Members of the basic/helix-loop-helix (bHLH) superfamily of eukaryotic transcription factors act as important transcriptional regulators in many organisms. In these transcription factors, which function as homo- or hetero- dimers, the conserved bHLH domain contains a basic region and a HLH region. The basic region is generally located at the N-terminus of the bHLH domain and binds to a consensus hexanucleotide E-box (CANNTG) (Heim et al., 2003). The HLH region is located at the C-terminus of the bHLH domain, contains about 50 amino acids, and is composed of two alpha helixes separated by a loop of variable length. Generally, the HLH region mediates interactions with other bHLH proteins to form homodimeric or heterodimeric complexes [3].

Based on their phylogenetic relationship and DNA binding function, the bHLH members in eukaryotes have been classified into six main groups (named A, B, C, D, E and F). In brief, Group A can specifically bind to the E-box core sequence, Group B (most ancestral) prefers to bind the G-box, and Group C binds to the ACTTG or GCGTG sequences. Group D lacks a typical basic region and mainly participates in heterodimerization with other bHLH family proteins. Group E can preferentially bind to the CACGNG sequence, and the Group F members can bind to specific DNA target sequences (Hao et al., 2021). At least 162 members of bHLH proteins have been identified in Arabidopsis, which could be clustered into 12 distinctive subfamilies (Group B being the largest) namely bHLH I to XII (Heim et al., 2003).

Members of the bHLH family in plants play vital roles in plant growth, development, light signal transduction and stress responses. They are also involved in the crosstalk of hormones signaling, including abscisic acid (ABA), jasmonic acid (JA), brassinosteroid (BR), salicylic acid (SA) and ethylene (ET), and they are pivotal for plant growth and survival in the environment (Hao et al., 2021).

A 2018 study performed a genome-wide analysis and identified 208 candidate bHLH family proteins (ZmbHLH proteins) in maize (Zea mays). These proteins were classified into 18 subfamilies by comparing the ZmbHLHs with Arabidopsis thaliana bHLH proteins (Zhang et al., 2018).

ZmbHLH1 (r1 for colored 1) encodes a bHLH transcription factor and is a duplicate gene of B1 (ZmbHLH2) (Ludwig et al., 1989). Dominant R1 controls kernel and plant coloration by regulating genes coding for enzymes of anthocyanin biosynthesis. The action of some alleles is subject to change by allelic association (paramutation) and by pollen vs. ovule transmission (imprinting). ZmbHLH65 (Phytochrome-interacting factor 3, PIF3) was found to activate light-responsive transcriptional network genes in coordination with the circadian clock and plant hormones to modulate plant growth and development as well as abiotic stress (Gao et al., 2015).

Last updated June 2023 by John Gray

References:

Heim MA, Jakoby M, Werber M, Martin C, Weisshaar B, Bailey PC. The basic helix-loop-helix transcription factor family in plants: a genome-wide study of protein structure and functional diversity. Mol Biol Evol. 2003 May;20(5):735-47. doi: 10.1093/molbev/msg088. Epub 2003 Apr 2. PMID: 12679534.

Zhang T, Lv W, Zhang H, Ma L, Li P, Ge L, Li G. Genome-wide analysis of the basic Helix-Loop-Helix (bHLH) transcription factor family in maize. BMC Plant Biol. 2018 Oct 16;18(1):235. doi: 10.1186/s12870-018-1441-z. PMID: 30326829; PMCID: PMC6192367.

Hao Y, Zong X, Ren P, Qian Y, Fu A. Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis. Int J Mol Sci. 2021 Jul 1;22(13):7152. doi: 10.3390/ijms22137152. PMID: 34281206; PMCID: PMC8267941.

Ludwig SR, Habera LF, Dellaporta SL, Wessler SR. Lc, a member of the maize R gene family responsible for tissue-specific anthocyanin production, encodes a protein similar to transcriptional activators and contains the myc-homology region. Proc Natl Acad Sci U S A. 1989 Sep;86(18):7092-6. doi: 10.1073/pnas.86.18.7092. PMID: 2674946; PMCID: PMC298000.

Gao Y, Jiang W, Dai Y, Xiao N, Zhang C, Li H, Lu Y, Wu M, Tao X, Deng D, Chen J. A maize phytochrome-interacting factor 3 improves drought and salt stress tolerance in rice. Plant Mol Biol. 2015 Mar;87(4-5):413-28. doi: 10.1007/s11103-015-0288-z. Epub 2015 Jan 31. PMID: 25636202.