bHLH Transcription Factor Family
The basic helix-loop-helix (bHLH) transcription factors form one of the largest families of transcription factors in plants
. The bHLH domain is approximately 60 amino acids long and contains two functionally distinct regions . Typically, there are
18 hydrophilic and basic amino acids at the N-terminus, followed by two regions of hydrophobic residues predicted to form
amphipathic ?-helices separated by an intervening loop . These ?-helices can interact with other proteins, allowing the
formation of homodimers or heterodimers with MYB, bHLH, WD40 or other proteins . The basic region determines the DNA binding
activity of the protein . A small number of bHLH proteins do not bind DNA, whereas the other bHLHs can be subdivided into
two categories: the E Box binders (CANNTG) and the G box binders (CACGTG). The subdivision is based on the presence or
absence of Glu-13 and Arg-16 in the basic region .
In Zea mays a group of bHLH genes (R, B, Lc, Sn and R-ch Hopi) are required for the production of the purple anthocyanin
pigments . These genes interact with the products of the R2R3MYB proteins C1 and P and together control pigmentation.
bHLH/MYB complexes are also involved in trichome development in Arabidopsis through the interaction of the bHLH protein
GLABRA3 and the R2R3MYB protein GLABROUS1 . One of most important roles of bHLH proteins in plants is in light sensing and
studies have shown that related bHLHs play key roles in phytochrome signaling . The bHLHs involved in light signaling are
found in subgroup E and several specifically interact with light-activated phytochrome. These bHLH proteins are called
phytochrome interacting factors (PIFs) or phytochrome interacting factor-like (PILs). They vary in their specificity for the
phytochromes phyA-E and primarily act as negative regulators of phytochrome signaling.
Phylogenetic analysis of the bHLH family is considerably more difficult than for most of the other families. This is
illustrated by two recent publications, that sought to analyse the complete bHLH gene family in Arabidopsis . Using slightly
different search strategies, Toledo-Ortiz and co-workers reported the discovery of 147 bHLH genes, whereas Heim and
co-workers reported the discovery of 133 genes. Both groups then cooperated in producing a combined dataset and arrived at a
final total of 162 bHLH genes . There were several reasons for these problems and some became apparent when we studied the
bHLH family in tobacco. One major problem is that the bHLH genes are relatively divergent and there are disagreements as to
what exactly constitutes a bHLH domain. This resulted in no single search ever isolating all 162 Arabidopsis genes . Another
problem is the presence of up to three introns in many bHLH domains, particularly very short introns in the loop domain.
This was a significant source of false negatives in the Arabidopsis analyses and was also a problem with the tobacco gene
family.
245 putative bHLH TF peptide,
CDS, and cDNA sequences;
blast HSP output, and multiple sequence alignment in
Soy - TFKB.
HLH domain peptide sequence with alignment
and phylogeny tree.
132 bHLH protein
and DNA
sequences with
annotations for soybean in PlantTFDB. most are partial sequences.
This page was setup on May 27, 2009, last updated by Dr. Jeff Chen on
June 16, 2009.
