Abstract
In plants, the basic helix-loop-helix (bHLH) transcription factors (TFs) play pivotal roles in many biological processes including growth, stress response, and secondary metabolite synthesis. To date, many bHLH genes have been identified and characterized in diverse plant species. However, little is known regarding the bHLH genes in Dimocarpus longan Lour. (D. longan). Based on RNA-seq data, we identified 42 putative bHLH genes from D. longan and determined their putative functions using the NCBI Conserved Domain Search Tool and Pfam databases. The physicochemical properties, phylogenetic relationships, conserved motifs, gene ontology (GO) annotations, protein-protein interactions, and tissue-specific expression patterns of these bHLH genes were systematically explored. In total, ten motifs were found in DlbHLH proteins using MEME, among which two were highly conserved. Phylogenetic tree analysis found that DlbHLH proteins can be divided into nine groups, with group 2 being the largest. GO annotation results showed that the DlHLH genes were involved in various molecular functions. RNA-seq and qRT-PCR results revealed important differences in the expression patterns of 17 of the DlbHLH genes. In particular, DlbHLH-9, DlbHLH-19, DlbHLH-25, DlbHLH-26, and DlbHLH-35 were found to show significantly different expression patterns in root and leaf tissues. The results of this study will further enrich our knowledge regarding bHLH transcription factor genes and lay a foundation for enhancing the production of active secondary metabolites by genetic engineering in D. longan.
 
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 In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 3, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue.
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Highlights
Transcription factors (TFs) are an important group of DNA-binding proteins that recognize and bind to specific DNA sequences to control transcription from DNA to mRNA at specific times and places
Using NR annotations, the NCBI Conserved Domain Search Tool, and the Pfam database to analyze D. longan RNA-seq data (NCBI accession number: SRP155595), we identified 42 genes as putative DlbHLH TF genes
We assessed the physicochemical properties of these TFs; our analyses included determinations of their open reading frame (ORF) length, theoretical isoelectric point, aliphatic index, molecular weight, instability index (II), and grand average of hydropathicity (GRAVY), as well as the number of alpha helices, extended strands, beta turns, and random coils
Summary
Transcription factors (TFs) are an important group of DNA-binding proteins that recognize and bind to specific DNA sequences to control transcription from DNA to mRNA at specific times and places. BHLH TFs are the second largest family after MYB TFs (Sun et al, 2018; Yu et al, 2019) These TFs contain the highly conserved bHLH domain, which includes both a basic region and a HLH region. The basic region is usually located at the N-terminus of the bHLH domain, and permits binding to E-box sequences (5’-CANNTG-3’) in target gene promoters (Heim et al, 2003). The HLH region is usually located at the C-terminus of the bHLH domain, and is approximately 50 amino acids long. It contains two alpha helixes separated by a loop, and forms homodimeric or heterodimeric complexes with other bHLH proteins, thereby regulating their activity (Massari and Murre, 2000)
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