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

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.

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

10.21203/rs.2.22819/v1 ◽

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 .

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.730692 ◽

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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Characterization and Tissue-specific Expression of bHLH Genes in Dimocarpus longan

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha47311531 ◽

2019 ◽

Vol 47 (3) ◽

Author(s):

Wei ZHENG ◽

Xueming DONG ◽

Xuefei YU ◽

Qiuying ZHANG ◽

Ning CHEN

Keyword(s):

Expression Patterns ◽

Digital Object Identifier ◽

Bhlh Transcription Factor ◽

Rna Seq ◽

Phylogenetic Tree Analysis ◽

Specific Expression ◽

Tissue Specific ◽

Tissue Specific Expression ◽

Bhlh Genes ◽

Dimocarpus Longan

In plants, the basic helix-loop-helix (bHLH) transcription factors (TFs) play pivotal roles in many biological processes including growth, stress response, and secondary metabolite synthesis. To date, many bHLH genes have been identified and characterized in diverse plant species. However, little is known regarding the bHLH genes in Dimocarpus longan Lour. (D. longan). Based on RNA-seq data, we identified 42 putative bHLH genes from D. longan and determined their putative functions using the NCBI Conserved Domain Search Tool and Pfam databases. The physicochemical properties, phylogenetic relationships, conserved motifs, gene ontology (GO) annotations, protein-protein interactions, and tissue-specific expression patterns of these bHLH genes were systematically explored. In total, ten motifs were found in DlbHLH proteins using MEME, among which two were highly conserved. Phylogenetic tree analysis found that DlbHLH proteins can be divided into nine groups, with group 2 being the largest. GO annotation results showed that the DlHLH genes were involved in various molecular functions. RNA-seq and qRT-PCR results revealed important differences in the expression patterns of 17 of the DlbHLH genes. In particular, DlbHLH-9, DlbHLH-19, DlbHLH-25, DlbHLH-26, and DlbHLH-35 were found to show significantly different expression patterns in root and leaf tissues. The results of this study will further enrich our knowledge regarding bHLH transcription factor genes and lay a foundation for enhancing the production of active secondary metabolites by genetic engineering in D. longan. ********* In press - Online First. Article has been peer reviewed, accepted for publication and published online without pagination. It will receive pagination when the issue will be ready for publishing as a complete number (Volume 47, Issue 3, 2019). The article is searchable and citable by Digital Object Identifier (DOI). DOI link will become active after the article will be included in the complete issue. *********

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Basic Helix-Loop-Helix (bHLH) transcription factor family in Yellow horn (Xanthoceras sorbifolia Bunge): Genome-wide characterization, chromosome location, phylogeny, structures and expression patterns

International Journal of Biological Macromolecules ◽

10.1016/j.ijbiomac.2020.05.253 ◽

2020 ◽

Vol 160 ◽

pp. 711-723 ◽

Cited By ~ 1

Author(s):

Yanhe Lang ◽

Zhi Liu

Keyword(s):

Transcription Factor ◽

Expression Patterns ◽

Bhlh Transcription Factor ◽

Chromosome Location ◽

Transcription Factor Family ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Genome Wide

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Genome-Wide Identification and Characterization of the NAC Transcription Factor Family in Musa Acuminata and Expression Analysis during Fruit Ripening

International Journal of Molecular Sciences ◽

10.3390/ijms21020634 ◽

2020 ◽

Vol 21 (2) ◽

pp. 634

Author(s):

Bin Li ◽

Ruiyi Fan ◽

Qiaosong Yang ◽

Chunhua Hu ◽

Ou Sheng ◽

...

Keyword(s):

Transcription Factor ◽

Fruit Ripening ◽

Expression Patterns ◽

Musa Acuminata ◽

Nac Transcription Factor ◽

Banana Fruit ◽

Transcription Factor Family ◽

Climacteric Fruit ◽

Identification And Characterization

Banana (Musa acuminata, AAA group) is a representative climacteric fruit with essential nutrients and pleasant flavors. Control of its ripening determines both the fruit quality and the shelf life. NAC (NAM, ATAF, CUC2) proteins, as one of the largest superfamilies of transcription factors, play crucial roles in various functions, especially developmental processes. Thus, it is important to conduct a comprehensive identification and characterization of the NAC transcription factor family at the genomic level in M. acuminata. In this article, a total of 181 banana NAC genes were identified. Phylogenetic analysis indicated that NAC genes in M. acuminata, Arabidopsis, and rice were clustered into 18 groups (S1–S18), and MCScanX analysis disclosed that the evolution of MaNAC genes was promoted by segmental duplication events. Expression patterns of NAC genes during banana fruit ripening induced by ethylene were investigated using RNA-Seq data, and 10 MaNAC genes were identified as related to fruit ripening. A subcellular localization assay of selected MaNACs revealed that they were all localized to the nucleus. These results lay a good foundation for the investigation of NAC genes in banana toward the biological functions and evolution.

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Genome-Wide Analysis of Basic Helix–Loop–Helix Superfamily Members Reveals Organization and Chilling-Responsive Patterns in Cabbage (Brassica oleracea var. capitata L.)

Genes ◽

10.3390/genes10110914 ◽

2019 ◽

Vol 10 (11) ◽

pp. 914

Author(s):

Shan ◽

Zhang ◽

Yu ◽

Wang ◽

Li ◽

...

Keyword(s):

Brassica Oleracea ◽

Expression Profiles ◽

Phylogenetic Analyses ◽

Chilling Stress ◽

Expression Patterns ◽

Comprehensive Analysis ◽

Bhlh Transcription Factor ◽

Specific Expression ◽

Basic Helix Loop Helix ◽

Helix Loop Helix

Basic helix–loop–helix (bHLH) transcription factor (TF) family is commonly found in eukaryotes, which is one of the largest families of regulator proteins. It plays an important role in plant growth and development, as well as various biotic and abiotic stresses. However, a comprehensive analysis of the bHLH family has not been reported in Brassica oleracea. In this study, we systematically describe the BobHLHs in the phylogenetic relationships, expression patterns in different organs/tissues, and in response to chilling stress, and gene and protein characteristics. A total of 234 BobHLH genes were identified in the B. oleracea genome and were further clustered into twenty-three subfamilies based on the phylogenetic analyses. A large number of BobHLH genes were unevenly located on nine chromosomes of B. oleracea. Analysis of RNA-Seq expression profiles revealed that 21 BobHLH genes exhibited organ/tissue-specific expression. Additionally, the expression of six BobHLHs (BobHLH003, -048, -059, -093, -109, and -148) were significantly down-regulated in chilling-sensitive cabbage (CS-D9) and chilling-tolerant cabbage (CT-923). At 24h chilling stress, BobHLH054 was significantly down-regulated and up-regulated in chilling-treated CS-D9 and CT-923. Conserved motif characterization and exon/intron structural patterns showed that BobHLH genes had similar structures in the same subfamily. This study provides a comprehensive analysis of BobHLH genes and reveals several candidate genes involved in chilling tolerance of B. oleracea, which may be helpful to clarify the roles of bHLH family members and understand the regulatory mechanisms of BobHLH genes in response to the chilling stress of cabbage.

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Potato MYB and bHLH transcription factors associated with anthocyanin intensity and common scab resistance

Botany ◽

10.1139/cjb-2012-0025 ◽

2013 ◽

Vol 91 (10) ◽

pp. 722-730 ◽

Cited By ~ 10

Author(s):

Helen H. Tai ◽

Claudia Goyer ◽

Agnes M. Murphy

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Common Scab ◽

Scab Resistance ◽

Bhlh Transcription Factor ◽

Bhlh Genes ◽

Transcription Factor Genes ◽

Key Enzyme ◽

Common Scab Resistance ◽

Highly Correlated

MYB and bHLH are large transcription factor families with largely uncharacterized biological functions. The patterns of expression of 42 MYB and 58 bHLH transcription factor genes were examined in potato clones that were demonstrated to have variation in anthocyanin intensity and common scab resistance to assess their possible involvement in regulating these traits. The control of expression of biosynthetic enzymes in regulation of anthocyanin intensity was also evaluated. The dihydroflavonol 4-reductase (DFR) gene, a key enzyme in the pathway, had the highest correlation with gene expression and anthocyanin intensity (quantified as levels of anthocyanidins). Expression of five uncharacterized MYB and three bHLH genes was also highly correlated with anthocyanin intensity, suggesting that they could be regulators of biosynthetic enzyme gene expression. The same potato clones were also demonstrated to have variation in resistance to Streptomyces scabiei, the causal pathogen of common scab in potato. Correlation analysis was used to show that anthocyanin intensity was not associated with common scab resistance. However, common scab resistance was correlated with expression of another two MYB and three bHLH genes, indicating that they might be involved in the regulation of the defense response of potato against the common scab pathogen.

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Structural analysis and tissue-specific expression patterns of a novel salt-inducible NAC transcription factor gene fromNicotiana tabacumcv. Xanthi

The Journal of Horticultural Science and Biotechnology ◽

10.1080/14620316.2014.11513140 ◽

2014 ◽

Vol 89 (6) ◽

pp. 700-706 ◽

Cited By ~ 6

Author(s):

Q. Q. Han ◽

P. Qiao ◽

Y. Z. Song ◽

J. Y. Zhang

Keyword(s):

Transcription Factor ◽

Structural Analysis ◽

Expression Patterns ◽

Nac Transcription Factor ◽

Transcription Factor Gene ◽

Specific Expression ◽

Tissue Specific ◽

Factor Gene ◽

Tissue Specific Expression

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

Journal of Experimental Botany ◽

10.1093/jxb/eraa363 ◽

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.

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