Genome-wide characterization and analysis of bHLH transcription factors related to anthocyanin biosynthesis in spine grapes (Vitis davidii)

AbstractAs one of the largest transcription factor family, basic helix-loop-helix (bHLH) transcription factor family plays an important role in plant metabolism, physiology and growth. Berry color is one of the important factors that determine grape quality. However, the bHLH transcription factor family’s function in anthocyanin synthesis of grape berry has not been studied systematically. We identified 115 bHLH transcription factors in grape genome and phylogenetic analysis indicated that bHLH family could be classified into 25 subfamilies. First, we screened six candidate genes by bioinformatics analysis and expression analysis. We found one of the candidate genes VdbHLH037 belonged to III (f) subfamily and interacted with genes related to anthocyanin synthesis through phylogenetic analysis and interaction network prediction. Therefore, we speculated that VdbHLH037 participated in the anthocyanin synthesis process. To confirm this, we transiently expressed VdbHLH037 in grape and Arabidopsis transformation. Compared with the control, transgenic materials can accumulate more anthocyanins. These results provide a good base to study the function of the VdbHLH family in anthocyanin synthesis of grape berry.

Download Full-text

Hemato-vascular specification requires arnt1 and arnt2 genes in zebrafish embryos

10.1101/2022.01.04.474920 ◽

2022 ◽

Author(s):

Hailey E Edwards ◽

Jaclyn Paige Souder ◽

Daniel A Gorelick

Keyword(s):

Endothelial Cells ◽

Transcription Factor ◽

Transcription Factors ◽

Progenitor Cells ◽

Bhlh Transcription Factor ◽

Zebrafish Embryos ◽

Pas Domain ◽

Hematopoietic Stem ◽

Vascular Progenitor Cells ◽

Bhlh Transcription Factors

During embryonic development, a subset of cells in the mesoderm germ layer are specified as hemato-vascular progenitor cells, which then differentiate into endothelial cells and hematopoietic stem and progenitor cells. In zebrafish, the transcription factor npas4l, also known as cloche, is required for the specification of hemato-vascular progenitor cells. However, it is unclear if npas4l is the sole factor at the top of the hemato-vascular specification cascade. Here we show that arnt1 and arnt2 genes are required for hemato-vascular specification. We found that arnt1;arnt2 double homozygous mutant zebrafish embryos (herein called arnt1/2 mutants), but not arnt1 or arnt2 single mutants, lack blood cells and most vascular endothelial cells. arnt1/2 mutants have reduced or absent expression of etv2 and tal1, the earliest known endothelial and hematopoietic transcription factor genes. npas4l and arnt genes are PAS domain-containing bHLH transcription factors that function as dimers. We found that Npas4l binds both Arnt1 and Arnt2 proteins in vitro, consistent with the idea that PAS domain-containing bHLH transcription factors act in a multimeric complex to regulate gene expression. Our results demonstrate that npas4l, arnt1 and arnt2 act together as master regulators of endothelial and hematopoietic cell fate. Our results also demonstrate that arnt1 and arnt2 act redundantly in a transcriptional complex containing npas4l, but do not act redundantly when interacting with another PAS domain-containing bHLH transcription factor, the aryl hydrocarbon receptor. Altogether, our data enhance our understanding of hemato-vascular specification and the function of PAS domain-containing bHLH transcription factors.

Download Full-text

Transcriptome Analysis Revealed the Mechanism by Which Exogenous ABA Increases Anthocyanins in Blueberry Fruit During Veraison

Frontiers in Plant Science ◽

10.3389/fpls.2021.758215 ◽

2021 ◽

Vol 12 ◽

Author(s):

Tianyu Han ◽

Wenlong Wu ◽

Weilin Li

Keyword(s):

Transcription Factors ◽

Fruit Ripening ◽

Expression Patterns ◽

Synthesis Process ◽

Mature Stage ◽

Anthocyanin Synthesis ◽

Bhlh Transcription Factor ◽

Anthocyanin Content ◽

Anthocyanin Pathway ◽

Green Stage

Blueberry (Vaccinium spp.) is a popular healthy fruit worldwide. The health value of blueberry is mainly because the fruit is rich in anthocyanins, which have a strong antioxidant capacity. However, because blueberry is a non-model plant, little is known about the structural and regulatory genes involved in anthocyanin synthesis in blueberries. Previous studies have found that spraying 1,000 mg/L abscisic acid at the late green stage of “Jersey” highbush blueberry fruits can increase the content of anthocyanins. In this experiment, the previous results were verified in “Brightwell” rabbiteye blueberry fruits. Based on the previous results, the anthocyanin accumulation process in blueberry can be divided into six stages from the late green stage to the mature stage, and the transcriptome was used to systematically analyze the blueberry anthocyanin synthesis process. Combined with data from previous studies on important transcription factors regulating anthocyanin synthesis in plants, phylogenetic trees were constructed to explore the key transcription factors during blueberry fruit ripening. The results showed that ABA increased the anthocyanin content of blueberry fruits during veraison. All structural genes and transcription factors (MYB, bHLH, and WD40) involved in the anthocyanin pathway were identified, and their spatiotemporal expression patterns were analyzed. The expression of CHS, CHI, DFR, and LDOX/ANS in ABA-treated fruits was higher in the last two stages of maturity, which was consistent with the change in the anthocyanin contents in fruits. In general, six MYB transcription factors, one bHLH transcription factor and four WD40 transcription factors were found to change significantly under treatment during fruit ripening. Among them, VcMYBA plays a major role in the regulation of anthocyanin synthesis in ABA signaling. This result preliminarily explained the mechanism by which ABA increases the anthocyanin content and improves the efficiency of the industrial use of blueberry anthocyanins.

Download Full-text

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 .

Download Full-text

Transcriptome Analysis Revealed The Mechanism of Exogenous ABA Increasing Anthocyanins in Blueberry Fruit During Veraison

10.21203/rs.3.rs-88852/v1 ◽

2020 ◽

Author(s):

Tianyu Han ◽

Zhixiang Yan ◽

Wenlong Wu ◽

Weilin Li

Keyword(s):

Transcription Factors ◽

Transcriptome Analysis ◽

Expression Patterns ◽

Synthesis Process ◽

Anthocyanin Synthesis ◽

Bhlh Transcription Factor ◽

Anthocyanin Content ◽

Structural Genes ◽

Anthocyanin Pathway ◽

Green Stage

Abstract Background: Blueberry（Vaccinium Spp）is a popular healthy fruit all over the world. The health value of blueberry is mainly due to the fact that blueberry is rich in anthocyanins, which have a strong antioxidant capacity. However, due to the fact that blueberry is a non model plant, little is known about the structural genes and regulatory genes involved in the anthocyanin synthesis of blueberries. Previous studies have found that spraying abscisic acid at the late green stage of blueberry fruit can increase the content of anthocyanins. Based on the former results, the anthocyanin accumulation process of blueberry can be divided into six stages from late green stage to mature stage to analyze the anthocyanin synthesis mechanism. In order to identify the important genes in the anthocyanin synthesis process of blueberry, the transcriptome analysis was conducted to explore the key genes in blueberry anthocyanin synthesis process.Results: The results showed that ABA could increase the anthocyanin content of blueberry fruits during the veraison. The effect of ABA on blueberry fruit development was systematically analyzed by KEGG and GO. All structural genes and transcription factors (MYB, bHLH and WD40) involved in anthocyanin pathway were identified and their spatiotemporal expression patterns were analyzed. The expression of CHS, CHI, DFR and LDOX / ANS in ABA treated fruits was higher in S5-S6, which was consistent with the change of anthocyanins in fruits.In general, six MYB transcription factors, one bHLH transcription factor and four WD40 transcription factors under treatment were found to have significant changes in transcripts during fruit ripening. Conclusions: Our results suggest that VcMYBA should play a major role in the regulation of anthocyanin synthesis in ABA signaling. This result preliminarily explained the mechanism of ABA increasing anthocyanin content and improves the efficiency of industrial use of blueberry anthocyanins.

Download Full-text

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.

Download Full-text

In silico genome-wide identification and phylogenetic analysis of the WRKY transcription factor family in sweet orange (Citrus sinensis)

Australian Journal of Crop Science ◽

10.21475/ajcs.17.11.06.p471 ◽

2017 ◽

Vol 11 (06) ◽

pp. 716-726 ◽

Cited By ~ 2

Author(s):

Eduardo Goiano da Silva ◽

◽

Tania Mayumi Ito ◽

Silvia Graciele Hülse de Souza ◽

◽

...

Keyword(s):

Phylogenetic Analysis ◽

Transcription Factor ◽

In Silico ◽

Citrus Sinensis ◽

Sweet Orange ◽

Wrky Transcription Factor ◽

Transcription Factor Family ◽

Genome Wide

Download Full-text

QTL Mapping Low-Temperature Germination Ability in the Maize IBM Syn10 DH Population

Plants ◽

10.3390/plants11020214 ◽

2022 ◽

Vol 11 (2) ◽

pp. 214

Author(s):

Qinghui Han ◽

Qingxiang Zhu ◽

Yao Shen ◽

Michael Lee ◽

Thomas Lübberstedt ◽

...

Keyword(s):

Transcription Factor ◽

Low Temperature ◽

Candidate Genes ◽

Temperature Tolerance ◽

Bhlh Transcription Factor ◽

Rna Seq ◽

Dh Population ◽

Low Temperature Tolerance ◽

Germination Ability ◽

Upregulated Genes

Chilling injury poses a serious threat to seed emergence of spring-sowing maize in China, which has become one of the main climatic limiting factors affecting maize production in China. It is of great significance to mine the key genes controlling low-temperature tolerance during seed germination and study their functions for breeding new maize varieties with strong low-temperature tolerance during germination. In this study, 176 lines of the intermated B73 × Mo17 (IBM) Syn10 doubled haploid (DH) population, which comprised 6618 bin markers, were used for QTL analysis of low-temperature germination ability. The results showed significant differences in germination related traits under optimum-temperature condition (25 °C) and low-temperature condition (10 °C) between two parental lines. In total, 13 QTLs were detected on all chromosomes, except for chromosome 5, 7, 10. Among them, seven QTLs formed five QTL clusters on chromosomes 1, 2, 3, 4, and 9 under the low-temperature condition, which suggested that there may be some genes regulating multiple germination traits at the same time. A total of 39 candidate genes were extracted from five QTL clusters based on the maize GDB under the low-temperature condition. To further screen candidate genes controlling low-temperature germination, RNA-Seq, in which RNA was extracted from the germination seeds of B73 and Mo17 at 10 °C, was conducted, and three B73 upregulated genes and five Mo17 upregulated genes were found by combined analysis of RNA-Seq and QTL located genes. Additionally, the variations of Zm00001d027976 (GLABRA2), Zm00001d007311 (bHLH transcription factor), and Zm00001d053703 (bZIP transcription factor) were found by comparison of amino sequence between B73 and Mo17. This study will provide a theoretical basis for marker-assisted breeding and lay a foundation for further revealing molecular mechanism of low-temperature germination tolerance in maize.

Download Full-text

Genome-Wide Identification and Characterization of the Potato bHLH Transcription Factor Family

Genes ◽

10.3390/genes9010054 ◽

2018 ◽

Vol 9 (1) ◽

pp. 54 ◽

Cited By ~ 32

Author(s):

Ruoqiu Wang ◽

Peng Zhao ◽

Nana Kong ◽

Ruize Lu ◽

Yue Pei ◽

...

Keyword(s):

Transcription Factor ◽

Bhlh Transcription Factor ◽

Transcription Factor Family ◽

Genome Wide ◽

Identification And Characterization

Download Full-text

Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis

International Journal of Molecular Sciences ◽

10.3390/ijms22137152 ◽

2021 ◽

Vol 22 (13) ◽

pp. 7152

Author(s):

Yaqi Hao ◽

Xiumei Zong ◽

Pan Ren ◽

Yuqi Qian ◽

Aigen Fu

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Target Genes ◽

Gene Families ◽

Bhlh Transcription Factor ◽

Basic Helix Loop Helix ◽

Helix Loop Helix ◽

Wide Range ◽

Range Of Functions ◽

Eukaryotic Organisms

The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor gene families in Arabidopsis thaliana, and contains a bHLH motif that is highly conserved throughout eukaryotic organisms. Members of this family have two conserved motifs, a basic DNA binding region and a helix-loop-helix (HLH) region. These proteins containing bHLH domain usually act as homo- or heterodimers to regulate the expression of their target genes, which are involved in many physiological processes and have a broad range of functions in biosynthesis, metabolism and transduction of plant hormones. Although there are a number of articles on different aspects to provide detailed information on this family in plants, an overall summary is not available. In this review, we summarize various aspects of related studies that provide an overview of insights into the pleiotropic regulatory roles of these transcription factors in plant growth and development, stress response, biochemical functions and the web of signaling networks. We then provide an overview of the functional profile of the bHLH family and the regulatory mechanisms of other proteins.

Download Full-text