Os06g0165600

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Annotated Information

Function

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 ).

Figure 2.Cold tolerance analysis of 35S OsDREB1D transgenic Arabidopsis.(from reference ).

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.. 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).. This OsDREB1D gene functions similarly as other DREB transcription factors .

Expression

The expression of OsDREB1D in rice may be controlled by a special mechanism for the redundancy of function.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.

Fig. 3.A model for signal transduction mediated by the DREB and ERF proteins.(from reference)

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.

Primer	Forward primer	Reverse primer
Gene amplication	5’ -TCGTTGTAGTAGCTCTGGTG-3’	5’-GGAAAAAGTTACCTCCTCCATCGAGCTC-3’
RT-PCR	5’-CGGCTGGGGTAAAGAAGTTGTC-3’	5’-CATGAGTCTCCGGGAGGAAGTG-3’

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 (Figure 4). The DREB subfamily proteins were further divided into six subgroups, A-1–A-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 .

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)

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..

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)

Knowledge Extension

The DREB proteins contain an ERF/AP2 DNA-binding domain. The ERF/AP2 domain is quite conserved in Fig.6..

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)

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. .

Fig. 7. Relationships among some DREB proteins as illustrated by Tree View produced by DNA STAR, ClustalW. Scale indicates branch length. (from reference)

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

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Structured Information

Gene Name	Os06g0165600
Description	CRT/DRE binding factor (Transcription factor RCBF4)
Version	NM_001063444.1 GI:115466619 GeneID:4340239
Length	904 bp
Definition	Oryza sativa Japonica Group Os06g0165600, 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 6
Location	Chromosome 6:3309920..3310823
Sequence Coding Region	3309944..3310705
Expression	GEO Profiles:Os06g0165600
Genome Context	<gbrowseImage1> name=NC_008399:3309920..3310823 source=RiceChromosome06 preset=GeneLocation </gbrowseImage1>
Gene Structure	<gbrowseImage2> name=NC_008399:3309920..3310823 source=RiceChromosome06 preset=GeneLocation </gbrowseImage2>
Coding Sequence	<cdnaseq>atggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtag</cdnaseq>
Protein Sequence	<aaseq>MEKNTAASGQLMTSSAEATPSSPKRPAGRTKFQETRHLVFRGVR WRGCAGRWVCKVRVPGSRGDRFWIGTSDTAEETARTHDAAMLALCGASASLNFADSAW LLHVPRAPVVSGLRPPAARCATRCLQGHRRVPAPGRGSTATATATSGDAASTAPPSAP VLSAKQCEFIFLSSLDCWMLMSKLISSSRAKGSLCLRKNPISFCMVTNSYTALLLEYI ILQMNSMIVLIHELSKYQVFLLLTMITHHLFQWRR</aaseq>
Gene Sequence	<dnaseqindica>25..786#actgcttgagacgtcgcacacgtcatggagaagaacaccgccgccagcgggcaattgatgacctcctccgcggaggcgacgccgtcgtcgccgaagcggccggcggggcgaaccaagttccaggagacgaggcacctagtgttccgtggggtgcgatggcgtgggtgcgcggggcggtgggtgtgcaaggtgcgtgtcccgggcagccgcggtgaccgtttctggataggcacgtctgacaccgccgaggagaccgcgcgcacgcacgacgccgccatgctcgccttgtgcggggcctccgccagcctcaacttcgccgactctgcctggctgctccacgtcccgcgcgcccccgtcgtctccggactccggccaccagctgcccgatgtgcaacgcgctgcctgcaaggccatcgccgagttccagcgccgggccgggggagcaccgccactgccactgccacctccggcgatgctgcatcgaccgctcctccgtcggcacccgttctgtcagccaaacaatgcgaattcatctttctttcttcactagattgttggatgttaatgtcaaagcttatcagcagtagcagagcaaaaggatcgttgtgcctgcgaaaaaatcccatttcattttgcatggttacaaattcttacactgctcttttgctcgaatacattatattgcagatgaattcaatgatcgttttaatccacgaattatcaaaatatcaagtctttctgctactaaccatgataacacaccacctttttcaatggaggaggtaggcgcggacgccctcgccatcatcgtcgatgtcgccactgatgacgaggtccgcgccgctcaccagctcgcacgcctcgtcgtcgtccatgctcgccacctcggtccagcagctgaacc</dnaseqindica>
External Link(s)	NCBI Gene:Os06g0165600, RefSeq:Os06g0165600