scholarly journals Genome-wide identification and characterization of melon bHLH transcription factors in regulation of fruit development

2020 ◽  
Author(s):  
Selinge Bai ◽  
Chao Tan ◽  
Yunyun Tian ◽  
Ming Ma ◽  
Agula Hasi
Keyword(s):  
Transcription Factor ◽  
Fruit Ripening ◽  
Distribution Patterns ◽  
Fruit Growth ◽  
Bhlh Transcription Factor ◽  
Transcription Factor Family ◽  
Helix Loop Helix ◽  
Bhlh Genes ◽  
Bhlh Transcription Factors ◽  
Intron Distribution

Abstract Background: The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor families in plants, and plays crucial roles in plant development. Melon is one of an important horticulture plants, and is an attractive model plant for studying fruit ripening. However, the bHLH gene family of melon has not been identified yet, and functions in fruit growth and ripening are seldom researched. Results: In this study, 118 bHLH genes were identified in the genome of melon. Phylogenetic analysis illustrated that these CmbHLHs could be classified into 16 subfamilies. Intron distribution pattern analysis of bHLH domain found 13 intron distribution patterns in CmbHLHs. CmbHLH genes were unevenly distributed on chromosomes 1 to 12 of the melon genome, and five CmbHLH s were tandem repeat on chromosomes 4 and 8. Expression characters of CmbHLH genes were studied using the transcriptome data. Tissue analysis of indicated CmbHLH32 high expressed in female flowers and early fruit growth stage. Transgenic plant lines of overexpression of CmbHLH32 were constructed, and overexpression of CmbHLH32 result in early fruit ripening compared to the wild type fruit. Conclusions: The bHLH transcription factor family was identified and analyzed for the first time in the melon, overexpression of CmbHLH32 will affect the ripening time of melon fruit, these findings laid a theoretical foundation for further study on the role of bHLH family members in the growth and development of melon .

scholarly journals Genome-Wide Identification and Characterization of Melon bHLH Transcription Factors in Regulation of Fruit Development

Plants ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 2721
Author(s):  
Chao Tan ◽  
Huilei Qiao ◽  
Ming Ma ◽  
Xue Wang ◽  
Yunyun Tian ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Fruit Ripening ◽  
Expression Patterns ◽  
Female Flower ◽  
Distribution Patterns ◽  
Early Developmental Stage ◽  
Bhlh Transcription Factor ◽  
Transcription Factor Family ◽  
Specific Expression ◽  
Bhlh Genes

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor families in plants and plays crucial roles in plant development. Melon is an important horticultural plant as well as an attractive model plant for studying fruit ripening. However, the bHLH gene family of melon has not yet been identified, and its functions in fruit growth and ripening are seldom researched. In this study, 118 bHLH genes were identified in the melon genome. These CmbHLH genes were unevenly distributed on chromosomes 1 to 12, and five CmbHLHs were tandem repeat on chromosomes 4 and 8. There were 13 intron distribution patterns among the CmbHLH genes. Phylogenetic analysis illustrated that these CmbHLHs could be classified into 16 subfamilies. Expression patterns of the CmbHLH genes were studied using transcriptome data. Tissue specific expression of the CmbHLH32 gene was analysed by quantitative RT-PCR. The results showed that the CmbHLH32 gene was highly expressed in female flower and early developmental stage fruit. Transgenic melon lines overexpressing CmbHLH32 were generated, and overexpression of CmbHLH32 resulted in early fruit ripening compared to wild type. The CmbHLH transcription factor family was identified and analysed for the first time in melon, and overexpression of CmbHLH32 affected the ripening time of melon fruit. These findings laid a foundation for further study on the role of bHLH family members in the growth and development of melon.

scholarly journals Identification and Characterization of the Basic Helix-Loop-Helix Transcription Factor Family in Pinus massoniana

Forests ◽  
2020 ◽  
Vol 11 (12) ◽  
pp. 1292
Author(s):  
Yu Chen ◽  
Peihuang Zhu ◽  
Fan Wu ◽  
Xiaofeng Wang ◽  
Jinfeng Zhang ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Pinus Massoniana ◽  
Pcr Analysis ◽  
Bhlh Protein ◽  
Transcription Factor Family ◽  
Masson Pine ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Genes ◽  
Bhlh Transcription Factors

The basic helix-loop-helix (bHLH) protein transcription factor family is the most widely distributed transcription factor family in eukaryotes. Members of this family play important roles in secondary metabolic biosynthesis, signal transduction, and plant resistance. Research on the bHLH family in animals is more extensive than that in plants, and members of the family in plants are classified according to the classification criteria for those in animals. To date, no research on the bHLH gene family in Pinus massoniana (Masson pine) has been reported. In this study, we identified 88 bHLH genes from four transcriptomes of Masson pine and performed bioinformatics analysis. These genes were divided into 10 groups in total. RT-PCR analysis revealed that the expression levels of the six genes increased under abiotic stress and hormone treatments. These findings will facilitate further studies on the functions of bHLH transcription factors.

The basic helix-loop-helix transcription factor bHLH95 affects fruit ripening and multiple metabolisms in tomato

2020 ◽  
Vol 71 (20) ◽  
pp. 6311-6327
Author(s):  
Lincheng Zhang ◽  
Jing Kang ◽  
Qiaoli Xie ◽  
Jun Gong ◽  
Hui Shen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Fruit Ripening ◽  
Tomato Fruit ◽  
Soluble Sugar ◽  
Glutathione Metabolism ◽  
Bhlh Transcription Factor ◽  
Total Carotenoids ◽  
Helix Loop Helix ◽  
Tomato Fruit Ripening

Abstract Ethylene signaling pathways regulate several physiological alterations that occur during tomato fruit ripening, such as changes in colour and flavour. The mechanisms underlying the transcriptional regulation of genes in these pathways remain unclear, although the role of the MADS-box transcription factor RIN has been widely reported. Here, we describe a bHLH transcription factor, SlbHLH95, whose transcripts accumulated abundantly in breaker+4 and breaker+7 fruits compared with rin (ripening inhibitor) and Nr (never ripe) mutants. Moreover, the promoter activity of SlbHLH95 was regulated by RIN in vivo. Suppression of SlbHLH95 resulted in reduced sensitivity to ethylene, decreased accumulation of total carotenoids, and lowered glutathione content, and inhibited the expression of fruit ripening- and glutathione metabolism-related genes. Conversely, up-regulation of SlbHLH95 in wild-type tomato resulted in higher sensitivity to ethylene, increased accumulation of total carotenoids, slightly premature ripening, and elevated accumulation of glutathione, soluble sugar, and starch. Notably, overexpression of SlbHLH95 in rin led to the up-regulated expression of fruit ripening-related genes (FUL1, FUL2, SAUR69, ERF4, and CNR) and multiple glutathione metabolism-related genes (GSH1, GSH2, GSTF1, and GSTF5). These results clarified that SlbHLH95 participates in the regulation of fruit ripening and affects ethylene sensitivity and multiple metabolisms targeted by RIN in tomato.

scholarly journals BMP and FGF signaling interact to pattern mesoderm by controlling basic helix-loop-helix transcription factor activity

eLife ◽  
2018 ◽  
Vol 7 ◽  
Author(s):  
Richard H Row ◽  
Amy Pegg ◽  
Brian A Kinney ◽  
Gist H Farr ◽  
Lisa Maves ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Bhlh Transcription Factor ◽  
Germ Layer ◽  
Transcription Factor Activity ◽  
Fgf Signaling ◽  
Factor Activity ◽  
Cell Fates ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Transcription Factors

The mesodermal germ layer is patterned into mediolateral subtypes by signaling factors including BMP and FGF. How these pathways are integrated to induce specific mediolateral cell fates is not well understood. We used mesoderm derived from post-gastrulation neuromesodermal progenitors (NMPs), which undergo a binary mediolateral patterning decision, as a simplified model to understand how FGF acts together with BMP to impart mediolateral fate. Using zebrafish and mouse NMPs, we identify an evolutionarily conserved mechanism of BMP and FGF-mediated mediolateral mesodermal patterning that occurs through modulation of basic helix-loop-helix (bHLH) transcription factor activity. BMP imparts lateral fate through induction of Id helix loop helix (HLH) proteins, which antagonize bHLH transcription factors, induced by FGF signaling, that specify medial fate. We extend our analysis of zebrafish development to show that bHLH activity is responsible for the mediolateral patterning of the entire mesodermal germ layer.

scholarly journals Systematic analysis of the basic/helix-loop-helix (bHLH) transcription factor family in pummelo (Citrus grandis) and identification of the key members involved in the response to iron deficiency

2019 ◽  
Author(s):  
Xiao-Yong Zhang ◽  
Jie-Ya Qiu ◽  
Qiu-Ling Hui ◽  
Yuan-Yuan Xu ◽  
Yi-Zhong He ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Protein Interactions ◽  
Bhlh Transcription Factor ◽  
Sequencing Data ◽  
Systematic Analysis ◽  
Go Annotation ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Bhlh Genes ◽  
Bhlh Proteins

Abstract Background As the second largest superfamily of transcription factors (TFs), the basic/helix-loop-helix (bHLH) proteins participate in regulating of a series of biological and developmental processes in plants. Although several bHLH genes of citrus have been identified and previously characterized, a large number of bHLH members are still unknown.Results In this study, we genome-widely identified a total of 128 CgbHLHs from pummelo (Citrus grandis) that were classified into 18 subfamilies by phylogenetic comparison with Arabidopsis thaliana bHLH proteins. All of these CgbHLHs were randomly distributed on nine known (125 genes) and one unknown (3 genes) chromosomes, and 12 and 47 of them were identified to be tandem and segmental duplicated genes, respectively. Sequence analysis showed detailed characteristics of their intron-exon structures, bHLH domain and conserved motifs. Gene ontology (GO) analysis suggested that most of CgbHLHs were annotated to the nucleus, DNA-binding transcription factor activity, response to abiotic stimulus, reproduction, post-embryonic development, flower development and photosynthesis. In addition, 37 CgbHLH proteins were predicted to have direct or indirect protein-protein interactions. Based on GO annotation, RNA sequencing data in public database and qRT-PCR results, 22 of CgbHLHs were identified as the key candidates that respond to iron deficiency.Conclusions In total, 128 CgbHLH proteins were identified from pummelo, and their detailed sequence and structure characteristics and putative functions were analyzed. This study provides comprehensive information for further functional elucidation of CgbHLH genes in citrus.

scholarly journals Genome-Wide Identification and Analysis of the Chicken Basic Helix-Loop-Helix Factors

2010 ◽  
Vol 2010 ◽  
pp. 1-12 ◽  
Author(s):  
Wu-yi Liu ◽  
Chun-jiang Zhao
Keyword(s):  
Transcription Factor ◽  
Phylogenetic Analyses ◽  
Bhlh Transcription Factor ◽  
Transcription Factor Family ◽  
Early Date ◽  
Basic Helix Loop Helix ◽  
Helix Loop Helix ◽  
Genome Wide ◽  
A Genome ◽  
Wide Range

Members of the basic helix-loop-helix (bHLH) family of transcription factors play important roles in a wide range of developmental processes. In this study, we conducted a genome-wide survey using the chicken (Gallus gallus) genomic database, and identified 104 bHLH sequences belonging to 42 gene families in an effort to characterize the chicken bHLH transcription factor family. Phylogenetic analyses revealed that chicken has 50, 21, 15, 4, 8, and 3 bHLH members in groups A, B, C, D, E, and F, respectively, while three members belonging to none of these groups were classified as ‘‘orphans’’. A comparison between chicken and human bHLH repertoires suggested that both organisms have a number of lineage-specific bHLH members in the proteomes. Chromosome distribution patterns and phylogenetic analyses strongly suggest that the bHLH members should have arisen through gene duplication at an early date. Gene Ontology (GO) enrichment statistics showed 51 top GO annotations of biological processes counted in the frequency. The present study deepens our understanding of the chicken bHLH transcription factor family and provides much useful information for further studies using chicken as a model system.

scholarly journals Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Anthocyanin Biosynthesis in Fig (Ficus carica L.)

2021 ◽  
Vol 12 ◽  
Author(s):  
Miaoyu Song ◽  
Haomiao Wang ◽  
Zhe Wang ◽  
Hantang Huang ◽  
Shangwu Chen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Anthocyanin Biosynthesis ◽  
Expression Patterns ◽  
Ficus Carica ◽  
Functional Study ◽  
Anthocyanin Synthesis ◽  
Bhlh Transcription Factor ◽  
Transcription Factor Family ◽  
Genome Database ◽  
Bhlh Genes

The basic helix–loop–helix (bHLH) transcription factor family is the second largest transcription factor family in plants, and participates in various plant growth and development processes. A total of 118 bHLH genes were identified from fig (Ficus carica L.) by whole-genome database search. Phylogenetic analysis with Arabidopsis homologs divided them into 25 subfamilies. Most of the bHLHs in each subfamily shared a similar gene structure and conserved motifs. Seventy-two bHLHs were found expressed at fragments per kilobase per million mapped (FPKM) > 10 in the fig fruit; among them, 15 bHLHs from eight subfamilies had FPKM > 100 in at least one sample. bHLH subfamilies had different expression patterns in the female flower tissue and peel during fig fruit development. Comparing green and purple peel mutants, 13 bHLH genes had a significantly different (≥ 2-fold) expression. Light deprivation resulted in 68 significantly upregulated and 22 downregulated bHLH genes in the peel of the fruit. Sixteen bHLH genes in subfamily III were selected by three sets of transcriptomic data as candidate genes related to anthocyanin synthesis. Interaction network prediction and yeast two-hybrid screening verified the interaction between FcbHLH42 and anthocyanin synthesis-related genes. The transient expression of FcbHLH42 in tobacco led to an apparent anthocyanin accumulation. Our results confirm the first fig bHLH gene involved in fruit color development, laying the foundation for an in-depth functional study on other FcbHLH genes in fig fruit quality formation, and contributing to our understanding of the evolution of bHLH genes in other horticulturally important Ficus species.

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