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Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon
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Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon
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Journal Article
Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon
2017
Overview
Background
As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in
Brachypodium distachyon
, an emerging model plant in Poaceae.
Results
A total of 146 bHLH TFs were identified in the
Brachypodium distachyon
genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions.
Conclusion
One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of
BdbHLH
genes.
Publisher
BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
Subject
/ Analysis
/ Animal Genetics and Genomics
/ Basic Helix-Loop-Helix Transcription Factors - chemistry
/ Basic Helix-Loop-Helix Transcription Factors - genetics
/ Basic Helix-Loop-Helix Transcription Factors - metabolism
/ bHLH
/ Binding
/ Biomedical and Life Sciences
/ Chromosomes, Plant - genetics
/ DNA
/ Domains
/ Gene Expression Regulation, Plant
/ Genes
/ Genomes
/ Genomics
/ Grasses
/ Helix-loop-helix proteins (basic)
/ Microbial Genetics and Genomics
/ Protein Structure, Quaternary
/ Proteins
/ Sorghum
