Os02g0725900

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Annotated Information

General information

Os02g0725900 is the gene loci name called HAP3 subunit of the CCAAT-box-binding transcription factor.Gene symbol is OsNF-YB1 locating at the second chromosome in rice.Now,rice has been identified 11 HAP3 genes in its genome.

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. OsHAP3A, OsHAP3B and OsHAP3C showed ubiquitous expression . They were expressed in all organs examined such as shoot apices, roots, young panicles, flowering panicles, young leaves, developing embryos and their surrounding tissues at 0, 2, 4, 6 and 8 DAP, and regenerating calli at 0, 2, 4 and 6 days after regeneration (DAR). The expression was also observed in developing young inflorescence with a panicle length of 1 and 3 mm, 2 and 3 cm[2]. The newly identified genes were named as OsHAP3D to OsHAP3K. OsHAP3K was identical to OsNF-YB1 . They encode a protein with a conserved domain in their middle, as do the OsHAP3A, OsHAP3B and OsHAP3C proteins[1]. A phylogenetic analysis based on the amino acid sequences of the conserved domain showed that the OsHAP3 proteins were located in several different clades (Fig1astro). Among them OsHAP3D and OsHAP3E belonged to a clade which include LEC1 and L1L, both of which play critical roles in embryogenesis (Fig1astro)[1].

We previously showed that OsHAP3A, OsHAP3B and OsHAP3C were expressed ubiquitously (Miyoshi et al. 2003), and Masiero et al. (2002) reported that OsHAP3K/OsNF-YB1 was expressed in seed. We examined expression patterns of the newly identified OsHAP3 genes. Because LEC1 and L1L were shown to be expressed in embryogenesis (Lotan et al. 1998; Kwong et al. 2003), the expression of the OsHAP3 genes at several different stages of embryogenesis and regeneration was examined in addition to various organs. Because it is extremely difficult to isolate early-stage embryo from ovary, RNAs isolated from ovary containing developing embryo were used for RT-PCR analysis and designated as embryo. The results showed that OsHAP3D to OsHAP3G showed expression at specific stages of embryogenesis [1]. Expression of OsHAP3D in callus was first detected at 2 day-after-regeneration (DAR) and continued weakly at later stages. Expression of OsHAP3D was also detected in 2 day-after-pollination (DAP) embryo. Expression of OsHAP3E in callus was detected weakly at 0 and 2 DARs, and became stronger at 4 DAR and further at 6 DAR. Expression of OsHAP3E in embryo was detected at 6 DAP and weakly at 8 DAP. Expression of OsHAP3E was also detected in panicle with a length of 2–3 cm. Expression of OsHAP3F was detected at 8 DAR callus, 0 DAP and 8 DAP embryos and young leaf. Very weak signals were also detected in shoot apex and root. Expression of OsHAP3G was detected in 0 DAP embryo and 10 cm panicle. No expression of OsHAP3I was detected in the organs and at the developmental stages examined (data not shown), although the database searches identified several OsHAP3I cDNAs from etiolated seedling, in which we did not examine the expression, and one more cDNA from seedling and callus. This indicates that OsHAP3I was mainly expressed in etiolated seedling. No expression of OsHAP3H was also detected by the RT-PCR analysis in the examined tissues (data not shown) and a few cDNA was identified as Heading date clones by the database search. OsHAP3J showed ubiquitous expression in almost all tissues examined here like OsHAP3A, OsHAP3B and OsHAP3C but at a low level, although no cDNAs or EST sequences have been identified in any DNA databases[1].

Evolution

The subunit contains an evolutionary conserved domain, which is responsible for DNA binding and protein–protein interaction, and non-conserved regions.

Extension

[[File:

Fig 1astro HAP genes in rice. Schematic presentation of OsHAP2 proteins (a), OsHAP3 proteins (b) and OsHAP5 proteins (c). Shaded boxes indicate conserved domains in each HAP subunit. Boxes with a one-letter code of amino acid residues indicate stretches of five or more corresponding amino acid residues. Phylogenetic trees of HAP2 (d), HAP3 (e) and HAP5 (f). The trees were drawn on the basis of the amino acid sequences of the conserved domains in each subunit. OsHAP5D and OsHAP5E, and AtNF-YC3 and AtNF-YC9 have identical amino acid sequences in the conserved domain, respectively. ScHAP2 (M15243), ScHAP3 (M59079) and ScHAP5 (U19932) are proteins from yeast Saccharomyces cerevisiae, and HsNF-YA (M59079), HsNF-YB (L06145) and HsNF-YC (U78774) are proteins from human Homo sapiens

Labs working on this gene

(1)Genetic Strains Research Center, National Institute of Genetics, Shizuoka-ken, Japan

(2)School of Life Science, Graduate University for Advanced Studies, 1111 Yata, Mishima, Shizuoka-ken 411-8540, Japan

(3)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

(4)Dipartimento di Genetica e Biologia dei Microrganismi and ‖Dipartimento di Biologia, Universitá di Milano, Italy and the §Dipartimento di Biologia Animale, Universitá di Modena e Reggio, Via Campi 213/d, 41100 Modena, Italy

References

[1]Thirumurugan T, 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

[2]Kazumaru Miyoshi, Yukihiro Ito, Akiko Serizawa1 andNori Kurata.(2003)OsHAP3 genes regulate chloroplast biogenesis in rice.Article first published online: 16 OCT 2003 DOI: 10.1046/j.1365-313X.2003.01897.x

[3]Simona Masiero, Carol Imbrian, Federica Ravasio, Rebecca Favaro, Nilla Pelucchi, Mirella Sari Gorla, Roberto Mantovani, Lucia Colombo and Martin M. Kater,(2002)Ternary Complex Formation between MADS-box Transcription Factors and the Histone Fold Protein NF-YB.First Published on April 23, 2002, doi: 10.1074/jbc.M202546200 July 19, 2002 The Journal of Biological Chemistry, 277, 26429-26435.

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	GEO Profiles:Os02g0725900
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)	NCBI Gene:Os02g0725900, RefSeq:Os02g0725900