The Arabidopsis Basic/Helix-Loop-Helix Transcription Factor Family[W]

Abstract

The basic/helix-loop-helix (bHLH) proteins are a superfamily of transcription factors that bind as dimers to specific DNA target sites and that have been well characterized in nonplant eukaryotes as important regulatory components in diverse biological processes. Based on evidence that the bHLH protein PIF3 is a direct phytochrome reaction partner in the photoreceptor's signaling network, we have undertaken a comprehensive computational analysis of the Arabidopsis genome sequence databases to define the scope and features of the bHLH family. Using a set of criteria derived from a previously defined consensus motif, we identified 147 bHLH protein-encoding genes, making this one of the largest transcription factor families in Arabidopsis. Phylogenetic analysis of the bHLH domain sequences permits classification of these genes into 21 subfamilies. The evolutionary and potential functional relationships implied by this analysis are supported by other criteria, including the chromosomal distribution of these genes relative to duplicated genome segments, the conservation of variant exon/intron structural patterns, and the predicted DNA binding activities within subfamilies. Considerable diversity in DNA binding site specificity among family members is predicted, and marked divergence in protein sequence outside of the conserved bHLH domain is observed. Together with the established propensity of bHLH factors to engage in varying degrees of homodimerization and heterodimerization, these observations suggest that the Arabidopsis bHLH proteins have the potential to participate in an extensive set of combinatorial interactions, endowing them with the capacity to be involved in the regulation of a multiplicity of transcriptional programs. We provide evidence from yeast two-hybrid and in vitro binding assays that two related phytochrome-interacting members in the Arabidopsis family, PIF3 and PIF4, can form both homodimers and heterodimers and that all three dimeric configurations can bind specifically to the G-box DNA sequence motif CACGTG. These data are consistent, in principle, with the operation of this combinatorial mechanism in Arabidopsis.

Duplication and expression analysis of multicopy miRNA gene family members in Arabidopsis and rice

“…In plants, miRNA genes are mostly discrete, independent transcription units, and about 50% of miRNAs are predicted to be multiple loci in the genome, similar to that seen with protein-coding genes (recent rice sequencing data showed that 29% of protein-coding genes appear in gene families) [43]. The evidence here suggesting that the expansion of miRNA genes in plants resulted from genome segmental and tandem duplication events during evolution is similar to that of many protein-coding gene families, especially transcription factor families [33,44]. Thus, these kinds of duplication events are proposed to have contributed to the expansion of both protein-coding gene families and miRNA gene families.…”

Tobacco Transcription Factors: Novel Insights into Transcriptional Regulation in the Solanaceae

“…bHLHs form one of the largest families of TFs in plants and regulate numerous processes. Analysis of the bHLH family is technically more difficult than for most of the other TF families Heim et al, 2003;Toledo-Ortiz et al, 2003); therefore, we performed a total of 30 independent searches using a representative bHLH domain from each of the 23 subfamilies described by Heim et al (2003). This resulted in the identification of 192 bHLH sequences representing a minimum of 190 bHLH genes.…”

Identification and Bioinformatics Analyses of the Basic Helix-loop-helix Transcription Factors in Xenopus laevis

“…Atchley et al (1999) computed and deduced a predictive motif for the bHLH domains based on 242 bHLH proteins, in which 19 conserved sites were found within the bHLH domain (Atchley et al, 1999). Their works showed that a sequence identified with less than 8 mismatches to the predictive motif was possibly a bHLH protein (Atchley and Fitch, 1997;Atchley et al, 1999;Atchley et al, 2000) and other researchers found that a sequence with nine mismatches might be a potential bHLH protein as well (Toledo-Ortiz et al, 2003).…”

“…Recently, more and more bHLH genes has been identified and bHLH TF families have been analyzed in many organisms whose genome drafts have been available (Ledent et al, 2002;Toledo-Ortiz et al, 2003;Buck and Atchley, 2003;Heim et al, 2003;Li et al, 2006a, b;Simionato et al, 2007;Stevens et al, 2008;Wang et al, 2007Wang et al, , 2008Wang et al, , 2009Pires and Dolan, 2010;Carretero-Paulet et al, 2010;Liu andZhao, 2010, 2011;Liu et al, 2012Liu and Chen, 2013). However, the family of bHLH TFs has not yet been studied and characterized in Xenopus laevis.…”