lyl-1 and tal-1/scl, two genes encoding closely related bHLH transcription factors, display highly overlapping expression patterns during cardiovascular and hematopoietic ontogeny

Tunicates are marine invertebrates whose tadpole-like larvae feature a highly simplified version of the chordate body plan. Similar to their distant vertebrate relatives, tunicate larvae develop a regionalized central nervous system and form distinct neural structures, which include a rostral sensory vesicle, a motor ganglion, and a caudal nerve cord. The sensory vesicle contains a photoreceptive complex and a statocyst, and based on the comparable expression patterns of evolutionarily conserved marker genes, it is believed to include proto-hypothalamic and proto-retinal territories. The evolutionarily conserved molecular fingerprints of these landmarks of the vertebrate brain consist of genes encoding for different transcription factors, and of the gene batteries that they control, and include several members of the bHLH family. Here we review the complement of bHLH genes present in the streamlined genome of the tunicate Ciona robusta and their current classification, and summarize recent studies on proneural bHLH transcription factors and their expression territories. We discuss the possible roles of bHLH genes in establishing the molecular compartmentalization of the enticing nervous system of this unassuming chordate.

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Expression profiles of four BES1/BZR1 homologous genes encoding bHLH transcription factors in Arabidopsis

Journal of Pesticide Science ◽

10.1584/jpestics.d20-001 ◽

2020 ◽

Vol 45 (2) ◽

pp. 95-104

Author(s):

Yui Otani ◽

Yusuke Tomonaga ◽

Kenya Tokushige ◽

Miyu Kamimura ◽

Azusa Sasaki ◽

...

Keyword(s):

Transcription Factors ◽

Expression Profiles ◽

Homologous Genes ◽

Genes Encoding ◽

Bhlh Transcription Factors

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The Proneural Proteins Atonal and Scute Regulate Neural Target Genes through Different E-Box Binding Sites

Molecular and Cellular Biology ◽

10.1128/mcb.24.21.9517-9526.2004 ◽

2004 ◽

Vol 24 (21) ◽

pp. 9517-9526 ◽

Cited By ~ 56

Author(s):

Lynn M. Powell ◽

Petra I. zur Lage ◽

David R. A. Prentice ◽

Biruntha Senthinathan ◽

Andrew P. Jarman

Keyword(s):

Transcription Factors ◽

Dna Binding ◽

Binding Sites ◽

Tandem Repeats ◽

Target Genes ◽

Expression Patterns ◽

Sense Organ ◽

Ample Evidence ◽

E Box ◽

Bhlh Transcription Factors

ABSTRACT For a particular functional family of basic helix-loop-helix (bHLH) transcription factors, there is ample evidence that different factors regulate different target genes but little idea of how these different target genes are distinguished. We investigated the contribution of DNA binding site differences to the specificities of two functionally related proneural bHLH transcription factors required for the genesis of Drosophila sense organ precursors (Atonal and Scute). We show that the proneural target gene, Bearded, is regulated by both Scute and Atonal via distinct E-box consensus binding sites. By comparing with other Ato-dependent enhancer sequences, we define an Ato-specific binding consensus that differs from the previously defined Scute-specific E-box consensus, thereby defining distinct EAto and ESc sites. These E-box variants are crucial for function. First, tandem repeats of 20-bp sequences containing EAto and ESc sites are sufficient to confer Atonal- and Scute-specific expression patterns, respectively, on a reporter gene in vivo. Second, interchanging EAto and ESc sites within enhancers almost abolishes enhancer activity. While the latter finding shows that enhancer context is also important in defining how proneural proteins interact with these sites, it is clear that differential utilization of DNA binding sites underlies proneural protein specificity.

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The identification and characterization of human Sister-of-Mammalian Grainyhead (SOM) expands the grainyhead-like family of developmental transcription factors

Biochemical Journal ◽

10.1042/bj20021476 ◽

2003 ◽

Vol 370 (3) ◽

pp. 953-962 ◽

Cited By ~ 64

Author(s):

Stephen B. TING ◽

Tomasz WILANOWSKI ◽

Loretta CERRUTI ◽

Lin-Lin ZHAO ◽

John M. CUNNINGHAM ◽

...

Keyword(s):

Transcription Factors ◽

Expression Patterns ◽

Large Family ◽

The Other ◽

Mammalian Development ◽

Ancestral Gene ◽

Activation Domains ◽

The Family ◽

Genes Encoding ◽

Functional Dna

The Drosophila gene grainyhead is the founding member of a large family of genes encoding developmental transcription factors that are highly conserved from fly to human. The family consists of two main branches, with grainyhead as the ancestral gene for one branch and the recently cloned DrosophilaCP2 as the ancestral gene for the other. We now extend this family with the identification of another novel mammalian member, Sister-of-Mammalian Grainyhead (SOM), which is phylogenetically aligned with grainyhead. SOM is closely related to the other mammalian homologues of grainyhead, including Mammalian Grainyhead (MGR) and Brother-of-MGR, sharing a high degree of sequence identity with these factors in the functional DNA-binding, protein dimerization and activation domains. Protein interaction studies demonstrate that SOM can heterodimerize with MGR and Brother-of-MGR, but not with the more distant members of the family. Like grainyhead, the SOM gene too produces several distinct isoforms with differing functional properties through alternative splicing. The tissue distributions of these isoforms differ and all display highly restricted expression patterns. These findings indicate that SOM, like its family members, may play important roles in mammalian development.

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REVEILLE Transcription Factors Contribute to the Nighttime Accumulation of Anthocyanins in ‘Red Zaosu’ (Pyrus Bretschneideri Rehd.) Pear Fruit Skin

International Journal of Molecular Sciences ◽

10.3390/ijms21051634 ◽

2020 ◽

Vol 21 (5) ◽

pp. 1634

Author(s):

Xieyu Li ◽

Ting Wu ◽

Hanting Liu ◽

Rui Zhai ◽

Yao Wen ◽

...

Keyword(s):

Transcription Factors ◽

Anthocyanin Biosynthesis ◽

Expression Patterns ◽

Luciferase Reporter ◽

Anthocyanin Accumulation ◽

Pear Fruit ◽

Biosynthetic Genes ◽

Expression Levels ◽

Fruit Skin ◽

Genes Encoding

Anthocyanin biosynthesis exhibits a rhythmic oscillation pattern in some plants. To investigate the correlation between the oscillatory regulatory network and anthocyanin biosynthesis in pear, the anthocyanin accumulation and the expression patterns of anthocyanin late biosynthetic genes (ALBGs) were investigated in fruit skin of ‘Red Zaosu’ (Pyrus bretschneideri Rehd.). The anthocyanin accumulated mainly during the night over three continuous days in the fruit skin, and the ALBGs’ expression patterns in ‘Red Zaosu’ fruit skin were oscillatory. However, the expression levels of typical anthocyanin-related transcription factors did not follow this pattern. Here, we found that the expression patterns of four PbREVEILLEs (PbRVEs), members of a class of atypical anthocyanin-regulated MYBs, were consistent with those of ALBGs in ‘Red Zaosu’ fruit skin over three continuous days. Additionally, transient expression assays indicated that the four PbRVEs promoted anthocyanin biosynthesis by regulating the expression of the anthocyanin biosynthetic genes encoding dihydroflavonol-4-reductase (DFR) and anthocyanidin synthase (ANS) in red pear fruit skin, which was verified using a dual-luciferase reporter assay. Moreover, a yeast one-hybrid assay indicated that PbRVE1a, 1b and 7 directly bound to PbDFR and PbANS promoters. Thus, PbRVEs promote anthocyanin accumulation at night by up-regulating the expression levels of PbDFR and PbANS in ‘Red Zaosu’ fruit skin.

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Insights into the Diversification of Subclade IVa bHLH Transcription Factors in Fabaceae

10.21203/rs.3.rs-52910/v1 ◽

2020 ◽

Author(s):

Hayato Suzuki ◽

Hikaru Seki ◽

Toshiya Muranaka

Keyword(s):

Transcription Factors ◽

Expression Patterns ◽

Lotus Japonicus ◽

Helix Loop Helix ◽

Saponin Biosynthesis ◽

Plant Families ◽

Almost All ◽

Bhlh Transcription Factors ◽

Bhlh Proteins ◽

Group 1

Abstract Background: Fabaceae plants appear to contain larger numbers of subclade IVa basic-helix-loop-helix (bHLH) transcription factors than other plant families, and some members of this subclade have been identified as saponin biosynthesis regulators. We aimed to systematically elucidate the diversification of this subclade and obtain insights into the evolutionary history of saponin biosynthesis regulation in Fabaceae.Results: In this study, we collected sequences of subclade IVa bHLH proteins from 40 species, including fabids and other plants, and found greater numbers of subclade IVa bHLHs in Fabaceae. We confirmed conservation of the bHLH domain, C-terminal ACT-like domain, and exon-intron organisation among almost all subclade IVa members in model legumes, supporting the results of our classification. Phylogenetic tree-based classification of subclade IVa revealed the presence of three different groups. Interestingly, most Fabaceae subclade IVa bHLHs fell into group 1, which contained all legume saponin biosynthesis regulators identified to date. These observations support the co-occurrence and Fabaceae-specific diversification of saponin biosynthesis regulators. Comparing the expression of orthologous genes in Glycine max, Medicago truncatula, and Lotus japonicus, orthologues of MtTSAR1 (the first identified soyasaponin biosynthesis regulatory transcription factor) were not expressed in the same tissues, suggesting that group 1 members have gained different expression patterns and contributions to saponin biosynthesis during their duplication and divergence. On the other hand, groups 2 and 3 possessed fewer members, and their phylogenetic relationships and expression patterns were highly conserved, indicating that their activities may be conserved across Fabaceae.Conclusions: This study suggests subdivision and diversification of subclade IVa bHLHs in Fabaceae plants. The results will be useful for candidate selection of unidentified saponin biosynthesis regulators. Furthermore, the functions of groups 2 and 3 members are interesting targets for clarifying the evolution of subclade IVa bHLH transcription factors in Fabaceae.

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Genome-Wide Characterization and Analysis of bHLH Transcription Factors Related to Crocin Biosynthesis in Gardenia jasminoides Ellis (Rubiaceae)

BioMed Research International ◽

10.1155/2020/2903861 ◽

2020 ◽

Vol 2020 ◽

pp. 1-11

Author(s):

Ya Tian ◽

Xiangdong Pu ◽

Haoying Yu ◽

Aijia Ji ◽

Ranran Gao ◽

...

Keyword(s):

Transcription Factors ◽

Regulatory Mechanism ◽

Expression Patterns ◽

Cancer Cell Growth ◽

Promoter Sequences ◽

Helix Loop Helix ◽

Gardenia Jasminoides ◽

Genome Wide ◽

Transcription Factor Genes ◽

Bhlh Transcription Factors

Crocins, enriched in Gardenia jasminoides fruits, have a pharmacological activity against central nervous system diseases, cardiovascular diseases, and cancer cell growth. The biosynthesis of crocins has been widely explored, but its regulatory mechanism remains unknown. Here, the basic helix-loop-helix (bHLH) transcription factors related to crocin biosynthesis were systematically identified on the basis of the genome of G. jasminoides. A total of 95 GjbHLH transcription factor genes were identified, and their phylogenetic analysis indicated that they could be classified into 23 subfamilies. The combination of gene-specific bHLH expression patterns, the coexpression analysis of biosynthesis genes, and the analysis of promoter sequences in crocin biosynthesis pathways suggested that nine bHLHs in G. jasminoides might negatively regulate crocin biosynthesis. This study laid a foundation for understanding the regulatory mechanism of crocin biosynthesis and the improvement and breeding of G. jasminoides varieties.

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AP2/ERF transcription factor NbERF-IX-33 is involved in the regulation of phytoalexin production for the resistance of Nicotiana benthamiana to Phytophthora infestans.

10.1101/2021.11.30.468885 ◽

2021 ◽

Author(s):

Sayaka Imano ◽

Mayuka Fushimi ◽

Maurizio Camagna ◽

Akiko Tsuyama-Koike ◽

Hitoshi Mori ◽

...

Keyword(s):

Transcription Factor ◽

Transcription Factors ◽

Expression Profiles ◽

Expression Patterns ◽

Acc Oxidase ◽

Defense Responses ◽

Hypersensitive Cell Death ◽

Gcc Box ◽

Genes Encoding ◽

Induced Genes

Plants recognize molecular patterns unique to a certain group of microbes to induce effective resistance mechanisms. Elicitins are secretory proteins produced by plant pathogenic oomycete genera including Phytophthora and Pythium. Treatment of INF1 (an elicitin produced by P. infestans) induces a series of defense responses in Nicotiana species, including reactive oxygen species (ROS) production, hypersensitive cell death and accumulation of the sesquiterpenoid phytoalexin capsidiol. In this study, we analyzed the expression profiles of N. benthamiana genes after INF1 treatment by RNAseq analysis. Based on their expression patterns, N. benthamiana genes were categorized into 20 clusters and 4,761 (8.3%) out of 57,140 genes were assigned to the clusters for INF1-induced genes. All genes encoding enzymes dedicated for capsidiol production, 5-epi-aristolochene (EA) synthase (NbEAS, 10 copies) and EA dehydrogenase (NbEAH, 6 copies) and some genes for ethylene production, such as 1-aminocyclopropane 1-carboxylate (ACC) synthase (NbACS) and ACC oxidase (NbACO), were significantly upregulated by INF1 treatment. Analysis of NbEAS1 and NbEAS4 promoters revealed that AGACGCC (GCC box-like motif) is the essential cis-element required for INF1-induced expression of NbEAS genes. Given that the GCC box is known to be targeted by ERF (ethylene-responsive factor) transcription factors, we created a complete list of N. benthamiana genes encoding AP2/ERF family transcription factors, and identified 45 out of 337 AP2/ERF genes in the clusters for INF1-induced genes. Among INF1-induced NbERF genes, silencing of NbERF-IX-33 compromised resistance against P. infestans and INF1-induced production of capsidiol. Recombinant NbERF-IX-33 protein can bind to the promoter sequence of NbEAS4, suggesting that NbERF-IX-33 is a transcription factor directly regulating the expression of genes for phytoalexin production.

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Insights into the diversification of subclade IVa bHLH transcription factors in Fabaceae

BMC Plant Biology ◽

10.1186/s12870-021-02887-w ◽

2021 ◽

Vol 21 (1) ◽

Author(s):

Hayato Suzuki ◽

Hikaru Seki ◽

Toshiya Muranaka

Keyword(s):

Transcription Factors ◽

Expression Patterns ◽

Lotus Japonicus ◽

Helix Loop Helix ◽

Saponin Biosynthesis ◽

Plant Families ◽

Almost All ◽

Bhlh Transcription Factors ◽

Bhlh Proteins ◽

Group 1

Abstract Background Fabaceae plants appear to contain larger numbers of subclade IVa basic-helix-loop-helix (bHLH) transcription factors than other plant families, and some members of this subclade have been identified as saponin biosynthesis regulators. We aimed to systematically elucidate the diversification of this subclade and obtain insights into the evolutionary history of saponin biosynthesis regulation in Fabaceae. Results In this study, we collected sequences of subclade IVa bHLH proteins from 40 species, including fabids and other plants, and found greater numbers of subclade IVa bHLHs in Fabaceae. We confirmed conservation of the bHLH domain, C-terminal ACT-like domain, and exon-intron organisation among almost all subclade IVa members in model legumes, supporting the results of our classification. Phylogenetic tree-based classification of subclade IVa revealed the presence of three different groups. Interestingly, most Fabaceae subclade IVa bHLHs fell into group 1, which contained all legume saponin biosynthesis regulators identified to date. These observations support the co-occurrence and Fabaceae-specific diversification of saponin biosynthesis regulators. Comparing the expression of orthologous genes in Glycine max, Medicago truncatula, and Lotus japonicus, orthologues of MtTSAR1 (the first identified soyasaponin biosynthesis regulatory transcription factor) were not expressed in the same tissues, suggesting that group 1 members have gained different expression patterns and contributions to saponin biosynthesis during their duplication and divergence. On the other hand, groups 2 and 3 possessed fewer members, and their phylogenetic relationships and expression patterns were highly conserved, indicating that their activities may be conserved across Fabaceae. Conclusions This study suggests subdivision and diversification of subclade IVa bHLHs in Fabaceae plants. The results will be useful for candidate selection of unidentified saponin biosynthesis regulators. Furthermore, the functions of groups 2 and 3 members are interesting targets for clarifying the evolution of subclade IVa bHLH transcription factors in Fabaceae.

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