Difference between revisions of "Os03g0722400"

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Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
 
Both rice OsDDM1a and OsDDM1b proteins contain the eight signature
 
amino acid motifs diagnostic for SWI2/SNF2 proteins.
 
amino acid motifs diagnostic for SWI2/SNF2 proteins.
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[[File:Osddm1a.jpg|left|thumb|200px|''Structure of OsDDM1 and Arabidopsis DDM1 (from reference <ref name="ref1" />).'']]
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[[File:Osddm1a.jpg|right|thumb|200px|''Structure of OsDDM1 and Arabidopsis DDM1 (from reference <ref name="ref1" />).'']]
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[[File:E_1.jpg|left|thumb|300px|''Alignment of proteins encoded by DDM1-like genes among speciecs (from reference <ref name="ref1" />).'']]
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[[File:E_1.jpg|right|thumb|300px|''Alignment of proteins encoded by DDM1-like genes among speciecs (from reference <ref name="ref1" />).'']]
 
By comparing the DDM1-like prteins encoded in the maize genome,Arabidopsis DDM1 and the mouse LSH with the two rice DDM1-like proteins,the envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
 
By comparing the DDM1-like prteins encoded in the maize genome,Arabidopsis DDM1 and the mouse LSH with the two rice DDM1-like proteins,the envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent
 
duplication event.
 
duplication event.

Revision as of 09:41, 19 May 2014

The rice DDM1 homologous gene (OsDDM1b) is well known as the "maintaining methylation gene" and controls the plant methylation level in genome.

Annotated Information

Function

OsDDM1b is required for the maintenance of DNA methylation on newly replicated DNA strands in rice genome like OsDDM1a.It mainly keeps the methylation level on repeated sequences rather than single copy sequences.

Expression

Cytosine methylation in the plant genome is very important in establishing the epigenetic states of chromosome regions. The Decrease in DNA Methylation 1 (DDM1) in Arabidopsis thaliana is one of the best well-studyed plant epigenetic regulators for maintenance of cytosine methylation in genomic DNA. Higo,Hiromi et al identified two rice genes with high similarity to Arabidopsis DDM1 and designated them OsDDM1a and OsDDM1b. Both of the rice DDM1 homologs are transcribed during development. Transgenic rice lines silencing the OsDDM1 exhibited genomic DNA hypomethylation.And in those mutant lines, repeated sequences were more severely affected than a single copy sequence. Transcripts derived from endogenous transposon- related loci were up-regulated in the antisense OsDDM1 lines.OsDDM1a and OsDDM1b are expressed during development with slight variations among various tissues, suggesting that there might be functional divergence of these two genes. Expression.jpg


Mutant Phenotype

We can observe dwarf phenotypes in OsDDM1 mutant lines generated through the antisense technology.
Dwarf phenotype in OsDDM1-mutant lines (from reference [1]).
Except the dwarf phenotypes, no other significant specific morphological aberration was observed in independent OsDDM1 mutant lines. However, in some sublines, researchers observed reduced fertility relative to normal lines.

Evolution

OsDDM1b(Os03g0722400) is 93% identical to another gene OsDDM1a(Os09g0442700) in the predicted amino acid sequences and shows 60 % identity to Arabidopsis DDM1. However, considering maize, no simple orthologous relationships exits between the two maize DDM1-like genes-CHR101,CHR106 and OsDDM1.OsDDM1b and OsDDM1a both consist of 15 exons and 14 introns and the DNA sequence similarity shared by these two genes is 81%, even including intron sequences. Compared to the Arabidopsis DDM1, these two genes' exon–intron structure is similar. The start codon of the Arabidopsis DDM1 locates in the first exon, but it is in the second exon for the OsDDM1 genes. The protein product of OsDDM1b gene is 849 amino acids in length. Both rice OsDDM1a and OsDDM1b proteins contain the eight signature amino acid motifs diagnostic for SWI2/SNF2 proteins.

Structure of OsDDM1 and Arabidopsis DDM1 (from reference [1]).
Alignment of proteins encoded by DDM1-like genes among speciecs (from reference [1]).

By comparing the DDM1-like prteins encoded in the maize genome,Arabidopsis DDM1 and the mouse LSH with the two rice DDM1-like proteins,the envolution relationship is showed as below.We can see that they appear to have arisen by a relatively recent duplication event.

envolution relationship in rice,maize,Arabidopsis and mouse (from reference [1]).

Labs working on this gene

CREST, Japan Science and Technology Agency,Kawaguchi 332-0012, Japan

Department of Molecular Genetics, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan

Department of Plant Science, University of Manitoba, Winnipeg R3T 2N2, Canada

Department of Integrated Genetics,National Institute of Genetics, Mishima 411-0801, Japan

Experimental Farm, National Institute of Genetics, Mishima 411-0801, Japan

References

Higo, Hiromi, et al. "DDM1 (Decrease in DNA Methylation) genes in rice (Oryza sativa)." Molecular Genetics and Genomics 287.10 (2012): 785-792.

Structured Information

Gene Name

Os03g0722400

Description

Conserved hypothetical protein

Version

NM_001057645.2 GI:297601601 GeneID:4333943

Length

3180 bp

Definition

Oryza sativa Japonica Group Os03g0722400, 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 3

Location

Chromosome 3:30070286..30073465

Sequence Coding Region

30072187..30072291

Expression

GEO Profiles:Os03g0722400

Genome Context

<gbrowseImage1> name=NC_008396:30070286..30073465 source=RiceChromosome03 preset=GeneLocation </gbrowseImage1>

Gene Structure

<gbrowseImage2> name=NC_008396:30070286..30073465 source=RiceChromosome03 preset=GeneLocation </gbrowseImage2>

Coding Sequence

<cdnaseq>atgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattga</cdnaseq>

Protein Sequence

<aaseq>MNIFILSTRAGGLGINLTSADTCILYDSDWVIPY</aaseq>

Gene Sequence

<dnaseqindica>1902..2006#aggggcatcggctaaagaattcaaagtgcatattattaagggagttaaagcgcctgccaatggataataagctccttttgactggaacacctcttcagaataatctagcagaactgtggtcactgctgaacttcattttgcctgatatattctcatcgcatcaggagttcgagtcatggtatgatccattttgctgagtatattccttctcaagtgtggtttgtgcttttatactatcacgtctcagcagtcagcactaaagtacaaatatgatagtataattgaagattttcttatcatgcactcgttcctatatccatcttaacctttccgtcaaataattgtttgtctcacttttgagtcattttcctgactgtttattgtcaacttcgttcatttgtatatgcattgagcagagcagatagtcttcttctcttcaagacaagacatttgtcaggatctctctaggtcattgagggctagcatattggtcaaaacaatgtaaaagaacctcttaaactgcataacagcaatttcaacactaatctcatcaactaaccctgtttatgtatatagttattccattagtttgttgctactcttaagacgtggctttattttttttctcattggcttgcctttatgaagtgtcgtaaagttgaatgccctatgtgttgtagcggttatgcatattgctttgatatgcgatgtctgctaacgtgtcttttgaatgtagcacaaatctatgctgtacatctactgatttatttggtgtttactgggatgctatgtttacttttgtgtctgccttatgtctgttgtacaggtttgatttttgtgcaaaagggggtgaagaagaacaagaggaaagtgaagagaagagaaaagtcgatgttgtttcaaagcttcatgccatattgcgccccttccttctaaggcggatgaaggaggatgtagagcatatgcttccacgaaagaaagagataatcatttatgctaacatgactaaccatcagaaagaaatccagaatcacttggttgaacaaacatttgatgaatacctgcatgaaaaatcagaaattggtacggatgcttgtgcacatagtctcctacatacattcctgttgacttaaaaagttaatctgacaagtgctgaggagtattgcagttctgcggagacctggcattaaggcgaagctgaataaccttttaattcaactgaggaaaaattgcaaccatcctgatcttttggagtccgcatatgactcatcaggttgttccacattggacatctgtagttaattgcttcacgtgctcatttcctaacatttttgtttttttttctttctgtaggtatgtacccacctgttgagaagctcttagaacaatgcggtaaatttcagctcttgaacagattgctaaatttgctgcttgcacggaagcacaaggtatatcattttctctgctattctgtttaattcaggattacattaatgcaaatgttagctcaaactttttttgaagaaaaaaaatcatagacctcaactggcgttctttgtaggttctaatattttcacagtggacaaaagttttggacattatcgagtactacttggaaacaaaaggccttcaggtttgccgaattgatggcagtgttaagttggaagagaggaggaggcaggtaaagcgggctgtgccaagcattgccgattaccatataatgtgtaaagttctagtcttctagatgcatataggctgactgcgctatcttaaaatacaattaggagtctcattttttcgccattgttatcttttatcatccattttaatgtaatacagttctcacaattttgtgcactattctcttgcagatagcagaatttaatgacttgaacagcagcatgaatatctttattctaagcacacgggctggtgggctgggtatcaatcttacttcggctgatacctgtatcctatatgatagtgactgggtaattccctattgacattattttacttcttcagactaaatattcatattatagcaagtacattgcaagattcttttgcatgccatccacctgttcgaacaggtggaatgtaggcatgtagactttaccttctattagctgattatgtgaattgttaaacttctgccatcattctgcagaatcctcagatggatttgcaggccatggatcgatgccaccggattggtcaaacacgcccagttcacgtctaccggttggcaacatcacattctgttgaggtgtgtcggatgatctttttgtctttagacatcggctacaccacctgttgtatagttgctcatcttaatggtgttgcagggccggatcatcaagaaagcatttggaaagttgaggctggaacatgtggtgatcgggaagggtcagtttgaacaagacagagccaaacctaatgcactagacgtaaatgttcccatccatcctcctgagtcctgactattaagataactactctttgttcacacttttttttggaaaacaagttctttcttcatagaggaacaccatatgaacaaatctacaaaattgacactgaaagaatgtccaccccgcggaaaatcctcatctcatattttccatttcttgtgattatgcaggaggcggagttgctggcgctgctcagggacgagcaggacgaggaggaccggatgatccagacggacatcaccgacgaggatctcctgaaggtgatggaccggagcgaccttacaggccctcctgccaacgccgacgccgcccctctcgtgcccctgaagggacccggctgggaggtggtggtgccgacgaagagcggcggcggcatgctcacgtcgctcaccagctagctgctttctttcatcgctcgctgcgcacctcaggccatagccctagtaaggctgccggctaaggtgcctcttgagctgtgctgcatctgctgatgagacgacgcttttgtgatcccaccccaagtaattactgactgggcattgcacttgcgccagtacactaggaagtgataaggtagtgtgcatctaatctgtcgtaagtatctctgttgttggctcagctgctgcatttcattttgcaaggcccaaagccttttctagaatgctagtgtaagaacgtggtatttgagaacataatatccttgtct</dnaseqindica>

External Link(s)

NCBI Gene:Os03g0722400, RefSeq:Os03g0722400

  1. ↑ 1.0 1.1 1.2 1.3 Cite error: Invalid <ref> tag; no text was provided for refs named ref1
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