Please input one-sentence summary here.

==Annotated Information==
===Function===
*OsERF3 (Os01g0797600), is AP2 domain-containing protein, it is found to be significantly up-regulated in both genotypes under cold stress.<ref name="ref1" />
*OsERF3 (Os01g0797600) belongs to class II ERFs with a conserved EAR-motif (DLNRPPP) at the C terminal (Nakano et al. 2006). In rice, OsERF3 participated in the resistance to disease and the herbivore-induced defense responses via mediating different hormone pathways (Luet al. 2011).We also found that OsERF3 negatively
affected ethylene production and drought tolerance in rice(Wan et al. 2011). However, little is known about whether its EAR motif is involved in the regulation of ethylene synthesis and drought response. Here, we generated transgenic rice overexpressing full-length (OE) and the mutation of OsERF3 with the A680/C substitution (mEAR), respectively. The phenotypic analyses suggested that mEAR lines showed better drought tolerance and more ethylene emission than those of OE lines and wild type (WT) plants. At the transcriptional level, the substitution of Leu/Ala disrupted the repression of ACO2 and ACS6 by OsERF3 in mEAR lines. Moreover, ACS2 was significantly up-regulated in mEAR lines compared with that in WT plants. Taken together, our results indicate that the EAR motif is required for OsERF3 to repress the expression of ethylene biosynthesis genes, deepening our understanding of the regulatory function of ERF proteins involved in ethylene biosynthesis and stress response.<ref name="ref2" />
*OsERF3 is a transcriptional repressor with an ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motif (F/LDLNxxP), which transcriptionally represses the ethylene emission and drought tolerance in rice. However, its molecular mechanism to explore repression function remains unknown.<ref name="ref2" />

===Expression===
*The expression of OsERF3 was induced by drought, salt, ACC and ABA treatment. In addition, it showed a higher expression level in the root and sheath than that in the leaf.
*The full length of OsERF3 gene was obtained from the cDNA library using specific primers.The full length of OsERF3 gene was obtained from the cDNA library using specific primers. The mutation of EAR motif of OsERF3 (mEAR) was obtained by replacing the base of A680 with C (Fig. 1a) through PCR amplifications using specific primers (Table S1). Then, the full-length cDNA of OsERF3 and mEAR were inserted into pCAMBIA1307 modified from pCAMBIA1300, respectively. For the modification of pCAMBIA1307 vector (Fig. S1), we inserted a fragment including a CaMV 35S promoter and multiple cloning sites from vector pBluescript into the SstI and KpnI of pCAMBIA1300 vector. To generate the ERF3:GUS construct, the 1.0 kb promoter region upstream to start codon of OsERF3 was amplified using specific primers (OsERF3P-F and OsERF3P-R) (Table S1). Then, the fragment digested with EcoRI and NcoI was cloned into the multiple cloning sites of pCAMBIA1391Z vector. All of the transgenic rice plants were generated through Agrobacterium-mediated transformation. T1 seedlings were examined by PCR amplifications at the DNA and RNA levels with specific primers (Table S1); T2 and T3 seeds were screened by germinating with the selection of 50 ng/l hygromycin.
[[File:zch.png|200px|thumb|left|Fig. 1. Comparison of EAR motif and phylogenetic analysis of EAR motif containing ERF proteins from rice and Arabidopsis.]]
*The expression of OsERF3 was highly induced by ABA at 1 h, and reached peak at 2 h. Similarly, it was rapidly inducible by ACC at 0.5 h and peaked at 2 h, and then it decreased to normal level at 8 h (Fig. 2a). Moreover, OsERF3 was up-regulated by drought and peaked at 2 h. Similarly, OsERF3 was quickly induced by high salinity and peaked at 0.5 h. These results indicate that OsERF3 might be associated with ethylene- and ABArelated environmental stimuli in rice.the potential cis-elements withinthe 1 kb region (1,040 bp) upstream to the start codon(Table S2). There were more important elements involved in different hormones or stress signaling (including ethylene, ABA, Auxin and GA as well as dehydration, cold and light) and specific tissues. These data also support the molecular cues for the expression of OsERF3 in response to different hormones and stress treatments.
*As shown in Fig. 2b, the expression of OsERF3 in the root and sheath was two and three times higher than that in the leaf at the seedling phase, respectively. Moreover, the expression of GUS driven by the promoter of OsERF3 in transgenic rice was analyzed. Consistently, the GUS staining was observed in all parts of seedlings, but it showed more intense in sheath and root than that in leaf(Fig. 2c), further confirming its expression in seedlings.
[[File:zch2.png|400px|thumb|right|Fig. 2.Expression of OsERF3 .]]

===Mutation===
*The physiological analysesransgenic of rice overexpressing full-length OsERF3 (OE) and its mutation of EAR motif with the A680/C substitution (mEAR), showed that mEAR lines showed better drought tolerance and more ethylene emission compared with those of OE lines and wild type plants.However, the repression of OsERF3 was eliminated in mEAR lines. Specifically, ACS2 was up-regulated in mEAR lines compared with that in OE lines andWTplants, suggesting that the Leu/Ala substitution
within the EAR motif resulted in loss of repression of OsERF3.theEARmotif is required for OsERF3 to transcriptionally regulate the ethylene synthesis and drought tolerance in rice, providing new insight to the roles of ethylene-response factor proteins in regulating ethylene biosynthesis and stress response.
*It has been reported that series stress-related genes (Luet al. 2011) and ethylene synthesis-related genes were regulated by OsERF3 in rice (Wan et al. 2011). In the present work, we focused on whether EAR motif is required for the repression of OsACS2, OsACS6, and OsACO2 by OsERF3 in rice. The expression level of these
genes in OE and mEAR lines was analyzed. As shown in Fig. 5, the expression level of ACO2, ACS2, and ACS6 was decreased in OE lines. Interestingly, the expression of
ACS2 in mEAR lines was much higher than that in WT; the expression level of ACO2 and ACS6 in mEAR lines showed similar to that in WT. These results revealed that the mutation of Leu227/Ala within the EAR motif disrupted the repression function of OsERF3, implying that the EAR motif is essential for OsERF3 to repress the expression of ACO2, ACS2, and ACS6 in rice.
[[File:zch4.png|300px|thumb|left|Fig. 4. Transcriptional repression of OsERF3 in the expression of ethylene biosynthesis-related genes via EAR motif.]]

===Evolution===
Compared the drought tolerance among the transgenic lines (OE and mEAR) and wild type (WT) Nipponbare. As shown in Fig. 3a, most of the OE seedling leaves turned withered after the 2-week-old seedlings were exposed to successive drought by withholding water for 6 days, while WT and mEAR lines still grew well. When the seedlings of WT and OE lines exhibited serious stress symptom at the eighth day, mEAR lines showed mild stress symptom (Fig. 3a). After treated for 9 days, the resulting seedlings were recovered normal growth with watering for 7 days. The survival rates of seedlings in WT, OE lines, and mEAR lines were about 40, 19.5–28, and 43–49 %, respectively (Fig. 3b). Student’s t test analyses showed thatthe differences among WT and two OE lines were significant(P\0 05 or P\0 01). Although there was no significantdifference between WT and mEAR lines, the survival rate in mEAR lines was slight higher than that in WT plants. These findings suggest that the Leu227/Ala substitution results in the complete loss of negative regulation of drought tolerance by OsERF3. We also found that the OE lines showed drought sensitive at the flowering stage (Fig. S4). Taken together, our research demonstrates that that the EAR motif is necessary for OsERF3 to negatively regulate drought tolerance in rice.
[[File:zch3.png|200px|thumb|left|Fig. 3. Negative regulation of OsERF3 in the drought tolerance through its EAR motif..]]

===sequence analysis===
The rice genome encodes for 163 putative AP2/ERF family proteins based on their conserved AP2 domain sequence (Sharoni et al. 2011). OsERF3 encodes 235 amino acids
and belongs to class II ERF proteins. Sequence alignments showed that OsERF3 has a conserved AP2 DNA-binding domain and an EAR motif (DLNRPPP), which were highly
similar to the other class II ERF genes from Arabidopsis and rice. Especially, the three amino acids (DLN) were highly conserved in all candidate proteins (Fig. 1b, Fig. S2), suggesting they might play important roles in EAR motif-containing proteins. Analyses with phylogenetic tree of the protein sequences showed that OsERF3 was grouped in a cluster with Os05g0497300, with identity of 67.2 %. These two proteins showed a close evolutionary relationship with Os04g0610400, AtERF4, AtERF8, and AtERF11 (Fig. 1c), coinciding with the recent report on the syntenic relationships of rice ERF proteins (Rashid et al. 2012). Of these candidate genes, AtERF11 (Li et al. 2011), AtERF3 (Ohta et al. 2001), AtERF4 (Yang et al. 2005), and AtERF7 (Song et al. 2005) were proved to function as transcriptional repressors involved in modulating hormone response and stress tolerance. These analyses imply that OsERF3 might be a transcriptional repressor and play roles in mediating stress response.

==Labs working on this gene==
*Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing100081, China
*Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518083, China
*Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
*Rice Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China

==References==
<references>
* <ref name="ref1">
Zhang et al. BMC Genomics 2012, 13:461.Fan Zhang, Liyu Huang, Wensheng Wang, Xiuqin Zhao, Linghua Zhu, Binying Fu and Zhikang Li;Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background
</ref>
* <ref name="ref2">
Haiwen Zhang • Jianfei Zhang • Ruidang Quan •Xiaowu Pan • Liyun Wan • Rongfeng Huang;EAR motif mutation of rice OsERF3 alters the regulation of ethylene biosynthesis and drought tolerance. Planta (2013) 237:1443–1451
</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os01g0797600|
Description = Ethylene responsive element binding factor3 (OsERF3)|
Version = NM_001051054.1 GI:115440478 GeneID:4327621|
Length = 1090 bp|
Definition = Oryza sativa Japonica Group Os01g0797600, 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 1:35522840..35523929|
CDS = 35522920..35523627|
GCID = <gbrowseImage1>
name=NC_008394:35522840..35523929
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:35522840..35523929
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgcccagagcagctacggtggagaaggttgctgtggcgccacccaccgggcttggtcttggcgtcggcggaggtgtcggagccgggggtcctcactacaggggcgtccgcaagcgcccgtgggggcgttacgcagcggagatccgtgaccctgccaagaagagccgggtgtggctcggtacctacgacacggcagaggaggccgcccgcgcctacgacgccgccgctcgagagttccggggtgccaaggcaaaaacaaactttccgtttgcatcacagtcgatggtcggctgtggcggcagccccagcagcaatagcacggtagacaccggtggcggcggggttcagacgcctatgcgggccatgcctctgccgccgactctggacttggatttgttccaccgcgcggctgctgtgactgcagtcgccggcaccggcgttcgctttcctttcagaggatatcccgttgcacgtccagcaacgcatccttactttttctatgagcaggctgcagcggctgccgcagctgaggctggataccgtatgatgaagcttgcaccgccggtcaccgtggcggcggttgcacaaagtgactccgactcctcgtcggtggttgatctcgcgccgtcacctccagcggttacggcgaacaaggcggcagctttcgatctggatctgaaccggccgccgccggtagagaactag</cdnaseq>|
AA = <aaseq>MAPRAATVEKVAVAPPTGLGLGVGGGVGAGGPHYRGVRKRPWGR YAAEIRDPAKKSRVWLGTYDTAEEAARAYDAAAREFRGAKAKTNFPFASQSMVGCGGS PSSNSTVDTGGGGVQTPMRAMPLPPTLDLDLFHRAAAVTAVAGTGVRFPFRGYPVARP ATHPYFFYEQAAAAAAAEAGYRMMKLAPPVTVAAVAQSDSDSSSVVDLAPSPPAVTAN KAAAFDLDLNRPPPVEN</aaseq>|
DNA = <dnaseqindica>81..788#cacacccaaacccaacctcccaaaacacccacccggtttaccagagatccgcgcccgccacttgtaaacctgctgcacccatggcgcccagagcagctacggtggagaaggttgctgtggcgccacccaccgggcttggtcttggcgtcggcggaggtgtcggagccgggggtcctcactacaggggcgtccgcaagcgcccgtgggggcgttacgcagcggagatccgtgaccctgccaagaagagccgggtgtggctcggtacctacgacacggcagaggaggccgcccgcgcctacgacgccgccgctcgagagttccggggtgccaaggcaaaaacaaactttccgtttgcatcacagtcgatggtcggctgtggcggcagccccagcagcaatagcacggtagacaccggtggcggcggggttcagacgcctatgcgggccatgcctctgccgccgactctggacttggatttgttccaccgcgcggctgctgtgactgcagtcgccggcaccggcgttcgctttcctttcagaggatatcccgttgcacgtccagcaacgcatccttactttttctatgagcaggctgcagcggctgccgcagctgaggctggataccgtatgatgaagcttgcaccgccggtcaccgtggcggcggttgcacaaagtgactccgactcctcgtcggtggttgatctcgcgccgtcacctccagcggttacggcgaacaaggcggcagctttcgatctggatctgaaccggccgccgccggtagagaactagctcaggatgggttagctgacgactttgtagtttctctcttattttcttctttgatggatatttctctccgatgttttggtcctctgtgtttttgtttagtagcctgtgagagacggaagagccttgtaaatagtttttctgccgagggcgaaattcatcttgggatctgttaattagaacagatcatgccggcgatgagatggactaaaccgtggagtgtatgtattcctttatattagtatgaagaaattattcagaaagtcacaaaaatatctgtgcacactgagtttgattgacgtttt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001051054.1 RefSeq:Os01g0797600]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Zch4.png

2014-05-25T06:45:30Z

Zhangs:

Os01g0797600

2014-05-25T06:45:14Z

Zhangs: /* Mutation */

Please input one-sentence summary here.

==Annotated Information==
===Function===
*OsERF3 (Os01g0797600), is AP2 domain-containing protein, it is found to be significantly up-regulated in both genotypes under cold stress.<ref name="ref1" />
*OsERF3 (Os01g0797600) belongs to class II ERFs with a conserved EAR-motif (DLNRPPP) at the C terminal (Nakano et al. 2006). In rice, OsERF3 participated in the resistance to disease and the herbivore-induced defense responses via mediating different hormone pathways (Luet al. 2011).We also found that OsERF3 negatively
affected ethylene production and drought tolerance in rice(Wan et al. 2011). However, little is known about whether its EAR motif is involved in the regulation of ethylene synthesis and drought response. Here, we generated transgenic rice overexpressing full-length (OE) and the mutation of OsERF3 with the A680/C substitution (mEAR), respectively. The phenotypic analyses suggested that mEAR lines showed better drought tolerance and more ethylene emission than those of OE lines and wild type (WT) plants. At the transcriptional level, the substitution of Leu/Ala disrupted the repression of ACO2 and ACS6 by OsERF3 in mEAR lines. Moreover, ACS2 was significantly up-regulated in mEAR lines compared with that in WT plants. Taken together, our results indicate that the EAR motif is required for OsERF3 to repress the expression of ethylene biosynthesis genes, deepening our understanding of the regulatory function of ERF proteins involved in ethylene biosynthesis and stress response.<ref name="ref2" />
*OsERF3 is a transcriptional repressor with an ethylene-responsive element-binding factor-associated amphiphilic repression (EAR) motif (F/LDLNxxP), which transcriptionally represses the ethylene emission and drought tolerance in rice. However, its molecular mechanism to explore repression function remains unknown.<ref name="ref2" />

===Expression===
*The expression of OsERF3 was induced by drought, salt, ACC and ABA treatment. In addition, it showed a higher expression level in the root and sheath than that in the leaf.
*The full length of OsERF3 gene was obtained from the cDNA library using specific primers.The full length of OsERF3 gene was obtained from the cDNA library using specific primers. The mutation of EAR motif of OsERF3 (mEAR) was obtained by replacing the base of A680 with C (Fig. 1a) through PCR amplifications using specific primers (Table S1). Then, the full-length cDNA of OsERF3 and mEAR were inserted into pCAMBIA1307 modified from pCAMBIA1300, respectively. For the modification of pCAMBIA1307 vector (Fig. S1), we inserted a fragment including a CaMV 35S promoter and multiple cloning sites from vector pBluescript into the SstI and KpnI of pCAMBIA1300 vector. To generate the ERF3:GUS construct, the 1.0 kb promoter region upstream to start codon of OsERF3 was amplified using specific primers (OsERF3P-F and OsERF3P-R) (Table S1). Then, the fragment digested with EcoRI and NcoI was cloned into the multiple cloning sites of pCAMBIA1391Z vector. All of the transgenic rice plants were generated through Agrobacterium-mediated transformation. T1 seedlings were examined by PCR amplifications at the DNA and RNA levels with specific primers (Table S1); T2 and T3 seeds were screened by germinating with the selection of 50 ng/l hygromycin.
[[File:zch.png|200px|thumb|left|Fig. 1. Comparison of EAR motif and phylogenetic analysis of EAR motif containing ERF proteins from rice and Arabidopsis.]]
*The expression of OsERF3 was highly induced by ABA at 1 h, and reached peak at 2 h. Similarly, it was rapidly inducible by ACC at 0.5 h and peaked at 2 h, and then it decreased to normal level at 8 h (Fig. 2a). Moreover, OsERF3 was up-regulated by drought and peaked at 2 h. Similarly, OsERF3 was quickly induced by high salinity and peaked at 0.5 h. These results indicate that OsERF3 might be associated with ethylene- and ABArelated environmental stimuli in rice.the potential cis-elements withinthe 1 kb region (1,040 bp) upstream to the start codon(Table S2). There were more important elements involved in different hormones or stress signaling (including ethylene, ABA, Auxin and GA as well as dehydration, cold and light) and specific tissues. These data also support the molecular cues for the expression of OsERF3 in response to different hormones and stress treatments.
*As shown in Fig. 2b, the expression of OsERF3 in the root and sheath was two and three times higher than that in the leaf at the seedling phase, respectively. Moreover, the expression of GUS driven by the promoter of OsERF3 in transgenic rice was analyzed. Consistently, the GUS staining was observed in all parts of seedlings, but it showed more intense in sheath and root than that in leaf(Fig. 2c), further confirming its expression in seedlings.
[[File:zch2.png|200px|thumb|left|Fig. 2.Expression of OsERF3 .]]

===Mutation===
*The physiological analysesransgenic of rice overexpressing full-length OsERF3 (OE) and its mutation of EAR motif with the A680/C substitution (mEAR), showed that mEAR lines showed better drought tolerance and more ethylene emission compared with those of OE lines and wild type plants.However, the repression of OsERF3 was eliminated in mEAR lines. Specifically, ACS2 was up-regulated in mEAR lines compared with that in OE lines andWTplants, suggesting that the Leu/Ala substitution
within the EAR motif resulted in loss of repression of OsERF3.theEARmotif is required for OsERF3 to transcriptionally regulate the ethylene synthesis and drought tolerance in rice, providing new insight to the roles of ethylene-response factor proteins in regulating ethylene biosynthesis and stress response.
*It has been reported that series stress-related genes (Luet al. 2011) and ethylene synthesis-related genes were regulated by OsERF3 in rice (Wan et al. 2011). In the present work, we focused on whether EAR motif is required for the repression of OsACS2, OsACS6, and OsACO2 by OsERF3 in rice. The expression level of these
genes in OE and mEAR lines was analyzed. As shown in Fig. 5, the expression level of ACO2, ACS2, and ACS6 was decreased in OE lines. Interestingly, the expression of
ACS2 in mEAR lines was much higher than that in WT; the expression level of ACO2 and ACS6 in mEAR lines showed similar to that in WT. These results revealed that the mutation of Leu227/Ala within the EAR motif disrupted the repression function of OsERF3, implying that the EAR motif is essential for OsERF3 to repress the expression of ACO2, ACS2, and ACS6 in rice.
[[File:zch4.png|300px|thumb|left|Fig. 4. Transcriptional repression of OsERF3 in the expression of ethylene biosynthesis-related genes via EAR motif.]]

===Evolution===
Compared the drought tolerance among the transgenic lines (OE and mEAR) and wild type (WT) Nipponbare. As shown in Fig. 3a, most of the OE seedling leaves turned withered after the 2-week-old seedlings were exposed to successive drought by withholding water for 6 days, while WT and mEAR lines still grew well. When the seedlings of WT and OE lines exhibited serious stress symptom at the eighth day, mEAR lines showed mild stress symptom (Fig. 3a). After treated for 9 days, the resulting seedlings were recovered normal growth with watering for 7 days. The survival rates of seedlings in WT, OE lines, and mEAR lines were about 40, 19.5–28, and 43–49 %, respectively (Fig. 3b). Student’s t test analyses showed thatthe differences among WT and two OE lines were significant(P\0 05 or P\0 01). Although there was no significantdifference between WT and mEAR lines, the survival rate in mEAR lines was slight higher than that in WT plants. These findings suggest that the Leu227/Ala substitution results in the complete loss of negative regulation of drought tolerance by OsERF3. We also found that the OE lines showed drought sensitive at the flowering stage (Fig. S4). Taken together, our research demonstrates that that the EAR motif is necessary for OsERF3 to negatively regulate drought tolerance in rice.
[[File:zch3.png|200px|thumb|left|Fig. 3. Negative regulation of OsERF3 in the drought tolerance through its EAR motif..]]

===sequence analysis===
The rice genome encodes for 163 putative AP2/ERF family proteins based on their conserved AP2 domain sequence (Sharoni et al. 2011). OsERF3 encodes 235 amino acids
and belongs to class II ERF proteins. Sequence alignments showed that OsERF3 has a conserved AP2 DNA-binding domain and an EAR motif (DLNRPPP), which were highly
similar to the other class II ERF genes from Arabidopsis and rice. Especially, the three amino acids (DLN) were highly conserved in all candidate proteins (Fig. 1b, Fig. S2), suggesting they might play important roles in EAR motif-containing proteins. Analyses with phylogenetic tree of the protein sequences showed that OsERF3 was grouped in a cluster with Os05g0497300, with identity of 67.2 %. These two proteins showed a close evolutionary relationship with Os04g0610400, AtERF4, AtERF8, and AtERF11 (Fig. 1c), coinciding with the recent report on the syntenic relationships of rice ERF proteins (Rashid et al. 2012). Of these candidate genes, AtERF11 (Li et al. 2011), AtERF3 (Ohta et al. 2001), AtERF4 (Yang et al. 2005), and AtERF7 (Song et al. 2005) were proved to function as transcriptional repressors involved in modulating hormone response and stress tolerance. These analyses imply that OsERF3 might be a transcriptional repressor and play roles in mediating stress response.

==Labs working on this gene==
*Institute of Crop Sciences/National Key Facility for Crop Gene Resources and Genetic Improvement, Chinese Academy of Agricultural Sciences, Beijing100081, China
*Shenzhen Institute of Breeding and Innovation, Chinese Academy of Agricultural Sciences, Shenzhen 518083, China
*Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
*National Key Facility of Crop Gene Resources and Genetic Improvement, Beijing 100081, China
*Rice Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, China

==References==
<references>
* <ref name="ref1">
Zhang et al. BMC Genomics 2012, 13:461.Fan Zhang, Liyu Huang, Wensheng Wang, Xiuqin Zhao, Linghua Zhu, Binying Fu and Zhikang Li;Genome-wide gene expression profiling of introgressed indica rice alleles associated with seedling cold tolerance improvement in a japonica rice background
</ref>
* <ref name="ref2">
Haiwen Zhang • Jianfei Zhang • Ruidang Quan •Xiaowu Pan • Liyun Wan • Rongfeng Huang;EAR motif mutation of rice OsERF3 alters the regulation of ethylene biosynthesis and drought tolerance. Planta (2013) 237:1443–1451
</ref>
==Structured Information==
{{JaponicaGene|
GeneName = Os01g0797600|
Description = Ethylene responsive element binding factor3 (OsERF3)|
Version = NM_001051054.1 GI:115440478 GeneID:4327621|
Length = 1090 bp|
Definition = Oryza sativa Japonica Group Os01g0797600, 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 1:35522840..35523929|
CDS = 35522920..35523627|
GCID = <gbrowseImage1>
name=NC_008394:35522840..35523929
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008394:35522840..35523929
source=RiceChromosome01
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atggcgcccagagcagctacggtggagaaggttgctgtggcgccacccaccgggcttggtcttggcgtcggcggaggtgtcggagccgggggtcctcactacaggggcgtccgcaagcgcccgtgggggcgttacgcagcggagatccgtgaccctgccaagaagagccgggtgtggctcggtacctacgacacggcagaggaggccgcccgcgcctacgacgccgccgctcgagagttccggggtgccaaggcaaaaacaaactttccgtttgcatcacagtcgatggtcggctgtggcggcagccccagcagcaatagcacggtagacaccggtggcggcggggttcagacgcctatgcgggccatgcctctgccgccgactctggacttggatttgttccaccgcgcggctgctgtgactgcagtcgccggcaccggcgttcgctttcctttcagaggatatcccgttgcacgtccagcaacgcatccttactttttctatgagcaggctgcagcggctgccgcagctgaggctggataccgtatgatgaagcttgcaccgccggtcaccgtggcggcggttgcacaaagtgactccgactcctcgtcggtggttgatctcgcgccgtcacctccagcggttacggcgaacaaggcggcagctttcgatctggatctgaaccggccgccgccggtagagaactag</cdnaseq>|
AA = <aaseq>MAPRAATVEKVAVAPPTGLGLGVGGGVGAGGPHYRGVRKRPWGR YAAEIRDPAKKSRVWLGTYDTAEEAARAYDAAAREFRGAKAKTNFPFASQSMVGCGGS PSSNSTVDTGGGGVQTPMRAMPLPPTLDLDLFHRAAAVTAVAGTGVRFPFRGYPVARP ATHPYFFYEQAAAAAAAEAGYRMMKLAPPVTVAAVAQSDSDSSSVVDLAPSPPAVTAN KAAAFDLDLNRPPPVEN</aaseq>|
DNA = <dnaseqindica>81..788#cacacccaaacccaacctcccaaaacacccacccggtttaccagagatccgcgcccgccacttgtaaacctgctgcacccatggcgcccagagcagctacggtggagaaggttgctgtggcgccacccaccgggcttggtcttggcgtcggcggaggtgtcggagccgggggtcctcactacaggggcgtccgcaagcgcccgtgggggcgttacgcagcggagatccgtgaccctgccaagaagagccgggtgtggctcggtacctacgacacggcagaggaggccgcccgcgcctacgacgccgccgctcgagagttccggggtgccaaggcaaaaacaaactttccgtttgcatcacagtcgatggtcggctgtggcggcagccccagcagcaatagcacggtagacaccggtggcggcggggttcagacgcctatgcgggccatgcctctgccgccgactctggacttggatttgttccaccgcgcggctgctgtgactgcagtcgccggcaccggcgttcgctttcctttcagaggatatcccgttgcacgtccagcaacgcatccttactttttctatgagcaggctgcagcggctgccgcagctgaggctggataccgtatgatgaagcttgcaccgccggtcaccgtggcggcggttgcacaaagtgactccgactcctcgtcggtggttgatctcgcgccgtcacctccagcggttacggcgaacaaggcggcagctttcgatctggatctgaaccggccgccgccggtagagaactagctcaggatgggttagctgacgactttgtagtttctctcttattttcttctttgatggatatttctctccgatgttttggtcctctgtgtttttgtttagtagcctgtgagagacggaagagccttgtaaatagtttttctgccgagggcgaaattcatcttgggatctgttaattagaacagatcatgccggcgatgagatggactaaaccgtggagtgtatgtattcctttatattagtatgaagaaattattcagaaagtcacaaaaatatctgtgcacactgagtttgattgacgtttt</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001051054.1 RefSeq:Os01g0797600]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 1]]
[[Category:Chromosome 1]]

File:Zch3.png

2014-05-25T06:39:28Z

Zhangs:

Os01g0797600

2014-05-25T04:47:34Z

Zhangs: /* References */

The rice '''''Os03g0149100''''' was reported as ''crown rootless1 ('''OsCrl1''')''<ref name="ref1" /> and ''Adventitious rootless1('''OsARL1''')'' <ref name="ref2" /> respectively in 2005 by researchers from Japan and China. (in chronological order)

==Annotated Information==
[[File:Crl_1.jpg|right|thumb|230px|'''Figure 1.''' ''Mutant VS. WT(from reference) <ref name="ref1" />.'']]
[[File:Crl_2.jpg|right|thumb|450px|'''Figure 2.''' ''Mutant VS. WT(from reference) <ref name="ref2" />.'']]
===Function===
'''''OsCrl1''''' encodes an ASYMMETRIC LEAVES2 (AS2) / LATERAL ORGAN BOUNDARIES (LOB) domain transcription factor which acts as a positive regulator for crown and lateral root formation in rice <ref name="ref1" /><ref name="ref2" />. As an auxin-responsive factor involved in auxin-mediated cell dedifferentiation, '''''OsCrl1''''' can promote the initial cell division in the pericycle cells adjacent to the peripheral vascular cylinder in the stem<ref name="ref2" />.Manipulation of the regulation of this gene (and its homologs in other crops) has great potential for increasing the ability of crops to absorb water and nutrients from the soil through improvement in their root architecture, which is required for achieving high yields<ref name="ref2" />.
OsCrl1 genes is well known as early auxin-response genes,an essential gene for crown root formation in rice.<ref name="ref6" />

.

===Mutation===
'''1. Mutation reported by ''Yoshiaki Inukai et al.'' <ref name="ref1" />:'''
* Two-week-old '''''OsCrl1''''' mutants had normal seminal root development but did not form any crown roots, whereas wild-type plants formed several crown roots at the same developmental stage(Figures 1A and 1B).
* In the wild type, crown root primordia (arrow in Figure 1C) formed on the outside, adjacent to the peripheral vascular cylinder (arrowhead in Figure 1C) of the stem. By contrast, '''''OsCrl1''''' did not produce any crown root primordia(Figure 1D).
* The number of lateral roots from a seminal root in '''''OsCrl1''''' also decreased to;70% of that in the wild type (Figures 1A and 1B), indicating that '''''OsCrl1''''' is involved in both crown root and lateral root formation.
* At later stages of development, wild type can produce significant crown root, while the '''''OsCrl1''''' only produce crown root occasionally (Figures 1E and 1F). 
'''2. Mutation reported by ''Hongjia Liu et al.'' <ref name="ref2" />:'''
* In contrast to a normal rice plant, '''''OsArl1''''' mutant seedlings lack adventitious roots (Figure 2a).
* Due to its lack of essential root structure, the homozygous '''''OsArl1''''' mutant cannot grow to maturity (Figure 2b), although at the seedling stage no significant difference was observed in shoot morphology between the wild type and the mutant.
* Cross sections at the base of the stem of 5-day-old seedlings revealed that the formation of adventitious primordium is impaired in the '''''OsArl1''''' mutant (Figure 2c,d).
* Adventitious root primordia were induced at the fourth node of 8-week-old wild-type plants by submergence for 24 h (Figure 1e), but were not induced in the '''''OsArl1''''' mutant (Figure 2f).
Interestingly,constitutive expression of the OsIAA4 and OsCrl1 genes was observed in the OsWRKY31 overexpressor lines of T2 progenies and their expressions were not increased further by the treatment of the overexpressor plants with IBA (Figure 8C). These results suggest that OsWRKY31 may be involved in auxin signaling.
We also found that the induction of OsWRKY31 was even faster than the expression of auxin-inducible OsIAA4 and OsCrl1 genes following treatment of rice seedlings with IBA (Figure 8B).The early auxin response of OsWRKY31 expression suggests that OsWRKY31 is a member of the early auxin response family. However, constitutive expression of auxin-inducible OsIAA4 and OsCrl1 genes in OsWRKY31 overexpressor lines did not exhibit corresponding phenotypes,such as more or longer lateral roots (Figure 8)<ref name="ref6" />.
An explanation for this dissimilarity may be that the constitutive expression in some of the rice Aux/IAA genes,such as OsIAA4, might lead to the stabilization of these proteins at some specific stage or condition of development.In support of this idea, some SLR1/IAA14 overexpressing Arabidopsis plants exhibit an slr (solitary-root)-1-like phenotype, which was interpreted by Fukaki et al. to be the accumulation of IAA14 proteins in these 35S::IAA14 plants at the CaMV35S promoter, which is constitutively active in most plant tissues. Furthermore, even though rice Crl1 is a positive regulator of crown and lateral root formation, its expression has been found to be insufficient to initiate crown or lateral root development.<ref name="ref6" />

===Expression Pattern===
* Semi-quantitative RT-PCR analysis by ''Yoshiaki Inukai et al.'' shows that '''''OsCrl1''''' transcripts accumulated in unelongating basal internodes. And the localized expression of '''''OsCrl1''''' in stems and roots corresponds well to the areas of crown and lateral root initiation, confirming that ''''''OsCrl1''''' is involved in the initiation of these root systems<ref name="ref1" />.
* The RNA ''in situ hybridization'' analysis by ''Hongjia Liu et al.'' showed that this gene is expressed at the beginning of primordium formation<ref name="ref2" />.
* The expression of '''''OsCrl1''''' was induced within 1 h and increased dramatically until 3 h after IAA treatment, then it gradually decreased. This suggests that '''''OsCrl1''''' is a member of the early auxin response family<ref name="ref1" />.
[[File:Crl_3.jpg|right|thumb|300px|'''Figure 3.''' ''An unrooted dendogram of the AS2/LOB family proteins in Arabidopsis, maize and rice(from reference) <ref name="ref1" />.'']]
The primers used were 5´-agc aac gtg tcc aag ctg ct-3´ and 5´-tgt agc cgc cgt acc cta at-3´ for OsCrl1 (AB200234).<ref name="ref6" />

===Subcellular localization===
* The subcellular localization analysis by ''Hongjia Liu et al.'' suggests that '''''OsCrl1''''' is a nuclear protein, which is expressed in nuclei<ref name="ref2" />.
===Evolution===
''Yoshiaki Inukai et al.'' made a BLAST search by using the AS2/LOB domain sequence of '''''OsCrl1'''''. They found that some AS2/LOB proteins in Arabidopsis, maize (Zea mays), and rice are more similar to '''''OsCrl1''''' than to other AS2/LOB
proteins (Figure 3)<ref name="ref1" />.

===Knowledge Extension===
* The ''LATERAL ORGAN BOUNDARIES DOMAIN '''(LBD)''' '' genes define a large, plant-specific family of largely unknown function<ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. The LOB protein encodes a conserved approximately 100-amino acid domain which contains a motif resembling a zinc finger and another similar to a leucine zipper<ref name="ref3" /><ref name="ref4" />. However, both motifs have atypical spacing and until now, the biochemical function of the LOB domain has not been defined, although proteins containing LOB domains have been assumed to be transcription factors<ref name="ref3" />.The discovery of '''''OsCrl1''''' implies that some members of the LOB domain gene family may play an important role in organ development in plants<ref name="ref2" />.
* In Arabidopsis, LOB defines a subgroup of LBD genes that also includes ''LBD10/ASL2, LBD25/ASL3, LBD36/ASL1, and AS2/LBD6''<ref name="ref4" /><ref name="ref5" />. Among this subgroup, '''''AS2''' (ASYMMETRIC LEAVES2)'' is the only gene with clearly defined functions. '''''AS2''''' is required to prevent expression of the class I ''KNOX'' homeobox genes ''BREVIPEDICELLUS ('''BP''')'', ''KNAT2'', and ''KNAT6'' in the leaf. '''''AS2''''' is expressed on the adaxial side of lateral organs and misexpression leads to the formation of adaxialized leaves implicating '''''AS2''''' in adaxial cell fate specification<ref name="ref5" />.

==Labs working on this gene==
* Bioscience and Biotechnology Center, Nagoya University, Nagoya, Aichi 464-8601, Japan
* Field Production Science Center, University of Tokyo, Nishi-Tokyo, Tokyo 188-0002, Japan
* State Key Laboratory of Plant Physiology and Biochemistry, College of Life Science, Zhejiang University, Hangzhou 310029,China
* Department of Biology and Environmental Science, School of Life Sciences, University of Sussex, Brighton BN1 9QG, UK
* Department of Crop Physiology, Tamil Nadu Agricultural University, Coimbatore 641003, Tamil Nadu, India
* University of Agriculture Faisalabad, Sub-Campus Depalpur, Okara 38040, Pakistan
* Graduate School of Agricultural and Life Sciences,University of Tokyo, Tokyo 113-8657
* Faculty of Agriculture, Kagawa University, Miki, Kagawa 761-0795, Japan
*1State Key Laboratory of Agrobiotechnology, Department of Plant Pathology, China Agricultural University,Yuanmingyuan West Road 2, Beijing 100094,China

==References==
<references>
* <ref name="ref1">
Inukai Y, Sakamoto T, Ueguchi-Tanaka M, et al. Crown rootless1, which is essential for crown root formation in rice, is a target of an AUXIN RESPONSE FACTOR in auxin signaling[J]. The Plant Cell Online, 2005, 17(5): 1387-1396.
</ref>
* <ref name="ref2">
Liu H, Wang S, Yu X, et al. ARL1, a LOB‐domain protein required for adventitious root formation in rice[J]. The Plant Journal, 2005, 43(1): 47-56.
</ref>
* <ref name="ref3">
Husbands A, Bell E M, Shuai B, et al. LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins[J]. Nucleic Acids Research, 2007, 35(19): 6663-6671.
</ref>
* <ref name="ref4">
Shuai B, Reynaga-Peña C G, Springer P S. The lateral organ boundaries gene defines a novel, plant-specific gene family[J]. Plant physiology, 2002, 129(2): 747-761.
</ref>
* <ref name="ref5">
Mangeon A, Bell E M, Lin W, et al. Misregulation of the LOB domain gene DDA1 suggests possible functions in auxin signalling and photomorphogenesis[J]. Journal of experimental botany, 2011, 62(1): 221-233.
</ref>
</references>
* <ref name="ref3">
Juan Zhang, Youliang Peng, Zejian Guo.Constitutive expression of pathogen-inducible OsWRKY31 enhances disease resistance and affects root growth and auxin response in transgenic rice plants,Cell Research (2008) 18:508-521.
</ref>

==Structured Information==
{{JaponicaGene|
GeneName = Os03g0149100|
Description = Adventitious rootless1 (LOB domain protein)|
Version = NM_001186339.1 GI:297721808 GeneID:9271993|
Length = 864 bp|
Definition = Oryza sativa Japonica Group Os03g0149100, 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 3:2705032..2705895|
CDS = 2705032..2705532,2705617..2705895|
GCID = <gbrowseImage1>
name=NC_008396:2705032..2705895
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage1>|
GSID = <gbrowseImage2>
name=NC_008396:2705032..2705895
source=RiceChromosome03
preset=GeneLocation
</gbrowseImage2>|
CDNA = <cdnaseq>atgacgggatttggatcgccgtgcggcgcgtgcaagtttctgcggcgcaagtgcgtgcgcgggtgcgtgttcgcgccatacttctgccacgagcaaggggcggcgcacttcgccgccatccacaaggtgttcggcgccagcaacgtgtccaagctgctcgcccacctgccgctcgccgaccgccccgaggccgccgtcactatctcctacgaggcgcaggcccgcctccgcgaccccatctatggctgcgtcgcccacatcttcgccctccagcagcaggtgatgacgctgcaggcgcagctggcgtcgctcaaggcggcggcggcgcaagggatacaccaccaggacgtcggcgccaccaccaagggcggctacatgagcgccgccgccaccgccgccgacgaccaattagggtacggcggctacaaccagtggtgcggcagcaatgggggcggcgcgccggcggcgtcgcagccgggcgcgtatagcagcaatggcggcgccggccacggccacgactccatcaccgcgctgctggcggccgggtcggactacatgcagcactcgctgtaccacgcgttcgagcactcggagggcgccggcgccgtggacgacgggcacgcggccgccgcggccttcgaggcggcggcggagtcgtcgtcgtgcggcatggcggcgtcgttcgccgccgacgagagcgtgtggaggtcgtcgtcgtcgggataccaagattgcgaggatctccagagcgtcgcctacgcttaccttaaccgctcgtaa</cdnaseq>|
AA = <aaseq>MTGFGSPCGACKFLRRKCVRGCVFAPYFCHEQGAAHFAAIHKVF GASNVSKLLAHLPLADRPEAAVTISYEAQARLRDPIYGCVAHIFALQQQVMTLQAQLA SLKAAAAQGIHHQDVGATTKGGYMSAAATAADDQLGYGGYNQWCGSNGGGAPAASQPG AYSSNGGAGHGHDSITALLAAGSDYMQHSLYHAFEHSEGAGAVDDGHAAAAAFEAAAE SSSCGMAASFAADESVWRSSSSGYQDCEDLQSVAYAYLNRS</aaseq>|
DNA = <dnaseqindica>364..864#1..279#atgacgggatttggatcgccgtgcggcgcgtgcaagtttctgcggcgcaagtgcgtgcgcgggtgcgtgttcgcgccatacttctgccacgagcaaggggcggcgcacttcgccgccatccacaaggtgttcggcgccagcaacgtgtccaagctgctcgcccacctgccgctcgccgaccgccccgaggccgccgtcactatctcctacgaggcgcaggcccgcctccgcgaccccatctatggctgcgtcgcccacatcttcgccctccagcagcaggttcgtatagttcattcgatcgatgtgtcgctcgtcggcgtcgctggtttgctgatcttggtgtcgcggcgcgtgttcgaacaggtgatgacgctgcaggcgcagctggcgtcgctcaaggcggcggcggcgcaagggatacaccaccaggacgtcggcgccaccaccaagggcggctacatgagcgccgccgccaccgccgccgacgaccaattagggtacggcggctacaaccagtggtgcggcagcaatgggggcggcgcgccggcggcgtcgcagccgggcgcgtatagcagcaatggcggcgccggccacggccacgactccatcaccgcgctgctggcggccgggtcggactacatgcagcactcgctgtaccacgcgttcgagcactcggagggcgccggcgccgtggacgacgggcacgcggccgccgcggccttcgaggcggcggcggagtcgtcgtcgtgcggcatggcggcgtcgttcgccgccgacgagagcgtgtggaggtcgtcgtcgtcgggataccaagattgcgaggatctccagagcgtcgcctacgcttaccttaaccgctcgtaa</dnaseqindica>|
Link = [http://www.ncbi.nlm.nih.gov/nuccore/NM_001186339.1 RefSeq:Os03g0149100]|
}}
[[Category:Genes]]
[[Category:Japonica mRNA]]
[[Category:Oryza Sativa Japonica Group]]
[[Category:Japonica Genes]]
[[Category:Japonica Chromosome 3]]
[[Category:Chromosome 3]]