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Evolution of the basic helix-loop-helix transcription factor SPATULA and its role in gynoecium development

ANNALS OF BOTANY 2024年第6期134卷 1037-1054页

作者： Rivarola-Sena, Ana C. Vialette, Aurelie C. Andres-Robin, Amelie Chambrier, Pierre Bideau, Loic Franco-Zorrilla, Jose M. Scutt, Charles P. Ecole Normale Super Lyon Lab Reprod & Dev Plantes CNRS UMR 5667 F-69364 Lyon 7 France CSIC Ctr Nacl Biotecnol C Darwin 3 Madrid 28049 Spain

Background and Aims SPATULA (SPT) encodes a basic helix-loop-helix transcription factor in Arabidopsis thaliana that functions in the development of the style, stigma and replum tissues, all of which arise from the carpel margin meristem of the gynoecium. Here we use a comparative approach to investigate the evolutionary history of SPT and identify changes that potentially contributed to its role in gynoecium *** We investigate SPT's molecular and functional evolution using phylogenetic reconstruction, yeast two-hybrid analyses of protein-protein interactions, microarray-based analyses of protein-DNA interactions, plant transformation assays, RNA in situ hybridization, and in silico analyses of promoter *** results We demonstrate the SPT lineage to have arisen at the base of euphyllophytes from a clade of potentially light-regulated transcription factors through gene duplication followed by the loss of an active phytochrome binding (APB) domain. We also clarify the more recent evolutionary history of SPT and its paralogue ALCATRAZ (ALC), which appear to have arisen through a large-scale duplication within Brassicales. We find that SPT orthologues from diverse groups of seed plants share strikingly similar capacities for protein-protein and protein-DNA interactions, and that SPT coding regions from a wide taxonomic range of plants are able to complement loss-of-function spt mutations in transgenic Arabidopsis. However, the expression pattern of SPT appears to have evolved significantly within angiosperms, and we identify structural changes in SPT's promoter region that correlate with the acquisition of high expression levels in tissues arising from the carpel margin meristem in *** We conclude that changes in SPT's expression pattern made a major contribution to the evolution of its developmental role in the gynoecium of Brassicaceae. By contrast, the main biochemical capacities of SPT, as well as many of its immediate t

关键词： SPATULA ALCATRAZ basic helix-loop-helix carpel gynoecium carpel margin meristem flower angiosperm Arabidopsis thaliana Amborella trichopoda Nymphaea thermarum Petunia axillaris

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Genome-wide identification and characterization of basic helix-loop-helix transcription factors in Spodoptera litura upon pathogen infection

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Insect Science 2022年第4期29卷 977-992页

作者： Jie Zhang Mengyao Zhu Qilin Li Ting Tang Liang Wen Jielai Zhong Ruonan Zhang Xiao-Qiang Yu Yuzhen Lu Guangdong Provincial Key Laboratory of Insect Developmental Biology and Applied Technology Institute of Insect Science and TechnologySchool of Life SciencesSouth China Normal UniversityGuangzhouChina Guangzhou Key Laboratory of Insect Development Regulation and Application Research Institute of Insect Science and TechnologySchool of Life SciencesSouth China Normal UniversityGuangzhouChina

basic helix-loop-helix(bHLH)transcription factors play an important role in a wide range of metabolic and developmental processes in eukaryotes,and bHLH proteins also participate in immune responses,especially in ***,their roles in insects upon entomopathogen infection are *** this study,54 bHLH genes in 41 families were identified in a polyphagous pest,Spodoptera litura,including a new bHLH gene in group B,which is specifically present in Lepidoptera and was thus named *** conserved amino acids in the bHLH domain,structural architecture,and chromosomal distribution of bHLH genes in *** were *** bHLH genes in Plutella xylostella and Apis mellifera were also updated,and genome-wide comparison and phylogenetic analysis of bHLH members in 5 holometabolous insects were *** expression profiles of *** bHLH(SlbHLH)genes in 3 tissues at different developmental stages and their responses to *** nucleopolyhedrovirus(SpltNPV),Nomuraea rileyi(Nr),and Bacillus thuringiensis(Bt)infection were *** SlbHLHs in group B were expressed and differentially expressed during pathogen infections,and SlbHLHs tended to be downregulated in the midgut of *** larvae after *** *** study provides an overview of bHLH family members in *** and their responses to different pathogens used for pest *** findings on bHLH members may contribute to uncovering the mechanism of host-pathogen interaction.

关键词： basic helix-loop-helix entomopathogen infection pest biocontrol Spodoptera liura

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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

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INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES 2020年第0期160卷 711-723页

作者： Lang, Yanhe Liu, Zhi Northeast Forest Univ Coll Life Sci Alkali Soil Nat Environm Sci Ctr ASNESC Harbin Heilongjiang Peoples R China

Yellow horn (Xanthoceras sorbifolia Bunge) is a oil-rich, woody deciduous shrub with exceptional economic and ecological values. basic helix-loop-helix (bHLH) transcription factor (TF) family fulfills crucial biological functions in plant. However, genome-wide survey of the bHLH genes in yellow horn has not been performed. In this study, 136 putative XsbHLH genes were identified from yellow horn genome which were divided into 26 subfamilies according to the sequence similarity and phylogenetic relationships. 130 XsbHLH genes were unevenly distributed on 15 chromosomes, with six XsbHLH genes locating on the scaffolds. The similar structural compositions of XsbHLHs in the same subfamily suggested that they were relatively conserved and therefore exhibited similar molecular functions. Cis-regulatory elements analysis revealed that most XsbHLH genes had many stress-responsive elements, such as MYB, ARE, ABRE and LTR. In addition. XsbHLHs showed differential expression profiles under various abiotic stresses. Transoriptorne analysis revealed that three XsbHLH genes, including XsbHLH 59, XsbHLH 71 and XsbHLH 102, were significantly up-regulated under salt, ABA and low temperature stresses over time, demonstrating their key roles in stress responses. The current study would provide a comprehensive information for further functional research on the stress-responsive bHLH gene candidates in yellow horn. (C) 2020 Elsevier B.V. All rights reserved.

关键词： Abiotic stresses Yellow horn basic helix-loop-helix

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Isolation and characterization of R2R3-MYB and basic helix-loop-helix (bHLH) transcription factors involved in anthocyanin biosynthesis in tulip tepals

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ACTA PHYSIOLOGIAE PLANTARUM 2020年第3期42卷 32-32页

作者： Yuan, Yuan Shi, Yimin Tang, Dongqin Shanghai Jiao Tong Univ Dept Landscape Architecture Shanghai 200240 Peoples R China Fujian Agr & Forestry Univ Coll Hort Fuzhou 350002 Peoples R China

Anthocyanin is a kind of secondary metabolites that contribute to flower color. Transcription factors R2R3-MYB and bHLH (basic helix-loop-helix) are required to regulate the transcription of structural genes involved in anthocyanin biosynthesis. In this study, full-length cDNAs of four R2R3-MYB (TfMYB2, TfMYB3, TfMYB4, TfMYB5) and two bHLH (TfbHLH1, TfBHLH2) genes were first cloned from tepals of Tulipa fosteriana 'Albert heijn' by RACE method. Four MYB genes belong to AN2 subgroup possessing high homology with lily MYBs, and bHLH genes share high homology with lily bHLHs. TfMYB3, TfMYB4, TfMYB5, and TfbHLH1 expressed highly in tulip tepal, while TfMYB2 and TfbHLH2 highly in stem and leaf. The spatial expression patterns of above four TFs also coincided well with some structural genes involving in the anthocyanin biosynthesis. The transcripts of TfMYB3, TfMYB4, TfMYB5, and TfbHLH1 constantly increased along with flower development, which were consistent with the expression of structural genes and accompanied by the anthocyanin accumulation. Y2H analysis revealed that TfMYB3, TfMYB4, or TfMYB5 interacted with TfbHLH1. The transient expression assay suggested that TfMYB5 activated the promoter of TfCHS1, while TfMYB3 or TfMYB4 promoted the promoter activity of TfANS1. Meanwhile, no significant promoting effect of TfbHLH1 was observed;however, the enhancing effect of TfMYBs on the promoters was much promoted when interacted with TfbHLH1. Taken together, our findings strongly suggested that TfMYB3, TfMYB4, TfMYB5, and TfbHLH1 were definitely participated in the regulating of anthocyanin biosynthesis in tepals of tulip.

关键词： Tulip Anthocyanin biosynthesis Transcription factor basic helix-loop-helix

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High-throughput sequencing of highbush blueberry transcriptome and analysis of basic helix-loop-helix transcription factors

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Journal of Integrative Agriculture 2017年第3期16卷 591-604页

作者： SONG Yang LIU Hong-di ZHOU Qiang ZHANG Hong-jun ZHANG Zhi-dong LI Ya-dong WANG Hai-bo LIU Feng-zhi Research Institute of Pomology Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (Germplasm Resources Utilization)Ministry of Agriculture College of Horticulture Jilin Agricultural University

The highbush blueberry（Vaccinium corymbosum）,Duke,was used to construct a de novo transcriptome sequence library and to perform data statistical *** 4,CLC Sequence Viewer 6 software,and quantitative PCR were employed for bioinformatics and expression analyses of the basic helix-loop-helix（BHLH）transcription factors of the sequencing *** results showed that 28.38 gigabytes of valid data were obtained from transcriptome sequencing and were assembled into 108 033 *** annotation showed that 32 244 unigenes were annotated into Clusters of Orthologous Groups（COG）and Gene Ontology（GO）databases,whereas the rest of the 75 789 unigenes had no matching *** using COG and GO classification tools,sequences with annotation information were divided into 25 and 52 categories,respectively,which involved transport and metabolism,transcriptional regulation,and signal *** of the transcriptome library identified a total of 59 BHLH *** analysis revealed that 55 genes of that contained a complete BHLH ***,phylogenetic analysis showed that BHLH genes of blueberry（Duke）could be divided into 13 *** results showed that 45 genes were expressed at various developmental stages of buds,stems,leaves,flowers,and fruits,suggesting that the function of BHLH was associated with the development of different tissues and organs of blueberry,*** present study would provided a foundation for further investigations on the classification and functions of the blueberry BHLH family.

关键词： blueberry bioinformatics transcdptome sequencing basic helix-loop-helix transcription factor

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Identification and Phylogenetic Analysis of basic helix-loop-helix Genes in the Diamondback Moth

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JOURNAL OF INSECT SCIENCE 2018年第3期18卷 1-11页

作者： Zeng, Zhen Wang, Yong Johnson, Nana Adwoa Nkuma Wang, Guang-Dong Yao, Qin Chen, Ke-Ping Jiangsu Univ Inst Life Sci 301 Xuefu Rd Zhenjiang 212013 Peoples R China Jiangsu Univ Sch Food & Biol Engn 301 Xuefu Rd Zhenjiang 212013 Peoples R China

basic helix-loop-helix (bHLH) transcription factors play essential roles in regulating eukaryotic developmental and physiological processes such as neuron generation, myocyte formation, intestinal tissue development, and response to environmental stress. In this study, the diamondback moth, Plutella xylostella (L.) (Lepidoptera: Plutellidae), genome was found to encode 52 bHLH genes. All 52 P. xylostella bHLH (PxbHLH) genes were classified into correspondent bHLH families according to their orthology with bHLHs from fruit fly and other insect species. Among these 52 PxbHLH genes, 19 have been annotated consistently with our classification in GenBank database. The remaining 33 PxbHLH genes are either annotated as general bHLH genes or as hypothetical genes. Therefore, our data provide useful information for updating annotations to PxbHLH genes. P. xylostella has four stem cell leukemia (SCL) genes (one of them has three copies), two Dys genes, two copies of MyoR, Mitf, and Sima genes, and three copies of Sage genes. Further studies may be conducted to elucidate functions of these specific bHLH genes in regulating P. xylostella growth and development.

关键词： basic helix-loop-helix Blastp search orthology phylogenetic analysis Plutella xylostella

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A genome-wide identification and analysis of basic helix-loop-helix transcription factors in cattle

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GENE 2017年 626卷 241-250页

作者： Zhang, Debao Li, Guanying Wang, Yong Shanghai Huaxin High Biotechnol Co Ltd 1150 Guiqiao Rd Shanghai 201206 Peoples R China Jiangsu Univ Sch Food & Biol Engn 301 Xuefu Rd Zhenjiang 212013 Peoples R China

basic helix-loop-helix (BHLH) transcription factors comprise a large family of regulatory proteins and play critical roles in the developmental processes of higher organisms. Complete lists of BHLH family members have been identified in about 50 organisms, including fruit fly, zebrafish, mouse, giant panda, worm, yeast, rice and apple. Cattle, Bos taurus, is important for agriculture and animal nutrition, and is also a good model organism for health research. In the present study, 116 putative BHLHs were identified in the cattle genome. Phylogenetic analyses revealed that 111 Bos taurus BHLH (BtBHLH: Bos taurus BHLH) members belong to 44 families, with 48, 26, 16, 4, 13 and 4 members in group A, B, C, D, E and F respectively, and the remaining 5 BtBHLHs are orphan members. All of them were named and assigned into the corresponding BHLH families based on acceptable bootstrap values from in-group phylogenetic analyses with orthologous BHLHs from mouse and other mammalian species. A comparison between annotations deposited in the GenBank and KEGG databases with our analyses indicated that the annotations of 2 of the 116 BtBHLH members were inconsistent with our analytical results. Microarray evidence and expressed sequence tags of only 14 BtBHLH genes was now not available. Chromosomal locations of the BtBHLHs showed that the distribution of the BtBHLHs was uneven and some genes, e.g., BtOligo, BtHes and BtMyf6, may arise from gene duplication. The test of positive selection showed episodic positive selection occurs only in 5 families among the studied mammalian BHLHs. These results provide a solid basis for further studies on BHLH protein regulation of key growth and developmental processes.

关键词： basic helix-loop-helix Transcription factor Cattle Phylogenetic analysis Episodic positive selection WebLogo

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A genome-wide survey and analysis of basic helix-loop-helix genes in the Asian citrus psyllid, Diaphorina citri (Hemiptera: Psyllidae)

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JOURNAL OF ASIA-PACIFIC ENTOMOLOGY 2017年第3期20卷 821-829页

作者： Peng, Ying Wang, Yong Tao, Xia-Fang Zeng, Zhen Johnson, Nana Adwoa Nkuma Yao, Qin Chen, Ke-Ping Jiangsu Univ Sch Food & Biol Engn 301 Xuefu Rd Zhenjiang 212013 Peoples R China Jiangsu Univ Inst Life Sci 301 Xuefu Rd Zhenjiang 212013 Peoples R China

The basic helix-loop-helix (bHLH) proteins are important player in regulation of various eukaryotic developmental processes such as neurogenesis, myogenesis and heart morphogenesis. The Asian citrus psyllid (Diaphorina citri) is a sap-sucking pest which is widely distributed in southern Asia and causes greening disease in citrus orchard. In this study, Diaphorina citri genome is found to encode 52 bHLH genes. Through in-depth phylogenetic analyses, all 52 Diaphorina citri bHLH (DcbHLH) genes are classified into correspondent bHLH families according to their orthology with bHLHs from fruit fly and other insect species. Examination of GenBank annotations of these 52 DcbHLH members indicated that annotations of only 21 DcbHLH proteins are consistent with our analysis. Therefore, our data provide useful information for updating annotations to other 31 DcbHLH proteins. Among the 52 DcbHLH proteins, DcClk, DcSima, DcCyc and DcCwo have dual HLH motifs, which have not been found in any other bHLH proteins. Diaphorina citri has 2, 3 and 2 bHLH members respectively in Net, Hand and SRC families while other insect species have only one member in these families. The existence of more Net, Hand and SRC family members probably means that Asian citrus psyllid possesses more complex regulatory network in controlling intervein emergence, heart morphogenesis and larval metamorphosis than other insects. These results provide a solid basis and interesting aspects for further investigations into the evolution and functions of bHLH genes in Diaphorina citri.

关键词： basic helix-loop-helix Phylogenetic analysis Orthology Blastp search tBlastn search Diaphorina citri

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The basic helix-loop-helix transcription factor BIS2 is essential for monoterpenoid indole alkaloid production in the medicinal plant Catharanthus roseus

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PLANT JOURNAL 2016年第1期88卷 3-12页

作者： Van Moerkercke, Alex Steensma, Priscille Gariboldi, Ivo Espoz, Javiera Purnama, Purin C. Schweizer, Fabian Miettinen, Karel Vanden Bossche, Robin De Clercq, Rebecca Memelink, Johan Goossens, Alain VIB Dept Plant Syst Biol Technol Pk 927 B-9052 Ghent Belgium Univ Ghent Dept Plant Biotechnol & Bioinformat Technol Pk 927 B-9052 Ghent Belgium Leiden Univ Inst Biol POB 9505 NL-2300 RA Leiden Netherlands

M onoterpenoid indole alkaloids (MIAs) are produced as plant defence compounds. In the medicinal plant Catharanthus roseus, they comprise the anticancer compounds vinblastine and vincristine. The iridoid (monoterpenoid) pathway forms one of the two branches that feed MIA biosynthesis and its activation is regulated by the transcription factor (TF) basic helix-loop-helix (bHLH) iridoid synthesis 1 (BIS1). Here, we describe the identification and characterisation of BIS2, a jasmonate (JA)-responsive bHLH TF expressed preferentially in internal phloem-associated parenchyma cells, which transactivates promoters of iridoid biosynthesis genes and can homodimerise or form heterodimers with BIS1. Stable overexpression of BIS2 in C. roseus suspension cells and transient ectopic expression of BIS2 in C. roseus petal limbs resulted in increased transcript accumulation of methylerythritol-4-phosphate and iridoid pathway genes, but not of other MIA genes or triterpenoid genes. Transcript profiling also indicated that BIS2 expression is part of an amplification loop, as it is induced by overexpression of either BIS1 or BIS2. Accordingly, silencing of BIS2 in C. roseus suspension cells completely abolished the JA-induced upregulation of the iridoid pathway genes and subsequent MIA accumulation, despite the presence of induced BIS1, indicating that BIS2 is essential for MIA production in C. roseus.

关键词： basic helix-loop-helix Catharanthus roseus Madagascar periwinkle jasmonate terpenoid iridoid monoterpenoid alkaloid

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Genome-wide analysis of basic helix-loop-helix family transcription factors and their role in responses to abiotic stress in carrot

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MOLECULAR BREEDING 2015年第5期35卷 1-12页

作者： Chen, Yi-Yun Li, Meng-Yao Wu, Xue-Jun Huang, Ying Ma, Jing Xiong, Ai-Sheng Nanjing Agr Univ State Key Lab Crop Genet & Germplasm Enhancement Coll Hort Nanjing 210095 Jiangsu Peoples R China

Environmental stresses significantly influence the growth and development of plants. To overcome these stresses, higher plants have evolved a variety of complicated molecular mechanisms. basic helix-loop-helix (bHLH) transcription factors (TFs) play important roles in plant growth and development in response to environmental stresses. Here, a total of 146 DcbHLH TFs were identified from carrot, based on a genomic and transcriptomic database. Based on the previous classification system of Arabidopsis thaliana, the DcbHLH TFs were divided into 17 subfamilies. Multiple sequence alignment of bHLH conserved domains indicated that 109 DcbHLH proteins were bound to DNA (83 proteins were E-box binders and 52 DcbHLHs were G-box binders). From evolutionary analysis, bHLH TFs selected from plants, metazoans, and fungi demonstrated that the number of bHLH TFs increased during the evolution of these species. The expression profiles of eight DcbHLH genes from subfamily 15 showed differences in three tissues and four abiotic stresses in two carrot cultivars, Junchuanhong and Kurodagosun. This study presented useful information on the structure and function of DcbHLH factors in the regulatory mechanisms of carrot.

关键词： basic helix-loop-helix Transcription factor Evolution Expression profile Abiotic stress Carrot

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