Genome-Wide Characterization and Analysis of the bHLH Transcription Factor Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cell C4 Anatomy

Wei, Xiaowei; Cao, Jing; Lan, Haiyan

doi:10.3389/fgene.2022.927830

Cited by 4 publications

(4 citation statements)

References 104 publications

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“…A subset of genes, encompassing CtbHLH88, CtbHLH99, CtbHLH12, CtbHLH26, CtbHLH102, CtbHLH24, CtbHLH105, and CtbHLH6, are characterized by the presence of MBS elements (n = 1 each) (Figure S4). Compared to the findings in other plants [28,77], these bHLH members demonstrate an array of defense and stress-responsive elements, including the drought-inducible MBS element. In comparison to G-box and ABRE, MBS elements might hold a lesser significance than G-box elements.…”

Section: Discussionmentioning

confidence: 68%

Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius

Tan,

Lu,

et al. 2023

Plants

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The basic helix–loop–helix (bHLH) transcription factors possess DNA-binding and dimerization domains and are involved in various biological and physiological processes, such as growth and development, the regulation of secondary metabolites, and stress response. However, the bHLH gene family in C. tinctorius has not been investigated. In this study, we performed a genome-wide identification and analysis of bHLH transcription factors in C. tinctorius. A total of 120 CtbHLH genes were identified, distributed across all 12 chromosomes, and classified into 24 subfamilies based on their phylogenetic relationships. Moreover, the 120 CtbHLH genes were subjected to comprehensive analyses, including protein sequence alignment, evolutionary assessment, motif prediction, and the analysis of promoter cis-acting elements. The promoter region analysis revealed that CtbHLH genes encompass cis-acting elements and were associated with various aspects of plant growth and development, responses to phytohormones, as well as responses to both abiotic and biotic stresses. Expression profiles, sourced from transcriptome databases, indicated distinct expression patterns among these CtbHLH genes, which appeared to be either tissue-specific or specific to certain cultivars. To further explore their functionality, we determined the expression levels of fifteen CtbHLH genes known to harbor motifs related to abiotic and hormone responses. This investigation encompassed treatments with ABA, salt, drought, and MeJA. The results demonstrated substantial variations in the expression patterns of CtbHLH genes in response to these abiotic and hormonal treatments. In summary, our study establishes a solid foundation for future inquiries into the roles and regulatory mechanisms of the CtbHLH gene family.

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Section: Discussionmentioning

confidence: 68%

Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius

Tan,

Lu,

et al. 2023

Plants

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“…Under drought stress, Arabidopsis AtMYC2 (bHLH) functions as a transcriptional activator in abscisic acid signaling and AtMYC2 and AtMYB2 proteins function as transcriptional activators in ABA-inducible gene expression in plants [42]. A number of cis-acting elements related to plant hormones and stress responses were also predicted in the promoter regions of SabHLHs, and most were involved in tolerance to drought and salinity [43]. In this study, the expression profile based on RNA-seq showed that most of the BpbHLH genes responded to osmotic treatment, indicating that these genes might be involved in drought resistance regulation mediated by the hormone signaling pathway in birch.…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization of bHLH Family Genes and Expression Analysis in Response to Osmotic Stress in Betula platyphylla

Zhao,

Bi,

Jia

et al. 2023

Plants

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The bHLH family, as a superfamily of transcription factors (TFs), has special functional characteristics in plants and plays a crucial role in a plant’s growth and development and helping the plant cope with various stresses. In this study, 128 bHLH family genes were screened in the birch (B. platyphylla) genome using conservative domain scan and blast analysis. These genes are clustered into 21 subfamilies based on the phylogenetic tree construction and are unevenly distributed among the 14 birch chromosomes. In all, 22 segmental duplication pairs with 27 BpbHLH genes were identified. The duplications were distributed on eight chromosomes. Analysis of gene structures and protein motifs revealed intra-group conservation of BpbHLHs. Of the BpbHLH family genes, 16 contain only one intron each. The BPChr14G06667 gene contains the most introns, that is, 19. The cis-elements, which respond to plant hormones, light, defense, and stress, were found on the promoter of BHLH family genes. As per RNA-seq data analysis, under PEG osmotic stress, most BpbHLH genes were differentially expressed, and eight were highly differentially expressed. The qRT-PCR analysis results further indicated that BPChr06G09475 was the gene with the highest expression level in leaves, roots, and stems, and that the expression of these eight genes was higher in leaves than in roots and stems and upregulated in all three tissues under osmotic stress compared to the controls. The above analysis suggests that the BpbHLH family genes have a certain biological effect under drought stress that provides a basis for molecular breeding for stress resistance in birch.

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“… Phylogenetic analysis of the species based on genome-wide association study of the basic helix-loop-helix (bHLH) family. The total number of bHLH transcription factors identified from the genome of each species are indicated [ 5 , 22 , 23 , 24 , 25 , 26 , 27 , 28 , 29 , 30 , 31 , 32 , 33 , 34 , 35 , 36 , 37 , 38 , 39 , 40 , 41 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 , 51 , 52 , 53 , 54 , 55 , 56 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 64 ]. …”

Section: Figurementioning

confidence: 99%

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

Zuo

Lee

Kang

2023

IJMS

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Plant basic helix-loop-helix (bHLH) transcription factors are involved in many physiological processes, and they play important roles in the abiotic stress responses. The literature related to genome sequences has increased, with genome-wide studies on the bHLH transcription factors in plants. Researchers have detailed the functionally characterized bHLH transcription factors from different aspects in the model plant Arabidopsis thaliana, such as iron homeostasis and abiotic stresses; however, other important economic crops, such as rice, have not been summarized and highlighted. The bHLH members in the same subfamily have similar functions; therefore, unraveling their regulatory mechanisms will help us to identify and understand the roles of some of the unknown bHLH transcription factors in the same subfamily. In this review, we summarize the available knowledge on functionally characterized bHLH transcription factors according to four categories: plant growth and development; metabolism synthesis; plant signaling, and abiotic stress responses. We also highlight the roles of the bHLH transcription factors in some economic crops, especially in rice, and discuss future research directions for possible genetic applications in crop breeding.

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Genome-Wide Characterization and Analysis of the bHLH Transcription Factor Family in Suaeda aralocaspica, an Annual Halophyte With Single-Cell C4 Anatomy

Cited by 4 publications

References 104 publications

Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius

Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius

Genome-Wide Characterization of bHLH Family Genes and Expression Analysis in Response to Osmotic Stress in Betula platyphylla

Basic Helix-Loop-Helix Transcription Factors: Regulators for Plant Growth Development and Abiotic Stress Responses

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