Global identification, structural analysis and expression characterization of bHLH transcription factors in wheat

Guo, Xiaojiang; Wang, Jirui

doi:10.1186/s12870-017-1038-y

Cited by 54 publications

(49 citation statements)

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“…The 19 subfamilies were designated I a, I b, II, III a, III b, III c, III d+e, III f, IV a, IV d, V a, V b, VII a+b, VIII a, VIII b+c, IX, X, XI, and XII ( Fig 1 ). Most of these subfamilies are common and are consistent with the subfamily classification reported in previous phylogenetic analyses in other plant species, such as tomato [ 9 ], peanut [ 8 ], Chinese cabbage [ 13 ], and wheat [ 27 ]. This finding indicated that the bHLH proteins in the conserved subfamilies among plant species may play a fundamental role during plant development and evolution.…”

Section: Resultssupporting

confidence: 86%

“…Compared with the number of bHLH genes identified in other plant species in previous studies, fewer bHLH superfamily genes were identified in peach in this study. In previous studies, 132, 124, 188, 225, 155, 167, 146 and 159 bHLH genes were identified in peanut [ 8 ], potato [ 26 ], apple [ 10 ], wheat [ 27 ], bean [ 17 ], rice [ 4 ], carrot [ 28 ], and tomato [ 9 ], respectively. These values are probably associated with differences in evolution and genome duplication or genome sizes in these plants.…”

Section: Resultsmentioning

confidence: 99%

“…Additionally, this result is consistent with the earlier finding that the bHLH superfamily in plants can be divided into 15–25 subfamilies [ 6 ]. Some previous studies have named the bHLH subfamilies using English letters [ 4 , 10 ], whereas most published reports have named them using Roman numerals [ 13 , 9 , 11 , 8 , 27 , 26 , 6 ], and some authors have named each subfamily using Arabic numerals [ 3 , 28 ]. For the peach bHLH subfamilies identified in this study, we adopted the nomenclature using Roman numerals, as employed for Chinese cabbage by Song et al [ 13 ] and for other plants by Pires and Dolan [ 6 ].…”

Section: Resultsmentioning

confidence: 99%

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Genome-wide analysis of basic helix-loop-helix superfamily members in peach

Zhang

Feng

et al. 2018

PLoS ONE

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The basic helix-loop-helix (bHLH) transcription factor family is a superfamily found in all eukaryotes that plays important roles in regulating growth and development. Over the past several decades, many bHLH superfamily genes have been identified and characterized in herbaceous and woody plants. However, the genes belonging to the bHLH superfamily in peach (Prunus persica) have not yet been comprehensively identified and characterized. Here, we identified 95 members of the bHLH superfamily in the peach genome, and these genes were classified into 19 subfamilies based on a phylogenetic comparison with bHLH proteins from Arabidopsis. The members within each subfamily were highly conserved according to the analysis of motif compositions and exon/intron organizations. The 95 bHLH genes were unevenly distributed on chromosomes 1 to 8 of the peach genome. We identified 57 pairs of bHLH members that were orthologous between peach and Arabidopsis. Additionally, 48 pairs of paralogous bHLH genes were identified on the eight chromosomes of the peach genome. Coupled with relative expression analysis of bHLH genes in red-fleshed peach fruit at five developmental stages, we identified several bHLH genes that might be involved in fruit development and anthocyanin biosynthesis. This study provides insight into the molecular mechanisms through which these genes are involved in the regulation of biological and biochemical processes in peach and lays the foundation for further studies on these genes.

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Section: Resultssupporting

confidence: 86%

Section: Resultsmentioning

confidence: 99%

Section: Resultsmentioning

confidence: 99%

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Genome-wide analysis of basic helix-loop-helix superfamily members in peach

Zhang

Feng

et al. 2018

PLoS ONE

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“…4A. The backbones of motif 1 and 2 are also conserved among plant species [10,20,47], which is believed to indicate that these highly conserved residues in bHLH domains are responsible for dimerization [10].…”

Section: Phylogenetic Analysis Gene Structure Conserved Motifs Analmentioning

confidence: 98%

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in papaya (Carica papaya L.)

Yang¹,

Kuang²,

Zhou³

et al. 2019

Preprint

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Background : As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been identified and functionally characterized in many plants. However, no comprehensive analysis of the bHLH family in papaya ( Carica papaya L. ) has been reported previously. Results: In this study, a total of 73 CpbHLH genes were found in papaya, and these genes were classified into 18 subfamilies based on phylogenetic analysis, with one orphans. Almost all of the CpbHLH in the same subfamily shared similar gene structures and protein motifs according to an analysis of exon/intron organizations and motif compositions. The number of exons in CpbHLH genes varied from 1 to 11 with an average of 5. The amino acid sequences of the bHLH domains were quite conservative, especially Leu-27 and Leu-63. Promoter cis -element analysis revealed that most of the CpbHLH genes contained cis -elements that can respond to various biotic/abiotic stress-related events. Gene ontology (GO) analysis revealed that Cp bHLH mainly functions in protein dimerization activity and DNA-binding, and most Cp bHLH proteins were predicted to localize in the nucleus. Abiotic stress treatment and quantitative real-time PCR (qRT-PCR) revealed some predicted CpbHLH genes that might be responsible for abiotic stress responses in papaya. Conclusions : A total of 73 bHLH transcription factors were identified from papaya, and their gene structures, conserved domains, sequence features, phylogenetic relationship, promoter cis -element, GO annotation and gene expression profiles responsible for abiotic stress were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of Cp bHLHs. Keywords : papaya, genome-wide analysis, bHLH transcription factors, abiotic stress

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“…The earliest reported bHLH protein in animals is the mouse transcription factors E12 and E47 (Murre et al, 1989;Massari and Murre, 2000;Stevens et al, 2008;Murre, 2019). Later studies suggested the animal bHLH proteins to be divided into six large categories of protein subclasses that were subdivided as 45 sub-families (Ledent and Vervoort, 2001;Ledent et al, 2002;Simionato et al, 2007;Stevens et al, 2008;Wang et al, 2010), whereas the plant bHLH proteins were divided into more than 20 subclasses with conserved motifs or domains identified (Carretero-Paulet et al, 2010;Yan et al, 2015;Liu et al, 2018;Wei and Chen, 2018;Gao et al, 2019), varying from 21 to 32 subfamilies (Carretero-Paulet et al, 2010;Song et al, 2014;Hudson and Hudson, 2014;Sun et al, 2015;Yan et al, 2015;Zhang et al, 2015;Kavas et al, 2016;Gao et al, 2017;Guo and Wang, 2017;Niu et al, 2017;Liu et al, 2018;Lu et al, 2018;Wei and Chen, 2018;Gao et al, 2019).…”

Section: Introductionmentioning

confidence: 99%

Comparative Functional Analysis of the Basic Helix-Loop-Helix Proteins in the Clawed Frogs' Genomes With Common Essential Pathways and Enriched Gene Ontology Terms

Liu

2019

American Journal of Biochemistry and Biotechnology

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The international Gene Ontology (GO) and pathway databases were used to functionally analyze the clawed frogs' Basic Helix-Loop-Helix (bHLH) transcription factors of Xenopus tropicalis and Xenopus laevis in a updated genome-wide survey. There were 41 GO terms and one pathway significantly enriched for Xenopus tropicalis, whereas there were 45 GO terms and 3 pathways significantly enriched for Xenopus laevis. Among those significantly enriched GO terms, the two clawed frogs share 31 common functional GO annotations of these bHLH genes, including DNA-dependent transcription and (negative) transcription regulation, DNA binding and bHLH binding, transcription factor complex and protein heterodimerization activity, (negative) regulation of RNA metabolic processes, nuclear translocator and repressor, myogenic basic muscle-specific protein, neurogenic differentiation factor and NeuroD. Furthermore, these frogs' bHLH genes were also found to play important roles in the regulation of gene expression in some important developmental or physiological processes, such as (skeletal) muscle cell differentiation, muscle organ development, biological rhythms and rhythmic process, hypoxia (adaption) and hypoxia-inducible factors, neurogenesis, neural tube development and neurogenic differentiation, whereas they were commonly significantly enriched in TGF-beta signaling pathway. These resulted data and information are very important for us to understand the functions, classification and evolution of frog bHLH genes.

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Global identification, structural analysis and expression characterization of bHLH transcription factors in wheat

Cited by 54 publications

References 50 publications

Genome-wide analysis of basic helix-loop-helix superfamily members in peach

Genome-wide analysis of basic helix-loop-helix superfamily members in peach

Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in papaya (Carica papaya L.)

Comparative Functional Analysis of the Basic Helix-Loop-Helix Proteins in the Clawed Frogs' Genomes With Common Essential Pathways and Enriched Gene Ontology Terms

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