Difference between revisions of "Os05g0346200"

From RiceWiki
Jump to: navigation, search
(→‎Expression)
(→‎Evolution)
Line 11: Line 11:
 
[[File:pic2.jpg|a Schematic models of OsDREB2B transcripts. The OsDREB2B gene contains three exons (E1, E2, E3) and two introns (I1, I2). Two kinds of transcripts are produced by alternative splicing. Arrows A and B indicate primers used for the PCR analyses in c and d. Arrows C and D indicate primers used for the qRT-PCR analysis in c. NLS, nuclear localisation signals; AP2, AP2/ERF DNAbinding domain. b Expression analysis of OsDREB2A under abiotic stress conditions. Total RNA was prepared from 2-week-old rice seedlings treated by high temperature (42°C), low temperature (4°C), drought and high salinity (250 mM NaCl) for the indicated time courses. H2O-treated plants were used as a control. The mRNA accumulation levels were analysed by qRT-PCR. The relative amounts of mRNA were calculated by defining the amount of OsDREB2B2 in the unstressed condition (0 min) as 1.0. Bars indicate standard deviations (SDs) (n = 3). c Expression analysis of OsDREB2B under abiotic stress conditions. RNA preparation and qRT-PCR were conducted as described in a. Specific primers for each transcript were used. d Analysis of the splicing mechanism of OsDREB2B. Two-week-old transgenic rice seedlings overexpressing OsDREB2B1 or OsDREB2B2 fused to sGFP were treated with high temperature (42°C) or H2O, and then total RNA was isolated. The control plant carried only empty vector. Transcripts were detected by RT-PCR. Transgene expression was detected using the primers indicated by black arrows in the schematic model of the transgenes. Endogenous OsDREB2B transcripts were detected using the primers A and B indicated in b. Actin was used as a control.]]
 
[[File:pic2.jpg|a Schematic models of OsDREB2B transcripts. The OsDREB2B gene contains three exons (E1, E2, E3) and two introns (I1, I2). Two kinds of transcripts are produced by alternative splicing. Arrows A and B indicate primers used for the PCR analyses in c and d. Arrows C and D indicate primers used for the qRT-PCR analysis in c. NLS, nuclear localisation signals; AP2, AP2/ERF DNAbinding domain. b Expression analysis of OsDREB2A under abiotic stress conditions. Total RNA was prepared from 2-week-old rice seedlings treated by high temperature (42°C), low temperature (4°C), drought and high salinity (250 mM NaCl) for the indicated time courses. H2O-treated plants were used as a control. The mRNA accumulation levels were analysed by qRT-PCR. The relative amounts of mRNA were calculated by defining the amount of OsDREB2B2 in the unstressed condition (0 min) as 1.0. Bars indicate standard deviations (SDs) (n = 3). c Expression analysis of OsDREB2B under abiotic stress conditions. RNA preparation and qRT-PCR were conducted as described in a. Specific primers for each transcript were used. d Analysis of the splicing mechanism of OsDREB2B. Two-week-old transgenic rice seedlings overexpressing OsDREB2B1 or OsDREB2B2 fused to sGFP were treated with high temperature (42°C) or H2O, and then total RNA was isolated. The control plant carried only empty vector. Transcripts were detected by RT-PCR. Transgene expression was detected using the primers indicated by black arrows in the schematic model of the transgenes. Endogenous OsDREB2B transcripts were detected using the primers A and B indicated in b. Actin was used as a control.]]
  
−
===Evolution===
+
===Evolution
−
  Sequence alignment analysis of whole proteins revealed that OsDREB2B shares high homology with ZmDREB2A<ref name="ref4" />, PgDREB2A<ref name="ref5" />,HvDRF1<ref name="ref6" /> and Wdreb2<ref name="ref7" />. ZmDREB2A, HvDRF1 and Wdreb2 were reported to have several alternatively spliced forms of transcripts, and one of the transcripts from each gene contains a short ORF like OsDREB2B. These short ORFs are also resulted from the 53-bp second exon of each gene. To know whether such a structure is conserved amongst OsDREB2B orthologues in the grass family, we searched other OsDREB2B orthologues from grass family plants in Phytozome(http://www.phytozome.net/index.php)and found two additional OsDREB2B orthologues. One orthologue was Sb09g016150, a gene from Sorghum bicolor, and the other was Bradi2g29960 from Brachypodium distachyon. According to their EST-based sequences,they were also expected to have a 53-bp exon that causes a transcript containing a short ORF.
+
Sequence alignment analysis of whole proteins revealed that OsDREB2B shares high homology with ZmDREB2A<ref name="ref4" />, PgDREB2A<ref name="ref5" />,HvDRF1<ref name="ref6" /> and Wdreb2<ref name="ref7" />. ZmDREB2A, HvDRF1 and Wdreb2 were reported to have several alternatively spliced forms of transcripts, and one of the transcripts from each gene contains a short ORF like OsDREB2B. These short ORFs are also resulted from the 53-bp second exon of each gene. To know whether such a structure is conserved amongst OsDREB2B orthologues in the grass family, we searched other OsDREB2B orthologues from grass family plants in Phytozome(http://www.phytozome.net/index.php)and found two additional OsDREB2B orthologues. One orthologue was Sb09g016150, a gene from Sorghum bicolor, and the other was Bradi2g29960 from Brachypodium distachyon. According to their EST-based sequences,they were also expected to have a 53-bp exon that causes a transcript containing a short ORF.
−
 
 
−
You can also add sub-section(s) at will.
 
  
 
==Labs working on this gene==
 
==Labs working on this gene==

Revision as of 04:24, 3 June 2014

Please input one-sentence summary here.

Annotated Information

Function

This gene is the most important gene amongst the rice DREB2-type genes for stress-responsive gene expression. It was strongly suggested that OsDREB2B2 works similarly to DREB2A CA in Arabidopsis because OsDREB2B2 could bind the DRE sequence and activate the reporter gene in Arabidopsis T87 protoplasts during the transactivation analysis. The degrees of morphological change, the expression levels of DREB2A target genes and the degrees of stress tolerance of the transgenic plants correlated with the expression levels of the transgene. These data suggest that OsDREB2B is a functional protein that improves stress tolerance in planta[1]. OsDREB2B activated target gene expression in both protoplasts and transgenic Arabidopsis.35S:OsDREB2B plants showed growth retardation as well as drought and heat-shock stress tolerance in a manner similar to 35S:DREB2A CA plants [2][3]. In addition, most of the DREB2A target genes tested were upregulated in 35S:OsDREB2B plants. These data indicate that OsDREB2B can function like DREB2A in Arabidopsis,but OsDREB2B does not require activation by posttranslational regulation. Phenotype, gene expression analysis and abiotic stress tolerance of 35S:OsDREB2B transgenic Arabidopsis. Three-week-old (a) and 40-day-old (b) transgenic Arabidopsis plants expressing Os-DREB2B2 under the control of the CaMV 35S promoter and TMV Ω sequence (35S:OsDREB2B). Control plants transformed with an empty vector (pGreenII0029) are also shown. c RNA gel blot analysis of the transgene and DREB2A target genes in transgenic Arabidopsis. Plants treated with drought (5 h) or high temperature (37°C, 5 h) stress and control plants (H2O) were used for RNA preparations. Ethidium bromide-stained rRNA images are shown as loading controls. d Drought stress tolerance tests of transgenic plants. Water was withheld from 3-week-old plants for 15 days. Photographs were taken 7 days after re-watering. Survival rates were obtained from three independent experiments and are indicated under the photographs. The plants with significantly higher survival rates compared to control plants are indicated by asterisks (χ2 test, *P < 0.05, **P < 0.001). e Heat-shock stress tolerance tests of transgenic plants. Nine-day-old plants were treated at 45°C for 1 h and returned to 22°C. Photographs were taken after two further weeks. Survival rates were obtained from three independent experiments and are indicated around the photograph. The plants with significantly higher survival rates as compared to control plants are indicated by asterisks, as described in d

Expression

Two forms of OsDREB2B transcripts were identified by RT-PCR. These transcripts were named OsDREB2B1 and OsDREB2B2. OsDREB2B1 was composed of three exons (E1, E2 and E3), whereas OsDREB2B2 was composed of exons E1 and E3. OsDREB2B2 contained a putative coding sequence of 373 amino acid (a.a.) residues, with putative nuclear localisation signals and a typical AP2/ERF DNA-binding domain. OsDREB2B1 contained a short ORF encoding a polypeptide of 93 a.a. residues without a nuclear localisation signal or an AP2/ERF DNA-binding domain because the 53-bp sequence of E2 causes a frame shift and premature termination. Thus, we regarded the protein encoded by OsDREB2B2 as OsDREB2B[1]. a Schematic models of OsDREB2B transcripts. The OsDREB2B gene contains three exons (E1, E2, E3) and two introns (I1, I2). Two kinds of transcripts are produced by alternative splicing. Arrows A and B indicate primers used for the PCR analyses in c and d. Arrows C and D indicate primers used for the qRT-PCR analysis in c. NLS, nuclear localisation signals; AP2, AP2/ERF DNAbinding domain. b Expression analysis of OsDREB2A under abiotic stress conditions. Total RNA was prepared from 2-week-old rice seedlings treated by high temperature (42°C), low temperature (4°C), drought and high salinity (250 mM NaCl) for the indicated time courses. H2O-treated plants were used as a control. The mRNA accumulation levels were analysed by qRT-PCR. The relative amounts of mRNA were calculated by defining the amount of OsDREB2B2 in the unstressed condition (0 min) as 1.0. Bars indicate standard deviations (SDs) (n = 3). c Expression analysis of OsDREB2B under abiotic stress conditions. RNA preparation and qRT-PCR were conducted as described in a. Specific primers for each transcript were used. d Analysis of the splicing mechanism of OsDREB2B. Two-week-old transgenic rice seedlings overexpressing OsDREB2B1 or OsDREB2B2 fused to sGFP were treated with high temperature (42°C) or H2O, and then total RNA was isolated. The control plant carried only empty vector. Transcripts were detected by RT-PCR. Transgene expression was detected using the primers indicated by black arrows in the schematic model of the transgenes. Endogenous OsDREB2B transcripts were detected using the primers A and B indicated in b. Actin was used as a control.

===Evolution Sequence alignment analysis of whole proteins revealed that OsDREB2B shares high homology with ZmDREB2A[4], PgDREB2A[5],HvDRF1[6] and Wdreb2[7]. ZmDREB2A, HvDRF1 and Wdreb2 were reported to have several alternatively spliced forms of transcripts, and one of the transcripts from each gene contains a short ORF like OsDREB2B. These short ORFs are also resulted from the 53-bp second exon of each gene. To know whether such a structure is conserved amongst OsDREB2B orthologues in the grass family, we searched other OsDREB2B orthologues from grass family plants in Phytozome(http://www.phytozome.net/index.php)and found two additional OsDREB2B orthologues. One orthologue was Sb09g016150, a gene from Sorghum bicolor, and the other was Bradi2g29960 from Brachypodium distachyon. According to their EST-based sequences,they were also expected to have a 53-bp exon that causes a transcript containing a short ORF.

Labs working on this gene

  • Japan International Research Center for Agricultural Sciences
  • Laboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
  • Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), Ibaraki 305-8686, Japan
  • RIKEN Plant Science Center, Yokohama 203-0045, Japan
  • CREST, Japan Science and Technology Corporation (JST), Japan

References

<references> [1] [2] [3] [4] [5] [6] [7]

Structured Information

Gene Name

Os05g0346200

Description

Similar to Ethylene response factor 1

Version

NM_001061795.1 GI:115463320 GeneID:4338484

Length

3312 bp

Definition

Oryza sativa Japonica Group Os05g0346200, 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

Chromosome 5

Location

Chromosome 5:16274887..16278198

Sequence Coding Region

16275185..16276081

Expression

GEO Profiles:Os05g0346200

Genome Context

<gbrowseImage1> name=NC_008398:16274887..16278198 source=RiceChromosome05 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008398:16274887..16278198 source=RiceChromosome05 preset=GeneLocation </gbrowseImage2>

Coding Sequence

<cdnaseq>atgaaggggaaaggaggaccggagaatacacgttgtgacttccgtggtgtgaggcaacgtacctggggcaagtgggttgctgaaattcgggagccgaatcagcaaagtagactctggttggggaccttcccaactgccgaagctgcagcttgtgcttatgacgaggcagccagagcaatgtatggtccaatggctcgcactaattttggccagcatcatgcccctgctgcttccgttcaggttgcactagcagctgtcaaatgtgctttacctggtggtggcttaacagcaagcaagtctagaacatccactcagggtgcatcagcagatgttcaagatgttttaactggtggcttatcagcatgcgagtccactacaacaacaattaataatcaatctgatgtcgtctctaccttacataagccagaagaggtttctgagatctctagtccactgagagctccaccagctgtcctggaagatggttctaatgaagacaaggctgaatcggttacctatgatgagaacattgtcagccagcagcgtgcccctcctgaagccgaggctagtaatggaagaggcgaggaggtctttgagcctctggaacctattgccagcctaccagaggaccaaggagattattgttttgatattgatgagatgctgagaatgatggaagctgaccctacgaacgagggtttgtggaaaggcgacaaagatggatcagacgccatcctggagcttggccaggatgaacctttctactacgaaggggttgatccaggcatgctggacaacttgctcaggtctgatgagccagcatggttattggcagatcctgcgatgttcatctccggtggcttcgaagatgactctcagttctttgagggcttgtga</cdnaseq>

Protein Sequence

<aaseq>MKGKGGPENTRCDFRGVRQRTWGKWVAEIREPNQQSRLWLGTFP TAEAAACAYDEAARAMYGPMARTNFGQHHAPAASVQVALAAVKCALPGGGLTASKSRT STQGASADVQDVLTGGLSACESTTTTINNQSDVVSTLHKPEEVSEISSPLRAPPAVLE DGSNEDKAESVTYDENIVSQQRAPPEAEASNGRGEEVFEPLEPIASLPEDQGDYCFDI DEMLRMMEADPTNEGLWKGDKDGSDAILELGQDEPFYYEGVDPGMLDNLLRSDEPAWL LADPAMFISGGFEDDSQFFEGL</aaseq>

Gene Sequence

<dnaseqindica>2118..3014#gcctttccttccgatctctctccctctctctcttcttcttcttcttccttccctctcaacccgacgacccacgcgaagcgaactctcgcgcgagacgagagtagtaaaccctagaaacctagaggagatccccaccaccaccatgacggtggatcagaggacgacggcgaaggcgatcatgccgccggtggagatgccgcccgtccagcccggaaggtgagatcttgctctccaacatcccttcactttcccctctctcttgtggttacttttagggggtggggtggttcgagtttgggcgggagttaggggttgggggttcgctcgattcgttggtggatcgagcgattttgggtgtatgggttgtggattttaggttggattggttgtatttgggcggggttgggtgctagggttggtggaatttggggggctagggtttcaggatctggttattttgcctgaatatgaattgggggtgaagggtgcagggttggattgtggggggtgaccgtgcggtgtagggatcatggaagatgttggggattttgttgggttgaaagctgggacagggtgggcgattgggggaggtgggatctctggatccccttttaattgggcggcagtgctttgctggagtccaaatcaatcgttgtgaattccatagctaatgtttgtagttgtatatattataggtaaattgagtgttttgggttcgaacccctttgcaagtttcggttttttcccctactgtgggtgactttggtagtagtattgtttcaatggtgtgattacctgttgattttgtgtgagactgttcgaattacttgttgtttagagtcttgagtagcaaagttatactactatggttctagtcagcaccatctccacagaaacgtgtcgtatgccccgagtcatctaacttaatgtcattctttgttgctgtacactgctgttatatttttgtaatttttgtcagtttaacttcgtaatacagtctctgatacatgtatgtctatttgtcttgtcttttggtaattagaaaatgtggaggcgaggaaagtactggaaaccttgattccgtccaaccgataggtatgactgctttgatttgaacacctttcgtaaacaggaagtactgattgagatgggtcccttgtgtccagcagtgaagtgtgagcacaaaataactgcttgtgtttcagcaggagctcttccctgtaatgagcatgcactcttggcccagcagacccccaagggagatgcgccatcagtgggctctaagatttggtgtgtttaaccgttctgatatgtctggcttgctcaatttgttggagcatgcgggctatgactaccaggcttaactggttttttagtatagagctgcacgaaagtattttttttccttgtcttttcaccagctggtttctgatcagctggtttaagcatattcggtttctctcttgatttgatcctgttcagctgttacattgtgtgaaatggaagaaacaataactgagtaggtccagtgaataaaataagcatcagtgcttttgagatgttacgagtatttttctaaacaattagctcgagcttgattgattgagtgaaatagtacatctatgtgcgtgttgcttgtatgaacttaaggaattgttcgcagaattcattgaaatgaataactggcaaattagagtttagttatcaagcgtgattatcatcataatagtacctgtttctgtggatatggtctgtttgtaggaacatatgaaagcatatgtgtttgtggagaacagttgatggcactggggttattgaacgcgtttagttcatgtttctgtggagatggtctaccttgtgggaaacattcattgttctgttctgctatgtccttttcccttggttatgtggatattttccctgaatctgtagaacaattactaaagttaagctccttgtttagcaggaaaaagcgaccacggagatcacgcgatggacctacttcagttgcagagaccatcaagcggtgggccgagctcaacaatcagcaggagcttgatccacagggtccaaagaaggcaaggaaggcacctgcaaagggttcaaagaagggctgcatgaaggggaaaggaggaccggagaatacacgttgtgacttccgtggtgtgaggcaacgtacctggggcaagtgggttgctgaaattcgggagccgaatcagcaaagtagactctggttggggaccttcccaactgccgaagctgcagcttgtgcttatgacgaggcagccagagcaatgtatggtccaatggctcgcactaattttggccagcatcatgcccctgctgcttccgttcaggttgcactagcagctgtcaaatgtgctttacctggtggtggcttaacagcaagcaagtctagaacatccactcagggtgcatcagcagatgttcaagatgttttaactggtggcttatcagcatgcgagtccactacaacaacaattaataatcaatctgatgtcgtctctaccttacataagccagaagaggtttctgagatctctagtccactgagagctccaccagctgtcctggaagatggttctaatgaagacaaggctgaatcggttacctatgatgagaacattgtcagccagcagcgtgcccctcctgaagccgaggctagtaatggaagaggcgaggaggtctttgagcctctggaacctattgccagcctaccagaggaccaaggagattattgttttgatattgatgagatgctgagaatgatggaagctgaccctacgaacgagggtttgtggaaaggcgacaaagatggatcagacgccatcctggagcttggccaggatgaacctttctactacgaaggggttgatccaggcatgctggacaacttgctcaggtctgatgagccagcatggttattggcagatcctgcgatgttcatctccggtggcttcgaagatgactctcagttctttgagggcttgtgatttccccttggcggcagccggccatactaaaattttctggtgctttggtcggctagctcctgcacatcgccctcaggatcagcaagagaaacactggaccggattgggttcgttggtggaactggatgagcatctagtagctaaggaaaaaagatccttttatttagttctgtaggcaatggaactccttgagaactccgtttcagtgtttgttaatttgataacgcttgcttgtttgtgtgtgtatatcgatctcttttgaagcaatgagaaaaaaaaaaggactgaagaaaatgtg</dnaseqindica>

External Link(s)

NCBI Gene:Os05g0346200, RefSeq:Os05g0346200

  1. ↑ 1.0 1.1 1.2 Matsukura S, Mizoi J, Yoshida T, et al. Comprehensive analysis of rice DREB2-type genes that encode transcription factors involved in the expression of abiotic stress-responsive genes[J]. Molecular Genetics and Genomics, 2010, 283(2): 185-196.
  2. ↑ 2.0 2.1 Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K, Yamaguchi-Shinozaki K (2006a) Functional analysis of an Arabidopsis transcription factor, DREB2A, involved in drought-responsive gene expression. Plant Cell 18:1292–1309
  3. ↑ 3.0 3.1 Sakuma Y, Maruyama K, Qin F, Osakabe Y, Shinozaki K, Yamaguchi-Shinozaki K (2006b) Dual function of an Arabidopsis transcription factor DREB2A in water-stress-responsive and heat-stress-responsive gene expression. Proc Natl Acad Sci USA 103:18822–18827
  4. ↑ 4.0 4.1 Qin F, Kakimoto M, Sakuma Y, Maruyama K, Osakabe Y, Tran LS,Shinozaki K, Yamaguchi-Shinozaki K (2007) Regulation and functional analysis of ZmDREB2A in response to drought and heat stresses in Zea mays L. Plant J 50:54–69
  5. ↑ 5.0 5.1 Agarwal P, Agarwal PK, Nair S, Sopory SK, Reddy MK (2007) Stress-inducible DREB2A transcription factor from Pennisetum glaucum is a phosphoprotein and its phosphorylation negatively regulates its DNA-binding activity. Mol Genet Genomics 277:189–198
  6. ↑ 6.0 6.1 Xue GP, Loveridge CW (2004) HvDRF1 is involved in abscisic acidmediated gene regulation in barley and produces two forms of AP2 transcriptional activators, interacting preferably with a CT-rich element. Plant J 37:326–339
  7. ↑ 7.0 7.1 Egawa C, Kobayashi F, Ishibashi M, Nakamura T, Nakamura C,Takumi S (2006) Differential regulation of transcript accumulation and alternative splicing of a DREB2 homolog under abiotic stress conditions in common wheat. Genes Genet Syst 81:77–91
Retrieved from "https://ngdc.cncb.ac.cn/ricewiki/index.php?title=Os05g0346200&oldid=176436"