title: Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis.
abstract: The basic/helix-loop-helix (bHLH) transcription factors and their homologs form a large family in plant and animal genomes. They are known to play important roles in the specification of tissue types in animals. On the other hand, few plant bHLH proteins have been studied functionally. Recent completion of whole genome sequences of model plants Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) allows genome-wide analysis and comparison of the bHLH family in flowering plants. We have identified 167 bHLH genes in the rice genome, and their phylogenetic analysis indicates that they form well-supported clades, which are defined as subfamilies. In addition, sequence analysis of potential DNA-binding activity, the sequence motifs outside the bHLH domain, and the conservation of intron/exon structural patterns further support the evolutionary relationships among these proteins. The genome distribution of rice bHLH genes strongly supports the hypothesis that genome-wide and tandem duplication contributed to the expansion of the bHLH gene family, consistent with the birth-and-death theory of gene family evolution. Bioinformatics analysis suggests that rice bHLH proteins can potentially participate in a variety of combinatorial interactions, endowing them with the capacity to regulate a multitude of transcriptional programs. In addition, similar expression patterns suggest functional conservation between some rice bHLH genes and their close Arabidopsis homologs.
authors.affiliation: Shanghai Jiao Tong University-Shanghai Institutes for Biological Sciences-Pennsylvania State University Joint Center for Life Sciences, Shanghai Jiao Tong University, Shanghai, People's Republic of China, 200240.
authors.forename: Xiaoxing
authors.initials: X
authors.lastname: Li
authors.forename: Xuepeng
authors.initials: X
authors.lastname: Duan
authors.forename: Haixiong
authors.initials: H
authors.lastname: Jiang
authors.forename: Yujin
authors.initials: Y
authors.lastname: Sun
authors.forename: Yuanping
authors.initials: Y
authors.lastname: Tang
authors.forename: Zheng
authors.initials: Z
authors.lastname: Yuan
authors.forename: Jingkang
authors.initials: J
authors.lastname: Guo
authors.forename: Wanqi
authors.initials: W
authors.lastname: Liang
authors.forename: Liang
authors.initials: L
authors.lastname: Chen
authors.forename: Jingyuan
authors.initials: J
authors.lastname: Yin
authors.forename: Hong
authors.initials: H
authors.lastname: Ma
authors.forename: Jian
authors.initials: J
authors.lastname: Wang
authors.forename: Dabing
authors.initials: D
authors.lastname: Zhang
mesh_terms: D000595:Amino Acid Sequence; D017360:Arabidopsis / Q000235:genetics* / Q000378:metabolism; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D051792:Basic Helix-Loop-Helix Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017124:Conserved Sequence; D019143:Evolution, Molecular; D020440:Gene Duplication; D018745:Genome, Plant; D005810:Multigene Family; D012275:Oryza / Q000235:genetics* / Q000378:metabolism; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry / Q000235:genetics* / Q000378:metabolism; D017434:Protein Structure, Tertiary; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein
chemical_list: D029681:Arabidopsis Proteins; D051792:Basic Helix-Loop-Helix Proteins; D010940:Plant Proteins