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Yu R, Hou Q, Deng H, Xiao L, Cai X, Shang C, Qiao G. Overexpression of PavHIPP16 from Prunus avium enhances cold stress tolerance in transgenic tobacco. BMC PLANT BIOLOGY 2024; 24:536. [PMID: 38862890 PMCID: PMC11167810 DOI: 10.1186/s12870-024-05267-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Accepted: 06/07/2024] [Indexed: 06/13/2024]
Abstract
BACKGROUND The heavy metal-associated isoprenylated plant protein (HIPP) is an important regulatory element in response to abiotic stresses, especially playing a key role in low-temperature response. RESULTS This study investigated the potential function of PavHIPP16 up-regulated in sweet cherry under cold stress by heterologous overexpression in tobacco. The results showed that the overexpression (OE) lines' growth state was better than wild type (WT), and the germination rate, root length, and fresh weight of OE lines were significantly higher than those of WT. In addition, the relative conductivity and malondialdehyde (MDA) content of the OE of tobacco under low-temperature treatment were substantially lower than those of WT. In contrast, peroxidase (POD), superoxide dismutase (SOD), catalase (CAT) activities, hydrogen peroxide (H2O2), proline, soluble protein, and soluble sugar contents were significantly higher than those of WT. Yeast two-hybrid assay (Y2H) and luciferase complementation assay verified the interactions between PavbHLH106 and PavHIPP16, suggesting that these two proteins co-regulated the cold tolerance mechanism in plants. The research results indicated that the transgenic lines could perform better under low-temperature stress by increasing the antioxidant enzyme activity and osmoregulatory substance content of the transgenic plants. CONCLUSIONS This study provides genetic resources for analyzing the biological functions of PavHIPPs, which is important for elucidating the mechanisms of cold resistance in sweet cherry.
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Affiliation(s)
- Runrun Yu
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Qiandong Hou
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Hong Deng
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Ling Xiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Xiaowei Cai
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Chunqiong Shang
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China
| | - Guang Qiao
- Key Laboratory of Plant Resource Conservation and Germplasm Innovation in Mountainous Region (Ministry of Education), College of Life Sciences, Institute of Agro-bioengineering, Guizhou University, Guiyang, 550025, Guizhou Province, China.
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Chen X, Yao C, Liu J, Liu J, Fang J, Deng H, Yao Q, Kang T, Guo X. Basic helix-loop-helix (bHLH) gene family in rye (Secale cereale L.): genome-wide identification, phylogeny, evolutionary expansion and expression analyses. BMC Genomics 2024; 25:67. [PMID: 38233751 PMCID: PMC10792839 DOI: 10.1186/s12864-023-09911-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 12/15/2023] [Indexed: 01/19/2024] Open
Abstract
BACKGROUND Rye (Secale cereale), one of the drought and cold-tolerant crops, is an important component of the Triticae Dumortier family of Gramineae plants. Basic helix-loop-helix (bHLH), an important family of transcription factors, has played pivotal roles in regulating numerous intriguing biological processes in plant development and abiotic stress responses. However, no systemic analysis of the bHLH transcription factor family has yet been reported in rye. RESULTS In this study, 220 bHLH genes in S. cereale (ScbHLHs) were identified and named based on the chromosomal location. The evolutionary relationships, classifications, gene structures, motif compositions, chromosome localization, and gene replication events in these ScbHLH genes are systematically analyzed. These 220 ScbHLH members are divided into 21 subfamilies and one unclassified gene. Throughout evolution, the subfamilies 5, 9, and 18 may have experienced stronger expansion. The segmental duplications may have contributed significantly to the expansion of the bHLH family. To systematically analyze the evolutionary relationships of the bHLH family in different plants, we constructed six comparative genomic maps of homologous genes between rye and different representative monocotyledonous and dicotyledonous plants. Finally, the gene expression response characteristics of 22 ScbHLH genes in various biological processes and stress responses were analyzed. Some candidate genes, such as ScbHLH11, ScbHLH48, and ScbHLH172, related to tissue developments and environmental stresses were screened. CONCLUSIONS The results indicate that these ScbHLH genes exhibit characteristic expression in different tissues, grain development stages, and stress treatments. These findings provided a basis for a comprehensive understanding of the bHLH family in rye.
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Affiliation(s)
- Xingyu Chen
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Caimei Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jiahao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jintao Liu
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Jingmei Fang
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Hong Deng
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Qian Yao
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China
| | - Tairan Kang
- School of Food and Biological Engineering, Chengdu University, Chengdu, 610106, PR China.
| | - Xiaoqiang Guo
- Sichuan Industrial Institute of Antibiotics, School of Pharmacy, Chengdu University, Chengdu, 610106, PR China.
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Tan Z, Lu D, Yu Y, Li L, Dong W, Xu L, Yang Q, Wan X, Liang H. Genome-Wide Identification and Characterization of the bHLH Gene Family and Its Response to Abiotic Stresses in Carthamus tinctorius. PLANTS (BASEL, SWITZERLAND) 2023; 12:3764. [PMID: 37960120 PMCID: PMC10648185 DOI: 10.3390/plants12213764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/16/2023] [Accepted: 11/02/2023] [Indexed: 11/15/2023]
Abstract
The basic helix-loop-helix (bHLH) transcription factors possess DNA-binding and dimerization domains and are involved in various biological and physiological processes, such as growth and development, the regulation of secondary metabolites, and stress response. However, the bHLH gene family in C. tinctorius has not been investigated. In this study, we performed a genome-wide identification and analysis of bHLH transcription factors in C. tinctorius. A total of 120 CtbHLH genes were identified, distributed across all 12 chromosomes, and classified into 24 subfamilies based on their phylogenetic relationships. Moreover, the 120 CtbHLH genes were subjected to comprehensive analyses, including protein sequence alignment, evolutionary assessment, motif prediction, and the analysis of promoter cis-acting elements. The promoter region analysis revealed that CtbHLH genes encompass cis-acting elements and were associated with various aspects of plant growth and development, responses to phytohormones, as well as responses to both abiotic and biotic stresses. Expression profiles, sourced from transcriptome databases, indicated distinct expression patterns among these CtbHLH genes, which appeared to be either tissue-specific or specific to certain cultivars. To further explore their functionality, we determined the expression levels of fifteen CtbHLH genes known to harbor motifs related to abiotic and hormone responses. This investigation encompassed treatments with ABA, salt, drought, and MeJA. The results demonstrated substantial variations in the expression patterns of CtbHLH genes in response to these abiotic and hormonal treatments. In summary, our study establishes a solid foundation for future inquiries into the roles and regulatory mechanisms of the CtbHLH gene family.
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Affiliation(s)
- Zhengwei Tan
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Dandan Lu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Yongliang Yu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lei Li
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Wei Dong
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Lanjie Xu
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Qing Yang
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
| | - Xiufu Wan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijng 100700, China;
| | - Huizhen Liang
- Institute of Chinese Herbel Medicines, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; (Z.T.); (D.L.); (Y.Y.); (L.L.); (W.D.); (L.X.); (Q.Y.)
- Henan Sesame Research Center, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China
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Kamran HM, Fu X, Wang H, Yang N, Chen L. Genome-Wide Identification and Expression Analysis of the bHLH Transcription Factor Family in Wintersweet ( Chimonanthus praecox). Int J Mol Sci 2023; 24:13462. [PMID: 37686265 PMCID: PMC10487621 DOI: 10.3390/ijms241713462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 08/12/2023] [Accepted: 08/18/2023] [Indexed: 09/10/2023] Open
Abstract
Wintersweet (Chimonanthus praecox (L.) Link, Calycanthaceae) is an esteemed ornamental flowering shrub known for its distinct blooming period in winter, vibrant color petals, and captivating floral fragrance. Basic helix-loop-helix (bHLH) transcription factors (TFs) play pivotal roles as key regulators in secondary metabolites biosynthesis, growth, and development in plants. However, the systematic analysis of the bHLH family members and their role in the regulation of floral traits in Wintersweet remains insufficiently understood. To bridge this knowledge gap, we conducted a comprehensive genome-wide analysis of the C. praecox bHLH (CpbHLH) gene family, identifying a total of 131 CpbHLH genes across 11 chromosomes. Phylogenetic analysis classified these CpbHLH genes into 23 subfamilies, wherein most members within the same subfamily exhibited analogous intron/exon patterns and motif composition. Moreover, the expansion of the CpbHLH gene family was primarily driven by segmental duplication, with duplicated gene pairs experiencing purifying selection during evolution. Transcriptomic analysis revealed diverse expression patterns of CpbHLH genes in various tissues and distinct stages of Wintersweet flower development, thereby suggesting their involvement in a diverse array of physiological processes. Furthermore, yeast 2-hybrid assay demonstrated interaction between CpbHLH25 and CpbHLH59 (regulators of floral scent and color) as well as with CpbHLH112 and CpMYB2, suggesting potential coordinately regulation of secondary metabolites biosynthesis in Wintersweet flowers. Collectively, our comprehensive analysis provides valuable insights into the structural attributes, evolutionary dynamics, and expression profiles of the CpbHLH gene family, laying a solid foundation for further explorations of the multifaceted physiological and molecular roles of bHLH TFs in Wintersweet.
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Affiliation(s)
| | | | | | - Nan Yang
- Yunnan Province Engineering Research Center for Functional Flower Resources and Industrialization, College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China; (H.M.K.)
| | - Longqing Chen
- Yunnan Province Engineering Research Center for Functional Flower Resources and Industrialization, College of Landscape Architecture and Horticulture Sciences, Southwest Forestry University, Kunming 650224, China; (H.M.K.)
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Yang M, Ma Y, Si X, Liu X, Geng X, Wen X, Li G, Zhang L, Yang C, Zhang Z. Analysis of the Glycoside Hydrolase Family 1 from Wild Jujube Reveals Genes Involved in the Degradation of Jujuboside A. Genes (Basel) 2023; 14:1135. [PMID: 37372316 DOI: 10.3390/genes14061135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/17/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Jujubosides are the major medicinal ingredients of Ziziphi Spinosae Semen (the seed of wild jujube). To date, a complete understanding of jujuboside's metabolic pathways has not been attained. This study has systematically identified 35 β-glucosidase genes belonging to the glycoside hydrolase family 1 (GH1) using bioinformatic methods based on the wild jujube genome. The conserved domains and motifs of the 35 putative β-glucosidases, along with the genome locations and exon-intron structures of 35 β-glucosidase genes were revealed. The potential functions of the putative proteins encoded by the 35 β-glucosidase genes are suggested based on their phylogenetic relationships with Arabidopsis homologs. Two wild jujube β-glucosidase genes were heterologously expressed in Escherichia coli, and the recombinant proteins were able to convert jujuboside A (JuA) into jujuboside B (JuB). Since it has been previously reported that JuA catabolites, including JuB and other rare jujubosides, may play crucial roles in the jujuboside's pharmacological activity, it is suggested that these two proteins can be used to enhance the utilization potential of jujubosides. This study provides new insight into the metabolism of jujubosides in wild jujube. Furthermore, the characterization of β-glucosidase genes is expected to facilitate investigations involving the cultivation and breeding of wild jujube.
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Affiliation(s)
- Mingjun Yang
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Yimian Ma
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xupeng Si
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xiaofeng Liu
- School of Life Science and Engineering, Lanzhou University of Technology, Lanzhou 730050, China
| | - Xin Geng
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xin Wen
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Guoqiong Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liping Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Chengmin Yang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Zheng Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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Zhang Z, Fang J, Zhang L, Jin H, Fang S. Genome-wide identification of bHLH transcription factors and their response to salt stress in Cyclocarya paliurus. FRONTIERS IN PLANT SCIENCE 2023; 14:1117246. [PMID: 36968403 PMCID: PMC10035414 DOI: 10.3389/fpls.2023.1117246] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
As a highly valued and multiple function tree species, the leaves of Cyclocarya paliurus are enriched in diverse bioactive substances with healthy function. To meet the requirement for its leaf production and medical use, the land with salt stress would be a potential resource for developing C. paliurus plantations due to the limitation of land resources in China. The basic helix-loop-helix (bHLH) transcription factor protein family, the second largest protein family in plants, has been found to play essential roles in the response to multiple abiotic stresses, especially salt stress. However, the bHLH gene family in C.paliurus has not been investigated. In this study, 159 CpbHLH genes were successfully identified from the whole-genome sequence data, and were classified into 26 subfamilies. Meanwhile, the 159 members were also analyzed from the aspects of protein sequences alignment, evolution, motif prediction, promoter cis-acting elements analysis and DNA binding ability. Based on transcriptome profiling under a hydroponic experiment with four salt concentrations (0%, 0.15%, 0.3%, and 0.45% NaCl), 9 significantly up- or down-regulated genes were screened, while 3 genes associated with salt response were selected in term of the GO annotation results. Totally 12 candidate genes were selected in response to salt stress. Moreover, based on expression analysis of the 12 candidate genes sampled from a pot experiment with three salt concentrations (0%, 0.2% and 0.4% NaCl), CpbHLH36/68/146 were further verified to be involved in the regulation of salt tolerance genes, which is also confirmed by protein interaction network analysis. This study was the first analysis of the transcription factor family at the genome-wide level of C. paliurus, and our findings would not only provide insight into the function of the CpbHLH gene family members involved in salt stress but also drive progress in genetic improvement for the salt tolerance of C. paliurus.
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Affiliation(s)
- Zijie Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Jie Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Lei Zhang
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing, China
| | - Huiyin Jin
- College of Forestry, Nanjing Forestry University, Nanjing, China
| | - Shengzuo Fang
- College of Forestry, Nanjing Forestry University, Nanjing, China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing, China
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Characterization and expression analysis of bHLH transcription factors reveal their putative regulatory effects on nectar spur development in Aquilegia species. Gene 2023; 852:147057. [PMID: 36410606 DOI: 10.1016/j.gene.2022.147057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 10/27/2022] [Accepted: 11/14/2022] [Indexed: 11/19/2022]
Abstract
Nectar spur is a hollow extension of certain flower parts and shows strikingly diverse size and shape in Aquilegia. Nectar spur development is involved in cell division and expansion processes. The basic helix-loop-helix (bHLH) transcription factors (TFs) control a diversity of organ morphogenesis, including cell division and cell expansion processes. However, the role of bHLH genes in nectar spur development in Aquilegia is mainly unknown. We conducted a genome-wide identification of the bHLH gene family in Aquilegia to determine structural characteristics and phylogenetic relationships, and to analyze expression profiles of these genes during the development of nectar spur in spurless and spurred species. A total of 120 AqbHLH genes were identified from the Aquilegia coerulea genome. The phylogenetic tree showed that AqbHLH proteins were divided into 15 subfamilies, among which S7 and S8 subfamilies occurred marked expansion. The AqbHLH genes in the same clade had similar motif composition and gene structure characteristics. Conserved residue analysis indicated nineteen residues with conservation of more than 50% were found in the four conserved regions. In the upstream sequence of AqbHLH genes, the light-responsive element was the most abundant cis-acting element. Eighteen AqbHLH genes showed syntenic relationships, and eight genes from four syntenic pairs underwent tandem duplications. According to the expression profiling analysis by public RNA-Seq data and qRT-PCR results, five AqbHLH genes, including AqbHLH027, AqbHLH046, AqbHLH082, AqbHLH083 and AqbHLH092, were differentially expressed between different tissues in A. coerulea at early developmental stages, as well as between spurless and spurred Aquilegia species. Of them, AqbHLH046 was not only highly expressed in spur compared with blade, but also showed higher expression levels in spurred species than spurless specie, suggesting it plays an essential role in the development of spur by regulating cell division. This study lays a foundation to investigate the function of AqbHLH genes family in nectar spur development, and has potential implications for speciation and genetic breeding in the genus Aquilegia.
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Ding Y, Wang X, Wang D, Jiang L, Xie J, Wang T, Song L, Zhao X. Identification of CmbHLH Transcription Factor Family and Excavation of CmbHLHs Resistant to Necrotrophic Fungus Alternaria in Chrysanthemum. Genes (Basel) 2023; 14:genes14020275. [PMID: 36833202 PMCID: PMC9957535 DOI: 10.3390/genes14020275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 01/15/2023] [Accepted: 01/16/2023] [Indexed: 01/22/2023] Open
Abstract
Chrysanthemum morifolium Ramat. 'Huaihuang' is a traditional Chinese medicinal plant. However, a black spot disease caused by Alternaria sp., a typical necrotrophic fungus, has a serious damaging influence on the field growth, yield, and quality of the plant. 'Huaiju 2#' being bred from 'Huaihuang', shows resistance to Alternaria sp. bHLH transcription factor has been widely studied because of their functions in growth development, signal transduction, and abiotic stress. However, the function of bHLH in biotic stress has rarely been studied. To characterize the resistance genes, the CmbHLH family was surveyed in 'Huaiju 2#'. On the basis of the transcriptome database of 'Huaiju 2#' after Alternaria sp. inoculation, with the aid of the Chrysanthemum genome database, 71 CmbHLH genes were identified and divided into 17 subfamilies. Most (64.8%) of the CmbHLH proteins were rich in negatively charged amino acids. CmbHLH proteins are generally hydrophilic proteins with a high aliphatic amino acid content. Among the 71 CmbHLH proteins, five CmbHLHs were significantly upregulated by Alternaria sp. infection, and the expression of CmbHLH18 was the most significant. Furthermore, heterologous overexpression of CmbHLH18 could improve the resistance of Arabidopsis thaliana to necrotrophic fungus Alternaria brassicicola by enhancing callose deposition, preventing spores from entering leaves, reducing ROS accumulation, increasing the activities of antioxidant enzymes and defense enzymes, and promoting their gene expression levels. These results indicate that the five CmbHLHs, especially CmbHLH18, may be considered candidate genes for resistance to necrotrophic fungus. These findings not only increase our understanding of the role CmbHLHs play in biotic stress but also provide a basis by using CmbHLHs to breed a new variety of Chrysanthemum with high resistance to necrotrophic fungus.
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Affiliation(s)
- Yifeng Ding
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiaomeng Wang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Dandan Wang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Liwei Jiang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Jing Xie
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Tianle Wang
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Lingyu Song
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
| | - Xiting Zhao
- Department of Biological Sciences, College of Life Sciences, Henan Normal University, Xinxiang 453007, China
- Engineering Technology Research Center of Nursing and Utilization of Genuine Chinese Crude Drugs in Henan Province, Xinxiang 453007, China
- Engineering Laboratory of Biotechnology for Green Medicinal Plant of Henan Province, Xinxiang 453007, China
- Correspondence: or ; Tel.: +86-182-3739-1085 or +86-135-6988-6182
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Wang N, Shu X, Zhang F, Wang Z. Transcriptome-wide characterization of bHLH transcription factor genes in Lycoris radiata and functional analysis of their response to MeJA. FRONTIERS IN PLANT SCIENCE 2023; 13:975530. [PMID: 36704164 PMCID: PMC9872026 DOI: 10.3389/fpls.2022.975530] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 12/12/2022] [Indexed: 06/18/2023]
Abstract
As one of the biggest plant specific transcription factor (TF) families, basic helix-loop-helix (bHLH) protein, plays significant roles in plant growth, development, and abiotic stress responses. However, there has been minimal research about the effects of methyl jasmonate (MeJA) treatment on the bHLH gene family in Lycoris radiata (L'Her.) Herb. In this study, based on transcriptome sequencing data, 50 putative L. radiata bHLH (LrbHLH) genes with complete open reading frames (ORFs), which were divided into 20 bHLH subfamilies, were identified. The protein motif analyses showed that a total of 10 conserved motifs were found in LrbHLH proteins and motif 1 and motif 2 were the most highly conserved motifs. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis of LrbHLH genes revealed their involvement in regulation of plant growth, jasmonic acid (JA) mediated signaling pathway, photoperiodism, and flowering. Furthermore, subcellular localization revealed that most LrbHLHs were located in the nucleus. Expression pattern analysis of LrbHLH genes in different tissues and at flower developmental stages suggested that their expression differed across lineages and might be important for plant growth and organ development in Lycoris. In addition, all LrbHLH genes exhibited specific spatial and temporal expression patterns under MeJA treatment. Moreover, protein-protein interaction (PPI) network analysis and yeast two-hybrid assay showed that numerous LrbHLHs could interact with jasmonate ZIM (zinc-finger inflorescence meristem) domain (JAZ) proteins. This research provides a theoretical basis for further investigation of LrbHLHs to find their functions and insights for their regulatory mechanisms involved in JA signaling pathway.
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Tao T, Hu W, Yang Y, Zou M, Zhou S, Tian S, Wang Y. Transcriptomics reveals the molecular mechanisms of flesh colour differences in eggplant (Solanum melongena). BMC PLANT BIOLOGY 2023; 23:5. [PMID: 36597026 PMCID: PMC9811765 DOI: 10.1186/s12870-022-04002-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 12/13/2022] [Indexed: 06/17/2023]
Abstract
BACKGROUND Fruit flesh colour is not only an important commodity attribute of eggplant but is also closely related to maturity. However, very little is known about its formation mechanism in eggplant. RESULTS Two inbred lines of eggplant, green 'NC7' and white 'BL', were used in this study to explain the differences in flesh colour. Transcriptome sequencing results revealed a total of 3304 differentially expressed genes (DEGs) in NC7 vs. BL. Of the DEGs obtained, 2050 were higher and 1254 were lower in BL. These DEGs were annotated to 126 pathways, where porphyrin and chlorophyll metabolism, flavonoid biosynthesis, and photosynthesis-antenna proteins play vital roles in the colour formation of eggplant flesh. At the same time, Gene Ontology (GO) enrichment significance analysis showed that a large number of unigenes involved in the formation of chloroplast structure were lower in BL, which indicated that the formation of chloroplasts in white-fleshed eggplant was blocked. This was confirmed by transmission electron microscopy (TEM), which found only leucoplasts but no chloroplasts in the flesh cells of white-fleshed eggplant. Several genes encoding ERF and bHLH transcription factors were predicted to participate in the regulation of chlorophyll biosynthetic genes. CONCLUSIONS The results of this study indicated that differences in the gene expression of the chlorophyll metabolic pathway were the main cause of the different flesh colour formations. These findings will increase our understanding of the genetic basis in eggplant flesh colors formation mechanism.
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Affiliation(s)
- Tao Tao
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Wei Hu
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Yang Yang
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Min Zou
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Shanshan Zhou
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China
| | - Shibing Tian
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
| | - Yongqing Wang
- Vegetable and Flower Institute of Chongqing Academy of Agricultural Sciences, Chongqing, 401329, China.
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11
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Liu W, Yi Y, Zhuang J, Ge C, Cao Y, Zhang L, Liu M. Genome-wide identification and transcriptional profiling of the basic helix-loop-helix gene family in tung tree ( Vernicia fordii). PeerJ 2022; 10:e13981. [PMID: 36193421 PMCID: PMC9526410 DOI: 10.7717/peerj.13981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 08/10/2022] [Indexed: 01/19/2023] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor gene family is one of the largest gene families and is extensively involved in plant growth, development, biotic and abiotic stress responses. Tung tree (Vernicia fordii) is an economically important woody oil plant that produces tung oil rich in eleostearic acid. However, the characteristics of the bHLH gene family in the tung tree genome are still unclear. Hence, VfbHLHs were first searched at a genome-wide level, and their expression levels in various tissues or under low temperature were investigated systematically. In this study, we identified 104 VfbHLHs in the tung tree genome, and these genes were classified into 18 subfamilies according to bHLH domains. Ninety-eight VfbHLHs were mapped to but not evenly distributed on 11 pseudochromosomes. The domain sequences among VfbHLHs were highly conserved, and their conserved residues were also identified. To explore their expression, we performed gene expression profiling using RNA-Seq and RT-qPCR. We identified five, 18 and 28 VfbHLH genes in female flowers, male flowers and seeds, respectively. Furthermore, we found that eight genes (VfbHLH29, VfbHLH31, VfbHLH47, VfbHLH51, VfbHLH57, VfbHLH59, VfbHLH70, VfbHLH72) were significant differential expressed in roots, leaves and petioles under low temperature stress. This study lays the foundation for future studies on bHLH gene cloning, transgenes, and biological mechanisms.
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Affiliation(s)
- Wenjuan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Yaqi Yi
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Jingyi Zhuang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Chang Ge
- School of Urban Design, Wuhan University, Wuhan, Hubei, China
| | - Yunpeng Cao
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Lin Zhang
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
| | - Meilan Liu
- Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, Ministry of Education, Central South University of Forestry and Technology, Changsha, Hunan, China,Key Lab of Non-wood Forest Products of State Forestry Administration, College of Forestry, Central South University of Forestry and Technology, Changsha, Hunan, China
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12
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Li C, Cai X, Shen Q, Chen X, Xu M, Ye T, Si D, Wu L, Chen D, Han Z, Si J. Genome-wide analysis of basic helix-loop-helix genes in Dendrobium catenatum and functional characterization of DcMYC2 in jasmonate-mediated immunity to Sclerotium delphinii. FRONTIERS IN PLANT SCIENCE 2022; 13:956210. [PMID: 35982703 PMCID: PMC9378844 DOI: 10.3389/fpls.2022.956210] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/29/2022] [Indexed: 06/15/2023]
Abstract
Dendrobium catenatum, belonging to the Orchidaceae, is a precious Chinese herbal medicine. Sclerotium delphinii (P1) is a broad-spectrum fungal disease, which causes widespread loss in the near-wild cultivation of D. catenatum. Thus, resistance breeding of D. catenatum has become the key to solve this problem. The basic helix-loop-helix (bHLH) gene family is closely related to plant resistance to external stresses, but the related research in D. catenatum is not deep enough yet. Phylogenetic analysis showed that 108 DcbHLH genes could be divided into 23 subgroups. Promoter cis-acting elements revealed that DcbHLHs contain a large number of stress-related cis-acting elements. Transcriptome analysis of MeJA and P1 treatment manifested that exogenous MeJA can change the expression pattern of most bHLH genes, especially the IIIe subgroup, including inhibiting the expression of DcbHLH026 (MYC2a) and promoting the expression of DcbHLH027 (MYC2b). Subcellular localization indicated that they were located in the nucleus. Furthermore, exogenous MeJA treatment significantly delayed disease time and reduced lesion size after infection with P1. DcMYC2b-overexpression Arabidopsis lines showed significantly smaller lesions after being infected with P1 than the wild type, indicating that DcMYC2b functions as an important positive regulator in D. catenatum defense against P1. Our findings shed more insights into the critical role of the DcbHLH family in plants and the resistance breeding of D. catenatum.
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13
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Panzade KP, Kale SS, Manoj ML, Kothawale SP, Damse DN. Genome-Wide Analysis and Expression Profile of Nuclear Factor Y (NF-Y) Gene Family in Z. jujuba. Appl Biochem Biotechnol 2022; 194:1373-1389. [PMID: 34731431 DOI: 10.1007/s12010-021-03730-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/21/2021] [Indexed: 10/19/2022]
Abstract
Nuclear factor-Y (NF-Y) is an important transcription factor in the plant species, which potentially provides a higher level of functional diversity including for abiotic stress tolerance. The genome-wide study and expression analysis of NF-Y gene family in Ziziphus, an elite abiotic stress-tolerant species, assist bioprospecting of genes. Here, a total of 32 NF-Y (8 NF-YA, 15 NF-YB, and 9 NF-YC) genes were identified in genome-wide search of Z. jujuba genome. Physicochemical properties, cellular localization, gene structure, chromosomal location, and protein motifs were analyzed for structural and functional understanding. Identified 12 NF-Ys were responsible for the expansion of NF-Y gene family by tandem duplication in Z. jujuba. Phylogenetic and comparative physical mapping of Z. jujuba NF-Ys with its orthologs illustrated evolutionary and functional insights into NF-Y gene family. A total of 45 perfect microsatellites (20bp to 40bp) were extracted across the ZjNF-Y genes. The promoter and gene ontology study suggested that Z. jujuba NF-Y gene family is functionally diverse and could play a wide-ranging role in plant abiotic stress, development, and cellular processes. An expression study revealed that large numbers of the NF-Ys are differentially expressed in response to drought and salinity. The total 15 and 18 ZjNF-Y genes that are upregulated under drought and salinity stress, respectively, are the potential candidates for further functional analysis for development of climate-resilient crops. The present study established a base for understanding the role of NF-Ys in Z. jujuba under abiotic stress conditions and paved a way for further research.
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Affiliation(s)
- Kishor Prabhakar Panzade
- Department of Plant Biotechnology, SDMVM College of Agricultural Biotechnology, Georai Tanda, Maharashtra, 431002, India.
| | - Sonam S Kale
- Department of Plant Biotechnology, MGM College of Agricultural Biotechnology, Aurangabad, Maharashtra, 431007, India
| | | | | | - Dipak N Damse
- Central Sugarcane Research Station, Padegaon, Mahatma Phule Agriculture University, Rahuri, Maharashtra, 415521, India
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14
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Bai G, Yang DH, Chao P, Yao H, Fei M, Zhang Y, Chen X, Xiao B, Li F, Wang ZY, Yang J, Xie H. Genome-wide identification and expression analysis of NtbHLH gene family in tobacco ( Nicotiana tabacum) and the role of NtbHLH86 in drought adaptation. PLANT DIVERSITY 2021; 43:510-522. [PMID: 35024520 PMCID: PMC8720692 DOI: 10.1016/j.pld.2020.10.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 10/12/2020] [Accepted: 10/18/2020] [Indexed: 06/12/2023]
Abstract
The bHLH transcription factors play pivotal roles in plant growth and development, production of secondary metabolites and responses to various environmental stresses. Although the bHLH genes have been well studied in model plant species, a comprehensive investigation of the bHLH genes is required for tobacco with newly obtained high-quality genome. In the present study, a total of 309 NtbHLH genes were identified and can be divided into 23 subfamilies. The conserved amino acids which are essential for their function were predicted for the NtbHLH proteins. Moreover, the NtbHLH genes were conserved during evolution through analyzing the gene structures and conserved motifs. A total of 265 NtbHLH genes were localized in the 24 tobacco chromosomes while the remained 44 NtbHLH genes were mapped to the scaffolds due to the complexity of tobacco genome. Moreover, transcripts of NtbHLH genes were obviously tissue-specific expressed from the gene-chip data from 23 tobacco tissues, and expressions of 20 random selected NtbHLH genes were further confirmed by quantitative real-time PCR, indicating their potential functions in the plant growth and development. Importantly, overexpressed NtbHLH86 gene confers improve drought tolerance in tobacco indicating that it might be involved in the regulation of drought stress. Therefore, our findings here provide a valuable information on the characterization of NtbHLH genes and further investigation of their functions in tobacco.
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Affiliation(s)
- Ge Bai
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Da-Hai Yang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Peijian Chao
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan, China
| | - Heng Yao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - MingLiang Fei
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Yihan Zhang
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Xuejun Chen
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Bingguang Xiao
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
| | - Feng Li
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan, China
| | - Zhen-Yu Wang
- Institute ofBioengineering, Guangdong Academy of Sciences, Guangzhou, Guangdong, 510316, China
| | - Jun Yang
- National Tobacco Gene Research Centre, Zhengzhou Tobacco Research Institute, Zhengzhou, Henan, China
| | - He Xie
- Tobacco Breeding and Biotechnology Research Center, Yunnan Academy of Tobacco Agricultural Sciences, Kunming, Yunnan, China
- Key Laboratory of Tobacco Biotechnological Breeding, Kunming, Yunnan, China
- National Tobacco Genetic Engineering Research Center, Kunming, Yunnan, China
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15
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Fan Y, Lai D, Yang H, Xue G, He A, Chen L, Feng L, Ruan J, Xiang D, Yan J, Cheng J. Genome-wide identification and expression analysis of the bHLH transcription factor family and its response to abiotic stress in foxtail millet (Setaria italica L.). BMC Genomics 2021; 22:778. [PMID: 34717536 PMCID: PMC8557513 DOI: 10.1186/s12864-021-08095-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 10/18/2021] [Indexed: 12/04/2022] Open
Abstract
Background Members of the basic helix-loop-helix (bHLH) transcription factor family perform indispensable functions in various biological processes, such as plant growth, seed maturation, and abiotic stress responses. However, the bHLH family in foxtail millet (Setaria italica), an important food and feed crop, has not been thoroughly studied. Results In this study, 187 bHLH genes of foxtail millet (SibHLHs) were identified and renamed according to the chromosomal distribution of the SibHLH genes. Based on the number of conserved domains and gene structure, the SibHLH genes were divided into 21 subfamilies and two orphan genes via phylogenetic tree analysis. According to the phylogenetic tree, the subfamilies 15 and 18 may have experienced stronger expansion in the process of evolution. Then, the motif compositions, gene structures, chromosomal spread, and gene duplication events were discussed in detail. A total of sixteen tandem repeat events and thirty-eight pairs of segment duplications were identified in bHLH family of foxtail millet. To further investigate the evolutionary relationship in the SibHLH family, we constructed the comparative syntenic maps of foxtail millet associated with representative monocotyledons and dicotyledons species. Finally, the gene expression response characteristics of 15 typical SibHLH genes in different tissues and fruit development stages, and eight different abiotic stresses were analysed. The results showed that there were significant differences in the transcription levels of some SibHLH members in different tissues and fruit development stages, and different abiotic stresses, implying that SibHLH members might have different physiological functions. Conclusions In this study, we identified 187 SibHLH genes in foxtail millet and further analysed the evolution and expression patterns of the encoded proteins. The findings provide a comprehensive understanding of the bHLH family in foxtail millet, which will inform further studies on the functional characteristics of SibHLH genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08095-y.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.,School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, People's Republic of China
| | - Liang Feng
- Chengdu Institute of Food Inspection, Chengdu, 610030, People's Republic of China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China
| | - Dabing Xiang
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China
| | - Jun Yan
- School of Food and Biological engineering, Chengdu University, Chengdu, 610106, People's Republic of China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang, Guizhou Province, 550025, People's Republic of China.
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Genome-Wide Identification and Functional Analysis of the Basic Helix-Loop-Helix (bHLH) Transcription Family Reveals Candidate PtFBH Genes Involved in the Flowering Process of Populus trichocarpa. FORESTS 2021. [DOI: 10.3390/f12111439] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
As one of the largest TF families+ in plants, the basic helix-loop-helix (bHLH) family plays an important part in the growth and development of many plants. FLOWERING BHLH (FBH) encodes a bHLH-type transcriptional factor related to the flowering process. Poplar is a model woody plant as well as an important economic tree species with a small genome. However, the characteristics of the bHLHs and FBHs gene family in the newest version of Populustrichocarpa genome have not been analyzed yet. We identified 233 PtbHLHs and 10 PtFBHs in the newest version genome, and PtbHLHs were classified into 21 groups with FBH subfamily occupying one, supported by phylogenetic analysis, exon–intron patterns, and conserved protein motifs. These PtHLHs were distributed on 19 chromosomes unevenly and expressed in nucleus mainly. Gene duplication and synteny analysis have indicated that the PtbHLHs gene family has undergone strong purification selection during the evolution process. The cis-elements analysis has suggested that PtbHLHs may be related to the growth and development. Conserved residues of FBHs among Arabidopsis and poplar were also identified. Expression of 227 PtHLH genes (6 unmatched, 13 no expressed) showed diverse patterns in different tissues, implying their multiple functions. Protein–protein interaction network prediction and expression patterns in three states of the flowering process (Flowers-Dormant, Flowers-Expanding and Flowers-Expanded) suggested that some members of PtbHLH and PtFBH family may be involved in the flowering process. Our comprehensive and systematic analysis can provide some valuable clues and basic reference toward further investigations on physiological and molecular functions of PtbHLHs.
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Wang F, Zhao J, Zhang M, Yang J, Zeng G. Genome-wide analysis of the mouse LIM gene family reveals its roles in regulating pathological cardiac hypertrophy. FEBS Lett 2021; 595:2271-2289. [PMID: 34328660 DOI: 10.1002/1873-3468.14168] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/27/2021] [Accepted: 07/17/2021] [Indexed: 11/08/2022]
Abstract
LIM-domain proteins have been shown to be associated with heart development and diseases. Systematic studies of LIM family members at the genome-wide level, which are crucial to further understand their functions in cardiac hypertrophy, are currently lacking. Here, 70 LIM genes were identified and characterised in mice. The expression patterns of LIM genes differ greatly during cardiac development and in the case of hypertrophy. Both Crip2 and Xirp2 are differentially expressed in cardiac hypertrophy and during heart failure. In addition, the hypertrophic state of cardiomyocytes is controlled by the relative expression levels of Crip2 and Xirp2. This study provides a foundation for further understanding of the special roles of LIM proteins in mammalian cardiac development and hypertrophy.
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Affiliation(s)
- Fangfang Wang
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Jieqiong Zhao
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Mingming Zhang
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Jingxiao Yang
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
| | - Guangwei Zeng
- Department of Cardiology, The Second Affiliated Hospital of Air Force Medical University, Xi'an, China
- Department of Cardiology, Xi'an International Medical Center Hospital, Northwest University, Xi'an, China
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18
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Pervaiz T, Liu T, Fang X, Ren Y, Li X, Liu Z, Fiaz M, Fang J, Shangguan L. Identification of GH17 gene family in Vitis vinifera and expression analysis of GH17 under various adversities. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1423-1436. [PMID: 34366587 PMCID: PMC8295436 DOI: 10.1007/s12298-021-01014-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 05/20/2021] [Accepted: 05/27/2021] [Indexed: 06/13/2023]
Abstract
Glycoside hydrolase (GH, EC 3.2.1) is a group of enzymes that hydrolyzes glycosidic bonds and play a role in the hydrolysis and synthesis of sugars in living organisms. Vitis vinifera is an important fruit crop and it harbors GH17 gene family however, their function in grapes has not been systematically investigated. In this study, a total of 870 GH17 genes were identified from 14 plant species and their structural domain, sequence alignment, phylogenetic tree, collinear analysis, with the expression profiles of VviGH17 gene family was performed. The promoter analysis of VviGH17 gene showed the presence of cis-acting elements, which are responsive to plant growth and development. In addition, elements for plant hormones were found that are triggered in response to abiotic/biological stress. Transcriptomic data led to the identification of several VviGH17 genes, which are associated with bud dormancy and in response to abiotic stress. Transcript analysis was carried out for some of the selected VviGH17 genes RT-qPCR. VviGH17-16 and VviGH17-30 genes were differentially expressed during bud dormancy, fruit development and different abiotic stresses. Moreover, VviGH17-37 and VviGH17-44 were differentially expressed at fruit development, in response to abiotic stress. In addition, subcellular localization predicts that the VviGH17-16, VviGH17-30, and VviGH17-37 genes were located in the cell membrane, while VviGH17-44 gene was located in the vacuole. In conclusion, our study led to the identification of several GH17s and their probable role in development and stress. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01014-1.
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Affiliation(s)
- Tariq Pervaiz
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Beijing Advanced Innovation Center for Tree Breeding By Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083 People’s Republic of China
| | - Tianhua Liu
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering, Center of Jiangsu Province, Nanjing, 210095 People’s Republic of China
| | - Xiang Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
| | - Yanhua Ren
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering, Center of Jiangsu Province, Nanjing, 210095 People’s Republic of China
| | - Xiyang Li
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering, Center of Jiangsu Province, Nanjing, 210095 People’s Republic of China
| | - Zhongjie Liu
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering, Center of Jiangsu Province, Nanjing, 210095 People’s Republic of China
| | - Muhammad Fiaz
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering, Center of Jiangsu Province, Nanjing, 210095 People’s Republic of China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering, Center of Jiangsu Province, Nanjing, 210095 People’s Republic of China
| | - Lingfei Shangguan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu Province 210095 People’s Republic of China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering, Center of Jiangsu Province, Nanjing, 210095 People’s Republic of China
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Wang M, Qiu X, Pan X, Li C. Transcriptional Factor-Mediated Regulation of Active Component Biosynthesis in Medicinal Plants. Curr Pharm Biotechnol 2021; 22:848-866. [PMID: 32568019 DOI: 10.2174/1389201021666200622121809] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2020] [Revised: 03/06/2020] [Accepted: 04/27/2020] [Indexed: 11/22/2022]
Abstract
Plants produce thousands of chemically diverse secondary metabolites, many of which have valuable pharmaceutical properties. There is much interest in the synthesis of these pharmaceuticallyvaluable compounds, including the key enzymes and the transcription factors involved. The function and regulatory mechanism of transcription factors in biotic and abiotic stresses have been studied in depth. However, their regulatory roles in the biosynthesis of bioactive compounds, especially in medicinal plants, have only begun. Here, we review what is currently known about how transcription factors contribute to the synthesis of bioactive compounds (alkaloids, terpenoids, flavonoids, and phenolic acids) in medicinal plants. Recent progress has been made in the cloning and characterization of transcription factors in medicinal plants on the genome scale. So far, several large transcription factors have been identified in MYB, WRKY, bHLH, ZIP, AP2/ERF transcription factors. These transcription factors have been predicted to regulate bioactive compound production. These transcription factors positively or negatively regulate the expression of multiple genes encoding key enzymes, and thereby control the metabolic flow through the biosynthetic pathway. Although the research addressing this niche topic is in its infancy, significant progress has been made, and advances in high-throughput sequencing technology are expected to accelerate the discovery of key regulatory transcription factors in medicinal plants. This review is likely to be useful for those interested in the synthesis of pharmaceutically- valuable plant compounds, especially those aiming to breed or engineer plants that produce greater yields of these compounds.
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Affiliation(s)
- Meizhen Wang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xiaoxiao Qiu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Xian Pan
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
| | - Caili Li
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, No. 151 Malianwa North Road, Haidian District, Beijing 100193, China
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Fan Y, Yang H, Lai D, He A, Xue G, Feng L, Chen L, Cheng XB, Ruan J, Yan J, Cheng J. 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 2021; 22:415. [PMID: 34090335 PMCID: PMC8178921 DOI: 10.1186/s12864-021-07652-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 12/11/2022] Open
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. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07652-9.
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Affiliation(s)
- Yu Fan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Hao Yang
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Dili Lai
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Ailing He
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Guoxing Xue
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Liang Feng
- Chengdu Food and Drug Inspection Institute, Chengdu, 610000, P.R. China
| | - Long Chen
- Department of Nursing, Sichuan Tianyi College, Mianzhu, 618200, P.R. China
| | - Xiao-Bin Cheng
- Department of Environmental and Life Sciences, Sichuan MinZu College, Kangding, 626001, P.R. China
| | - Jingjun Ruan
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China
| | - Jun Yan
- School of Pharmacy and Bioengineering, Chengdu University, Chengdu, 610106, P.R. China.
| | - Jianping Cheng
- College of Agriculture, Guizhou University, Huaxi District, Guiyang City, 550025, Guizhou Province, P.R. China.
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21
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Wang Y, Liu A. Genomic Characterization and Expression Analysis of Basic Helix-Loop-Helix (bHLH) Family Genes in Traditional Chinese Herb Dendrobium officinale. PLANTS (BASEL, SWITZERLAND) 2020; 9:plants9081044. [PMID: 32824436 PMCID: PMC7463459 DOI: 10.3390/plants9081044] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Revised: 08/12/2020] [Accepted: 08/13/2020] [Indexed: 05/26/2023]
Abstract
Dendrobium officinale Kimura et Migo is of great importance as a traditional Chinese herb due to its abundant metabolites. The family of basic helix-loop-helix (bHLH) transcription factors widely exists in plants and plays an essential role in plant growth and development, secondary metabolism as well as responses to environmental changes. However, there is limited information on bHLH genes in D. officinale. In the present study, a total of 98 putative DobHLH genes were identified at the genomic level, which could be classified into 18 clades. Gene structures and conserved motifs in DobHLH genes showed high conservation during their evolution. The conserved amino acids and DNA bindings of DobHLH proteins were predicted, both of which are pivotal for their function. Furthermore, gene expression from eight tissues showed that some DobHLH genes were ubiquitously expressed while other DobHLH genes were expressed in the specific tissues. Expressional changes of DobHLH genes under MeJA and ABA treatments were detected by qRT-PCR. The protein-protein interactions between DobHLHs were predicted and several interactions were confirmed by yeast two hybrid. Therefore, our results here contribute to the understanding of bHLH genes in D. officinale and lay a foundation for the further functional study of its biological processes.
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Affiliation(s)
- Yue Wang
- Key Laboratory of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan, China;
- Bio-Innovation Center of DR PLANT, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201 Yunnan, China
| | - Aizhong Liu
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming, 650224 Yunnan, China
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Liu M, Wang J, Wang L, Liu P, Zhao J, Zhao Z, Yao S, Stănică F, Liu Z, Wang L, Ao C, Dai L, Li X, Zhao X, Jia C. The historical and current research progress on jujube-a superfruit for the future. HORTICULTURE RESEARCH 2020; 7:119. [PMID: 32821402 PMCID: PMC7395136 DOI: 10.1038/s41438-020-00346-5] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Revised: 05/12/2020] [Accepted: 05/22/2020] [Indexed: 05/02/2023]
Abstract
Jujube (Ziziphus jujuba Mill.), or Chinese date, is the most important species of Rhamnaceae, a large cosmopolitan family, and is one of the oldest cultivated fruit trees in the world. It originates from the middle and lower reaches of the Yellow River, the 'mother river' of the Chinese people. It is distributed in at least 48 countries on all continents except Antarctica and is becoming increasingly important, especially in arid and semiarid marginal lands. Based on a systematic analysis of the unique characteristics of jujube, we suggest that it deserves to be recognized as a superfruit. We summarized historical research achievements from the past 3000 years and reviewed recent research advances since 1949 in seven fields, including genome sequencing and application, germplasm resources and systematic taxonomy, breeding and genetics, cultivation theory and techniques, pest control, postharvest physiology and techniques, and nutrition and processing. Based on the challenges facing the jujube industry, we discuss eight research aspects to be focused on in the future.
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Affiliation(s)
- Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071001 Hebei China
- College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
- Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing, 100000 China
| | - Jiurui Wang
- College of Forestry, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Lili Wang
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Ping Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Zhihui Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Shengrui Yao
- Department of Plant and Environmental Sciences, Sustainable Agriculture Science Center at Alcalde, New Mexico State University, 371 County Road 40, Alcalde, NM 87511 USA
| | - Florin Stănică
- Faculty of Horticulture, University of Agronomic Sciences and Veterinary Medicine of Bucharest, 011464 Bucharest, Romania
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Lixin Wang
- College of Horticulture, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Changwei Ao
- College of Food Science and Technology, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Li Dai
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Xiansong Li
- National Engineering Research Center for Agriculture in Northern Mountainous Areas, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Xuan Zhao
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, 071001 Hebei China
| | - Chunxiang Jia
- Propaganda Department, Hebei Agricultural University, Baoding, 071001 Hebei China
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Zhang Y, Gao W, Li H, Wang Y, Li D, Xue C, Liu Z, Liu M, Zhao J. Genome-wide analysis of the bZIP gene family in Chinese jujube (Ziziphus jujuba Mill.). BMC Genomics 2020; 21:483. [PMID: 32664853 PMCID: PMC7362662 DOI: 10.1186/s12864-020-06890-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Accepted: 07/07/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Among several TF families unique to eukaryotes, the basic leucine zipper (bZIP) family is one of the most important. Chinese jujube (Ziziphus jujuba Mill.) is a popular fruit tree species in Asia, and its fruits are rich in sugar, vitamin C and so on. Analysis of the bZIP gene family of jujube has not yet been reported. In this study, ZjbZIPs were identified firstly, their expression patterns were further studied in different tissues and in response to various abiotic and phytoplasma stresses, and their protein-protein interactions were also analyzed. RESULTS At the whole genome level, 45 ZjbZIPs were identified and classified into 14 classes. The members of each class of bZIP subfamily contain a specific conserved domain in addition to the core bZIP conserved domain, which may be related to its biological function. Relative Synonymous Codon Usage (RSCU) analysis displayed low values of NTA and NCG codons in ZjbZIPs, which would be beneficial to increase the protein production and also indicated that ZjbZIPs were at a relative high methylation level. The paralogous and orthologous events occurred during the evolutionary process of ZjbZIPs. Thirty-four ZjbZIPs were mapped to but not evenly distributed among 10 pseudo- chromosomes. 30 of ZjbZIP genes showed diverse tissue-specific expression in jujube and wild jujube trees, indicating that these genes may have multiple functions. Some ZjbZIP genes were specifically analyzed and found to play important roles in the early stage of fruit development. Moreover, some ZjbZIPs that respond to phytoplasma invasion and abiotic stress environmental conditions, such as salt and low temperature, were found. Based on homology comparisons, prediction analysis and yeast two-hybrid, a protein interaction network including 42 ZjbZIPs was constructed. CONCLUSIONS The bioinformatics analyses of 45 ZjbZIPs were implemented systematically, and their expression profiles in jujube and wild jujube showed that many genes might play crucial roles during fruit ripening and in the response to phytoplasma and abiotic stresses. The protein interaction networks among ZjbZIPs could provide useful information for further functional studies.
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Affiliation(s)
- Yao Zhang
- College of Life Science, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Weilin Gao
- College of Life Science, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Hongtai Li
- College of Life Science, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Yongkang Wang
- Pomology Institute, Shanxi Academy of Agricultural Sciences, Taigu, China
| | - Dengke Li
- Pomology Institute, Shanxi Academy of Agricultural Sciences, Taigu, China
| | - Chaoling Xue
- College of Life Science, Hebei Agricultural University, Baoding, China.,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China
| | - Zhiguo Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Mengjun Liu
- Research Center of Chinese Jujube, Hebei Agricultural University, Baoding, China
| | - Jin Zhao
- College of Life Science, Hebei Agricultural University, Baoding, China. .,Hebei Key Laboratory of Plant Physiology and Molecular Pathology, Hebei Agricultural University, Baoding, China.
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24
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Wang Z, Jia C, Wang JY, Miao HX, Liu JH, Chen C, Yang HX, Xu B, Jin Z. Genome-Wide Analysis of Basic Helix-Loop-Helix Transcription Factors to Elucidate Candidate Genes Related to Fruit Ripening and Stress in Banana ( Musa acuminata L. AAA Group, cv. Cavendish). FRONTIERS IN PLANT SCIENCE 2020; 11:650. [PMID: 32536932 PMCID: PMC7267074 DOI: 10.3389/fpls.2020.00650] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 04/27/2020] [Indexed: 05/25/2023]
Abstract
The basic helix-loop-helix (bHLH) proteins are a superfamily of transcription factors (TFs) that can bind to specific DNA target sites, playing a central role in a wide range of metabolic, physiological, and developmental processes in higher organisms. However, no systemic analysis of bHLH TFs has been reported in banana, a typical climacteric fruit in tropical and subtropical regions. In our study, 259 MabHLH TF genes were identified in the genome of Musa acuminata (A genome), and phylogenetic analysis indicated that these MabHLHs could be classified into 23 subfamilies with the bHLHs from rice and Arabidopsis. The amino acid sequences of the bHLH domain in all MabHLH protein sequences were quite conserved, especially Arg-12, Arg-13, Leu-23, and Leu-79. Distribution mapping results showed that 258 MabHLHs were localized on the 11 chromosomes in the M. acuminata genome. The results indicated that 40.7% of gene duplication events were located in collinear fragments, and segmental duplications might have played a key role in the expansion of MabHLHs. Moreover, the expression profiles of MabHLHs in different fruit development and ripening stages and under various abiotic and biotic stresses were investigated using available RNA-sequencing data to obtain fruit development, ripening-specific, and stress-responsive candidate genes. Finally, a co-expression network of MabHLHs was constructed by weighted gene co-expression network analysis to elucidate the MabHLHs that might participate in important metabolic biosynthesis pathways in banana during development and the response to stress. A total of 259 MabHLHs were identified, and their sequence features, conserved domains, phylogenetic relationships, chromosomal distributions, gene duplications, expression profiles, and co-expression networks were investigated. This study systematically identified the MabHLHs in the M. acuminata genome at the genome-wide level, providing important candidate genes for further functional analysis. These findings improve our understanding of the molecular basis of developmental and stress tolerance in an important banana cultivar.
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Affiliation(s)
- Zhuo Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Caihong Jia
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Jing-Yi Wang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Hong-Xia Miao
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Ju-Hua Liu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Cui Chen
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Hui-Xiao Yang
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Biyu Xu
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
| | - Zhiqiang Jin
- Key Laboratory of Tropical Crop Biotechnology, Ministry of Agriculture and Rural Affairs, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
- Hainan Academy of Tropical Agricultural Resource, Chinese Academy of Tropical Agricultural Sciences, Hainan, China
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