Difference between revisions of "Os07g0592600"
(→Labs working on this gene) |
|||
| Line 17: | Line 17: | ||
===Evolution=== | ===Evolution=== | ||
| − | + | GH3 family genes are divided into three groups (I, II, and III) based on their sequence similarities and the substrate specificities of their products in Arabidopsis, which harbors 19 GH3 members and one incomplete GH3 protein. Group I GH3 enzymes are JA-amido or SAamido synthetases. Arabidopsis Group II enzymes were demonstrated to be active on IAA. Group III enzymes have only been identified in Arabidopsis to date. Members of this gene family are known to be regulated by phytohormones and biotic/abiotic stress factors, including abscisic acid (ABA), SA, JA, drought, cold, salt, pathogen infection, and light. GH3-mediated auxin homeostasis is an essential constituent of the complex network of auxin activity that regulates stress adaptation responses.GH3 family genes were divided into three groups (I, II, and III) based on their sequence similarities and the substrate specificities of their products in Arabidopsis, which harbors 19 GH3 members and one incomplete GH3 protein. Group III GH3 enzymes, of which there are nine in Arabidopsis, have only been identified in Arabidopsis to date. | |
[[File:Figure 2 dyf.jpg]] | [[File:Figure 2 dyf.jpg]] | ||
'''Figure 2 Phylogenetic analysis and gene structure of apple GH3 members.''' | '''Figure 2 Phylogenetic analysis and gene structure of apple GH3 members.''' | ||
| + | |||
| + | A hylogeny of apple GH3 proteins, generated using MEGA5 (using the neighbor-joining method and a bootstrap test with 1000 iterations). B Gene structure of the corresponding apple GH3 proteins, generated by a gene structure display server. The black boxes represent exons and lines represent introns. 0, 1, and 2 represent phase 0, 1, and 2 introns. | ||
==Labs working on this gene== | ==Labs working on this gene== | ||
Revision as of 06:09, 6 June 2014
Please input one-sentence summary here.
Contents
Annotated Information
Function
OsMGH3 (OsGH3-8) is a member of group II GH3 proteins whose closest Arabidopsis sequence homolog AtGH3.2 functions as a negative component in auxin signaling by regulating auxin level and activity[1][2] Auxin plays a central role in nearly all aspects of plant growth and development. The final molecular and cellular outcome of auxin signaling in a specific tissue/spatially localized domain depends very critically on the level of its biologically active pool. This is mostly regulated by a homeostasis between its biosynthesis and inactivation. The significance of auxin homeostasis is underscored by the finding that in Arabidopsis_99% of the IAA pool is maintained in the conjugated inactive form generated by various GH3 proteins, and only 1% of IAA occurs as the biologically active form[3]. Thus, regulated expression of GH3 factors can contribute to auxin signaling and these genes are ideal targets for transcription regulators to execute their developmental functions.
Expression
Rice GH3 genes are expressed at varying levels in various wild-type tissues and organs, with the transcript levels for OsGH3-1, 2, 3, 4, 5, 7, 8 and 11 being the highest in flowers (Jain et al. 2006a). The expression of six GH3 genes is de-regulated in OsMADS1 mutant panicles as seen in our analysis of transcript levels using whole-genome microarrays (Prasad et al. 2005, S. R. Yadav, I. Khanday and U. Vijayraghavan, unpublished data). OsMGH3 (OsGH3-8) is a member of group II GH3 proteins whose closest Arabidopsis sequence homolog AtGH3.2 functions as a negative component in auxin signaling by regulating auxin level and activity (Takase et al. 2004, Staswick et al. 2005). OsMGH3/OsGH3-8 (hence forth referred to as OsMGH3) is one amongst this family of genes whose expression is reduced in dsRNAi (double-stranded RNA interference) OsMADS1 panicles and in osmads6 mutant flowers (Prasad et al. 2005, Zhang et al. 2010).The expression domain of OsMGH3 overlaps with that of OsMADS1 at early stages of floret development (figure 1). In florets at later stages of development with differentiating organs, its expression overlaps more with OsMADS6 [4][5][6].
_OsMADS1_profile_in_developing_inflorescence_branch_primordia_and_spikelets._Silver_grains_reveal_regions_with_expression.jpg)
Figure 1 In situ RNA expression patterns of OsMADS1 compared with OsMGH3. (a–f) OsMADS1 profile in developing inflorescence branch primordia and spikelets. Silver grains reveal regions with expression. (a) Sense OsMADS1 RNA probe as a control. (b–f) Hybridizations with antisense RNA probes. (b) No transcripts in the very young branching panicle. (c) Near-uniform early expression in the incipient floret meristem. Expression is excluded from the glume primordia (green arrows). Red arrow indicates the future carpel anlagen. (d) Spikelet during an early stage of organ differentiation with OsMADS1 expression in the developing lemma (le)/palea (pa) and weak expression in the carpel (ca). (e, f) Spikelets showing expression in differentiated lemma (le), palea (pa) and carpels (ca). No expression in lodicules (lo) and glumes (gl). (g–l) Non-radioactive RNA in situ analysis of OsMGH3 RNAs in panicles and florets at stages similar to that shown for OsMADS1. (g) No OsMGH3 transcripts in the vegetative SAM (red arrow) or (h) branching panicles (black arrows). (i) Uniform RNA distribution in young spikelet primordia similar to OsMADS1 (compare c, i). Green arrow points to the glume, red arrows to the emerging lemma and palea and the blue arrow indicates the carpel anlagen. (j) Spikelet during organ emergence. OsMGH3 profile begins to deviates from OsMADS1. (k,l) Spikelets with differentiated organs. Greatly reduced expression in the near mature lemma (le) and palea (pa); continued lack of expression in the glumes (gl). Expression is maintained in the lodicules (lo), stamens (st) and carpel (ca). Scale bar is 100 lm in all panels.
Evolution
GH3 family genes are divided into three groups (I, II, and III) based on their sequence similarities and the substrate specificities of their products in Arabidopsis, which harbors 19 GH3 members and one incomplete GH3 protein. Group I GH3 enzymes are JA-amido or SAamido synthetases. Arabidopsis Group II enzymes were demonstrated to be active on IAA. Group III enzymes have only been identified in Arabidopsis to date. Members of this gene family are known to be regulated by phytohormones and biotic/abiotic stress factors, including abscisic acid (ABA), SA, JA, drought, cold, salt, pathogen infection, and light. GH3-mediated auxin homeostasis is an essential constituent of the complex network of auxin activity that regulates stress adaptation responses.GH3 family genes were divided into three groups (I, II, and III) based on their sequence similarities and the substrate specificities of their products in Arabidopsis, which harbors 19 GH3 members and one incomplete GH3 protein. Group III GH3 enzymes, of which there are nine in Arabidopsis, have only been identified in Arabidopsis to date.
Figure 2 Phylogenetic analysis and gene structure of apple GH3 members.
A hylogeny of apple GH3 proteins, generated using MEGA5 (using the neighbor-joining method and a bootstrap test with 1000 iterations). B Gene structure of the corresponding apple GH3 proteins, generated by a gene structure display server. The black boxes represent exons and lines represent introns. 0, 1, and 2 represent phase 0, 1, and 2 introns.
Labs working on this gene
1 Wang Shiping, National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China.
2 Usha Vijayraghavan, Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore-560012, India.
References
- ↑ Takase, T., Nakazawa, M., Ishikawa, A., Kawashima, M., Ichikawa, T., Takahashi, N. et al. (2004) ydk1-D, an auxin-responsive GH3 mutant that is involved in hypocotyl and root elongation. Plant J. 37:471–483.
- ↑ Staswick, P.E., Serban, B., Rowe, M., Tiryaki, I., Maldonado, M.T., Maldonado, M.C. et al. (2005) Characterization of an Arabidopsis enzyme family that conjugates amino acids to indole-3-acetic acid. Plant Cell 17: 616–627.
- ↑ Woodward, C., Bemis, S.M., Hill, E.J., Sawa, S., Koshiba, T. and Torii, K.U. (2005) Interaction of auxin and ERECTA in elaborating Arabidopsis inflorescence architecture revealed by the activation tagging of a new member of the YUCCA family putative flavin monooxygenases. Plant Physiol. 139: 192–203.
- ↑ Prasad, K., Parameswaran, S. and Vijayraghavan, U. (2005) OsMADS1, a rice MADS-box factor, controls differentiation of specific cell types in the lemma and palea and is an early-acting regulator of inner floral organs. Plant J. 43: 915–928.
- ↑ Li, H., Liang, W., Jia, R., Yin, C., Zong, J., Kong, H. et al. (2010) The AGL6-like gene OsMADS6 regulates floral organ and meristem identities in rice. Cell Res. 20: 299–313.
- ↑ Zhang, J., Nallamilli, B.R., Mujahid, H. and Peng, Z. (2010) OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa). Plant J. 64:604–617.
Structured Information
| Gene Name |
Os07g0592600 |
|---|---|
| Description |
Similar to Indole-3-acetic acid-amido synthetase GH3.3 (EC 6.3.2.-) (Auxin- responsive GH3-like protein 3) (AtGH3-3) |
| Version |
NM_001066698.1 GI:115473128 GeneID:4343785 |
| Length |
2357 bp |
| Definition |
Oryza sativa Japonica Group Os07g0592600, 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 | |
| Location |
Chromosome 7:24809875..24812231 |
| Sequence Coding Region |
24810162..24811536,24811631..24812073 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008400:24809875..24812231 source=RiceChromosome07 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008400:24809875..24812231 source=RiceChromosome07 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggcggtgatgactgatgtgtcgaccaccgggacggcactccggaccccggcggcgggggcggtgaaggagggcgacgtcgagaagctccggttcatcgacgagatgaccaccaacgtcgacgccgtgcaggagcgcgtcctgggggagatcctcggccgcaacgccggcacggagtacctgaccaagtgcggcctcgacggcgccaccgaccgcgccgccttccgggccaaggttccggtggtgtcgtacgacgacctgcagccgtacatccagcgcattgcgaacggggaccgctcgccgatcctgtccacccaccccgtctccgagttcctcaccagctccggcacgtcggccggcgagcgcaagctgatgcccaccatcatggacgagctcgaccgccgtcagctgctctacagcctcctcatgccggtcatgaacttgtatgtgcctgggcttgacaaggggaaggggctctacttcctgttcgtcaagtcggagacgaagacgccgggaggcctgacggcgaggcccgtgctgacgagctactacaagagcgaccacttcaagaaccggccgtacgacccgtaccacaactacacgagcccgacggcggccatcctctgcgccgacgcgttccagagcatgtacgcgcagatggtgtgcggcctgtgccagcgcaacgacgtgctgcgcctcggcgccgtgttcgcctccggcctcctccgggccatccgcttcctccagctcaactgggagcagctcgccgacgacatcgagtccggcgagctcacccctcgcgtcaccgacccgtcggtgcgcgaggctgtcgccgccatcctcctcccggaccccgagctcgccaagctcatccgcgccgagtgctccaagggcgactgggccggcatcatcacccgcgtgtggccgaacaccaagtacctcgacgtcatcgtcaccggcgcgatggcgcagtacatcccgaccctggagttctacagcggcgggcttcccatggcgtgcaccatgtacgcgtcatccgagtgctacttcggcctcaacctccgccccatgtgcgacccctccgaggtgtcctacaccatcatgcctaacatgggctacttcgagttcctccccgtggacgagaccggcgcggcttcgggcgacgccacccagctcgtggacctcgcccgcgtggaggtggggcgcgagtacgagctggtgatcaccacctacgccgggctgaaccggtaccgcgtcggcgacgtcctccgcgtgacggggttccacaacgcggcgccgcagttcaggttcgtgcgccgcaagaacgtgctcctctccatcgagtccgacaagaccgacgaggccgagctgcagcgcgccgtggagcgcgcgtcggcgctgctccgcccgcacggcgcgtccgtggtggagtacaccagccaagcgtgcaccaagcgcatcccgggccactacgtcatctactgggagctcctgaccaagggcgccggcgccacggtggtggacgcggacacgctgggcaggtgctgcctcgagatggaggaggcgctgaacacggtgtacaggcagagccgcgtcgcggacggctcgattgggccgctcgagatccgggtcgtccgcccgggcacattcgaggagctcatggactacgccatctcccgcggcgcgtccatcaaccagtacaaggtgccacgctgcgtcacgttcccgcccatcgtcgagctgctcgactcgcgcgtcgtgtccagccacttcagcccggcgctcccacactggactccggcgcgacggtccgaatag</cdnaseq> |
| Protein Sequence |
<aaseq>MAVMTDVSTTGTALRTPAAGAVKEGDVEKLRFIDEMTTNVDAVQ ERVLGEILGRNAGTEYLTKCGLDGATDRAAFRAKVPVVSYDDLQPYIQRIANGDRSPI LSTHPVSEFLTSSGTSAGERKLMPTIMDELDRRQLLYSLLMPVMNLYVPGLDKGKGLY FLFVKSETKTPGGLTARPVLTSYYKSDHFKNRPYDPYHNYTSPTAAILCADAFQSMYA QMVCGLCQRNDVLRLGAVFASGLLRAIRFLQLNWEQLADDIESGELTPRVTDPSVREA VAAILLPDPELAKLIRAECSKGDWAGIITRVWPNTKYLDVIVTGAMAQYIPTLEFYSG GLPMACTMYASSECYFGLNLRPMCDPSEVSYTIMPNMGYFEFLPVDETGAASGDATQL VDLARVEVGREYELVITTYAGLNRYRVGDVLRVTGFHNAAPQFRFVRRKNVLLSIESD KTDEAELQRAVERASALLRPHGASVVEYTSQACTKRIPGHYVIYWELLTKGAGATVVD ADTLGRCCLEMEEALNTVYRQSRVADGSIGPLEIRVVRPGTFEELMDYAISRGASINQ YKVPRCVTFPPIVELLDSRVVSSHFSPALPHWTPARRSE</aaseq> |
| Gene Sequence |
<dnaseqindica>696..2070#159..601#aggccacacaccaccaacacaaaacatttccttgtccctcgccttcctcgcctcgcctcggctctcacacgacgcctcttcctctcgctactactagctcaagctaagctagcaagagcattccttgggctttttttcttgttcggggttgagaggcaatggcggtgatgactgatgtgtcgaccaccgggacggcactccggaccccggcggcgggggcggtgaaggagggcgacgtcgagaagctccggttcatcgacgagatgaccaccaacgtcgacgccgtgcaggagcgcgtcctgggggagatcctcggccgcaacgccggcacggagtacctgaccaagtgcggcctcgacggcgccaccgaccgcgccgccttccgggccaaggttccggtggtgtcgtacgacgacctgcagccgtacatccagcgcattgcgaacggggaccgctcgccgatcctgtccacccaccccgtctccgagttcctcaccagctccggcacgtcggccggcgagcgcaagctgatgcccaccatcatggacgagctcgaccgccgtcagctgctctacagcctcctcatgccggtcatgaacttgtaagttgatactactcctatcattgtctcattctgatagcacacacacgtacaagaagcagatgatgattaatggccatgaatcattgcataggtatgtgcctgggcttgacaaggggaaggggctctacttcctgttcgtcaagtcggagacgaagacgccgggaggcctgacggcgaggcccgtgctgacgagctactacaagagcgaccacttcaagaaccggccgtacgacccgtaccacaactacacgagcccgacggcggccatcctctgcgccgacgcgttccagagcatgtacgcgcagatggtgtgcggcctgtgccagcgcaacgacgtgctgcgcctcggcgccgtgttcgcctccggcctcctccgggccatccgcttcctccagctcaactgggagcagctcgccgacgacatcgagtccggcgagctcacccctcgcgtcaccgacccgtcggtgcgcgaggctgtcgccgccatcctcctcccggaccccgagctcgccaagctcatccgcgccgagtgctccaagggcgactgggccggcatcatcacccgcgtgtggccgaacaccaagtacctcgacgtcatcgtcaccggcgcgatggcgcagtacatcccgaccctggagttctacagcggcgggcttcccatggcgtgcaccatgtacgcgtcatccgagtgctacttcggcctcaacctccgccccatgtgcgacccctccgaggtgtcctacaccatcatgcctaacatgggctacttcgagttcctccccgtggacgagaccggcgcggcttcgggcgacgccacccagctcgtggacctcgcccgcgtggaggtggggcgcgagtacgagctggtgatcaccacctacgccgggctgaaccggtaccgcgtcggcgacgtcctccgcgtgacggggttccacaacgcggcgccgcagttcaggttcgtgcgccgcaagaacgtgctcctctccatcgagtccgacaagaccgacgaggccgagctgcagcgcgccgtggagcgcgcgtcggcgctgctccgcccgcacggcgcgtccgtggtggagtacaccagccaagcgtgcaccaagcgcatcccgggccactacgtcatctactgggagctcctgaccaagggcgccggcgccacggtggtggacgcggacacgctgggcaggtgctgcctcgagatggaggaggcgctgaacacggtgtacaggcagagccgcgtcgcggacggctcgattgggccgctcgagatccgggtcgtccgcccgggcacattcgaggagctcatggactacgccatctcccgcggcgcgtccatcaaccagtacaaggtgccacgctgcgtcacgttcccgcccatcgtcgagctgctcgactcgcgcgtcgtgtccagccacttcagcccggcgctcccacactggactccggcgcgacggtccgaatagtcggtcaaatccccacctcgtcgttggaccgtgtccaagaatctgaagtagtagaagccggatgcctccacctaaaaacacttatctgttatttttggaattaattttgatggttgctgtcaactctgtcagttagtggcaagagggtacctctgatgtgagggagagaactgcagaacgaacggaagaaagtgttgatgtaagaggttaccactagtagtactgtttgtctgtatcaggaatgtgattataatttaacctgtcctccaaaaccgtacgagtcctgc</dnaseqindica> |
| External Link(s) |
