Difference between revisions of "Os06g0165600"

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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" />.
  
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===Mutation===
 
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To identify genes involved in the control of rice tillering, Li et al. have screened for mutants with altered tiller numbers from collections derived from spontaneous mutations or g-ray radiation and ethyl methanesulphonate (EMS) mutagenesis, and they found that '''''moc1''''' plants nearly completely lose their tillering ability after a spontaneous '''''moc1''''' mutant, producing only one main culm, in contrast to the multiple tillers in wild-type plants<ref name="ref1" />. They amplified the corresponding ORF from '''''moc1''''' and wild-type plants with polymerase chain reaction (PCR) and sequenced it. DNA sequence comparison revealed a 1.9-kb retrotransposon inserted in this ORF in the '''''moc1''''' mutant. Confirmation of the retrotransposon-interrupted ORF as '''''MOC1''''' was achieved by functional complementation<ref name="ref1" />. Genetic analysis with reciprocal crosses between moc1 and wild-type plants revealed that '''''moc1''''' possesses a recessive mutation in a single nuclear locus<ref name="ref1" />.
 
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We can see the effects of '''''moc1''''' mutant on rice tillering from the following picture 2.
 
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[[File:Moc1 mutant.jpg|right|thumb|150px|''Figure 2． Phenotype and complementation of the moc1 mutant.(from reference <ref name="ref1" />).'']]
 
  
 
===Expression===
 
===Expression===
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The '''''MOC1''''' spatial and temporal expression patterns revealed by RNA in situ hybridization are consistent with the function of '''''MOC1''''' for axillary meristem initiation and tiller bud formation. '''''MOC1''''' expression is detectable in a small number of epidermal or subepidermal cells at the leaf axils before any visible morphological changes at the position where axillary meristems will initiate. Thereafter, '''''MOC1''''' is mainly expressed in the protuberance and axillary meristem and extended to the entire tiller bud including the axillary leaf primordia and young leaves, whereas no signal could be observed in the shoot apical meristem (SAM) <ref name="ref1" />.
+
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" />.
−
Slight overexpression of the '''''MOC1''''' gene can increased tiller number and reduced plant height<ref name="ref1" />.
+
[[File:Evolution fig3.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"
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|-
 
|-
 
| rowspan="1"|Gene amplication
 
| rowspan="1"|Gene amplication
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| | 5’ -TCGTTGTAGTAGCTCT GGTG-3’
+
| | 5’ -TCGTTGTAGTAGCTCTGGTG-3’
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| | 5’-CTAACTAGAGATCGAGTAGC-3'<ref name="ref1" />
+
| | 5’-GGAAAAAGTTACCTCCTCCATCGAGCTC-3’<ref name="ref1" />
 
|-
 
|-
 
| rowspan="1"|RT-PCR
 
| rowspan="1"|RT-PCR
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| | 5'-AGACGCTCGCCGTGAACT-3'
+
| | 5’-CGGCTGGGGTAAAGAAGTTGTC-3’
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| | 5'-GCCTTCACCCACTTCAAGA-3'<ref name="ref8" />
+
| | 5’-CATGAGTCTCCGGGAGGAAGTG-3’<ref name="ref1" />
 
|}
 
|}
  
 
===Evolution===
 
===Evolution===
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'''''MONOCULM1'''''('''''MOC1''''') genomic regions were sequenced and compared across 14 Oryza genomes by Lu et al, and the result of genomic alignment of the '''''MOC1''''' region in 18 Oryza genomes or subgenomes can be seen from Fig.3<ref name="ref2" />.
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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
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[[File:Evolution fig3.jpg|right|thumb|150px|Fig. 3. Genomic alignment of the MOC1 region in 18 Oryza genomes or subgenomes. The species are ordered by genome type. Horizontal light blue bars represent genomic sequence in the MOC1 region. Gene models are shown in black rectangles. Transposons (at least 1 kb) are shown in red and pink for retrotransposons and DNA transposons, respectively. Lines/curves connect orthologous genes with each other and orthologous transposons with each other(from reference<ref name="ref2" />)'']]
+
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>
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Sequencing and annotation of the '''''MOC1''''' region of the 14 Oryza species, including 10 diploids and 4 allotetraploids, revealed highly conserved gene colinearity and structure in the '''''MOC1''''' region<ref name="ref2" />. Large and apparently noncoding sequences flanking the '''''MOC1''''' gene were observed to be under strong purifying selection<ref name="ref2" />. '''''MOC1''''' is highly homologous with the tomato Lateral suppressor ('''''Ls''''') gene. Rice '''''MONOCULM1''''' ('''''MOC1''''') and Arabidopsis '''''LATERAL SUPPRESSOR''''' ('''''LAS''''') are orthologs, which play important roles in axillary meristems initiation in rice and Arabidopsis<ref name="ref1" /><ref name="ref9" />.
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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===
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'''''TEOSINTE BRANCHED1''''' ('''''TB1''''') encodes a putative transcription factor of the TCP protein family, and impairment of '''''TB1''''' leading to enhance lateral branching in maize suggests its negative regulatory role in controlling the axillary bud outgrowth<ref name="ref10" /><ref name="ref11" />. The rice ortholog '''''OsTB1'''''/'''''FINE CULM1''''' ('''''FC1''''') shows similar characteristics and therefore also negatively regulates rice tillering <ref name="ref12" />. Consistent with the function of '''''TB1''''' in maize, overexpression of '''''OsTB1''''' reduces rice tillers severely while its loss-of-function mutation in the classical mutant fine culm (fcn1) promotes the outgrowth of rice tillers<ref name="ref7" />. The results reveal that the pivotal role of '''''OsTB1''''' is to control the outgrowth of rice tiller buds rather than the initiation of tiller buds<ref name="ref12" />. D10 also functions as a negative regulator and works independently of '''''OsTB1'''''/'''''FC1''''' in rice<ref name="ref13" />.
+
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" />)'']]
  
 
===Evolution===
 
===Evolution===

Revision as of 09:06, 22 May 2014

Please input one-sentence summary here.

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 [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])

Evolution

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Labs working on this gene

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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

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Cite error: Invalid <ref> tag; no text was provided for refs named ref1
  2. ↑ 2.0 2.1 2.2 Cite error: Invalid <ref> tag; no text was provided for refs named ref2
  3. ↑ 3.0 3.1 3.2 3.3 3.4 3.5 Cite error: Invalid <ref> tag; no text was provided for refs named ref3
  4. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref4
  5. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref5
  6. ↑ 6.0 6.1 6.2 6.3 6.4 Cite error: Invalid <ref> tag; no text was provided for refs named ref6
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