants than in the wild types. These accumulations may be secondary effects of the reduction of the contents of very long chains of aliphatic suberin monomers in the hypodermis.
In rice, the endodermis is also well suberized. The RCN1/OsABCG5 gene was expressed not only in the hypodermis but also in the endodermis under stagnant deoxygenated conditions (Figure 2e,f). However, in rcn1, very-long-chain fatty acids (≥C28) of suberin main monomers were reduced in the hypodermis but not in the endodermis (Figures 4b and S5b). Under waterlogged soil and stagnant deoxygenated conditions, the rcn1 mutants clearly lacked suberization at the hypodermis (Figures 3, S3 and S4) and had noticeably abnormal root systems (Figures 1 and S2). The rcn1 mutants were originally isolated by their smaller number of culms <ref name="ref19" />. However, stagnant deoxygenated treatments did not change the culm (i.e. tiller) number of rcn1 mutants (Figure S8). The reduced number of culms (tillers) in rcn1 mutants may be caused by a mechanism that differs from the mechanism of suberization in the hypodermis. Because RCN1/OsABCG5 belongs to the half-size WBC/WHITE subgroup of ABCG proteins <ref name="ref19" />, it is thought to form a homo-dimer or hetero-dimer to function as a transporter to mediate the movement of substrates across the membrane. Some human ABCG proteins function as homo-dimers, although their substrate and their localization can be altered when they form hetero-dimers with other subfamily members <ref name="ref20" /> <ref name="ref21" /> <ref name="ref22" />. RCN1/OsABCG5 might function with a different partner in the hypodermis and endodermis under waterlogged conditions, and also in developing tillers. Further studies are needed to test this hypothesis.

===Mutation===
[[File: Shijc-Os03g0281900-Fig3.png|right|thumb|200px|'' A rice mutant, reduced culm number1 (rcn1), cannot develop long roots under waterlogged soil conditions or stagnant deoxygenated conditions. (from reference <ref name="ref1" />).'']]
two allelic lines of the rice rcn1 mutants, reduced culm number1-1 (rcn1-1, whose background cultivar is ‘Akamuro’) and rcn1-2 (whose background cultivar is ‘Shiokari’), showed a reduced tillering phenotype <ref name="ref19" />. rcn1-1 and rcn1-2 had single point mutations in the RCN1/OsABCG5 gene (LOC_Os03g17350), causing amino acid substitutions R488C and A684P, respectively (Figure S1) <ref name="ref19" />. In waterlogged soil conditions, the roots of rcn1-1 and rcn1-2 were shorter (maximum root length was about 100 mm), and less flexible than those of the wild type (the roots did not droop when the plant was held in the air) (Figures 1a and S2b). This phenotype was more severe in rcn1-2 (Figure S2). rcn1-1 and rcn1-2 also developed short and inflexible roots when grown in stagnant deoxygenated nutrient solution, which mimics waterlogged soil conditions (Figures 1b and S2d). In stagnant deoxygenated conditions, the roots of rcn1 mutants were brownish compared with those of the wild type (white roots) (Figures 1b and S2d). The abnormal root phenotypes were not observed when the mutants were grown under well drained soil conditions (Figure S2a) or in well-aerated nutrient solution (Figure S2c), suggesting that the mutations in the RCN1/OsABCG5 gene affected root morphology under hypoxic conditions, but not under aerobic conditions. The rcn1-1 roots were completely recovered by introduction of a wild-type RCN1/OsABCG5 gene, but not by introduction of empty vector plasmid (without RCN1/OsABCG5 gene) (Figure 1b). Together, these results suggest that RCN1/OsABCG5 plays an important role in root growth in a hypoxia-specific manner.

===Expression===
[[File: Shijc-Os03g0281900-Fig4.png|right|thumb|200px|'' RCN1/OsABCG5 is expressed in the hypodermis as well as the endodermis in roots. (from reference <ref name="ref1" />).'']]
RCN1/OsABCG5 gene expression was analyzed in the wild type (cv. Shiokari) by quantitative RT-PCR in three different zones (zone I: 0–15 mm behind the root apex, zone II: 15–25 mm behind the root apex, and zone III: 50–70 mm behind the root apex) (Figure 2a) of roots grown in aerated or stagnant deoxygenated nutrient solution. In all of the zones (I, II and III) of wild-type roots, RCN1/OsABCG5 expression was 4- to 187-times greater under stagnant deoxygenated conditions than under aerated conditions (Figure 2b). In particular, RCN1/OsABCG5 was highly expressed in zone II under stagnant deoxygenated conditions (Figure 2b).
To determine whether RCN1/OsABCG5 expression in roots is specific to a cell type or to a tissue. RCN1/OsABCG5 expression was enhanced by stagnant deoxygenated treatment in all CC, CP and OPR tissues (Figure 2c). The transcript levels were especially high in OPR and CC under stagnant deoxygenated conditions (Figure 2c).
To confirm these results, GUS activity in RCN1/OsABCG5Pro::GFP:GUS plants was observed. GUS activity was high in zone II of roots grown under stagnant deoxygenated conditions (Figure 2d). Moreover, GUS activity was observed in the hypodermis (Figure 2e) and the endodermis (Figure 2f) of zone II in RCN1/OsABCG5Pro::GFP:GUS plants grown under stagnant conditions. These results suggest that RCN1/OsABCG5 was expressed specifically in the hypodermis as well as in the endodermis in rice roots under stagnant deoxygenated conditions (waterlogged conditions). Additionally, GFP-tagged RCN1/OsABCG5 was localized in the plasma membrane of hypodermal cells (Figure 2g,h), suggesting that RCN1/OsABCG5 works as an ABC transporter at the plasma membrane.

==Labs working on this gene==
1.Department of Bioscience, Fukui Prefectural University, Eiheiji, Fukui, Japan
2.Graduate School of Agricultural and Life Sciences, The University of Tokyo, Bunkyo, Tokyo, Japan
3.Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, Japan
4.Department of Crop Science, Obihiro University of Agricultural and Veterinary Medicine, Obihiro, Hokkaido, Japan
5.Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
6.Institute of Cellular and Molecular Botany, University of Bonn, Bonn, Germany
7.Graduate School of Pharmaceutical Sciences, Kobe Pharmaceutical University, Kobe, Hyougo, Japan
8.Research Institute for Bioresources and Biotechnology, Ishikawa Prefectural University, Ishikawa, Japan
9.Graduate School of Agriculture, Hokkaido University, Sapporo, Hokkaido, Japan
10.NARO Institute of Crop Science, Tsukuba, Ibaraki, Japan
11.Institute for Sustainable Humanosphere, Kyoto University, Gokasho, Uji, Kyoto, Japan

==References==
<references>
<ref name="ref1">Shiono, K., Ando, M., Nishiuchi, S., Takahashi, H., Watanabe, K., Nakamura, M., Matsuo, Y., Yasuno, N., Yamanouchi, U., Fujimoto, M., Takanashi, H., Ranathunge, K., Franke, R. B., Shitan, N., Nishizawa, N. K., Takamure, I., Yano, M., Tsutsumi, N., Schreiber, L., Yazaki, K., Nakazono, M. and Kato, K. (2014), RCN1/OsABCG5, an ATP-binding cassette (ABC) transporter, is required for hypodermal suberization of roots in rice (Oryza sativa). The Plant Journal, 80: 40–51. doi: 10.1111/tpj.12614</ref>
<ref name="ref2">Armstrong, W. (1979) Aeration in higher plants. Adv. Bot. Res. 7, 225–332. </ref>
<ref name="ref3">Soukup, A., Armstrong, W., Schreiber, L., Franke, R. and Votrubová, O. (2007) Apoplastic barriers to radial oxygen loss and solute penetration: a chemical and functional comparison of the exodermis of two wetland species, Phragmites australis and Glyceria maxima. New Phytol. 173, 264–278. </ref>
<ref name="ref4">Kotula, L., Ranathunge, K., Schreiber, L. and Steudle, E. (2009) Functional and chemical comparison of apoplastic barriers to radial oxygen loss in roots of rice (Oryza sativa L.) grown in aerated or deoxygenated solution. J. Exp. Bot. 60, 2155–2167. </ref>
<ref name="ref5">Ranathunge, K., Schreiber, L. and Franke, R. (2011b) Suberin research in the genomics era - new interest for an old polymer. Plant Sci. 180, 399–413. </ref>
<ref name="ref6">Watanabe, K., Nishiuchi, S., Kulichikhin, K. and Nakazono, M. (2013) Does suberin accumulation in plant roots contribute to waterlogging tolerance? Front. Plant Sci. 4, 1–7. </ref>
<ref name="ref7">Schönherr, J. (1982) Resistance of plant surfaces to water loss: transport properties of cutin, suberin and associated lipids. In Physiological Plant Ecology II, Water Relations and Carbon Assimilation, Encyclopedia of Plant Physiology New Series Volume 12B (Lange, O.L., Nobel, P.S., Osmond, C.B. and Ziegler, H., eds). Berlin, Heidelberg, New York: Springer, pp. 154–179. </ref>
<ref name="ref8">Vogt, E., Schönherr, J. and Schmidt, H.W. (1983) Water permeability of periderm membranes isolated enzymatically from potato tubers (Solanum tuberosum L.). Planta, 158, 294–301. </ref>
<ref name="ref9">Schreiber, L., Franke, R., Hartmann, K.D., Ranathunge, K. and Steudle, E. (2005) The chemical composition of suberin in apoplastic barriers affects radial hydraulic conductivity differently in the roots of rice (Oryza sativa L. cv. IR64) and corn (Zea mays L. cv. Helix). J. Exp. Bot. 56, 1427–1436.</ref>
<ref name="ref10">Ranathunge, K., Lin, J., Steudle, E. and Schreiber, L. (2011a) Stagnant deoxygenated growth enhances root suberization and lignifications, but differentially affects water and NaCl permeabilities in rice (Oryza sativa L.) roots. Plant, Cell Environ. 34, 1223–1240. </ref>
<ref name="ref11">Panikashvili, D., Shi, J.X., Bocobza, S., Franke, R.B., Schreiber, L. and Aharoni, A. (2010) The Arabidopsis DSO/ABCG11 transporter affects cutin metabolism in reproductive organs and suberin in roots. Mol. Plant 3, 563–575. </ref>
<ref name="ref12">Franke, R. and Schreiber, L. (2007) Suberin – a biopolyester forming apoplastic plant interfaces. Curr. Opin. Plant Biol. 10, 252–259. </ref>
<ref name="ref13">Beisson, F., Li-Beisson, Y. and Pollard, M. (2012) Solving the puzzles of cutin and suberin polymer biosynthesis. Curr. Opin. Plant Biol. 15, 329–337.</ref>
<ref name="ref14"> Pighin, J.A., Zheng, H., Balakshin, L.J., Goodman, I.P., Western, T.L., Jetter, R., Kunst, L. and Samuels, A.L. (2004) Plant cuticular lipid export requires an ABC transporter. Science, 306, 702–704. </ref>
<ref name="ref15">Bird, D., Beisson, F., Brigham, A., Shin, J., Greer, S., Jetter, R., Kunst, L., Wu, X., Yephremov, A. and Samuels, L. (2007) Characterization of Arabidopsis ABCG11/WBC11, an ATP binding cassette (ABC) transporter that is required for cuticular lipid secretion. Plant J. 52, 485–498. </ref>
<ref name="ref16">Luo, B., Xue, X., Hu, W., Wang, L. and Chen, X. (2007) An ABC transporter gene of Arabidopsis thaliana, AtWBC11, is involved in cuticle development and prevention of organ fusion. Plant Cell Physiol. 48, 1790–1802. </ref>
<ref name="ref17">Panikashvili, D., Savaldi-Goldstein, S., Mandel, T., Yifhar, T., Franke, R.B., Höfer, R., Schreiber, L., Chory, J. and Aharoni, A. (2007) The Arabidopsis DESPERADO/AtWBC11 transporter is required for cutin and wax secretion. Plant Physiol. 145, 1345–1360. </ref>
<ref name="ref18">Chen, G., Komatsuda, T., Ma, J.F. et al. (2011) An ATP-binding cassette subfamily G full transporter is essential for the retention of leaf water in both wild barley and rice. Proc. Natl Acad. Sci. USA, 108, 12354–12359. </ref>
<ref name="ref19"> Yasuno, N., Takamure, I., Kidou, S., Tokuji, Y., Ureshi, A., Funabiki, A., Ashikaga, K., Yamanouchi, U., Yano, M. and Kato, K. (2009) Rice shoot branching requires an ATP-binding cassette subfamily G protein. New Phytol. 182, 91–101. </ref>
<ref name="ref20"> Graf, G.A., Li, W., Gerard, R.D., Gelissen, I., White, A., Cohen, J.C. and Hobbs, H.H. (2002) Coexpression of ATP-binding cassette proteins ABCG5 and ABCG8 permits their transport to the apical surface. J. Clin. Invest. 110, 659–669. </ref>
<ref name="ref21">Graf, G.A., Yu, L., Li, W., Gerard, R., Tuma, P.L., Cohen, J.C. and Hobbs, H.H. (2003) ABCG5 and ABCG8 are obligate heterodimers for protein trafficking and biliary cholesterol excretion. J. Biol. Chem. 278, 48275–48282. </ref>
<ref name="ref22">Hirata, T., Okabe, M., Kobayashi, A., Ueda, K. and Matsuo, M. (2009) Molecular mechanisms of subcellular localization of ABCG5 and ABCG8. Biosci. Biotechnol. Biochem. 73, 619–626. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0281900|
Description = ABC transporter related domain containing protein|
Version = NM_001056281.1 GI:115452290 GeneID:4332449|
Length = 2692 bp|
Definition = Oryza sativa Japonica Group Os03g0281900, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 3|Chromosome 3]]|
AP = Chromosome 3:9704996..9707687|
CDS = 9705038..9707401|
GCID = <gbrowseImage1>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:9704996..9707687
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtag</cdnaseq>|
AA = <aaseq>MSRFVDKLPLFDRRPSPMEEAEGLPRSGYLGQLHHHQYYQPHSN MLPLEQSPPTSTKHTSVTLAQLLKRVNDARSGSSTPISSPRYTIELGGSKPESVSSES DDHHSDDGGSEGQPRALVLKFTDLTYSVKQRRKGSCLPFRRAAADEPELPAMRTLLDG ISGEARDGEIMAVLGASGSGKSTLIDALANRIAKESLHGSVTINGESIDSNLLKVISA YVRQEDLLYPMLTVEETLMFAAEFRLPRSLPTREKKKRVKELIDQLGLKRAANTIIGD EGHRGVSGGERRRVSIGVDIIHNPIMLFLDEPTSGLDSTSAFMVVTVLKAIAQSGSVV VMSIHQPSYRILGLLDRLLFLSRGKTVYYGPPSELPPFFLDFGKPIPDNENPTEFALD LIKEMETETEGTKRLAEHNAAWQLKHHGEGRGYGGKPGMSLKEAISASISRGKLVSGA TDGTVSVAASDHSAPPPSSSSVSKFVNPFWIEMGVLTRRAFINTKRTPEVFIIRLAAV LVTGFILATIFWRLDESPKGVQERLGFFAIAMSTMYYTCSDALPVFLSERYIFLRETA YNAYRRSSYVLSHTIVGFPSLVVLSFAFALTTFFSVGLAGGVNGFFYFVAIVLASFWA GSGFATFLSGVVTHVMLGFPVVLSTLAYFLLFSGFFINRDRIPRYWLWFHYISLVKYP YEAVMQNEFGDPTRCFVRGVQMFDNTPLAALPAAVKVRVLQSMSASLGVNIGTGTCIT TGPDFLKQQAITDFGKWECLWITVAWGFLFRILFYISLLLGSRNKRR</aaseq>|
DNA = <dnaseqindica>43..2406#tacttgtattggtaagagactaagagagtgagcttgccggagatgtcgcggtttgtcgacaagctgccgctgttcgaccggaggccgtcgccgatggaggaggccgagggcctcccgcgcagtggctatcttgggcagctgcaccaccaccagtactaccagccgcacagcaacatgctgccgctggagcagtcgccgccgacgagcacgaagcacacgtcggtcacgctcgcgcagctcctgaagcgcgtgaacgacgcgcgcagcgggtcgtcgacgcccatctcgtcgccgcgctacaccatcgagctgggcgggtccaagccggagtccgtcagcagcgagagcgacgaccaccactccgacgacggcggcagcgaggggcagccgagggcgctcgtgctcaagttcaccgacctgacgtacagcgtgaagcagcggaggaaggggtcgtgcctgccgttccgtcgtgcggcggcggacgagcccgagctgcccgcgatgaggacgctgctcgacggcatctccggcgaggcccgggacggcgagatcatggcggtgctcggcgcgagcgggtccggcaagagcacgctcatcgacgcgctcgccaaccgcatcgccaaggagagcctccacggctccgtcacgatcaacggcgagtccatcgacagcaacctgctcaaggtcatctcagcgtacgtccggcaggaggaccttctgtacccgatgctcaccgtcgaggagacgctcatgttcgccgccgagttccgcctgccgcgctccctccccaccagggagaagaagaagcgggtgaaggagctaatcgaccagctcggcctgaagagagcggcgaacacgatcatcggcgacgagggccaccgcggcgtgtcgggaggcgagcgccggcgcgtctccatcggtgtcgacatcatccacaacccgatcatgctgttcctcgacgagcccacctccgggctggactccaccagcgcgttcatggtggtgacggtcctcaaggccatcgcgcagagcggcagcgtcgtcgtcatgtccatccaccagccgagctaccgcatcctcggcctcctcgaccgcctcctgttcctctcccgcgggaagacggtgtactacggcccgccgagcgagctgccgccgttcttcctcgacttcggcaagcccatcccggacaacgagaacccgacggagttcgcgctggacctcatcaaggagatggagaccgagacggaggggaccaagcgtctcgccgagcacaacgcggcgtggcagctgaagcaccacggggaaggccgcgggtacggcggcaagccggggatgtccctcaaggaggccatcagcgccagcatctcgcgcgggaagctcgtgtccggcgcgaccgacggcaccgtgtcggtcgccgcctccgaccattctgcgccgccgccgtcgtcgtcgtccgtgtccaagttcgtcaacccgttctggatcgagatgggggtgctgacgcgtcgcgcgttcatcaacacgaagcgcacgccggaggtgttcatcatccgcctcgcggcggtgctggtcaccgggttcatcctcgccaccatcttctggcgcctggacgagtcgcccaagggcgtgcaggagcggctgggcttcttcgccatcgccatgtccaccatgtactacacctgctccgacgcgctcccggtgttcctcagcgagcgctacatcttcctcagggagacggcgtacaacgcgtaccgccgctcatcctacgtgctctcccacaccatcgtcggcttcccgtcgctcgtggttctctccttcgcgttcgcgctcaccaccttcttctccgtggggctcgccggtggcgtgaacgggttcttctacttcgtggcaatcgtgctggcctccttctgggcggggagcggcttcgccacgttcctctccggcgtggtgacgcacgtgatgctggggttccccgtggtgctctccacgctcgcctacttcctcctcttcagcggcttcttcatcaaccgcgacaggatcccgcgctactggctgtggttccactacatctcgctcgtcaagtacccgtacgaggcggtgatgcagaacgagttcggcgacccgacgaggtgcttcgtccgcggcgtgcagatgttcgacaacacgccgctggcggcgctgccggcggcggtcaaggtgcgggtgctgcagtccatgtcggcgtcgctcggcgtgaacatcggcacggggacgtgcatcaccacgggaccggacttcctgaagcagcaggcgatcaccgacttcggcaagtgggagtgcctctggatcaccgtcgcgtggggattcctcttccgcatcctcttctacatctcgctgctgctcggcagcaggaacaagcggaggtagacgacgacgacgaccaccttgctgatcgatcagtagctcgtacgtgatagcgatcgtcacctcgtctcaccgcagcggcggcgtggaccggccggcttcgttggagcaagcgacgcgtgggacaccattggttgcatggtttcccttgttttttttttcacttgttaaacatttcgatgttttttgattaaccgcctgtgattaacatgggacgggagttgtttgtaaaatttgtgtgcaagttgcaagtcgaaattgtatctggatgatatgacatttttttttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001056281.1 RefSeq:Os03g0281900]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]

Os02g0736400

2014-12-27T13:25:18Z

Shijc:

“OsDHODH” encoding a putative cytosolic dihydroorotate dehydrogenase (DHODH) in rice. cytosolic dihydroorotate dehydrogenase is involved in plant stress response and that OsDHODH1 could be used in engineering crop plants with enhanced tolerance to salt and drought. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os02g0736400-Fig1.gif|right|thumb|200px|'' OsDHODH1-OX plants showed increased salt tolerance. (from reference <ref name="ref1" />).'']]
As OsDHODH1 was induced in rice seedlings upon salt and drought stresses, it was of interest to investigate the function of OsDHODH1 in vivo. The tolerance of E. coli cells harboring the OsDHODH1 gene to salt and osmotic stresses was assayed; recombinant cells with OsDHODH1 significantly improved the salt and osmotic tolerance.

Two OsDHODH1-OX lines (S1 and S2) and two OsDHODH1-KD lines (A1 and A2) were analyzed for salinity and osmotic tolerance. There was no significant difference in the growth rates between WT and transgenic plants at the seedlings stage under normal conditions. However, in comparison to WT, when cultured on 1/2 MS medium supplied with 200 mM NaCl, OsDHODH1-OX lines showed improved tolerance to salt, and OsDHODH1-KD lines were more sensitive. The seedling heights of S1 and S2 were higher than those of WT, A1 and A2. The chlorophyll content, proline content and relative electrolyte leakage were also tested. Under normal conditions, the chlorophyll and proline contents and relative electrolyte leakage showed no significant difference between the WT and transgenic lines. After salt treatment, the chlorophyll and proline contents in OsDHODH1-OX were higher than in WT and OsDHODH1-KD. The relative electrolyte leakages in OsDHODH1-OX were lower than in WT and OsDHODH1-KD.
[[File: Shijc-Os02g0736400-Fig2.gif|right|thumb|200px|'' OsDHODH1-OX plants showed increased drought tolerance. (from reference <ref name="ref1" />).'']]

===Transgenic Types===
The transgenic rice plants with sense-OsDHODH1 and antisense-OsDHODH1 were obtained by Agrobacterium-mediated transformation. The expression of OsDHODH1 in transgenic lines and wild type (WT) were analyzed by semi-quantitative RT-PCR. The results showed that the expression levels of OsDHODH1 in three independent OsDHODH1-overexpression lines (OsDHODH1-OX lines S1, S2 and S3) were significantly higher than those in WT plants and three independent OsDHODH1-knock-down lines (OsDHODH1-KD lines A1, A2 and A3). Furthermore, we compared the DHODH activities among the WT and transgenic lines and found that the enzymatic activity of DHODH in the OsDHODH1-OX lines was 90% higher than those in the WT. However, the enzymatic activity of DHODH did not show a significant reduction from the OsDHODH1-KD lines.

===Expression===
[[File: Shijc-Os02g0736400-Fig3.gif|right|thumb|200px|'' Expression and subcellular localization of OsDHODH1. (from reference <ref name="ref1" />).'']]

The tissue-specific expression analysis suggested that OsDHODH1 is constitutively expressed in rice culms, leaves, roots and immature spikes at the adult stage, and shoots and roots at the seedling stage. To test whether OsDHODH1 exactly encodes a cytosolic protein, the OsDHODH1-GUS fusion gene is introduced into onion epidermal cells by an Agrobacterium-mediated transient expression. The OsDHODH1-GUS fusion protein is localized throughout the cells, indicating that OsDHODH1 is a cytosolic protein.
The expression of OsDHODH1 in rice seedlings under NaCl, temperature, drought, abscisic acid (ABA) and H2O2 treatments by semi-quantitative RT-PCR showed that the expression of OsDHODH1 is induced by salt, drought and high-temperature stresses and ABA treatment, but not markedly affected by low temperature or H2O2 treatment.

===Evolution===
[[File: Shijc-Os02g0736400-Fig4.gif|right|thumb|200px|'' Characterization of OsDHODH1. (from reference <ref name="ref1" />).'']]
The predicted protein of OsDHODH1 is composed of 414 amino acids with a molecular weight of 45.31 kDa and an isoelectric point (pI) of 6.29. There are no signal peptides or transmembrane domains in the OsDHODH1 sequence. A comparison with its genomic sequence revealed that OsDHODH1 comprises seven exons and six introns. A homology search against the GenBank database showed that OsDHODH1 is homologous to various cytosolic DHODH proteins in eukaryotes, with 84–87% amino acid similarities with the corresponding proteins from Arabidopsis thaliana, Pyrus pyrifolia and Lycopersicon esculentum. A multiple sequence alignment indicated that the DHO_dh domains are conserved among all known plant cytosolic DHODH proteins. To investigate the evolutionary relationships among dihydroorotate dehydrogenase proteins from different organisms, a phylogenetic tree is constructed using the neighbor-joining method. The tree could clearly divide into two big families: family 1 and family 2. The position of OsDHODH1 in the tree also supported that OsDHODH1 belongs to the family 1, the plant cytosolic DHODH proteins.

==Labs working on this gene==
1. State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China

==References==
<references>
<ref name="ref1">
Liu, W.-Y., Wang, M.-M., Huang, J., Tang, H.-J., Lan, H.-X. and Zhang, H.-S. (2009), The OsDHODH1 Gene is Involved in Salt and Drought Tolerance in Rice. Journal of Integrative Plant Biology, 51: 825–833. doi: 10.1111/j.1744-7909.2009.00853.x </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os02g0736400|
Description = Dihydroorotate dehydrogenase family protein|
Version = NM_001054588.1 GI:115448546 GeneID:4330657|
Length = 3602 bp|
Definition = Oryza sativa Japonica Group Os02g0736400, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 2|Chromosome 2]]|
AP = Chromosome 2:31632631..31636232|
CDS = 31632760..31632916,31633568..31633677,31633946..31634129,31634225..31634337,31634610..31634780 ,31634861..31635124,31635905..31636150|
GCID = <gbrowseImage1>
name=NC_008395:31632631..31636232
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008395:31632631..31636232
source=RiceChromosome02
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggagtcgctgactctccgggcatcgccgtcgacggccgcgccgttgcgccgcgtccccgggcggcggcacgcggcggtgtccgtccgcgcctccgccggcgccggcgagccggacctctccgtgcgcgtgaacgggctgaagatgcccaacccgttcgtgatcgggtcggggcccccgggcaccaactacaccgtcatgaagcgcgcgttcgacgaggggtggggcggcgtcatcgccaaaaccgtatccttggatgctgagaaagttatcaacgtaacccctcgctatgcccggctcagggcggaccccaatggatctactaagagtcctatcatcggatggcagaacattgaacttatcagtgatcggcctctagaaactatgctgaatgaattcaagcaactgaagaaagagtatcctgacaggatactcattggctcaataatggaggagtacaacaaagctgcatggcatgagcttattgaacgcgttgaagagagcggagtggatgctcttgagattaatttctcatgcccacatggcatgccagagcgaaaaatgggtgctgccgtgggacaagactgtgacttgttagaggaggtctgcggttggataaatgagaaggctacagtgcctgtttgggcaaagatgactcctaacattacagatattacaaagcctgcaagaatttctcttaagtcaggatgtgaaggagtttctgctattaacacaatcatgagtgtgatgggaattaacctcaaaactttgcgaccagaaccttgtgtggagggttattccacgcctggaggctattctgcgagagccgtgcaccctatagcacttgcgaaagtcatgcagatagcaaggatgatgaaagaagaatttgctgatggacagtcactctctgctattggaggcgtggagactggcaatgatgctgctgagtttattctacttggcgcagatacagtacaggtatgtacgggcgtaatgatgcatggttatggccttgtaaagaagctttgtgcagagctgcaggattttatgagacaacacaacttttcctcaatagaagatttccggggggcctctctcccgtatttcaccacacacaccgatttggtacatcggcaaagggaggcgatcaaccagaggaaggctattaggaagggcctggaatcagacaaggactggaccggtgatggattcgtcaaggagacagaaagcatggtgtccaactga</cdnaseq>|
AA = <aaseq>MESLTLRASPSTAAPLRRVPGRRHAAVSVRASAGAGEPDLSVRV NGLKMPNPFVIGSGPPGTNYTVMKRAFDEGWGGVIAKTVSLDAEKVINVTPRYARLRA DPNGSTKSPIIGWQNIELISDRPLETMLNEFKQLKKEYPDRILIGSIMEEYNKAAWHE LIERVEESGVDALEINFSCPHGMPERKMGAAVGQDCDLLEEVCGWINEKATVPVWAKM TPNITDITKPARISLKSGCEGVSAINTIMSVMGINLKTLRPEPCVEGYSTPGGYSARA VHPIALAKVMQIARMMKEEFADGQSLSAIGGVETGNDAAEFILLGADTVQVCTGVMMH GYGLVKKLCAELQDFMRQHNFSSIEDFRGASLPYFTTHTDLVHRQREAINQRKAIRKG LESDKDWTGDGFVKETESMVSN</aaseq>|
DNA = <dnaseqindica>3317..3473#2556..2665#2104..2287#1896..2008#1453..1623#1109..1372#83..328#atccgtgatactcccaaagattcttatcgattgaagaaaaaaaaaagccggagaaaaggatagagagggaaagcaaccagccatggagtcgctgactctccgggcatcgccgtcgacggccgcgccgttgcgccgcgtccccgggcggcggcacgcggcggtgtccgtccgcgcctccgccggcgccggcgagccggacctctccgtgcgcgtgaacgggctgaagatgcccaacccgttcgtgatcgggtcggggcccccgggcaccaactacaccgtcatgaagcgcgcgttcgacgaggggtggggcggcgtcatcgccaaaaccgtaatcctctcaaccctcgcaaccgcaattctcctggatggatgacttttcctgctctaattttccgttgaaacagcgcacaaggataggatctatgtgatgtagttagcatttcagtgtttgagataagttcgcgtattaacgagagtgccttttggctgtatgatttgattccgatctgggttgggtttggagtgggagtgggagtgggagtggaggtgggggccaattcaagctcacttgaaaacaggtagctgctaacatgatgtcaggaaaggtggcggtgtgagtttgctattttggttgcggcaaaatcgaatcatggagtcgtggctacgttagatttggtggtggatcttatgataggttttgatgggtggccatacgagaattgatagattgatgggtgccggatgagaattcagttagttatatatatggctggttagagttaggatctttgcatattctaggagaatttggtctgtatgtactacttgtgttcactatgactgactactgacaaacgtcttgcttgaagatgagatggcctaatttttgtgagatgagcattgcatcctcagtattaaacatgagaaattagtttcaatttcttttgttctgcattaaccctttgcaatcatcatttccacctttttcacatacacattgttgtttccattgtgcatagtgcctttgcagtcatcactttcacctatcacttccaacggttgaatcatcaactttgtggctaattgttggtatgattatgaatggtaggtatccttggatgctgagaaagttatcaacgtaacccctcgctatgcccggctcagggcggaccccaatggatctactaagagtcctatcatcggatggcagaacattgaacttatcagtgatcggcctctagaaactatgctgaatgaattcaagcaactgaagaaagagtatcctgacaggatactcattggctcaataatggaggagtacaacaaagctgcatggcatgagcttattgaacgcgttgaagagagcggagtggtaaccttcccttatgtgcattttggtgcattcttggtcgaacttatcatgttggaatgttaatgatctgtttctatcaggatgctcttgagattaatttctcatgcccacatggcatgccagagcgaaaaatgggtgctgccgtgggacaagactgtgacttgttagaggaggtctgcggttggataaatgagaaggctacagtgcctgtttgggcaaagatgactcctaacattacagatattacaaaggttagtcaaacatatacatcttcgcagcacttaaatgagatcctaaattagtttttatcccacccggttttcacattgttttggacatcgtgttcgcgaattattatttagcgttcgtgtaacatgttttggacatctcttgaagccctagcatcaccatctatggaattaccactacattagaataccaagatttaggtgctttttaagatctaccaagaattagttttttttatgggtcaatgttttcattccttacttgcattgtgcagcctgcaagaatttctcttaagtcaggatgtgaaggagtttctgctattaacacaatcatgagtgtgatgggaattaacctcaaaactttgcgaccagaaccttgtgtggaggggttagattcaattccctgagttctttttttccctatggaacatattcctttactgttaccattttttttcttataaaaaccacttgattccacagttattccacgcctggaggctattctgcgagagccgtgcaccctatagcacttgcgaaagtcatgcagatagcaaggatgatgaaagaagaatttgctgatggacagtcactctctgctattggaggcgtggagactggcaatgatgctgctgagtttattctacttggcgcagatacagtacaggtaagctctaacatggtactaatgttagtattatgcatgtttatattctacttgatgctgctgttattacacatgtttccaatctggcaacctatgtggctccctttactatggattttgaagatcataatgtgtgctgctcgtgtacagttgatgttgaattatattctagattttttcaggcatcatttttgcaattaattgattagctccatgcttatcttgaacagcataataataagacttgactaatggccattcattgtaggtatgtacgggcgtaatgatgcatggttatggccttgtaaagaagctttgtgcagagctgcaggattttatgagacaacacaacttttcctcaatagaagatttccgggggtatgttatcaccacttcccttcttctgactcttgttgatttgttgttggaaatcatctggagaaatcaccttagtttagagtactgtactatgatatgttgcctacgaatgaacttaggaagaaatggaaaatcaccaacatgagtgttcatgaaacttttcttgtaaaagaacatgctcaggggggttacacatcttttcttgcagttttattttccacatttctaagtagaagcaaggacgggacactctattgttaaaaacagacttgaggtaatgattgaaggcagacttataggttgttagcggtagtcattatgggcttgaaccttcattatgacatgtttaggcaagccttccaatggctctgccttgcacgcctgaccctactatgtgtgaatggtgtagattaaagtcttgtgtaccttatgattaattctgtgtcactttggccttgttttactcattctcaaggaagcctttcagagctattgtttagttcggtactttttccactcgcagaggacactaggaccatctcttttcaaattgtcgaaaagcataatgttgttttattgaactaaaatatggtttatttttttcctttgttaacaaattatcactaatccaagctcttcacatcatctcagggcctctctcccgtatttcaccacacacaccgatttggtacatcggcaaagggaggcgatcaaccagaggaaggctattaggaagggcctggaatcagacaaggactggaccggtgatggattcgtcaaggagacagaaagcatggtgtccaactgattcgactctgaactcacacccccttccaccatacttccaacttgtgattaaacagggaccatgttcagcccaaaacagcagaaacttttgcatcatctcgttcaaataaaaagcataccaaattacttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001054588.1 RefSeq:Os02g0736400]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 2]]
[[Category:Chromosome 2]]

Os01g0921200

2014-12-27T13:24:27Z

Shijc:

OsMOGS involves in N-glycan formation, is required for auxin-mediated root development in rice. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os01g0921200-Fig1.png|right|thumb|200px|'' The osmogs mutant was defective in root hair development. (from reference <ref name="ref1" />).'']]
To characterize further any alteration of the osmogs root system, the PRs of 5-day-old WT and osmogs seedlings were photographed using a stereomicroscope. The resulting images of adventitious root (AR) initiation, LR outgrowth and root tips, respectively, showed that the osmogs had fewer and shorter root hairs than the WT (Figure 2). Scanning electron microscopy (SEM) images also showed same result in the mature zone of osmogs root tips, compared with dense and long root hairs on the surface of the same segment of WT (Figure 2). These results confirmed that roots of osmogs were defective in root hair initiation and elongation.
In plants, the newly formed oligosaccharides in the ER require further maturation in the Golgi to form high-mannose-, paucimannosidic-, hybrid- and/or complex-type N-glycans <ref name="ref2" />. To investigate whether disruption of N-glycan processing in the ER would change overall N-glycosylation of glycoproteins, total proteins from WT and osmogs roots were immunoblotted by a lectin concanavalin A (Con A) and anti-HRP antibody. The immunoblot analysis showed a much weaker reaction with proteins from osmogs than from WT plants (Figure 6a), and suggested that formation of high-mannose, paucimannose and complex N-glycans was dramatically inhibited in osmogs.
To know whether N-glycan structures were altered in osmogs, the structures of N-glycans released from glycoproteins with peptide-N-glycosidase A (PNGase A) treatment were subjected to matrix-assisted laser desorption/Ionization time-of-flight (MALDI-TOF) and electrospray ionization-fourier transform mass spectrometry (ESI-FTMS) analysis. The MALDI-TOF-MS result showed that the full MS analysis of 12 N-linked glycans contains high-mannose and complex N-glycans. The high-mannose N-glycans obviously decreased while high-mannose N-glycan with glucose residues increased in osmogs (Figure 6b and Table S3). Then three of high-mannose N-glycans and Glc3Man7GlcNAc2 from MALD-MS spectra were further quantified using ESI-FTMS analysis. From the most abundant peak areas of full ESI-FTMS, in osmogs, the three high-mannose N-glycans, Man5GlcNAc2, Man6GlcNAc2 and Man7GlcNAc2 derived from the unique MALD-MS spectra were about 1/5, 1/4 and 1/4 of that in WT respectively, while high-mannose N-glycan with glucose residues, Glc3Man7GlcNAc2 increased about 5.3 folds (Figure 6c and Table S3). Moreover, the oligosaccharide Glc3Man8GlcNAc2, which could not be detected in WT was excessively accumulated in osmogs (Table S3). These results provided solid evidence for that OsMOGS activity is required for terminal glucose trimming of N-glycan, N-glycan formation and maturation.
[[File: Shijc-Os01g0921200-Fig2.png|right|thumb|200px|'' N-linked glycans analysis in wild-type (WT) and osmogs. (from reference <ref name="ref1" />).'']]
In order to clarify the relationship between the short-root phenotype and auxin signaling in osmogs seedlings, the auxin reporter DR5-GUS staining in 3-day-old WT and osmogs roots was observed. The staining in osmogs root tips and LRs, was much weaker than that in the WT (Figure 9a), and decreased free IAA contents in osmogs roots (Figure 9b) was consistent with the reduced DR5-GUS expression. To determine whether the lower auxin content was derived from impaired auxin transport, the rate of polar auxin transport in root tips of 3-day-old seedlings was measured. Interestingly, the IAA acropetal transport rate in the osmogs root was just half of that in the WT, and there also less inhibition by 1-naphthylphthalamic acid (NPA) on IAA acropetal transport was found in osmogs roots (Figure 9c), while basipetal IAA transport was almost not influenced in the tips of osmogs roots (Figure S5). These all indicated that the deficient auxin content was due to the decreased capacity for auxin transport in osmogs roots. To confirm whether alteration of auxin transport was involved in N-glycosylation of auxin transporters, the western blotting of two ABCB proteins, OsABCB2 and OsABCB14, was performed using OsABCB2 and OsABCB14- specific antibodies. The result clearly showed that the sizes of part of OsABCB2 and OsABCB14 decreased in osmogs roots and the smaller sizes were equal to the sizes of peptide-N-glycosidase F (PNGase F) treated OsABCB2 and OsABCB14 (Figure 9d), and suggested that involvement of OsMOGS in N-glycan processing was required for N-glycosylation of OsABCB proteins. The data demonstrated that the altered N-glycosylation of the OsABCB proteins led to an obstacle to auxin transport and abnormality of auxin signaling in osmogs roots.
[[File: Shijc-Os01g0921200-Fig3.png|right|thumb|200px|'' Analysis of auxin contents, auxin transport and glycosylation level of auxin transporters in WT and osmogs roots. (from reference <ref name="ref1" />).'']]
===Mutation===
[[File: Shijc-Os01g0921200-Fig4.png|right|thumb|200px|'' Map-based cloning of OsMOGS. (from reference <ref name="ref1" />).'']]
The mutant was named osmogs based on a mutation in OsMOGS (Figure 3). Compared with 7-day-old wild type (WT) plants, the osmogs plants showed retarded growth in post-embryonic roots (Figure 1a). Primary root (PR) and lateral root (LR) elongation of osmogs was inhibited dramatically and their length was approximately one-fourth and one-third of that in WT plants, respectively (Figure 1b,c). A mitotic marker reporter ProOsCYCB1;1-GUS <ref name="ref3" /> was introduced into the WT and osmogs calli. GUS staining of 5-day-old transgenic plants showed that intensity of cell division and size of the cell-dividing region had declined greatly in root tips of osmogs plants (Figure 1d), with lower cell division activity also observed in their LR primordia (Figure 1e). Longitudinal sections of the root tips of 3-day-old WT and osmogs seedlings showed root meristems of osmogs were much smaller than in the WT (Figure 1f). Moreover, cell length in the elongation zone of osmogs roots was only two-thirds of that in the WT (Figure 1g). The results clearly indicated that the shortened root phenotype of osmogs resulted from decreased cell division and elongation in the root.
[[File: Shijc-Os01g0921200-Fig5.png|right|thumb|200px|'' Phenotypic analysis of the osmogs mutant. (from reference <ref name="ref1" />).'']]
===Expression===
To examine the OsMOGS expression pattern, the total RNA from various tissues of 4-month-old WT seedlings, including flower, panicle, flag leaf, stem, stem base and root was extracted. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) showed that OsMOGS was expressed in all tissues and organs, with its stronger expression in the root than in the shoot (Figure 4a), and suggested that roles of OsMOGS in the developing root might be more important than in the shoot. The osmogs plants displayed severe defects in the root (Figures 1a and 2), leading us to monitor dynamic OsMOGS expression in roots at early developmental stages. Total RNA from different root sections of 1–5 days after germination (DAG) in WT seedlings was isolated. The qRT-PCR result showed that OsMOGS was expressed throughout the PR, with stronger expression in the rapidly growing root and sections near the root tip than in the mature root and sections (Figure 4b), and indicated that OsMOGS was expressed predominantly in root regions where cells were undergoing rapid division and elongation.
It has been predicted that the Arabidopsis GCS1/KNF possesses cytoplasmic N-terminus, ER-lumenal C-terminus and a transmembrane domain in between, but further experimental evidence is lacking <ref name="ref4" />. Transient expression of OsMOGS–sGFP (green fluorescent protein) in leaf epidermal cells of Nicotiana benthamiana was used to determine subcellular localization of OsMOGS. The green fluorescence was found predominantly in several widespread spots on reticulum-like structures (Figure 5a). To label clearly the reticulate ER network, the OsMOGS–sGFP was co-expressed transiently with ER marker ER-rb CD3-mcherry (red fluorescence protein, RFP) <ref name="ref5" />; the red fluorescence from RFP was also detected predominantly in punctate bodies distributed on the ER (Figure 5b). The highly overlapping GFP and RFP fluorescence signals were observed in the epidermal cells (Figure 5c), and indicated that the OsMOGS protein was localized in the ER.
[[File: Shijc-Os01g0921200-Fig6.png|right|thumb|200px|''OsMOGS expression profile. (from reference <ref name="ref1" />).'']]
==Labs working on this gene==
1. State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
2. Key Laboratory of Crop Germplasm Resources of Zhejiang Province, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
3. Department of Chemistry, Changwon National University, Changwon, Gyeongnam, 641-773, Korea
4. Complex Carbohydrate Research Center, The University of Georgia, Athens, Georgia, USA
5. Department of Biochemistry and PMBBRC, Gyeongsang National University, Jinju, Korea
6. State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
7. State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
==References==
<references>
<ref name="ref1">Wang, S., Xu, Y., Li, Z., Zhang, S., Lim, J.-M., Lee, K. O., Li, C., Qian, Q., Jiang, D. A. and Qi, Y. (2014), OsMOGS is required for N-glycan formation and auxin-mediated root development in rice (Oryza sativa L.). The Plant Journal, 78: 632–645. doi: 10.1111/tpj.12497 </ref>
<ref name="ref2">Lerouge, P., Cabanes-Macheteau, M., Rayon, C., Fischette-Lainé, A.C., Gomord, V. and Faye, L. (1998) N-glycoprotein biosynthesis in plants: recent developments and future trends. Plant Mol. Biol. 38, 31–48. </ref>
<ref name="ref3">Colón-Carmona, A., You, R., Haimovitch-Gal, T. and Doerner, P. (1999) Technical advance: spatio-temporal analysis of mitotic activity with a labile cyclin-GUS fusion protein. Plant J. 20, 503–508. </ref>
<ref name="ref4">Gillmor, C.S., Poindexter, P., Lorieau, J., Palcic, M.M. and Somerville, C. (2002) α-Glucosidase I is required for cellulose biosynthesis and morphogenesis in Arabidopsis. J. Cell Biol. 156, 1003–1013. </ref>
<ref name="ref5"> Nelson, B.K., Cai, X. and Nebenführ, A. (2007) A multicolored set of in vivo organelle markers for co-localization studies in Arabidopsis and other plants. Plant J. 51, 1126–1136. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0921200|
Description = Similar to Alpha-glucosidase I|
Version = NM_001051760.2 GI:297598204 GeneID:4327748|
Length = 8576 bp|
Definition = Oryza sativa Japonica Group Os01g0921200, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:41976801..41985376|
CDS = 41976801..41977151,41977608..41977681,41978032..41978283,41978515..41978689,41978831..41978917 ,41979033..41979101,41979226..41979322,41979598..41979680,41979961..41980068 ,41980206..41980381,41980509..41980616,41980709..41980782,41981080..41981205 ,41982243..41982310,41982518..41982667,41982752..41982802,41983266..41983322 ,41983412..41983558,41983652..41983743,41984104..41984213,41984316..41984379 ,41984471..41984620,41985142..41985376|
GCID = <gbrowseImage1>
name=NC_008394:41976801..41985376
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:41976801..41985376
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgagcggcggcggcggcagcagcagtgtccggcgacccgtagccgccgccaggagccgctcaggtccagagccggacgcgcgccgggcggccgccgccgccgccgccgccgccgcagcagcagcgcggcgccgtggccgcggcgaccatggccccctgcggctcatggaggtgagcccacggaacctcctccttgtagggactgcttccgtcgccctcctcgccgtcgccttcgtggtgtataccggcgtgtggcagggtaaggcggatggggaggtcgagacgcctctgcgcagggccgtgcgctccgtcacgccgcttgacgcgcccaggatgatggatctgcctcagttccaaggagatcacaaggaaagcttgtattggggtacctacaggccgaatgtatatcttggaattcgtgcaagaaccccgttgtctctaattgctgggataatgtggattggtgcaaagaatgggcaatactttcttcgtcatgtttgccaagattctgatgagcttagcacatatgggtggacagatcacaatgggagggattatggacatcaagtgttggttgatcatggcttgttgttgaccacgagtttcctgaaagagaaaggagagggtagcggttatggtggagattgggcagttcgattgaatgcgaagactgatgggccaagtttaagtgaagaccaagaaagcaccacacacctgtttttctacatcgcggatgaagcagggaactcaatcactatggattcgcatataccttcgtcaagaggtcatgttcttttggcatctggatcccgtgaggagattggtgattggaaagtctatttgagatctgaggaaaatttggaaattcacagagctggattcaaatcaattagtatgcacaatctaagtgacctagtacagcaagcccttgcgactaatgcaatgcaaagtgggaaccttaaccttccagacatggcagaagattcttcaaatgtaatagtatatcaggtttccatgaaacgttctgccgaagtcgacatagtcttcttgtcaggggccgcctcagaaaacccaatgattgaagagcgcattaacaggctaacaggtcctgttctgagcactcgtcttgaatcaaaacagaaggattttgaaaagagatatgaccaaattttcaatgcaaataataagattaatcccaaagaattatctgttggtgttgctgctttatcaaatcttcttggtggaattggctatttctatgggcagtcaaaaattgcacttccaaaaggttttacagcgattacacatcacactcaaacaaaatctaatgcttcaagagtttccttgcagcaaaaaaatggggataaatatatcccatattggccagctgcactatatacagctgtgcctagtcgctcattcttcccaaggggatttctatgggatgagggcttccatcagttagtcatttggcgctgggatgtgcatatatcgatggatataattggtcactggttagatctaataaatgcggatggatggattcctcgggagcaaatattaggagctgaagctttaagtaaagttcctgaggaatttgttctgcagtacccttccaatggaaatcccccaaccttatttcttgcactgcgtgatttggcaagtggaatacatgcaaaccagttttcagatgaggaatctgaaaagatatccactttccttaaaagggcttatgtaaggctgaactcttggtttcagtggttcaatagcacacaaacagggaaatacgaaggcaccttttattggcatggaagagacagcatggccaccagggagttgaatccgaagactttgacatctggtttggatgactatccacgggcatctcatcctaatgatgaagagcgccatgttgacctccggtgttggatgcttttagctacgaattgtatgtgctcaattgcagagtttcttaaaacagacagctctcttgagaaggattactacaagatgtcaaatcaactttcagattttgggatacttaacaagatgcacttggatgataaaaccggtgcctatttcgactatggtaaccacacagaaaaggttcgattgagatggtatgaagttagagagaatgatgttatgagacgagagcttttgcgtgaaacattacaaccccctcagctgcaattagtacctcatgtcggttatgtcagcatgttccctttcatgatgggggccattccacctgaatcatgggttcttgagaagcagcttgatcttatatcaaatagctctatcctgtggacaaattacggacttcggtcactttctcgaacaagttcaatatatatgaagcgcaacactgagcatgatcccccatattggagaggtgccatttggataaacatgaactacatgattctttcaggactacaccactatgcacatgaggatggtccatacaaggacagggcaaaggaactgtatgatgagctaagatcaaacctgatcaggaacatcgtgaagaattaccatgaaactgggttcttctgggaaaactatgaccagaagaacaaaggaaagggtaagggtgcgaggtcctttactggatggacttcgcttgttgttcttatcatgggcgagtcctacccgaccctacatagaagagatgactacccaaatctgtcatggttctcgtggatcaatatttgcctgagccttcgagtgaactttgcttgctacttctgcaagcatatgatctcactctctaatgcaagcaaagtaccggaagattatcgtgatcgtactgcagcagtaacagcacgatcttctgtcatgaaaacggatactgctaatacgacaaactcaatccctaccatctgtcccgataaaaactaa</cdnaseq>|
AA = <aaseq>MSGGGGSSSVRRPVAAARSRSGPEPDARRAAAAAAAAAAAAARR RGRGDHGPLRLMEVSPRNLLLVGTASVALLAVAFVVYTGVWQGKADGEVETPLRRAVR SVTPLDAPRMMDLPQFQGDHKESLYWGTYRPNVYLGIRARTPLSLIAGIMWIGAKNGQ YFLRHVCQDSDELSTYGWTDHNGRDYGHQVLVDHGLLLTTSFLKEKGEGSGYGGDWAV RLNAKTDGPSLSEDQESTTHLFFYIADEAGNSITMDSHIPSSRGHVLLASGSREEIGD WKVYLRSEENLEIHRAGFKSISMHNLSDLVQQALATNAMQSGNLNLPDMAEDSSNVIV YQVSMKRSAEVDIVFLSGAASENPMIEERINRLTGPVLSTRLESKQKDFEKRYDQIFN ANNKINPKELSVGVAALSNLLGGIGYFYGQSKIALPKGFTAITHHTQTKSNASRVSLQ QKNGDKYIPYWPAALYTAVPSRSFFPRGFLWDEGFHQLVIWRWDVHISMDIIGHWLDL INADGWIPREQILGAEALSKVPEEFVLQYPSNGNPPTLFLALRDLASGIHANQFSDEE SEKISTFLKRAYVRLNSWFQWFNSTQTGKYEGTFYWHGRDSMATRELNPKTLTSGLDD YPRASHPNDEERHVDLRCWMLLATNCMCSIAEFLKTDSSLEKDYYKMSNQLSDFGILN KMHLDDKTGAYFDYGNHTEKVRLRWYEVRENDVMRRELLRETLQPPQLQLVPHVGYVS MFPFMMGAIPPESWVLEKQLDLISNSSILWTNYGLRSLSRTSSIYMKRNTEHDPPYWR GAIWINMNYMILSGLHHYAHEDGPYKDRAKELYDELRSNLIRNIVKNYHETGFFWENY DQKNKGKGKGARSFTGWTSLVVLIMGESYPTLHRRDDYPNLSWFSWINICLSLRVNFA CYFCKHMISLSNASKVPEDYRDRTAAVTARSSVMKTDTANTTNSIPTICPDKN</aaseq>|
DNA = <dnaseqindica>1..351#808..881#1232..1483#1715..1889#2031..2117#2233..2301#2426..2522#2798..2880#3161..3268#3406..3581#3709..3816#3909..3982#4280..4405#5443..5510#5718..5867#5952..6002#6466..6522#6612..6758#6852..6943#7304..7413#7516..7579#7671..7820#8342..8576#atgagcggcggcggcggcagcagcagtgtccggcgacccgtagccgccgccaggagccgctcaggtccagagccggacgcgcgccgggcggccgccgccgccgccgccgccgccgcagcagcagcgcggcgccgtggccgcggcgaccatggccccctgcggctcatggaggtgagcccacggaacctcctccttgtagggactgcttccgtcgccctcctcgccgtcgccttcgtggtgtataccggcgtgtggcagggtaaggcggatggggaggtcgagacgcctctgcgcagggccgtgcgctccgtcacgccgcttgacgcgcccaggatgatggatctgcctcaggtgatgaccattaagttcgtcgcattgtttcttcaagcctccaatgctctgtgaaatagctttagattacaatctcgcgcggttgtagtctattagtgcgcttctgcttaatctgctgcaacagtagtagttaagaacttaattgaattgtgtaaaaatgctaggagaataacggaatcgaccactgcttgtttggattttacaagggctgctttatgtttgaaccacatagtggatacgactggtttgtcataggtaaaatgaatatgaattgtgcatagccgcaaatgtcatctgagctaggacagacgacctaaaatgtaccagtttctgttaaatatcctcctgtaagctagttctgattgatttatacgtaacatcatgttattccatactgttgagtttggatggtaattatggttagctttctgatggctcatagttgactgtttacagttccaaggagatcacaaggaaagcttgtattggggtacctacaggccgaatgtatatcttggaattcgtgcaaggtgcttaactttgatcttccccttgattcttatagcgtgctaatttaagcaattcagttctcttagtccaccatggcatgctagaaatatgcagggaagttcatattgctagcatcatatgttttttatgctttaaacacttctatggagttttgttcccatttgcttagtccatatgtgtcgagaacaaagatgttgttatatttcctgcttgattccttgaatgcgtattgtttttgtttctggtttagaatgttgccaccttaccacctcatagttggaattctattgctgtatgatgatgatatggtggcactctcaacttcttgctaatagtatttctatttcagaaccccgttgtctctaattgctgggataatgtggattggtgcaaagaatgggcaatactttcttcgtcatgtttgccaagattctgatgagcttagcacatatgggtggacagatcacaatgggagggattatggacatcaagtgttggttgatcatggcttgttgttgaccacgagtttcctgaaagagaaaggagagggtagcggttatggtggagattgggcagttcgattgaatgcgaagactgatgggtaagtgtatatttgtcagttacaaaactgaaaagttttttttactgaagagatgtaaacaattttccagttttaagtacaaggtgaaaagaccaataaattttactggattgactttttcattccctattcacaaaccaggatgatattaacaatcatttatttgctacctatataaagttaccaaaggaaccaaaagaaatttattccatgtagttatacttaatttaggccaagtttaagtgaagaccaagaaagcaccacacacctgtttttctacatcgcggatgaagcagggaactcaatcactatggattcgcatataccttcgtcaagaggtcatgttcttttggcatctggatcccgtgaggagattggtgattggaaagtctatttgagatctgaggtagcatatttcagtatgctcgtcacattgttgctactatttttttatttttctattttactcgctactggtatatagcattacaattccatataaactgatgttaatattgacatgtacagaactgtgtttttctcgcaggaaaatttggaaattcacagagctggattcaaatcaattagtatgcacaatctaagtgacctagtacagcaagcccttgcgactaatgtatgtcttagctccttacatttacctttttttttggggggggggtcaaaaacaagtctcagtttttttttatgaactcaagttgccatttagctgctcctgtgtacctttctaggcaatgcaaagtgggaaccttaaccttccagacatggcagaagattcttcaaatgtaatagtatatcaggtgcgtcaaagatgaaaaagaaagttattctgtcaatatgagaatccaatgagtcaacgtacacccagatttaaatagtgttctcttccggcattgtgatctatgctctctctcatcttcacaggtttccatgaaacgttctgccgaagtcgacatagtcttcttgtcaggggccgcctcagaaaacccaatgattgaagagcgcattaacaggctaacaggtgactctactgcatagctcatactgcatggagataggatatgtgattttccttttgttctattcattttgggatggcaatcatgccatagataccatgtcctccataatttggtatgcataggctcttgaccttttcttttgctgccttgcatttggtatccattccttttttttccttgcctgcatcttttccttctgttgaacctgaaattcagagatgttgaaagcaatatttcatcttgcttgttgattttatatcactaatgttgccaggtcctgttctgagcactcgtcttgaatcaaaacagaaggattttgaaaagagatatgaccaaattttcaatgcaaataataaggtgtgatctcttggatgagctttgtagttttgacaatcttcttttagcagtctatacagttgttttcttctcattatgctcctgttcctatgattatataaaattgctattgcgtataaatgatagtgtccttgccattttgttcaagtctgtacacttttcatagttgaaagaacctttaaaagctatttttcccctggaagataagtagtgtgactggctgcataatcagaagaaagtttgtgatggagcagttgatattattgtttcactgatgcagattaatcccaaagaattatctgttggtgttgctgctttatcaaatcttcttggtggaattggctatttctatgggcagtcaaaaattgcacttccaaaaggttttacagtaagttttagagtgttacctgataattagatccttttcctaatagctattgcagctgaactttatgctatctgatttagtcccccccccccttcttattactgtgctatcttttgtagatctgatataaatcctaggcgattacacatcacactcaaacaaaatctaatgcttcaagagtttccttgcagcaaaaaaatggggataaatatatcccatattggccagctgcactatatacagctgtgcctagtcgctcattcttcccaaggggatttctatgggatgagggcttccatcagttagtcatttggtaagcatttcatcgatcttgatgtgtagcgcagggcttctgccactatatcatcactcgctttttttttgaatctgtgctggtattattgctgcttgtttaacacatccttgatggtgatgtataggcgctgggatgtgcatatatcgatggatataattggtcactggttagatctaataaatgcggatggatggattcctcgggagcaaatattaggagctgaagctttaaggtggttcccctggcgagcaatgaaccattgtcatatctagctatgagtttagagtgtcagttcttatataatctgtttttacatttctgcagtaaagttcctgaggaatttgttctgcagtacccttccaatggaaatcccccaaccttatttcttgcactgcgtggtgagacaatgctttcttccttgctcttcactgtcatgacacattaaatgcagtatagcagtactgttgagaatcaaagtatctaaattatctgacttgagtatatctcagaaaatcaagttaccacaaaaacattattttgcactgttttcagtgcgtttgtctcaaatttataatattgagaattttcacgctgtctgcgattttggtttagcacaacaaggttgctactgtatggaagtgcataaactgtgatcgaacatcctattgagtttaacttgccactttttggtacagatttggcaagtggaatacatgcaaaccagttttcagatgaggaatctgaaaagatatccactttccttaaaagggcttatgtaaggctgaactcttggtttcagtggttcaatagcacacaaacaggtgagttaagttatgacattttatggtccatactatttattaggaacttggtaaccaatgatgcttgattgcttgtgaataactgcagacagaataacctgccctctttctggcaagtatggaatttgtatggattggatcttcactttaatttaggcctattattatgttaattaatgttcagaaaatacatgcctgaacacatgaacatgatgagccattaatatcttacttttcagtaaaaaaaagggtgatattttggggatgcatgcagtcagtgtatctatttatagctttataaatattttgattggatatacaaatatgacatgttcacattttatgaatggtttgattggataaaagagtactatcataaattatagttttatcattttttaagtgtactatcatatttgtgatttgtgaataggattgtgaccagcaaaattttctggccgttttgtcttgcagaagctactagtttttgcatcagttttggatgatgttagtcttcagatatccctggcactctatattttacatacactcaaggcagtgcatgctatatgaaataataattttgatcgtcaacttattcagtagtcgttgtttcactcatttactgttcctggacgagagagttatgaacccaaattcctgactctttagaaagtaactttaattcactgccacccaagaggaaccatgcaattgagatgttcaaacttacttagcgaagggaataaccttctgctcctgtgctaagcaaaatttagcttagtgtcattgcaaactatagccaccattccacatagctagaaattatgcaattactgttatctttaccttttccatcaccttgttgattgtttttttcctttttggcggacattgttgattgttatgtcaatgaacattggctgtactttccatgtgtggaataaccaatatttttgtttgtcatgccaacttttttcaccttcgacttatctatcctatatagcttctttgactttcaaacttgttttttttagggaaatacgaaggcaccttttattggcatggaagagacagcatggccaccagggagttgaatccgaaggttttggaacacttcatagttgctttcttccacagactaattggtcccaaataatagcaaaagaaatttgtttttgagcttttgtcatgcctacattacagtttatgtttttgagcttttgtcatgcctacgctacagtttcttgccttgtctttctatgtcatttctactaaccgttcactcctgatgttgctgactactctacagactttgacatctggtttggatgactatccacgggcatctcatcctaatgatgaagagcgccatgttgacctccggtgttggatgcttttagctacgaattgtatgtgctcaattgcagagtttcttaaaacagacagctctcttgagaaggtactgcagagtgaatggactgtgccttatgctttgtctcagcctttggttctcttgaaaaaaatctgtcttgaacttctacaggattactacaagatgtcaaatcaactttcagattttgggatacttaacaaggtattgctctgagagttctgactgtttcttcttgttctgagcttttgtcctttttaggtcagatagatacttaatctgcatatcaatccaccaatggctgctacattttggatataattaatggcttgatactccaacactaacacttgcgcctataacaataatggtttcttatattaacattttacatactagacgaagctaatagtttttgttttgtgcttggttttctgttcgtgatcattgcaatattatggttacatacttatatatgccataaagataataaactttgcataaacgcctgctgtgtcaggaagtcttacttttgatcaaacgttcaaagatcatatagcaactaaaatggtttttatcaattgccgccaatcattttgtgtcacaggaagggttttgatggtcacatttatcctatagtaatttgaaagtattggcatttttacagatgcacttggatgataaaaccggtgcctatttcgactatggtaaccacacagaaaaggtctctcttgcagttcctctatcttgccatcttgcctttcggacatgattcataactttcaaactctgatgacaatattattcttacaggttcgattgagatggtatgaagttagagagaatgatgttatgagacgagagcttttgcgtgaaacattacaaccccctcagctgcaattagtacctcatgtcggttatgtcagcatgttccctttcatgatgggggccattccacctgtatgctctttacctacatatacttgttctcacttttaccaatccagtgatgctcatcccctaaagtattaactaccattcaactctgttcaggaatcatgggttcttgagaagcagcttgatcttatatcaaatagctctatcctgtggacaaattacggacttcggtcactttctcgaacaaggtatatataaagataataactcatttaacctgaatcatgggcaaaatttcctacttgatctccagcaacctaaacttgcatcaagacgattagttatgaagctgatacttctggaataaatgagatatttcatttcatttatttatttgaaaagtgtaatttctttagaggatccaatactcaattggtaagacttgtcccgggggatgaagtgggtataagtctgcattgcccccaacacctaaatgtttatcgtttgagcttgttaatgaattaaaatcaacataacaatgtatacatagcattattgtttggtcttttggttactctgatctgaattatctgttgtccatggtccagttcaatatatatgaagcgcaacactgagcatgatcccccatattggagaggtgccatttggataaacatgaactacatgattctttcaggactacaccactatgcacatggtaaactctataacagatgctgctaaacaactattcagcttttacccttctgtaaattttactgtttgcacgatgatctaataacattgttctgctctgaagaggatggtccatacaaggacagggcaaaggaactgtatgatgagctaagatcaaacctgatcaggtatatccctctctcttccctaagctgaataaaatagttaaattgcagcctctttaatagattgctgttgctacttttgtgcttcttacaggaacatcgtgaagaattaccatgaaactgggttcttctgggaaaactatgaccagaagaacaaaggaaagggtaagggtgcgaggtcctttactggatggacttcgcttgttgttcttatcatgggcgagtcctacccgaccctacataggtaagcgaatattccaacagagaaacaacacaacaaatcccaattggaaatttggaatggaagacctgaacatgatttagctcgattttgaccccaaagaaaaaccctcggaaaaactttgatcgtgggggttttgaacaataaccggtgattactccgtgctgcatatatggtttgtgccttcttgagacagtagttacgtagctaatgataacatttatcctagattctgtaactagtgtctcgataaacattttttttggggctttgagatccctttggaggagcaaagtatgcactagaatcgagaggtaatgaaattctaacgtaatctgcccatgtctacgcgttgttggcttcttgctgcagtctgtagcgttggccttgtgttaaacaatttttatgttaagaaaagaaacttgatcacggggattcagggagctgtaacctgtaaggtccatctacggctaatggagtaatagctcggcactaatacagttcttaccgtttctgccatgaagaagagatgactacccaaatctgtcatggttctcgtggatcaatatttgcctgagccttcgagtgaactttgcttgctacttctgcaagcatatgatctcactctctaatgcaagcaaagtaccggaagattatcgtgatcgtactgcagcagtaacagcacgatcttctgtcatgaaaacggatactgctaatacgacaaactcaatccctaccatctgtcccgataaaaactaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001051760.2 RefSeq:Os01g0921200]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

Os01g0169800

2014-12-27T13:23:30Z

Shijc:

FIB plays a pivotal role in IAA biosynthesis in rice and that auxin biosynthesis, transport and sensitivity are closely interrelated. <ref name="ref1" />

==Annotated Information==
===Function===
[[File: Shijc-Os01g0169800-Fig1.png|right|thumb|200px|'' Measurement of auxin content and auxin responses in fib. (from reference <ref name="ref1" />).'']]
IAA content in fib-1 was reduced to about half of the wild-type in both shoot and root apices. FIB plays a pivotal role in rice IAA biosynthesis similar to that of TAA1 and VT2 in Arabidopsis and maize, respectively. The application of IAA enhanced lateral and crown root formation in a dose-dependent manner in both the wild-type and fib-1. However, the abnormal phenotypes of the fib mutant could not be fully rescued. Although the fib-1 seminal root was about three times longer than the wild-type under IAA-free conditions, the application of IAA resulted in a shorter fib-1 seminal root than the wild-type. Root growth inhibition was first observed at a dose as low as 0.003 μm IAA in fib-1, while the growth of wild-type roots was inhibited at doses higher than 0.09 μm IAA. These results indicate that fib is more sensitive to IAA than the wild-type. It is well known that NAA and 2,4-D are good substrates for auxin efflux and influx carriers, respectively <ref name="ref2" />. fib-1 also showed higher sensitivity to 2,4-D than the wild-type, but a higher sensitivity was not observed in NAA treatment. These different sensitivities of fib to IAA, 2,4-D and NAA indicated the possibility that fib is defective in auxin polar transport.
[[File: Shijc-Os01g0169800-Fig2.png|right|thumb|200px|'' Analysis of polar auxin transport (PAT) activity in fib and PAT inhibition by naphthyl-phtalamic acid (NPA) treatment. (from reference <ref name="ref1" />).'']]
In the fib-1 inflorescence stem (rachis), basipetal auxin transport decreased to ~10% of the wild-type, and acropetal auxin transport was suppressed in the roots to ~28% of the wild-type. Therefore, it is clear that PAT activity is reduced in both above- and below-ground parts of the fib-1 mutant. To test whether fib phenotypes were mimicked by PAT inhibition in the wild-type. Wild-type plants treated with NPA showed abnormal phyllotaxis, disrupted vascular tissue differentiation, decreased crown and lateral roots and defective root gravitropism. All of these abnormalities were observed in fib. Thus, the fib phenotypes are considered to be due, at least in part, to defects in PAT. The application of 7.29 μm IAA alone caused a 42% inhibition of wild-type seminal root growth, while simultaneous application of IAA and NPA resulted in more severe inhibition (68%). This result indicated that NPA application, which resulted in reduced PAT activity, enhanced sensitivity to auxin.

===Mutation===
[[File: Shijc-Os01g0169800-Fig3.png|right|thumb|200px|'' Phenotypes of fib plants. (from reference <ref name="ref1" />).'']]
In the vegetative shoots, fib showed an extremely dwarf phenotype together with narrow and adaxially rolled short leaves. The leaf blade was highly bent at the lamina joint. In the reproductive phase, fib formed small inflorescences, about half of the wild-type, and set a reduced number of spikelets, about a tenth of the wild-type. In flowers, partial or complete homeotic conversion of lodicules (equivalent to petals) into stamens occurred frequently. In roots, fib plants lacked gravitropism and developed the seminal root two- to three-fold longer than the wild-type, but formed fewer crown and lateral roots than the wild-type. Cross-sections of leaf primordia revealed a significantly reduced number of vascular bundles. Abnormal development was also observed in the transverse veins of the leaf blade, such as aberrant orientation and fragmentation. In addition, fib plants showed aberrant phyllotaxy that deviated from the normal distichous one. These phenotypes suggested the possibility that fib mutants were defective in auxin-related processes as many of these phenotypes resembled those found in auxin-related mutants of rice and Arabidopsis <ref name="ref3" /><ref name="ref4" /><ref name="ref5" /><ref name="ref6" /><ref name="ref7" /><ref name="ref8" />.

===Expression===
[[File: Shijc-Os01g0169800-Fig4.png|right|thumb|200px|'' Analysis of FIB expression. (from reference <ref name="ref1" />).'']]
FIB was expressed in all organs examined, including the embryo, shoot apex, leaf, inflorescence, flower and root, throughout the life cycle, suggesting a fundamental function for FIB in rice development. This expression pattern corresponded to the pleiotropic phenotypes of fib mutants. In the vegetative shoot apex, FIB was expressed predominantly in parenchymatous cells of vascular tissues and epidermal cells of leaf primordia. These signals were detected from the incipient stage of the leaf primordia and appeared clearly in the P3 leaf primordium. Tao et al. <ref name="ref9" /> reported the expression pattern of TAA1 in developing Arabidopsis embryos, in which the signals were detected in the developing vasculature as well as in the L1 layer of the presumptive shoot apical meristem and the adaxial epidermis of the developing cotyledons. The similar expression pattern between FIB and TAA1 supported the idea that FIB had functional similarity to TAA1.

==Labs working on this gene==
1. Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo, Japan
2. Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan
3. Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
4. School of Agricultural Regional Vitalization, Kibi International University, Minamiawaji, Japan
5. National Institute for Basic Biology, Okazaki, Japan
6. Maebashi Institute of Technology, Maebashi, Japan
7. National Institute of Agrobiological Sciences, Tsukuba, Japan

==References==
<references>
<ref name="ref1"> Yoshikawa, T., Ito, M., Sumikura, T., Nakayama, A., Nishimura, T., Kitano, H., Yamaguchi, I., Koshiba, T., Hibara, K.-I., Nagato, Y. and Itoh, J.-I. (2014), The rice FISH BONE gene encodes a tryptophan aminotransferase, which affects pleiotropic auxin-related processes. The Plant Journal, 78: 927–936. </ref>
<ref name="ref2">Delbarre, A., Muller, P., Imhoff, V. and Guern, J. (1996) Comparison of mechanisms controlling uptake and accumulation of 2,4-dichlorophenoxy acetic acid, naphthalene-1-acetic acid, and indole-3-acetic acid in suspension-cultured tobacco cells. Planta, 198, 532–541. </ref>
<ref name="ref3">Vernoux, T., Kronenberger, J., Grandjean, O., Laufs, P. and Traas, J. (2000) PIN-FORMED 1 regulates cell fate at the periphery of the shoot apical meristem. Development, 127, 5157–5165. </ref>
<ref name="ref4">Scarpella, E., Marcos, D., Friml, J. and Berleth, T. (2006) Control of leaf vascular patterning by polar auxin transport. Genes Dev. 20, 1015–1027. </ref>
<ref name="ref5">Bainbridge, K., Guyomarc'h, S., Bayer, E., Swarup, R., Bennett, M., Mandel, T. and Kuhlemeier, C. (2008) Auxin influx carriers stabilize phyllotactic patterning. Genes Dev. 22, 810–823. </ref>
<ref name="ref6">Kitomi, Y., Ogawa, A., Kitano, H. and Inukai, Y. (2008) CRL4 regulates crown root formation through auxin transport in rice. Plant Root, 2, 19–28. </ref>
<ref name="ref7">Křeček, P., Skůpa, P., Libus, J., Naramoto, S., Tejos, R., Friml, J. and Zažímalová, E. (2009) The PIN-formed (PIN) protein family of auxin transporters. Genome Biol. 10(12), 249. </ref>
<ref name="ref8">Mei, Y., Jia, W.J., Chu, Y.J. and Xue, H.W. (2012) Arabidopsis phosphatidylinositol monophosphate 5-kinase 2 is involved in root gravitropism through regulation of polar auxin transport by affecting the cycling of PIN proteins. Cell Res. 22, 581–597. </ref>
<ref name="ref9">Tao, Y., Ferrer, J.L., Ljung, K. et al. (2008) Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell, 133(1), 164–176. </ref>
</references>

==Structured Information==
{{JaponicaGene|
GeneName = Os01g0169800|
Description = Allinase, C-terminal domain containing protein|
Version = NM_001048670.1 GI:115434753 GeneID:4325198|
Length = 1563 bp|
Definition = Oryza sativa Japonica Group Os01g0169800, complete gene.|
Source = Oryza sativa Japonica Group

ORGANISM Oryza sativa Japonica Group
Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
Spermatophyta; Magnoliophyta; Liliopsida; Poales; Poaceae; BEP
clade; Ehrhartoideae; Oryzeae; Oryza.
|
Chromosome = [[:category:Japonica Chromosome 1|Chromosome 1]]|
AP = Chromosome 1:3576473..3578035|
CDS = 3576989..3577173,3577476..3577795,3577895..3578034|
GCID = <gbrowseImage1>
name=NC_008394:3576473..3578035
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:3576473..3578035
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>ccaaagaccggcaatggcaggacggtccatgacctggcctactactggcctcagtacacccccatcaccaagcgtgcttcccatgacatcatgctcttcaccgtctccaagagcaccggccatgccgggaccaggatcgggtgggcgttggtgaaggaccgggcgatcgcgaggaagatgacgaagtttgtggagctgaacacgatcggggtgtccaaggactcgcagatgcgggcggccaaggtgctcgccgccgtctccgacggctacgagcggcggccggagcagacgaaagagacgatgaccactcctcttcgcctgttcgactttggtcgacgcaagatggtggagcggtggagcatgctccgcgctgctgccgccgcctccggcatcttcagcctcccggaggagacctccggcttctgcaacttcaccaaggagaccgccgcgaccaaccctgcgttcgcgtggctgcggtgcgatagggaggatgtggaggattgtgcggggtttctccgtgggcacaagatcctgacgaggagcggggcgcagttcggggcggatgcgaggtacgtgcgggtgagcatgctcgacagggacgacgcgttcgacatcttcatcaaccgcctctcgtcgctcaagtga</cdnaseq>|
AA = <aaseq>PKTGNGRTVHDLAYYWPQYTPITKRASHDIMLFTVSKSTGHAGT RIGWALVKDRAIARKMTKFVELNTIGVSKDSQMRAAKVLAAVSDGYERRPEQTKETMT TPLRLFDFGRRKMVERWSMLRAAAAASGIFSLPEETSGFCNFTKETAATNPAFAWLRC DREDVEDCAGFLRGHKILTRSGAQFGADARYVRVSMLDRDDAFDIFINRLSSLK</aaseq>|
DNA = <dnaseqindica>863..1047#241..560#2..141#tccaaagaccggcaatggcaggacggtccatgacctggcctactactggcctcagtacacccccatcaccaagcgtgcttcccatgacatcatgctcttcaccgtctccaagagcaccggccatgccgggaccaggatcgggtatgtagatagagcttttcggtcgaactggttggtgcatgaaacacggtcgttttgagtagtgtaaactgagttgaatgtttttgtgtgtgtgtgaaggtgggcgttggtgaaggaccgggcgatcgcgaggaagatgacgaagtttgtggagctgaacacgatcggggtgtccaaggactcgcagatgcgggcggccaaggtgctcgccgccgtctccgacggctacgagcggcggccggagcagacgaaagagacgatgaccactcctcttcgcctgttcgactttggtcgacgcaagatggtggagcggtggagcatgctccgcgctgctgccgccgcctccggcatcttcagcctcccggaggagacctccggcttctgcaacttcaccaaggagaccgccgcgaccaaccctggtatgatttgatggataagatttttattcctcaagagggcatcccctattgtttacatgacatctaaatagttattaaaatttttttaaaaaaatgacaatataaattaatatgaaatatatcactctataaacatgtaagattaaattcagcttttaccagatgaaaaaaaaataaattaaactgaaaatagttatcatacatccacatctatatttattatttttgtggatgttacctcgatctcattggctttgctcatcgtatcaatggcggtgtgccggtgtggatgtggtttgcagcgttcgcgtggctgcggtgcgatagggaggatgtggaggattgtgcggggtttctccgtgggcacaagatcctgacgaggagcggggcgcagttcggggcggatgcgaggtacgtgcgggtgagcatgctcgacagggacgacgcgttcgacatcttcatcaaccgcctctcgtcgctcaagtgaaagaagacggcggagagagagaggacgctgcagcgtgttcgtccgtgcgctagcaagcaaagcatgcccatgactcatgagagcatgagtagaaccgttaactgtgtatctgtatcagtatttggagagcctttttggtagagcttcagagcataaccaaacggtttcagctttactcgaaatgggagtgaggttgattgaagtgctatcacagaatgatctagagatgtagagttggatttagactattttacagctacactttagaaccaactcttgaagttaaatttgtaagttgaagtcctgccaaataggttctcagtagtagtagtaggtagaagaagaggagcttgcttttctctagcttttctttttctcttaaatatttgtttctcgatgttgtgttttatggttaagaatggcctgcaatgtagatcagtgcctgcgtgatttcacatacggaaaataaataaataaatgttcttgttcttccttttttggaagatctaatgtttc</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001048670.1 RefSeq:Os01g0169800]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Shijc-Os03g0332400-Fig4.png

2014-12-27T13:22:27Z

Shijc: A binuclear metal centre is essential for OsGLYII-2 activity.

A binuclear metal centre is essential for OsGLYII-2 activity.

File:Shijc-Os03g0332400-Fig3.png

2014-12-27T13:22:08Z

Shijc: Expression analysis and subcellular localization of OsGLYII-2.

Expression analysis and subcellular localization of OsGLYII-2.

File:Shijc-Os03g0332400-Fig2.png

2014-12-27T13:21:55Z

Shijc: Comparison of various growth and yield parameters of wild-type (WT) and OsGLYII-2 ectopically expressing tobacco plants, continuously grown under saline conditions.

Comparison of various growth and yield parameters of wild-type (WT) and OsGLYII-2 ectopically expressing tobacco plants, continuously grown under saline conditions.

File:Shijc-Os03g0332400-Fig1.png

2014-12-27T13:21:38Z

Shijc: Transgenic plants ectopically expressing OsGLYII-2 maintained physiological balance under salinity stress.

Transgenic plants ectopically expressing OsGLYII-2 maintained physiological balance under salinity stress.

File:Shijc-Os06g0706400-Fig6.png

2014-12-27T10:20:55Z

Shijc: OsPTR9 expression is regulated by light and N source.

OsPTR9 expression is regulated by light and N source.

File:Shijc-Os06g0706400-Fig5.png

2014-12-27T10:18:38Z

Shijc: Expression analysis of OsPTR9.

Expression analysis of OsPTR9.

File:Shijc-Os06g0706400-Fig4.png

2014-12-27T10:18:24Z

Shijc: Subcellular localization of OsPTR9-eGFP fusion protein.

Subcellular localization of OsPTR9-eGFP fusion protein.

File:Shijc-Os06g0706400-Fig3.png

2014-12-27T10:18:03Z

Shijc: Phenotypes of rice plants with altered expression of OsPTR9.

Phenotypes of rice plants with altered expression of OsPTR9.

File:Shijc-Os06g0706400-Fig2.png

2014-12-27T10:17:48Z

Shijc: Root architecture is affected by altered expression of OsPTR9.

Root architecture is affected by altered expression of OsPTR9.

File:Shijc-Os06g0706400-Fig1.png

2014-12-27T10:14:39Z

Shijc: The effect of OsPTR9 on the formation of roots.

The effect of OsPTR9 on the formation of roots.

File:Shijc-Os01g0169800-Fig4.png

2014-12-27T07:12:45Z

Shijc: Analysis of FIB expression.

Analysis of FIB expression.

File:Shijc-Os01g0169800-Fig3.png

2014-12-27T07:12:29Z

Shijc: Phenotypes of fib plants.

Phenotypes of fib plants.

File:Shijc-Os01g0169800-Fig2.png

2014-12-27T07:12:13Z

Shijc: Analysis of polar auxin transport (PAT) activity in fib and PAT inhibition by naphthyl-phtalamic acid (NPA) treatment.

Analysis of polar auxin transport (PAT) activity in fib and PAT inhibition by naphthyl-phtalamic acid (NPA) treatment.

File:Shijc-Os01g0169800-Fig1.png

2014-12-27T07:11:57Z

Shijc: Measurement of auxin content and auxin responses in fib.

Measurement of auxin content and auxin responses in fib.

File:Shijc-Os10g0513200-Fig4.png

2014-12-27T05:52:56Z

Shijc: Rooted phylogenetic tree of sub-group II NIP proteins and their close relatives inA. thaliana (At), Lotus japonicus (Lj), grape (Vv), rice (Os), sorghum (Sb) and maize (Zm).

Rooted phylogenetic tree of sub-group II NIP proteins and their close relatives inA. thaliana (At), Lotus japonicus (Lj), grape (Vv), rice (Os), sorghum (Sb) and maize (Zm).

File:Shijc-Os10g0513200-Fig3.png

2014-12-27T05:52:35Z

Shijc: Subcellular localization of GFP–OsNIP3;1.

Subcellular localization of GFP–OsNIP3;1.

File:Shijc-Os10g0513200-Fig2.png

2014-12-27T05:52:18Z

Shijc: Growth defect of OsNIP3;1 RNAi plants under boron-deficient conditions.

Growth defect of OsNIP3;1 RNAi plants under boron-deficient conditions.

File:Shijc-Os10g0513200-Fig1.png

2014-12-27T05:52:02Z

Shijc: Altered boron distribution in shoots of OsNIP3;1 RNAi plants.

Altered boron distribution in shoots of OsNIP3;1 RNAi plants.

File:Shijc-Os01g0921200-Fig6.png

2014-12-26T16:39:42Z

Shijc: OsMOGS expression profile.

OsMOGS expression profile.

File:Shijc-Os01g0921200-Fig5.png

2014-12-26T16:39:27Z

Shijc: Phenotypic analysis of the osmogs mutant.

Phenotypic analysis of the osmogs mutant.

File:Shijc-Os01g0921200-Fig4.png

2014-12-26T16:39:09Z

Shijc: Map-based cloning of OsMOGS.

Map-based cloning of OsMOGS.

File:Shijc-Os01g0921200-Fig3.png

2014-12-26T16:38:22Z

Shijc: Analysis of auxin contents, auxin transport and glycosylation level of auxin transporters in WT and osmogs roots.

Analysis of auxin contents, auxin transport and glycosylation level of auxin transporters in WT and osmogs roots.

File:Shijc-Os01g0921200-Fig2.png

2014-12-26T16:38:07Z

Shijc: N-linked glycans analysis in wild-type (WT) and osmogs.

N-linked glycans analysis in wild-type (WT) and osmogs.