Abstract
As one of the largest TF families+ in plants, the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. FLOWERING BHLH (FBH) encodes a bHLH-type transcriptional factor related to the flowering process. Poplar is a model woody plant as well as an important economic tree species with a small genome. However, the characteristics of the bHLHs and FBHs gene family in the newest version of Populustrichocarpa genome have not been analyzed yet. We identified 233 PtbHLHs and 10 PtFBHs in the newest version genome, and PtbHLHs were classified into 21 groups with FBH subfamily occupying one, supported by phylogenetic analysis, exon–intron patterns, and conserved protein motifs. These PtHLHs were distributed on 19 chromosomes unevenly and expressed in nucleus mainly. Gene duplication and synteny analysis have indicated that the PtbHLHs gene family has undergone strong purification selection during the evolution process. The cis-elements analysis has suggested that PtbHLHs may be related to the growth and development. Conserved residues of FBHs among Arabidopsis and poplar were also identified. Expression of 227 PtHLH genes (6 unmatched, 13 no expressed) showed diverse patterns in different tissues, implying their multiple functions. Protein–protein interaction network prediction and expression patterns in three states of the flowering process (Flowers-Dormant, Flowers-Expanding and Flowers-Expanded) suggested that some members of PtbHLH and PtFBH family may be involved in the flowering process. Our comprehensive and systematic analysis can provide some valuable clues and basic reference toward further investigations on physiological and molecular functions of PtbHLHs.
Highlights
There are four types of transcription factors (TFs) in higher plants categorized by the sequence of arginine and lysine residues in the DNA binding region: Zinc finger, HTH, bZIP, and HLH [1,2,3,4]
A total of 233 basic helix-loop-helix (bHLH) genes, named PtbHLH1-PtbHLH233 according to their accession number, were identified in P. trichocarpa (Table S1)
We analyzed physicochemical properties and predicted subcellular location of proteins encoded by these 233 PtbHLH genes (Tables S2 and S3)
Summary
There are four types of transcription factors (TFs) in higher plants categorized by the sequence of arginine and lysine residues in the DNA binding region: Zinc finger, HTH, bZIP, and HLH [1,2,3,4]. As one of the largest TF families in plants [5], the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. Each member of bHLH family contains a bHLH domain, which consists of around 50–60 conserved amino acid sequences. The bHLH domain contains two functional regions: a basic amino acid region and an HLH region. The basic region is composed of approximately 15 amino acids at the N-terminal and responsible for binding to the cis-element E-box (CANNTG) or G-box (CACGTG) while the HLH region of a length of approximately 50 amino acids in a structure of two alpha helixes separated by a loop of variable length is located at the C-terminal [6,7,8]. It has been reported that two HLH proteins form homodimeric or heterodimeric complexes by the interaction of the HLH region’s hydrophobic amino acids to regulate the expression of downstream target genes
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