Difference between revisions of "Os06g0165600"
(→Annotated Information) |
(→Structured Information) |
||
| (25 intermediate revisions by one other user not shown) | |||
| Line 3: | Line 3: | ||
==Annotated Information== | ==Annotated Information== | ||
===Function=== | ===Function=== | ||
| + | [[File:Figure 1.Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.png|right|thumb|150px|Figure 1. Over-expression of '''''OsDREB1D''''' and high-salt tolerance analysis in transgenic plants. (A) Over-expression of '''''OsDREB1D''''' gene was analyzed in transgenic Arabidopsis.(from reference <ref name="ref1" />).'']] | ||
| + | [[File:Figure 2.Cold tolerance analysis of 35S '''''OsDREB1D''''' transgenic Arabidopsis.jpg|right|thumb|150px|Figure 2.Cold tolerance analysis of 35S '''''OsDREB1D''''' transgenic Arabidopsis.(from reference <ref name="ref1" />).'']] | ||
The '''''OsDREB1D'''''， a special DREB (dehydration responsive element binding protein) homologous gene, whose transcripts cannot be detected in rice (Oryza sativa L), either with or without stress treatments, was amplified from the rice genome DNA.<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The over-expression of '''''OsDREB1D''''',a gene encoding a protein that is the closest homolog of the C-repeat (CRT)binding factor/dehydration-responsiveelementbinding protein 1(CBF/DREB1) in rice, conferred cold and high-salt tolerance in transgenic plants, and that transgenic plants were also insensitive to ABA (abscisic acid).<ref name="ref1" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. This '''''OsDREB1D''''' gene functions similarly as other DREB transcription factors <ref name="ref1" />. | The '''''OsDREB1D'''''， a special DREB (dehydration responsive element binding protein) homologous gene, whose transcripts cannot be detected in rice (Oryza sativa L), either with or without stress treatments, was amplified from the rice genome DNA.<ref name="ref1" /><ref name="ref2" /><ref name="ref3" />. The over-expression of '''''OsDREB1D''''',a gene encoding a protein that is the closest homolog of the C-repeat (CRT)binding factor/dehydration-responsiveelementbinding protein 1(CBF/DREB1) in rice, conferred cold and high-salt tolerance in transgenic plants, and that transgenic plants were also insensitive to ABA (abscisic acid).<ref name="ref1" /><ref name="ref3" /><ref name="ref4" /><ref name="ref5" />. This '''''OsDREB1D''''' gene functions similarly as other DREB transcription factors <ref name="ref1" />. | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
===Expression=== | ===Expression=== | ||
| − | The ''''' | + | The expression of '''''OsDREB1D''''' in rice may be controlled by a special mechanism for the redundancy of function<ref name="ref1" />.'''''OsDREB1D''''' gene expression was up-regulated by drought stress and ABA treatment, but not by low temperature. Over-expression of CBF4 in transgenic Arabidopsis plants improved tolerance to freezing and drought stress. The '''''OsDREB1D''''' mRNA in any organs including roots, leaves, shoots, growing points, spike at late bolting stage and seeds of rice (Oryza sativaL.) with, or without stress treatments. The expression of '''''OsDREB1D''''' is not detected in rice plants, either with or without stress treatment. However，an independent group submitted the cDNA sequence for '''''OsDREB1D''''' to GeneBank (AF243384.1). Therefore, it is possible that '''''OsDREB1D''''' is expressed in a different specific growth stage or organ. The mRNA of '''''OsDREB1D''''' was likely to be degraded in particular developmental stage for its redundant function<ref name="ref1" />. |
| − | + | [[File:fig3A model for.jpg|right|thumb|150px|Fig. 3.A model for signal transduction mediated by the DREB and ERF proteins.(from reference<ref name="ref6" />)'']] | |
| + | DNA-gel blot analysis of '''''OsDREB1D''''' revealed multiple bands, implying multiple copies. The '''''OsDREB1D''''' mRNA was not detected in any plants either with or without stress treatments<ref name="ref2" />. | ||
{| class='wikitable' style="text-align:center" | {| class='wikitable' style="text-align:center" | ||
| Line 22: | Line 20: | ||
|- | |- | ||
| rowspan="1"|Gene amplication | | rowspan="1"|Gene amplication | ||
| − | | | 5’ - | + | | | 5’ -TCGTTGTAGTAGCTCTGGTG-3’ |
| − | | | 5’- | + | | | 5’-GGAAAAAGTTACCTCCTCCATCGAGCTC-3’<ref name="ref1" /> |
|- | |- | ||
| rowspan="1"|RT-PCR | | rowspan="1"|RT-PCR | ||
| − | | | | + | | | 5’-CGGCTGGGGTAAAGAAGTTGTC-3’ |
| − | | | | + | | | 5’-CATGAGTCTCCGGGAGGAAGTG-3’<ref name="ref1" /> |
|} | |} | ||
===Evolution=== | ===Evolution=== | ||
| − | + | We previously classified 145 ERF/AP2-related proteins in Arabidopsisinto five groups–AP2 subfamily, RAV subfamily, DREB subfamily, ERF subfamily, and one very specific gene,AL079349–on the basis of similarity of the amino acid sequence of the DNA-binding domain <ref name="ref6" />(Figure 4). The DREB subfamily proteins were further divided into six subgroups, A-1–A-6 <ref name="ref6" />. We analyzed the similarities of the ERF/AP2 domains of the | |
| − | [[File:Evolution | + | OsDREB proteins and compared them with those inArabidopsisand other genera. The OsDREB1 proteins were classified into the A-1 (DREB1/CBF) subgroup. The |
| + | DREB1-type ERF/AP2 domains in the three monocots were closely related to each other but distant from those in the dicots <ref name="ref2" /><ref name="ref6" />. | ||
| + | [[File:Evolution fig4.jpg|right|thumb|150px|Fig. 4. Phylogenic tree of ERF/AP2-related proteins. The bootstrapped tree file was produced by CLUSTAL W from sequences shown in Fig. 3. A-1 to A-6 and B-1 to B-6 indicate subgroups shown in Fig. 3. Scale indicates branch length. To simplify the dendrogram, amino acid sequences deduced from genomic sequences were excluded, except for the members of the B-5 subgroup and the AP2-like group. ORCA1 and ORCA2 (41), and ORCA3 (42) were isolated from Catharanthus roseus,BnDREB (AF084185) fromBrassica napus, and Tsi1 (AF058827) fromNicotiana tabacum.(from reference<ref name="ref6" />)'']] | ||
<br> | <br> | ||
| − | + | Phylogenetic analysis was carried out based on the similarities of AP2 domains in AP2/EREBP proteins from rice and Arabidopsis(Fig. 5). The '''''OsDREB1D''''' was closest to '''''OsDREB1A''''' on the phylogenetic tree. These two genes show 70% identity at the amino acid level over the entire ORFs (data not shown), and they are the highest homologs in the genes included in the phylogenetic tree. It seems likely that '''''OsDREB1D''''' and '''''OsDREB1A''''' may be orthologous and play similar roles under stress conditions.<ref name="ref1" />. | |
| + | [[File:Evolution fig5.jpg|right|thumb|150px|Fig. 5. Phylogenetic analysis of '''''OsDREB1D'''''.Phylogenetic tree showing the relationships between '''''OsDREB1D''''' and other DREB proteins from Arabidopsisand rice (AtCBF1: NM118681; AtCBF2:NM118679; AtCBF3:AF074602; AtCBF4:NM124578; AtDREB2A: AB016570; AtDREB2C:NC003071; OsDREB1A: AF300970; OsDREB1B: AF300972; OsDREB1C: AP001168; OsDREB2A: AF300971). The neighbor-joining tree was based on an alignment of the conserved sequence of AP2 domain. Bootstrap values are shown on branches(from reference<ref name="ref1" />)'']] | ||
| + | |||
===Knowledge Extension=== | ===Knowledge Extension=== | ||
| − | + | The DREB proteins contain an ERF/AP2 DNA-binding domain. The ERF/AP2 domain is quite conserved in Fig.6.<ref name="ref3" />. | |
| + | [[File:Evolution fig6.jpg|right|thumb|150px|Fig.6. Comparison of amino acid alignment of the DREB proteins.aDREB1-typeAhDREB1(AF274033), AtDREB1A(AB007787), | ||
| + | AtDREB1B(AB007788), AtDREB1C(AB007789), CaDREBLP1(AY496155), OsDREB1A(AF300970), OsDREB1B(AF300972),OsDREB1C(AP001168), OsDREB1D(AB023482)(from reference<ref name="ref3" />)'']] | ||
| + | <br> | ||
| + | The DREB1/CBF1-type NLS consensus PKRPAGRTKFRETRHP distinguishes these proteins from other ERF/AP2 proteins. The DSAW motif at the end of the ERF/AP2 domain and LWSY motif at the end of the C-terminal are conserved in most of the DREB1-type proteins. Phylogenetic relationship among some of the reported DREB-type proteins is shown in Fig.7. <ref name="ref3" />. | ||
| + | [[File:Evolution fig7.jpg|right|thumb|150px|Fig. 7. Relationships among some DREB proteins as illustrated by Tree View produced by DNA STAR, ClustalW. Scale indicates branch length. (from reference<ref name="ref3" />)'']] | ||
| − | === | + | ==Labs working on this gene== |
| − | |||
| − | + | *College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China | |
| − | + | *Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China | |
| − | + | *Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan | |
| − | + | *Japan Society for the Promotion of Science, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan | |
| + | *Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan | ||
| + | *Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan | ||
| + | *Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha,China | ||
| + | *Department of Life Science, Sogang University, Seoul 121-742, Korea | ||
==References== | ==References== | ||
| − | + | <references> | |
| + | <ref name="ref1">Zhang Y, et al. (2009) Expression of a rice DREB1 gene, OsDREB1D, enhances cold and high-salt tolerance in transgenic Arabidopsis. BMB reports 42(8):486-492.</ref> | ||
| + | <ref name="ref2">Dubouzet JG, et al. (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. The Plant journal : for cell and molecular biology 33(4):751-763.</ref> | ||
| + | <ref name="ref3">Agarwal P, Agarwal P, Reddy MK, & Sopory S (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25(12):1263-1274.</ref> | ||
| + | <ref name="ref4">Mao D & Chen C (2012) Colinearity and Similar Expression Pattern of Rice <italic>DREB1s</italic> Reveal Their Functional Conservation in the Cold-Responsive Pathway. PloS one 7(10):e47275.</ref> | ||
| + | <ref name="ref5">Lee SC, Kim SH, & Kim SR (2013) Drought inducible OsDhn1 promoter is activated by OsDREB1A and OsDREB1D. Journal of Plant Biology 56(2):115-121.</ref> | ||
| + | <ref name="ref6">Sakuma Y, et al. (2002) DNA-Binding Specificity of the ERF/AP2 Domain of Arabidopsis DREBs, Transcription Factors Involved in Dehydration- and Cold-Inducible Gene Expression. Biochemical and Biophysical Research Communications 290(3):998-1009.</ref> | ||
| + | </references> | ||
==Structured Information== | ==Structured Information== | ||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
[[Category:Genes]] | [[Category:Genes]] | ||
[[Category:Japonica mRNA]] | [[Category:Japonica mRNA]] | ||
Latest revision as of 08:07, 12 June 2015
Please input one-sentence summary here.
Contents
Annotated Information
Function
_Over-expression_of_%27%27%27%27%27OsDREB1D%27%27%27%27%27_gene_was_analyzed_in_transgenic_Arabidopsis.png){kind=spacer}
Figure 1. Over-expression of OsDREB1D and high-salt tolerance analysis in transgenic plants. (A) Over-expression of OsDREB1D gene was analyzed in transgenic Arabidopsis.(from reference [1]).
Figure 2.Cold tolerance analysis of 35S OsDREB1D transgenic Arabidopsis.(from reference [1]).
The OsDREB1D， a special DREB (dehydration responsive element binding protein) homologous gene, whose transcripts cannot be detected in rice (Oryza sativa L), either with or without stress treatments, was amplified from the rice genome DNA.[1][2][3]. The over-expression of OsDREB1D,a gene encoding a protein that is the closest homolog of the C-repeat (CRT)binding factor/dehydration-responsiveelementbinding protein 1(CBF/DREB1) in rice, conferred cold and high-salt tolerance in transgenic plants, and that transgenic plants were also insensitive to ABA (abscisic acid).[1][3][4][5]. This OsDREB1D gene functions similarly as other DREB transcription factors [1].
Expression
The expression of OsDREB1D in rice may be controlled by a special mechanism for the redundancy of function[1].OsDREB1D gene expression was up-regulated by drought stress and ABA treatment, but not by low temperature. Over-expression of CBF4 in transgenic Arabidopsis plants improved tolerance to freezing and drought stress. The OsDREB1D mRNA in any organs including roots, leaves, shoots, growing points, spike at late bolting stage and seeds of rice (Oryza sativaL.) with, or without stress treatments. The expression of OsDREB1D is not detected in rice plants, either with or without stress treatment. However，an independent group submitted the cDNA sequence for OsDREB1D to GeneBank (AF243384.1). Therefore, it is possible that OsDREB1D is expressed in a different specific growth stage or organ. The mRNA of OsDREB1D was likely to be degraded in particular developmental stage for its redundant function[1].
Fig. 3.A model for signal transduction mediated by the DREB and ERF proteins.(from reference[6])
DNA-gel blot analysis of OsDREB1D revealed multiple bands, implying multiple copies. The OsDREB1D mRNA was not detected in any plants either with or without stress treatments[2].
| Primer | Forward primer | Reverse primer |
|---|---|---|
| Gene amplication | 5’ -TCGTTGTAGTAGCTCTGGTG-3’ | 5’-GGAAAAAGTTACCTCCTCCATCGAGCTC-3’[1] |
| RT-PCR | 5’-CGGCTGGGGTAAAGAAGTTGTC-3’ | 5’-CATGAGTCTCCGGGAGGAAGTG-3’[1] |
Evolution
We previously classified 145 ERF/AP2-related proteins in Arabidopsisinto five groups–AP2 subfamily, RAV subfamily, DREB subfamily, ERF subfamily, and one very specific gene,AL079349–on the basis of similarity of the amino acid sequence of the DNA-binding domain [6](Figure 4). The DREB subfamily proteins were further divided into six subgroups, A-1–A-6 [6]. We analyzed the similarities of the ERF/AP2 domains of the OsDREB proteins and compared them with those inArabidopsisand other genera. The OsDREB1 proteins were classified into the A-1 (DREB1/CBF) subgroup. The DREB1-type ERF/AP2 domains in the three monocots were closely related to each other but distant from those in the dicots [2][6].
Fig. 4. Phylogenic tree of ERF/AP2-related proteins. The bootstrapped tree file was produced by CLUSTAL W from sequences shown in Fig. 3. A-1 to A-6 and B-1 to B-6 indicate subgroups shown in Fig. 3. Scale indicates branch length. To simplify the dendrogram, amino acid sequences deduced from genomic sequences were excluded, except for the members of the B-5 subgroup and the AP2-like group. ORCA1 and ORCA2 (41), and ORCA3 (42) were isolated from Catharanthus roseus,BnDREB (AF084185) fromBrassica napus, and Tsi1 (AF058827) fromNicotiana tabacum.(from reference[6])
Phylogenetic analysis was carried out based on the similarities of AP2 domains in AP2/EREBP proteins from rice and Arabidopsis(Fig. 5). The OsDREB1D was closest to OsDREB1A on the phylogenetic tree. These two genes show 70% identity at the amino acid level over the entire ORFs (data not shown), and they are the highest homologs in the genes included in the phylogenetic tree. It seems likely that OsDREB1D and OsDREB1A may be orthologous and play similar roles under stress conditions.[1].
Fig. 5. Phylogenetic analysis of OsDREB1D.Phylogenetic tree showing the relationships between OsDREB1D and other DREB proteins from Arabidopsisand rice (AtCBF1: NM118681; AtCBF2:NM118679; AtCBF3:AF074602; AtCBF4:NM124578; AtDREB2A: AB016570; AtDREB2C:NC003071; OsDREB1A: AF300970; OsDREB1B: AF300972; OsDREB1C: AP001168; OsDREB2A: AF300971). The neighbor-joining tree was based on an alignment of the conserved sequence of AP2 domain. Bootstrap values are shown on branches(from reference[1])
Knowledge Extension
The DREB proteins contain an ERF/AP2 DNA-binding domain. The ERF/AP2 domain is quite conserved in Fig.6.[3].
Fig.6. Comparison of amino acid alignment of the DREB proteins.aDREB1-typeAhDREB1(AF274033), AtDREB1A(AB007787), AtDREB1B(AB007788), AtDREB1C(AB007789), CaDREBLP1(AY496155), OsDREB1A(AF300970), OsDREB1B(AF300972),OsDREB1C(AP001168), OsDREB1D(AB023482)(from reference[3])
The DREB1/CBF1-type NLS consensus PKRPAGRTKFRETRHP distinguishes these proteins from other ERF/AP2 proteins. The DSAW motif at the end of the ERF/AP2 domain and LWSY motif at the end of the C-terminal are conserved in most of the DREB1-type proteins. Phylogenetic relationship among some of the reported DREB-type proteins is shown in Fig.7. [3].
Fig. 7. Relationships among some DREB proteins as illustrated by Tree View produced by DNA STAR, ClustalW. Scale indicates branch length. (from reference[3])
Labs working on this gene
- College of Bioscience and Biotechnology, Yangzhou University, Yangzhou 225009, China
- Biotechnology Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai 201106, China
- Biological Resources Division, Japan International Research Center for Agricultural Sciences (JIRCAS), 1-1 Ohwashi, Tsukuba, Ibaraki 305-8686, Japan
- Japan Society for the Promotion of Science, 4-1-8 Motomachi, Kawaguchi, Saitama 332-0012, Japan
- Laboratory of Plant Molecular Biology, RIKEN Tsukuba Institute, 3-1-1 Koyadai, Tsukuba, Ibaraki 305-0074, Japan
- Plant Functional Genomics Research Group, RIKEN Genomic Sciences Center, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama City, Kanagawa 230-0045, Japan
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences, Changsha,China
- Department of Life Science, Sogang University, Seoul 121-742, Korea
References
- ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Zhang Y, et al. (2009) Expression of a rice DREB1 gene, OsDREB1D, enhances cold and high-salt tolerance in transgenic Arabidopsis. BMB reports 42(8):486-492.
- ↑ 2.0 2.1 2.2 Dubouzet JG, et al. (2003) OsDREB genes in rice, Oryza sativa L., encode transcription activators that function in drought-, high-salt- and cold-responsive gene expression. The Plant journal : for cell and molecular biology 33(4):751-763.
- ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Agarwal P, Agarwal P, Reddy MK, & Sopory S (2006) Role of DREB transcription factors in abiotic and biotic stress tolerance in plants. Plant Cell Rep 25(12):1263-1274.
- ↑ Mao D & Chen C (2012) Colinearity and Similar Expression Pattern of Rice <italic>DREB1s</italic> Reveal Their Functional Conservation in the Cold-Responsive Pathway. PloS one 7(10):e47275.
- ↑ Lee SC, Kim SH, & Kim SR (2013) Drought inducible OsDhn1 promoter is activated by OsDREB1A and OsDREB1D. Journal of Plant Biology 56(2):115-121.
- ↑ 6.0 6.1 6.2 6.3 6.4 Sakuma Y, et al. (2002) DNA-Binding Specificity of the ERF/AP2 Domain of Arabidopsis DREBs, Transcription Factors Involved in Dehydration- and Cold-Inducible Gene Expression. Biochemical and Biophysical Research Communications 290(3):998-1009.
