Abstract
BackgroundAs 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.ResultsA 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.ConclusionOne 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.
Highlights
As a superfamily of transcription factors (TFs), the basic helix-loop-helix 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
In order to verify the reliability of our identification, a BlastN program was used to search for all the expressed sequence tags (EST) in Brachypodium distachyon (Additional file 1: Table S3). 57.5% (84/ 146) of BdbHLHs were supported by the EST hits
To study the basic helix-loop-helix (bHLH) gene family in the Brachypodium distachyon, an emerging model plant in grass, we identified 146 bHLH genes distributed in 5 chromosomes
Summary
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. Development and productivity are continuously threatened by various adverse environmental factors including biotic and abiotic stresses for their sessile nature. They have evolved complicated physiological and biochemical responses by regulating the expression of a series of genes to survive and flourish under extreme living conditions. The basic region, located at the N-terminus of the domain, consisting of approximately 17 amino acids, is a DNA-binding region that enables bHLH TFs to bind to E-box (CANNTG) [7, 8]; the HLH region includes two amphipathic α helices separated by a variable (both in length and primary sequence) loop and participates in the formation of homodimers or heterodimers [8, 9]
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