Reference "Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis"

Reference ID

11280

Title

Genome-wide analysis of basic/helix-loop-helix transcription factor family in rice and Arabidopsis

Source

Plant physiology, 2006, vol. 141, pp. 1167-1184

Authors (13)

Li-X	Duan-X	Jiang-H	Sun-Y
Tang-Y	Yuan-Z	Guo-J	Liang-W
Chen-L	Yin-J	Ma-H	Wang-J
Zhang-D

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.