Difference between revisions of "Os06g0165600"

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(→‎Annotated Information)
(→‎Annotated Information)
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==Annotated Information==
 
==Annotated Information==
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'''Function'''
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===Function===
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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" />.
 +
[[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. From left to right is 8217-1, 8217-2, 8217-4, respectively. RT-PCR was used to determine transcript abundance in two-week-old plants. (B-D) The seed germination rates of transgenic and wildtype plants were measured on MS plates containing 0 (B) 75 (C) 100 mM (D) NaCl at 3 to 10 d after sowing. Each value is the average of ＞ 80 transformants with the standard error of at least two replicates. Percentages of germinated seeds were obtained and scored as germination rates.jpg|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 left to right is 8217-1, 8217-2, 8217-4, respectively. RT-PCR was used to determine transcript abundance in two-week-old plants. (B-D) The seed germination rates of transgenic and wildtype plants were measured on MS plates containing 0 (B) 75 (C) 100 mM (D) NaCl at 3 to 10 d after sowing. Each value is the average of ＞ 80 transformants with the standard error of at least two replicates. Percentages of germinated seeds were obtained and scored as germination rates.(from reference <ref name="ref1" />).'']]
  
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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
+
===Mutation===
−
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]
+
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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[[File:BC12_1.jpg|right|thumb|320px|'''Figure 1.''' '' '''BC12''' Mutant VS. WT(from reference) <ref name="ref2" />.'']]
+
We can see the effects of '''''moc1''''' mutant on rice tillering from the following picture 2.
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'''Expression'''
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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" />).'']]
  
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The expression of OsDREB1D in rice may be controlled by a special mechanism for the redundancy of function. [1]
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===Expression===
 +
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" />.
 +
Slight overexpression of the '''''MOC1''''' gene can increased tiller number and reduced plant height<ref name="ref1" />.
 +
 
 +
{| class='wikitable' style="text-align:center"
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|-
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! | Primer
 +
! | Forward primer
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! | Reverse primer
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|-
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| rowspan="1"|Gene amplication
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| | 5’ -TCGTTGTAGTAGCTCT GGTG-3’
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| | 5’-CTAACTAGAGATCGAGTAGC-3'<ref name="ref1" />
 +
|-
 +
| rowspan="1"|RT-PCR
 +
| | 5'-AGACGCTCGCCGTGAACT-3'
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| | 5'-GCCTTCACCCACTTCAAGA-3'<ref name="ref8" />
 +
|}
 +
 
 +
===Evolution===
 +
'''''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" />.
 +
[[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" />)'']]
 +
<br>
 +
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" />.
 +
 
 +
===Knowledge Extension===
 +
'''''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" />.
  
 
===Evolution===
 
===Evolution===

Revision as of 07:57, 22 May 2014

Please input one-sentence summary here.

Annotated Information

Function

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]. [[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. From left to right is 8217-1, 8217-2, 8217-4, respectively. RT-PCR was used to determine transcript abundance in two-week-old plants. (B-D) The seed germination rates of transgenic and wildtype plants were measured on MS plates containing 0 (B) 75 (C) 100 mM (D) NaCl at 3 to 10 d after sowing. Each value is the average of ＞ 80 transformants with the standard error of at least two replicates. Percentages of germinated seeds were obtained and scored as germination rates.jpg|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 left to right is 8217-1, 8217-2, 8217-4, respectively. RT-PCR was used to determine transcript abundance in two-week-old plants. (B-D) The seed germination rates of transgenic and wildtype plants were measured on MS plates containing 0 (B) 75 (C) 100 mM (D) NaCl at 3 to 10 d after sowing. Each value is the average of ＞ 80 transformants with the standard error of at least two replicates. Percentages of germinated seeds were obtained and scored as germination rates.(from reference [1]).]]

Mutation

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[1]. 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[1]. Genetic analysis with reciprocal crosses between moc1 and wild-type plants revealed that moc1 possesses a recessive mutation in a single nuclear locus[1]. We can see the effects of moc1 mutant on rice tillering from the following picture 2.

Figure 2． Phenotype and complementation of the moc1 mutant.(from reference [1]).

Expression

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) [1]. Slight overexpression of the MOC1 gene can increased tiller number and reduced plant height[1].

Primer Forward primer Reverse primer
Gene amplication 5’ -TCGTTGTAGTAGCTCT GGTG-3’ 5’-CTAACTAGAGATCGAGTAGC-3'[1]
RT-PCR 5'-AGACGCTCGCCGTGAACT-3' 5'-GCCTTCACCCACTTCAAGA-3'[6]

Evolution

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[2].

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[2])


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[2]. Large and apparently noncoding sequences flanking the MOC1 gene were observed to be under strong purifying selection[2]. 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[1][7].

Knowledge Extension

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[8][9]. The rice ortholog OsTB1/FINE CULM1 (FC1) shows similar characteristics and therefore also negatively regulates rice tillering [10]. 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[11]. 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[10]. D10 also functions as a negative regulator and works independently of OsTB1/FC1 in rice[12].

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 1.11 Cite error: Invalid <ref> tag; no text was provided for refs named ref1
  2. ↑ 2.0 2.1 2.2 2.3 2.4 Cite error: Invalid <ref> tag; no text was provided for refs named ref2
  3. ↑ 3.0 3.1 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. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref8
  7. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref9
  8. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref10
  9. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref11
  10. ↑ 10.0 10.1 Cite error: Invalid <ref> tag; no text was provided for refs named ref12
  11. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref7
  12. ↑ Cite error: Invalid <ref> tag; no text was provided for refs named ref13
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