Difference between revisions of "Os02g0725900"
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==Annotated Information== | ==Annotated Information== | ||
===Function=== | ===Function=== | ||
| − | A HAP complex, which consists of three subunits, namely HAP2 (also called NF-YA or CBF-B), HAP3 (NF-YB/CBF-A) and HAP5 (NF-YC/CBF-C), binds to CCAAT sequences in a promoter to control the expression of target genes. We identified 10 HAP2 genes, 11 HAP3 genes and 7 HAP5 genes in the rice genome. All the three HAP family genes encode a protein with a conserved domain in each family and various non-conserved regions in both length and amino acid sequence. These genes showed various expression patterns depending on genes, and various combinations of overlapped expression of the HAP2, HAP3 and HAP5genes were observed. Furthermore, protein interaction analyses showed interaction of OsHAP3A, a ubiquitously expressed HAP3 subunit of rice, with specific members of HAP5. These results indicate that the formation of specific complex with various HAP subunits combinations can be achieved by both tissue specific expression of three subunit genes and specific interaction of three subunit proteins. This may suggest that the HAP complexes may control various aspects of rice growth and development through tissue specific expression and complex formation of three subunit members. | + | A HAP complex, which consists of three subunits, namely HAP2 (also called NF-YA or CBF-B), HAP3 (NF-YB/CBF-A) and HAP5 (NF-YC/CBF-C), binds to CCAAT sequences in a promoter to control the expression of target genes. We identified 10 HAP2 genes, 11 HAP3 genes and 7 HAP5 genes in the rice genome[1]. All the three HAP family genes encode a protein with a conserved domain in each family and various non-conserved regions in both length and amino acid sequence. These genes showed various expression patterns depending on genes, and various combinations of overlapped expression of the HAP2, HAP3 and HAP5genes were observed. Furthermore, protein interaction analyses showed interaction of OsHAP3A, a ubiquitously expressed HAP3 subunit of rice, with specific members of HAP5. These results indicate that the formation of specific complex with various HAP subunits combinations can be achieved by both tissue specific expression of three subunit genes and specific interaction of three subunit proteins. This may suggest that the HAP complexes may control various aspects of rice growth and development through tissue specific expression and complex formation of three subunit members. |
| − | In rice OsHAP3A and possibly its close homologues OsHAP3B andOsHAP3C were shown to control chloroplast biogenesis | + | In rice OsHAP3A and possibly its close homologues OsHAP3B andOsHAP3C were shown to control chloroplast biogenesis[2]. These studies indicate that the functions of the HAP3 genes are diverged from embryogenesis and chloroplast biogenesis, and suggest that each HAP3 gene has a specific role. |
| + | |||
===Expression=== | ===Expression=== | ||
Rice has 11 HAP3 genes in its genome. The newly identified genes were named as OsHAP3D to OsHAP3K. OsHAP3K was identical to OsNF-YB1 (Masiero et al. 2002). They encode a protein with a conserved domain in their middle, as do the OsHAP3A, OsHAP3B and OsHAP3C proteins. A phylogenetic analysis based on the amino acid sequences of the conserved domain showed that the OsHAP3 proteins were located in several different clades (Fig. 1e). Among them OsHAP3D and OsHAP3E belonged to a clade which include LEC1 and L1L, both of which play critical roles in embryogenesis (Fig. 1e, Lotan et al. 1998; Kwong et al. 2003). | Rice has 11 HAP3 genes in its genome. The newly identified genes were named as OsHAP3D to OsHAP3K. OsHAP3K was identical to OsNF-YB1 (Masiero et al. 2002). They encode a protein with a conserved domain in their middle, as do the OsHAP3A, OsHAP3B and OsHAP3C proteins. A phylogenetic analysis based on the amino acid sequences of the conserved domain showed that the OsHAP3 proteins were located in several different clades (Fig. 1e). Among them OsHAP3D and OsHAP3E belonged to a clade which include LEC1 and L1L, both of which play critical roles in embryogenesis (Fig. 1e, Lotan et al. 1998; Kwong et al. 2003). | ||
Revision as of 02:03, 8 June 2014
Please input one-sentence summary here.
Contents
Annotated Information
Function
A HAP complex, which consists of three subunits, namely HAP2 (also called NF-YA or CBF-B), HAP3 (NF-YB/CBF-A) and HAP5 (NF-YC/CBF-C), binds to CCAAT sequences in a promoter to control the expression of target genes. We identified 10 HAP2 genes, 11 HAP3 genes and 7 HAP5 genes in the rice genome[1]. All the three HAP family genes encode a protein with a conserved domain in each family and various non-conserved regions in both length and amino acid sequence. These genes showed various expression patterns depending on genes, and various combinations of overlapped expression of the HAP2, HAP3 and HAP5genes were observed. Furthermore, protein interaction analyses showed interaction of OsHAP3A, a ubiquitously expressed HAP3 subunit of rice, with specific members of HAP5. These results indicate that the formation of specific complex with various HAP subunits combinations can be achieved by both tissue specific expression of three subunit genes and specific interaction of three subunit proteins. This may suggest that the HAP complexes may control various aspects of rice growth and development through tissue specific expression and complex formation of three subunit members. In rice OsHAP3A and possibly its close homologues OsHAP3B andOsHAP3C were shown to control chloroplast biogenesis[2]. These studies indicate that the functions of the HAP3 genes are diverged from embryogenesis and chloroplast biogenesis, and suggest that each HAP3 gene has a specific role.
Expression
Rice has 11 HAP3 genes in its genome. The newly identified genes were named as OsHAP3D to OsHAP3K. OsHAP3K was identical to OsNF-YB1 (Masiero et al. 2002). They encode a protein with a conserved domain in their middle, as do the OsHAP3A, OsHAP3B and OsHAP3C proteins. A phylogenetic analysis based on the amino acid sequences of the conserved domain showed that the OsHAP3 proteins were located in several different clades (Fig. 1e). Among them OsHAP3D and OsHAP3E belonged to a clade which include LEC1 and L1L, both of which play critical roles in embryogenesis (Fig. 1e, Lotan et al. 1998; Kwong et al. 2003).
Evolution
The subunit contains an evolutionary conserved domain, which is responsible for DNA binding and protein–protein interaction, and non-conserved regions.
Labs working on this gene
Please input related labs here. (1)Thiruvengadam Thirumurugan1, 2, Yukihiro Ito1, 3, Takahiko Kubo1, Akiko Serizawa1 and Nori Kurata1, 2
(2)Genetic Strains Research Center, National Institute of Genetics, Shizuoka-ken, Japan
(3)School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan
(4)Present address: Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai 981-8555, Japan
Nori Kurata
Email: nkurata@lab.nig.ac.jp
References
[1]Thirumurugan T1, Ito Y, Kubo T, Serizawa A, Kurata N. Identification, characterization and interaction of HAP family genes in rice.Mol Genet Genomics. 2008 Mar;279(3):279-89. doi: 10.1007/s00438-007-0312-3. Epub 2008 Jan 9
Structured Information
| Gene Name |
Os02g0725900 |
|---|---|
| Description |
Histone-like transcription factor/archaeal histone/DNA topoisomerase family protein |
| Version |
NM_001054522.1 GI:115448414 GeneID:4330587 |
| Length |
997 bp |
| Definition |
Oryza sativa Japonica Group Os02g0725900, 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}}} |
| Location |
Chromosome 2:31078346..31079342 |
| Sequence Coding Region |
31078587..31079125,31079266..31079287 |
| Expression | |
| Genome Context |
<gbrowseImage1> name=NC_008395:31078346..31079342 source=RiceChromosome02 preset=GeneLocation </gbrowseImage1> |
| Gene Structure |
<gbrowseImage2> name=NC_008395:31078346..31079342 source=RiceChromosome02 preset=GeneLocation </gbrowseImage2> |
| Coding Sequence |
<cdnaseq>atggcagggaacaaaaagcgtggtggcaggaacatggatcaggtcaagaaggcggcagtgagatcggatggggtgggaggtagtgcgaccaacgccgagctgccgatggccaacctcgtacgcctgataaagaaggtgctcccagggaaagcgaagatcgggggagcagccaagggtctcacccatgattgcgcggtggagttcgtcgggttcgtcggcgacgaggcctccgagaaggccaaggcagagcaccgccgcaccgtagcgccggaagactacttgggctcattcggcgaccttggcttcgatcgctacgtcgaccccatggatgcctacatccatggttaccgtgagtttgagagggctggtgggaataggagggtggcgccgcctcctccggcggcagctacaccgctgacgcccggtggaccgacattcactgacgcagagctgcagtttctccggtcggtgatcccctccagaagtgatgatgaatatagcggctcatcaccagccataggcggctatggctatggatatggctatggaaaaaatatgtga</cdnaseq> |
| Protein Sequence |
<aaseq>MAGNKKRGGRNMDQVKKAAVRSDGVGGSATNAELPMANLVRLIK KVLPGKAKIGGAAKGLTHDCAVEFVGFVGDEASEKAKAEHRRTVAPEDYLGSFGDLGF DRYVDPMDAYIHGYREFERAGGNRRVAPPPPAAATPLTPGGPTFTDAELQFLRSVIPS RSDDEYSGSSPAIGGYGYGYGYGKNM</aaseq> |
| Gene Sequence |
<dnaseqindica>218..756#56..77#tccaatacaagttcacaacataagcatagtacaggtcattgagacttgagagagcatggcagggaacaaaaagcgtggtatagtagtatagtcagtactaggattagtacttgataactagcacaacaaaaagctactatcatttttgcattcaaagtggtaattaagaatcggatgatcattttgattgttcctcttcatttgttttggatgtcaggtggcaggaacatggatcaggtcaagaaggcggcagtgagatcggatggggtgggaggtagtgcgaccaacgccgagctgccgatggccaacctcgtacgcctgataaagaaggtgctcccagggaaagcgaagatcgggggagcagccaagggtctcacccatgattgcgcggtggagttcgtcgggttcgtcggcgacgaggcctccgagaaggccaaggcagagcaccgccgcaccgtagcgccggaagactacttgggctcattcggcgaccttggcttcgatcgctacgtcgaccccatggatgcctacatccatggttaccgtgagtttgagagggctggtgggaataggagggtggcgccgcctcctccggcggcagctacaccgctgacgcccggtggaccgacattcactgacgcagagctgcagtttctccggtcggtgatcccctccagaagtgatgatgaatatagcggctcatcaccagccataggcggctatggctatggatatggctatggaaaaaatatgtgaacaacttgatgcatgtgtgtgtgtacactgcatgcatgcgtggagggtcaaacagagtcaagactcttgtggtggtttcaataagtctctagtgacaatataagttgtgtatcgttgtttcctttgtaaaaaaaaacgtcatgtatcgttgtgtgtcctcatccggtaatcctttacgtgggtgggttatgcgagaaaaagaaaatgacgttgcatcaaataaaatgcttgatgtttgcgt</dnaseqindica> |
| External Link(s) |
