Abstract
The basic helix–loop–helix (bHLH) transcription factor family is the second largest transcription factor family in plants, and participates in various plant growth and development processes. A total of 118 bHLH genes were identified from fig (Ficus carica L.) by whole-genome database search. Phylogenetic analysis with Arabidopsis homologs divided them into 25 subfamilies. Most of the bHLHs in each subfamily shared a similar gene structure and conserved motifs. Seventy-two bHLHs were found expressed at fragments per kilobase per million mapped (FPKM) > 10 in the fig fruit; among them, 15 bHLHs from eight subfamilies had FPKM > 100 in at least one sample. bHLH subfamilies had different expression patterns in the female flower tissue and peel during fig fruit development. Comparing green and purple peel mutants, 13 bHLH genes had a significantly different (≥ 2-fold) expression. Light deprivation resulted in 68 significantly upregulated and 22 downregulated bHLH genes in the peel of the fruit. Sixteen bHLH genes in subfamily III were selected by three sets of transcriptomic data as candidate genes related to anthocyanin synthesis. Interaction network prediction and yeast two-hybrid screening verified the interaction between FcbHLH42 and anthocyanin synthesis-related genes. The transient expression of FcbHLH42 in tobacco led to an apparent anthocyanin accumulation. Our results confirm the first fig bHLH gene involved in fruit color development, laying the foundation for an in-depth functional study on other FcbHLH genes in fig fruit quality formation, and contributing to our understanding of the evolution of bHLH genes in other horticulturally important Ficus species.
Highlights
Transcription factors are key regulatory elements in life processes (Yamasaki et al, 2013; Guo and Wang, 2017)
According to the number of lysine and arginine residues in the DNAbinding domain, transcription factors are divided into four categories: zinc finger (ZF) type, FcbHLHs Related to Anthocyanin Biosynthesis helix–turn–helix (HLH), basic helix–loop–helix, and basic leucine zipper
A total of 118 bHLH genes were obtained from the published fig genome, and named FcbHLH1 to FcbHLH118 according to the equivalent classification for Arabidopsis thaliana (Figure 1A, and Supplementary Table 1)
Summary
Transcription factors are key regulatory elements in life processes (Yamasaki et al, 2013; Guo and Wang, 2017). The most commonly found transcription factors in higher plants are members of the WD40, MYB, WRKY, bHLH, and bZIP families (Kosugi and Ohashi, 2002). The bHLH domain is approximately 60 amino acids long, containing a basic region and an HLH region. The basic region, located next to the N-terminus, contains the DNA cis-acting elements E-box (5’-CANNTG-3’) and G-box (5’-CACGTG-3’) that regulate gene expression, whereas the HLH region consists of two amphipathic α-helices linked by a loop that serve as the dimerization domain to promote protein interactions, producing homodimers or heterodimers (Massari and Murre, 2000). BHLHs can act as either repressors or activators of gene transcription and play important roles in various physiological processes, such as sexual maturation, metabolism, and development (Feller et al, 2011) The basic region, located next to the N-terminus, contains the DNA cis-acting elements E-box (5’-CANNTG-3’) and G-box (5’-CACGTG-3’) that regulate gene expression, whereas the HLH region consists of two amphipathic α-helices linked by a loop that serve as the dimerization domain to promote protein interactions, producing homodimers or heterodimers (Massari and Murre, 2000). bHLHs can act as either repressors or activators of gene transcription and play important roles in various physiological processes, such as sexual maturation, metabolism, and development (Feller et al, 2011)
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