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

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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A66. Collagen Iα2 gene expression is regulated by the bHLH transcription factor scleraxis

Journal of Molecular and Cellular Cardiology ◽

10.1016/j.yjmcc.2006.03.303 ◽

2006 ◽

Vol 40 (6) ◽

pp. 870

Author(s):

L. Espira ◽

L. Lamoureux ◽

S.C. Jones ◽

I.M.C. Dixon ◽

M.P. Czubryt

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Bhlh Transcription Factor

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Genomic Characterization of Endothelial Enhancers Reveals a Multifunctional Role for NR2F2 in Regulation of Arteriovenous Gene Expression

Circulation Research ◽

10.1161/circresaha.119.316075 ◽

2020 ◽

Vol 126 (7) ◽

pp. 875-888 ◽

Cited By ~ 6

Author(s):

Samir Sissaoui ◽

Jun Yu ◽

Aimin Yan ◽

Rui Li ◽

Onur Yukselen ◽

...

Keyword(s):

Gene Expression ◽

Endothelial Cells ◽

Transcription Factor ◽

Deep Sequencing ◽

Chromatin Immunoprecipitation ◽

Regulatory Elements ◽

Bhlh Transcription Factor ◽

Genome Wide ◽

A Genome

Rationale: Significant progress has revealed transcriptional inputs that underlie regulation of artery and vein endothelial cell fates. However, little is known concerning genome-wide regulation of this process. Therefore, such studies are warranted to address this gap. Objective: To identify and characterize artery- and vein-specific endothelial enhancers in the human genome, thereby gaining insights into mechanisms by which blood vessel identity is regulated. Methods and Results: Using chromatin immunoprecipitation and deep sequencing for markers of active chromatin in human arterial and venous endothelial cells, we identified several thousand artery- and vein-specific regulatory elements. Computational analysis revealed that NR2F2 (nuclear receptor subfamily 2, group F, member 2) sites were overrepresented in vein-specific enhancers, suggesting a direct role in promoting vein identity. Subsequent integration of chromatin immunoprecipitation and deep sequencing data sets with RNA sequencing revealed that NR2F2 regulated 3 distinct aspects related to arteriovenous identity. First, consistent with previous genetic observations, NR2F2 directly activated enhancer elements flanking cell cycle genes to drive their expression. Second, NR2F2 was essential to directly activate vein-specific enhancers and their associated genes. Our genomic approach further revealed that NR2F2 acts with ERG (ETS-related gene) at many of these sites to drive vein-specific gene expression. Finally, NR2F2 directly repressed only a small number of artery enhancers in venous cells to prevent their activation, including a distal element upstream of the artery-specific transcription factor, HEY2 (hes related family bHLH transcription factor with YRPW motif 2). In arterial endothelial cells, this enhancer was normally bound by ERG, which was also required for arterial HEY2 expression. By contrast, in venous endothelial cells, NR2F2 was bound to this site, together with ERG, and prevented its activation. Conclusions: By leveraging a genome-wide approach, we revealed mechanistic insights into how NR2F2 functions in multiple roles to maintain venous identity. Importantly, characterization of its role at a crucial artery enhancer upstream of HEY2 established a novel mechanism by which artery-specific expression can be achieved.

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Metallothionein and bZIP Transcription Factor Genes from Velvetleaf and Their Differential Expression Following Colletotrichum coccodes Infection

Phytopathology ◽

10.1094/phyto-96-1116 ◽

2006 ◽

Vol 96 (10) ◽

pp. 1116-1123 ◽

Cited By ~ 9

Author(s):

Amélie L. Dauch ◽

Suha H. Jabaji-Hare

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Leucine Zipper ◽

Expression Patterns ◽

Bzip Transcription Factor ◽

Colletotrichum Coccodes ◽

Transcription Factor Genes ◽

Pathogen Attack ◽

Fungal Genes ◽

Type 3

Colletotrichum coccodes is a biocontrol agent of velvetleaf (Abutilon theophrasti), a noxious weed of corn and soybean. Metallothioneins (MTs) and basic region/leucine zipper motif (bZIP) are heavy-metal-binding proteins and transcription factors, respectively, that have been related to several plant processes, including the responses of plants to pathogen attack. Previous investigation of the determinants involved in the velvet-leaf-C. coccodes interaction had shed light on particular plant and fungal genes expressed in this pathosystem. Here, we report on the temporal expression patterns of two distinct types (2 and 3) of MT and bZIP transcription factor genes in velvetleaf leaves following infection with C. coccodes using quantitative reverse-transcription polymerase chain reaction. Gene expression ratios were significantly upregulated 1 day after infection (DAI), a time at which velvetleaf leaves appeared symptomless. At 2 DAI, bZIP and type 3 MT expression ratios dropped to levels significantly lower than those estimated for noninfected plants. Necrotic symptoms appeared 5 DAI and increased with time, during which gene expression levels were maintained either below or at levels observed in the control. These findings indicate that C. coccodes altered the expression of type 2 and 3 MT and bZIP genes. In addition, this is the first report on induction of a type 3 MT in plants in response to a pathogen attack.

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FvbHLH9 Functions as a Positive Regulator of Anthocyanin Biosynthesis by Forming a HY5–bHLH9 Transcription Complex in Strawberry Fruits

Plant and Cell Physiology ◽

10.1093/pcp/pcaa010 ◽

2020 ◽

Vol 61 (4) ◽

pp. 826-837 ◽

Cited By ~ 4

Author(s):

Yang Li ◽

Pengbo Xu ◽

Guanqun Chen ◽

Jun Wu ◽

Zhongchi Liu ◽

...

Keyword(s):

Transcription Factor ◽

Promoter Region ◽

Anthocyanin Biosynthesis ◽

Anthocyanin Synthesis ◽

Bhlh Transcription Factor ◽

Anthocyanin Accumulation ◽

Positive Regulator ◽

Key Enzyme ◽

Synergistic Regulation ◽

Transient Overexpression

Abstract Anthocyanin accumulation is transcriptionally regulated by the MYB–bHLH–WD40 complex. Light is indispensable for anthocyanin accumulation, and light-inducible MYB and HY5 were considered to promote anthocyanin accumulation in many fruits. Whether and how light-inducible bHLH transcription factor and HY5 regulate anthocyanin synthesis in strawberry is unknown. In this study, we identified a bHLH transcription factor, FvbHLH9, which was induced by light as well as FvHY5, and found that, similar to FvHY5, the transient overexpression and interference FvbHLH9 in strawberry fruits can promote and decrease anthocyanin accumulation, respectively, indicating FvbHLH9 functions as a positive regulator of anthocyanin biosynthesis. Furthermore, we confirmed that both FvHY5 and FvbHLH9 specifically bind to the promoter region of some key enzyme genes, including FvDFR, and the expression of FvDFR was activated through the heterodimer formation between FvHY5 and FvbHLH9. Finally, we confirmed that FvbHLH9-promoted anthocyanin accumulation is dependent on HY5–bHLH heterodimerisation in Arabidopsis. Our findings provide insights into a mechanism involving the synergistic regulation of light-dependent coloration and anthocyanin biosynthesis via a HY5–bHLH heterodimer formed by the interaction of FvHY5 and FvbHLH9 in strawberry fruits.

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Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in sorghum [Sorghum bicolor (L.) Moench]

BMC Genomics ◽

10.1186/s12864-021-07652-9 ◽

2021 ◽

Vol 22 (1) ◽

Author(s):

Yu Fan ◽

Hao Yang ◽

Dili Lai ◽

Ailing He ◽

Guoxing Xue ◽

...

Keyword(s):

Gene Expression ◽

Transcription Factor ◽

Sorghum Bicolor ◽

Higher Plants ◽

Bhlh Transcription Factor ◽

Tissue Development ◽

Functional Identification ◽

Transcription Factor Family ◽

Gene Expression Response ◽

Genome Wide

Abstract Background Basic helix-loop-helix (bHLH) is a superfamily of transcription factors that is widely found in plants and animals, and is the second largest transcription factor family in eukaryotes after MYB. They have been shown to be important regulatory components in tissue development and many different biological processes. However, no systemic analysis of the bHLH transcription factor family has yet been reported in Sorghum bicolor. Results We conducted the first genome-wide analysis of the bHLH transcription factor family of Sorghum bicolor and identified 174 SbbHLH genes. Phylogenetic analysis of SbbHLH proteins and 158 Arabidopsis thaliana bHLH proteins was performed to determine their homology. In addition, conserved motifs, gene structure, chromosomal spread, and gene duplication of SbbHLH genes were studied in depth. To further infer the phylogenetic mechanisms in the SbbHLH family, we constructed six comparative syntenic maps of S. bicolor associated with six representative species. Finally, we analyzed the gene-expression response and tissue-development characteristics of 12 typical SbbHLH genes in plants subjected to six different abiotic stresses. Gene expression during flower and fruit development was also examined. Conclusions This study is of great significance for functional identification and confirmation of the S. bicolor bHLH superfamily and for our understanding of the bHLH superfamily in higher plants.

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Analyses of Key Gene Networks Controlling Carotenoid Metabolism in Xiangfen 1 Banana

10.21203/rs.3.rs-1049305/v1 ◽

2021 ◽

Author(s):

Chen Dong ◽

Jiuxiang Wang ◽

Yulin Hu ◽

Weijun Xiao ◽

Huigang Hu ◽

...

Keyword(s):

Gene Expression ◽

Fruit Development ◽

Gene Networks ◽

Physiological Role ◽

Carotenoid Content ◽

Banana Fruit ◽

Genome Wide ◽

Transcription Factor Genes ◽

Key Enzyme ◽

Late Stages

Abstract Background: Banana fruits are rich in various high-value metabolites and play a key role in the human diet. Of these components, carotenoids have attracted considerable attention due to their physiological role and human health care functions. However, the accumulation patterns of carotenoids and genome-wide analysis of gene expression during banana fruit development have not been comprehensively evaluated. Results: In the present study, an integrative analysis of metabolome and transcriptome profiles in banana fruit with three different development stages was performed. A total of 11 carotenoid compounds were identified, and most of these compounds showed markedly higher abundances in mature green and/or mature fruit than in young fruit. Results were linked to the high expression of carotenoid synthesis and regulatory genes in the middle and late stages of fruit development. Co-expression network analysis revealed that 79 differentially expressed transcription factor genes may be responsible for the regulation of LCYB, a key enzyme catalyzing the biosynthesis of α- and β-carotene. Conclusions: Collectively, the study provided new insights into the understanding of dynamic changes in carotenoid content and gene expression level during banana fruit development.

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

Plants ◽

10.3390/plants10122721 ◽

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.

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