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Song W, Zhang S, Li Q, Xiang G, Zhao Y, Wei F, Zhang G, Yang S, Hao B. Genome-wide profiling of WRKY genes involved in flavonoid biosynthesis in Erigeron breviscapus. FRONTIERS IN PLANT SCIENCE 2024; 15:1412574. [PMID: 38895611 PMCID: PMC11184973 DOI: 10.3389/fpls.2024.1412574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 05/20/2024] [Indexed: 06/21/2024]
Abstract
The transcription factors of WRKY genes play essential roles in plant growth, stress responses, and metabolite biosynthesis. Erigeron breviscapus, a traditional Chinese herb, is abundant in flavonoids and has been used for centuries to treat cardiovascular and cerebrovascular diseases. However, the WRKY transcription factors that regulate flavonoid biosynthesis in E. breviscapus remain unknown. In this study, a total of 75 EbWRKY transcription factors were predicted through comprehensive genome-wide characterization of E. breviscapus and the chromosomal localization of each EbWRKY gene was investigated. RNA sequencing revealed transient responses of 74 predicted EbWRKY genes to exogenous abscisic acid (ABA), salicylic acid (SA), and gibberellin 3 (GA3) after 4 h of treatment. In contrast, the expression of key structural genes involved in flavonoid biosynthesis increased after 4 h in GA3 treatment. However, the content of flavonoid metabolites in leaves significantly increased at 12 h. The qRT-PCR results showed that the expression patterns of EbWRKY11, EbWRKY30, EbWRKY31, EbWRKY36, and EbWRKY44 transcription factors exhibited a high degree of similarity to the 11 structural genes involved in flavonoid biosynthesis. Protein-DNA interactions were performed between the key genes involved in scutellarin biosynthesis and candidate WRKYs. The result showed that F7GAT interacts with EbWRKY11, EbWRKY36, and EbWRKY44, while EbF6H has a self-activation function. This study provides comprehensive information on the regulatory control network of flavonoid accumulation mechanisms, offering valuable insights for breeding E. breviscapus varieties with enhanced scutellarin content.
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Affiliation(s)
- Wanling Song
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Shuangyan Zhang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Qi Li
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Guisheng Xiang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Yan Zhao
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Fan Wei
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Guanghui Zhang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Shengchao Yang
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
| | - Bing Hao
- The Key Laboratory of Medicinal Plant Biology of Yunnan Province, National & Local Joint Engineering Research Center on Germplasms Innovation & Utilization of Chinese Medicinal Materials in Southwest China, Yunnan Agricultural University, Kunming, China
- Yunnan Characteristic Plant Extraction Laboratory, Kunming, Yunnan, China
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Zhang J, Sun L, Wang Y, Li B, Li X, Ye Z, Zhang J. A Calcium-Dependent Protein Kinase Regulates the Defense Response in Citrus sinensis. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2024; 37:459-466. [PMID: 38597923 DOI: 10.1094/mpmi-12-23-0208-r] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Citrus Huanglongbing (HLB), which is caused by 'Candidatus Liberibacter asiaticus' (CLas), is one of the most destructive citrus diseases worldwide, and defense-related Citrus sinensis gene resources remain largely unexplored. Calcium signaling plays an important role in diverse biological processes. In plants, a few calcium-dependent protein kinases (CDPKs/CPKs) have been shown to contribute to defense against pathogenic microbes. The genome of C. sinensis encodes dozens of CPKs. In this study, the role of C. sinensis calcium-dependent protein kinases (CsCPKs) in C. sinensis defense was investigated. Silencing of CsCPK6 compromised the induction of defense-related genes in C. sinensis. Expression of a constitutively active form of CsCPK6 (CsCPK6CA) triggered the activation of defense-related genes in C. sinensis. Complementation of CsCPK6 rescued the defense-related gene induction in an Arabidopsis thaliana cpk4/11 mutant, indicating that CsCPK6 carries CPK activity and is capable of functioning as a CPK in Arabidopsis. Moreover, an effector derived from CLas inhibits defense induced by the expression of CsCPK6CA and autophosphorylation of CsCPK6, which suggests the involvement of CsCPK6 and calcium signaling in defense. These results support a positive role for CsCPK6 in C. sinensis defense against CLas, and the autoinhibitory regulation of CsCPK6 provides a potential genome-editing target for improving C. sinensis defense. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Jinghan Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- School of Life Sciences, Hebei University, Baoding, Hebei 071002, China
| | - Lifan Sun
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Yu Wang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Baiyang Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Xiangguo Li
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- College of Agronomy, Shanxi Agricultural University, Taigu 030801, China
| | - Ziqin Ye
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jie Zhang
- State Key Laboratory of Plant Genomics, Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
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Li Q, Xian B, Yu Q, Jia R, Zhang C, Zhong X, Zhang M, Fu Y, Liu Y, He H, Li M, Chen S, He Y. The CsAP2-09-CsWRKY25-CsRBOH2 cascade confers resistance against citrus bacterial canker by regulating ROS homeostasis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:534-548. [PMID: 38230828 DOI: 10.1111/tpj.16623] [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: 09/06/2023] [Revised: 12/04/2023] [Accepted: 12/18/2023] [Indexed: 01/18/2024]
Abstract
Citrus bacterial canker (CBC) is a serious bacterial disease caused by Xanthomonas citri subsp. citri (Xcc) that adversely impacts the global citrus industry. In a previous study, we demonstrated that overexpression of an Xcc-inducible apetala 2/ethylene response factor encoded by Citrus sinensis, CsAP2-09, enhances CBC resistance. The mechanism responsible for this effect, however, is not known. In the present study, we showed that CsAP2-09 targeted the promoter of the Xcc-inducible WRKY transcription factor coding gene CsWRKY25 directly, activating its transcription. CsWRKY25 was found to localize to the nucleus and to activate transcriptional activity. Plants overexpressing CsWRKY25 were more resistant to CBC and showed higher expression of the respiratory burst oxidase homolog (RBOH) CsRBOH2, in addition to exhibiting increased RBOH activity. Transient overexpression assays in citrus confirmed that CsWRKY25 and CsRBOH2 participated in the generation of reactive oxygen species (ROS) bursts, which were able to restore the ROS degradation caused by CsAP2-09 knockdown. Moreover, CsWRKY25 was found to bind directly to W-box elements within the CsRBOH2 promoter. Notably, CsRBOH2 knockdown had been reported previously to reduce the CBC resistance, while demonstrated in this study, CsRBOH2 transient overexpression can enhance the CBC resistance. Overall, our results outline a pathway through which CsAP2-09-CsWRKY25 transcriptionally reprograms CsRBOH2-mediated ROS homeostasis in a manner conducive to CBC resistance. These data offer new insight into the mechanisms and regulatory pathways through which CsAP2-09 regulates CBC resistance, highlighting its potential utility as a target for the breeding of CBC-resistant citrus varieties.
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Affiliation(s)
- Qiang Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
| | - Baohang Xian
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Qiyuan Yu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Ruirui Jia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
| | - Chenxi Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Xin Zhong
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Miao Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Yongyao Fu
- School of Advanced Agriculture and Bioengineering, Yangtze Normal University, Chongqing, 408100, China
| | - Yiqi Liu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Houzheng He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Man Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
| | - Shanchun Chen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
| | - Yongrui He
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Citrus Research Institute, Southwest University, Chongqing, 400712, China
- National Citrus Engineering Research Center, Chongqing, 400712, China
- National Citrus Improvement Center, Southwest University, Chongqing, 400712, China
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Yin Y, Fu H, Mi F, Yang Y, Wang Y, Li Z, He Y, Yue Z. Genomic characterization of WRKY transcription factors related to secoiridoid biosynthesis in Gentiana macrophylla. BMC PLANT BIOLOGY 2024; 24:66. [PMID: 38262919 PMCID: PMC10804491 DOI: 10.1186/s12870-024-04727-z] [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: 09/02/2023] [Accepted: 01/03/2024] [Indexed: 01/25/2024]
Abstract
Gentiana macrophylla is one of Chinese herbal medicines in which 4 kinds of iridoids or secoiridoids, such as loganic acid, sweroside, swertiamarin, and gentiopicroside, are identified as the dominant medicinal secondary metabolites. WRKY, as a large family of transcription factors (TFs), plays an important role in the synthesis of secondary metabolites in plants. Therefore, WRKY genes involved in the biosynthesis of secoiridoids in G. macrophylla were systematically studied. First, a comprehensive genome-wide analysis was performed, and 42 GmWRKY genes were identified, which were unevenly distributed in 12 chromosomes. Accordingly, gene structure, collinearity, sequence alignment, phylogenetic, conserved motif and promoter analyses were performed, and the GmWRKY proteins were divided into three subfamilies based on phylogenetic and multiple sequence alignment analyses. Moreover, the enzyme-encoding genes of the secoiridoid biosynthesis pathway and their promoters were then analysed, and the contents of the four secoiridoids were determined in different tissues. Accordingly, correlation analysis was performed using Pearson's correlation coefficient to construct WRKY gene-enzyme-encoding genes and WRKY gene-metabolite networks. Meanwhile, G. macrophylla seedlings were treated with methyl jasmonate (MeJA) to detect the dynamic change trend of GmWRKYs, biosynthetic genes, and medicinal ingredient accumulation. Thus, a total of 12 GmWRKYs were identified to be involved in the biosynthesis of secoiridoids, of which 8 (GmWRKY1, 6, 12, 17, 33, 34, 38 and 39) were found to regulate the synthesis of gentiopicroside, and 4 (GmWRKY7, 14, 26 and 41) were found to regulate the synthesis of loganic acid. Taken together, this study systematically identified WRKY transcription factors related to the biosynthesis of secoiridoids in G. macrophylla, which could be used as a cue for further investigation of WRKY gene functions in secondary metabolite accumulation.
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Affiliation(s)
- Yangyang Yin
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Coconstruction Collaborative Innovation Center for Chinese Medicinal Resources Industrialization By Shaanxi & Education Ministry, Shaanxi Innovative Drug Research Center, School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, People's Republic of China
| | - Huanhuan Fu
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Coconstruction Collaborative Innovation Center for Chinese Medicinal Resources Industrialization By Shaanxi & Education Ministry, Shaanxi Innovative Drug Research Center, School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, People's Republic of China
| | - Fakai Mi
- College of Life Science, Qinghai Normal University, Xining, 810016, People's Republic of China
| | - Ye Yang
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Coconstruction Collaborative Innovation Center for Chinese Medicinal Resources Industrialization By Shaanxi & Education Ministry, Shaanxi Innovative Drug Research Center, School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, People's Republic of China
| | - Yaomin Wang
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Coconstruction Collaborative Innovation Center for Chinese Medicinal Resources Industrialization By Shaanxi & Education Ministry, Shaanxi Innovative Drug Research Center, School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, People's Republic of China
| | - Zhe Li
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Coconstruction Collaborative Innovation Center for Chinese Medicinal Resources Industrialization By Shaanxi & Education Ministry, Shaanxi Innovative Drug Research Center, School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, People's Republic of China
| | - Yihan He
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Coconstruction Collaborative Innovation Center for Chinese Medicinal Resources Industrialization By Shaanxi & Education Ministry, Shaanxi Innovative Drug Research Center, School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, People's Republic of China.
| | - Zhenggang Yue
- State Key Laboratory of Research & Development of Characteristic Qin Medicine Resources (Cultivation), Coconstruction Collaborative Innovation Center for Chinese Medicinal Resources Industrialization By Shaanxi & Education Ministry, Shaanxi Innovative Drug Research Center, School of Pharmacy, Shaanxi University of Chinese Medicine, Xianyang, 712046, People's Republic of China.
- College of Life Science, Qinghai Normal University, Xining, 810016, People's Republic of China.
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Zhang M, Lu W, Yang X, Li Q, Lin X, Liu K, Yin C, Xiong B, Liao L, Sun G, He S, He J, Wang X, Wang Z. Comprehensive analyses of the citrus WRKY gene family involved in the metabolism of fruit sugars and organic acids. FRONTIERS IN PLANT SCIENCE 2023; 14:1264283. [PMID: 37780491 PMCID: PMC10540311 DOI: 10.3389/fpls.2023.1264283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 08/24/2023] [Indexed: 10/03/2023]
Abstract
Sugars and organic acids are the main factors determining the flavor of citrus fruit. The WRKY transcription factor family plays a vital role in plant growth and development. However, there are still few studies about the regulation of citrus WRKY transcription factors (CsWRKYs) on sugars and organic acids in citrus fruit. In this work, a genome-wide analysis of CsWRKYs was carried out in the citrus genome, and a total of 81 CsWRKYs were identified, which contained conserved WRKY motifs. Cis-regulatory element analysis revealed that most of the CsWRKY promoters contained several kinds of hormone-responsive and abiotic-responsive cis-elements. Furthermore, gene expression analysis and fruit quality determination showed that multiple CsWRKYs were closely linked to fruit sugars and organic acids with the development of citrus fruit. Notably, transcriptome co-expression network analysis further indicated that three CsWRKYs, namely, CsWRKY3, CsWRKY47, and CsWRKY46, co-expressed with multiple genes involved in various pathways, such as Pyruvate metabolism and Citrate cycle. These CsWRKYs may participate in the metabolism of fruit sugars and organic acids by regulating carbohydrate metabolism genes in citrus fruit. These findings provide comprehensive knowledge of the CsWRKY family on the regulation of fruit quality.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Xun Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zhihui Wang
- College of Horticulture, Sichuan Agricultural University, Chengdu, Sichuan, China
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Dai WS, Peng T, Wang M, Liu JH. Genome-wide identification and comparative expression profiling of the WRKY transcription factor family in two Citrus species with different Candidatus Liberibacter asiaticus susceptibility. BMC PLANT BIOLOGY 2023; 23:159. [PMID: 36959536 PMCID: PMC10037894 DOI: 10.1186/s12870-023-04156-4] [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: 09/17/2022] [Accepted: 03/06/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Salicylic Acid (SA) is a pivotal phytohormone in plant innate immunity enhancement of triggered by various pathogens, such as Candidatus Liberibacter asiaticus (CLas), the causal agent of Huanglongbing (HLB). WRKY is a plant specific transcription factor (TF) family, which plays crucial roles in plant response to biotic stresses. So far, the evolutionary history, functions, and expression patterns under SA treatment and CLas infection of WRKY family are poorly understood in Citrus, despite the release of the genome of several Citrus species. A comprehensive genomic and expressional analysis is worth to conduct for this family. RESULTS Here, a genome-wide identification of WRKY TFs was performed in two Citrus species: Citrus sinensis (HLB-sensitive) and Poncirus trifoliata (HLB-tolerant). In total, 52 CsWRKYs and 51 PtrWRKYs were identified, whose physical and chemical properties, chromosome locations, phylogenetic relationships and structural characteristics were comparatively analyzed. Especially, expression patterns of these WRKY genes before and after SA treatment and CLas infection were compared. Based on this result, seven pairs of orthologous WRKY genes showing opposite expression patterns in two Citrus species were screened out. Moreover, two pairs of orthologous WRKY genes with significant differences in the number or type of stress-responsive cis-elements in the promoter regions were discovered. Subcellular localization and transcriptional activation activity assays revealed that these two pairs of orthologous genes are classic WRKY TFs localize in the nucleus and could function as transcriptional activators. CONCLUSION In this study, we systematically analyzed the genomic characterization of WRKY family in two Citrus species, together with the analyses of expression patterns under SA signaling and CLas infection. Our study laid a foundation for further study on the function of WRKY TFs in HLB response and SA signaling of Citrus.
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Affiliation(s)
- Wen-Shan Dai
- College of Life Sciences, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Ting Peng
- College of Life Sciences, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China
| | - Min Wang
- College of Life Sciences, National Navel Orange Engineering Research Center, Gannan Normal University, Ganzhou, Jiangxi, 341000, China.
| | - Ji-Hong Liu
- College of Horticulture and Forestry Sciences, National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, Hubei, 430070, China
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Xi D, Yin T, Han P, Yang X, Zhang M, Du C, Zhang H, Liu X. Genome-Wide Identification of Sweet Orange WRKY Transcription Factors and Analysis of Their Expression in Response to Infection by Penicillium digitatum. Curr Issues Mol Biol 2023; 45:1250-1271. [PMID: 36826027 PMCID: PMC9954951 DOI: 10.3390/cimb45020082] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2022] [Revised: 01/17/2023] [Accepted: 01/29/2023] [Indexed: 02/08/2023] Open
Abstract
WRKY transcription factors (TFs) play a vital role in plant stress signal transduction and regulate the expression of various stress resistance genes. Sweet orange (Citrus sinensis) accounts for a large proportion of the world's citrus industry, which has high economic value, while Penicillium digitatum is a prime pathogenic causing postharvest rot of oranges. There are few reports on how CsWRKY TFs play their regulatory roles after P. digitatum infects the fruit. In this study, we performed genome-wide identification, classification, phylogenetic and conserved domain analysis of CsWRKY TFs, visualized the structure and chromosomal localization of the encoded genes, explored the expression pattern of each CsWRKY gene under P. digitatum stress by transcriptome data, and made the functional prediction of the related genes. This study provided insight into the characteristics of 47 CsWRKY TFs, which were divided into three subfamilies and eight subgroups. TFs coding genes were unevenly distributed on nine chromosomes. The visualized results of the intron-exon structure and domain are closely related to phylogeny, and widely distributed cis-regulatory elements on each gene played a global regulatory role in gene expression. The expansion of the CSWRKY TFs family was probably facilitated by twenty-one pairs of duplicated genes, and the results of Ka/Ks calculations indicated that this gene family was primarily subjected to purifying selection during evolution. Our transcriptome data showed that 95.7% of WRKY genes were involved in the transcriptional regulation of sweet orange in response to P. digitatum infection. We obtained 15 differentially expressed genes and used the reported function of AtWRKY genes as references. They may be involved in defense against P. digitatum and other pathogens, closely related to the stress responses during plant growth and development. Two interesting genes, CsWRKY2 and CsWRKY14, were expressed more than 60 times and could be used as excellent candidate genes in sweet orange genetic improvement. This study offers a theoretical basis for the response of CSWRKY TFs to P. digitatum infection and provides a vital reference for molecular breeding.
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Affiliation(s)
- Dengxian Xi
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Tuo Yin
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Peichen Han
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Xiuyao Yang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
| | - Mengjie Zhang
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China
| | - Chaojin Du
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China
| | - Hanyao Zhang
- Key Laboratory for Forest Resources Conservation and Utilization in the Southwest Mountains of China, Ministry of Education, Southwest Forestry University, Kunming 650224, China
- Correspondence: (H.Z.); (X.L.)
| | - Xiaozhen Liu
- Key Laboratory of Biodiversity Conservation in Southwest China, National Forest and Grassland Administration, Southwest Forestry University, Kunming 650224, China
- Correspondence: (H.Z.); (X.L.)
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Khoso MA, Hussain A, Ritonga FN, Ali Q, Channa MM, Alshegaihi RM, Meng Q, Ali M, Zaman W, Brohi RD, Liu F, Manghwar H. WRKY transcription factors (TFs): Molecular switches to regulate drought, temperature, and salinity stresses in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1039329. [PMID: 36426143 PMCID: PMC9679293 DOI: 10.3389/fpls.2022.1039329] [Citation(s) in RCA: 45] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 10/19/2022] [Indexed: 06/01/2023]
Abstract
The WRKY transcription factor (TF) belongs to one of the major plant protein superfamilies. The WRKY TF gene family plays an important role in the regulation of transcriptional reprogramming associated with plant stress responses. Change in the expression patterns of WRKY genes or the modifications in their action; participate in the elaboration of numerous signaling pathways and regulatory networks. WRKY proteins contribute to plant growth, for example, gamete formation, seed germination, post-germination growth, stem elongation, root hair growth, leaf senescence, flowering time, and plant height. Moreover, they play a key role in many types of environmental signals, including drought, temperature, salinity, cold, and biotic stresses. This review summarizes the current progress made in unraveling the functions of numerous WRKY TFs under drought, salinity, temperature, and cold stresses as well as their role in plant growth and development.
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Affiliation(s)
- Muneer Ahmed Khoso
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
- Department of Life Science, Key Laboratory of Saline-alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin, China
| | - Amjad Hussain
- College of Plant Science and Technology, National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei, China
| | | | - Qurban Ali
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University, Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Education, Nanjing, China
| | | | - Rana M. Alshegaihi
- Department of Biology, College of Science, University of Jeddah, Jeddah, Saudi Arabia
| | - Qinglin Meng
- Department of Biology and Food Engineering, Bozhou University, Bozhou, China
| | - Musrat Ali
- Department of Plant Sciences, Faculty of Biological Sciences, Quaid-i-Azam University Islamabad Pakistan, Islamabad, Pakistan
| | - Wajid Zaman
- Department of Life Sciences, Yeungnam University, Gyeongsan, South Korea
| | - Rahim Dad Brohi
- Department of Animal Reproduction/Theriogenology, Faculty of Veterinary Science, Shaheed Benazir Bhutto University of Veterinary and Animal Sciences, Sakrand, Pakistan
| | - Fen Liu
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
| | - Hakim Manghwar
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, Jiangxi, China
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9
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Liu G, Zhang D, Zhao T, Yang H, Jiang J, Li J, Zhang H, Xu X. Genome-wide analysis of the WRKY gene family unveil evolutionary history and expression characteristics in tomato and its wild relatives. Front Genet 2022; 13:962975. [PMID: 36186453 PMCID: PMC9520452 DOI: 10.3389/fgene.2022.962975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
WRKY transcription factors (WRKYs) are one of the largest plant gene families in plants involved in various biotic and abiotic stress responses. Based on the conservation of WRKY proteins, we identified a total of 642 WRKYs in Amborella trichopoda (33), Vitis vinifera (64), Arabidopsis thaliana (48), Solanum lycopersicoides (88), S. pennellii (77), S. pimpinellifolium (80), S. lycopersicum var. cerasiforme (85), S. lycopersicum cv. Heinz1706 (85), and S. lycopersicum cv. M82 (82) genomes. Phylogenetic analysis clustered WRKYs from nine genomes above into two clusters (Cluster1 and Cluster2). Evolutionary analysis revealed that most of the WRKYs in tomato and its wild relatives were expanded after the whole genome triplication (WGT) event of Solanum ancestor. Effects of tandem duplication (TD) event for WRKYs revealed that several WRKYs have experienced TD event and drove the expansion of the WRKY gene family in tomato and its wild relatives. Comparative analysis of WRKYs derived from WGT and TD events indicated that the WGT event performed a stronger influence on the expansion of the WRKY gene family than the effects of the TD event. Transcriptome profiling of WRKYs in S. lycopersicum cv. Heinz1706 under the biotic stress condition relative to the control condition uncovered a number of up-regulated WRKYs in response to biotic stress. The diversified expression pattern among paralogs derived from TD and WGT implied the impact of gene duplication events on gene functional divergence and diversity in tomato. We hope that this project will supply novel knowledge for studying the evolutionary history and functional characteristics of WRKYs involved in biotic stress in tomato.
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Affiliation(s)
- Guan Liu
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Dongye Zhang
- College of Advanced Agriculture and Ecological Environment, Heilongjiang University, Harbin, China
| | - Tingting Zhao
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Huanhuan Yang
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Jingbin Jiang
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Jingfu Li
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - He Zhang
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
| | - Xiangyang Xu
- Laboratory of Genetic Breeding in Tomato, College of Horticulture and Landscape Architecture, Northeast Agricultural University, Harbin, China
- *Correspondence: Xiangyang Xu,
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Genome-Wide Identification and Transcriptional Expression Profiles of Transcription Factor WRKY in Common Walnut ( Juglans regia L.). Genes (Basel) 2021; 12:genes12091444. [PMID: 34573426 PMCID: PMC8466090 DOI: 10.3390/genes12091444] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 09/07/2021] [Accepted: 09/17/2021] [Indexed: 11/16/2022] Open
Abstract
The transcription factor WRKY is widely distributed in the plant kingdom, playing a significant role in plant growth, development and response to stresses. Walnut is an economically important temperate tree species valued for both its edible nuts and high-quality wood, and its response to various stresses is an important factor that determines the quality of its fruit. However, in walnut trees themselves, information about the WRKY gene family remains scarce. In this paper, we perform a comprehensive study of the WRKY gene family in walnut. In total, we identified 103 WRKY genes in the common walnut that are clustered into 4 groups and distributed on 14 chromosomes. The conserved domains all contained a WRKY domain, and motif 2 was observed in most WRKYs, suggesting a high degree of conservation and similar functions within each subfamily. However, gene structure was significantly differentiated between different subfamilies. Synteny analysis indicates that there were 56 gene pairs in J. regia and A. thaliana, 76 in J. regia and J. mandshurica, 75 in J. regia and J. microcarpa, 76 in J. regia and P. trichocarpa, and 33 in J. regia and Q. robur, indicating that the WRKY gene family may come from a common ancestor. GO and KEGG enrichment analysis showed that the WRKY gene family was involved in resistance traits and the plant-pathogen interaction pathway. In anthracnose-resistant F26 fruits (AR) and anthracnose-susceptible F423 fruits (AS), transcriptome and qPCR analysis results showed that JrWRKY83, JrWRKY73 and JrWRKY74 were expressed significantly more highly in resistant cultivars, indicating that these three genes may be important contributors to stress resistance in walnut trees. Furthermore, we investigate how these three genes potentially target miRNAs and interact with proteins. JrWRKY73 was target by the miR156 family, including 12 miRNAs; this miRNA family targets WRKY genes to enhance plant defense. JrWRKY73 also interacted with the resistance gene AtMPK6, showing that it may play a crucial role in walnut defense.
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11
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Wang J, Sheng J, Zhu J, Hu Z, Diao Y. Comparative transcriptome analysis and identification of candidate adaptive evolution genes of Miscanthus lutarioriparius and Miscanthus sacchariflorus. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1499-1512. [PMID: 34366592 PMCID: PMC8295449 DOI: 10.1007/s12298-021-01030-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Revised: 06/24/2021] [Accepted: 06/27/2021] [Indexed: 06/13/2023]
Abstract
UNLABELLED Miscanthus species are perennial C4 grasses that are considered promising energy crops because of their high biomass yields, excellent adaptability and low management costs. Miscanthus lutarioriparius and Miscanthus sacchariflorus are closely related subspecies that are distributed in different habitats. However, there are only a few reports on the mechanisms by which Miscanthus adapts to different environments. Here, comparative transcriptomic and morphological analyses were used to study the evolutionary adaptation of M. lutarioriparius and M. sacchariflorus to different habitats. In total, among 7586 identified orthologs, 2060 orthologs involved in phenylpropanoid biosynthesis and plant hormones were differentially expressed between the two species. Through an analysis of the Ka/Ks ratios of the orthologs, we estimated that the divergence time between the two species was approximately 4.37 Mya. In addition, 37 candidate positively selected orthologs (PSGs) that played important roles in the adaptation of these species to different habitats were identified. Then, the expression levels of 20 PSGs in response to flooding and drought stress were analyzed, and the analysis revealed significant changes in their expression levels. These results facilitate our understanding of the evolutionary adaptation to habitats and the speciation of M. lutarioriparius and M. sacchariflorus. We hypothesise that lignin synthesis genes are the main cause of the morphological differences between the two species. In summary, the plant nonspecific phospholipase C gene family and the receptor-like protein kinase gene family played important roles in the evolution of these two species. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01030-1.
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Affiliation(s)
- Jia Wang
- School of Medicine, Anhui University of Science and Technology, Huainan, 232001 People’s Republic of China
| | - Jiajing Sheng
- College of Life Sciences, Nantong University, Nantong, 226019 People’s Republic of China
| | - Jianyong Zhu
- College of Forestry and Life Sciences, Chongqing University of Arts and Sciences, Chongqing, 402160 People’s Republic of China
| | - Zhongli Hu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Hubei Lotus Engineering Center, Wuhan University, Wuhan, 430072 People’s Republic of China
| | - Ying Diao
- School of Life Science and Technology, Wuhan Polytechnic University, Wuhan, 430023 People’s Republic of China
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12
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Yin X, He T, Yi K, Zhao Y, Hu Y, Liu J, Zhang X, Meng L, Wang L, Liu H, Li Y, Cui G. Comprehensive evaluation of candidate reference genes for quantitative real-time PCR-based analysis in Caucasian clover. Sci Rep 2021; 11:3269. [PMID: 33558610 PMCID: PMC7870939 DOI: 10.1038/s41598-021-82633-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 01/19/2021] [Indexed: 11/08/2022] Open
Abstract
The forage species Caucasian clover (Trifolium ambiguum M. Bieb.), a groundcover plant, is resistant to both cold and drought. However, reference genes for qRT-PCR-based analysis of Caucasian clover are lacking. In this study, 12 reference genes were selected on the basis of transcriptomic data. These genes were used to determine the most stably expressed genes in various organs of Caucasian clover under cold, salt and drought stress for qRT-PCR-based analysis. Reference gene stability was analyzed by geNorm, NormFinder, BestKeeper, the ∆Ct method and RefFinder. Under salt stress, RCD1 and PPIL3 were the most stable reference genes in the leaves, and NLI1 and RCD1 were the most stable references genes in the roots. Under low-temperature stress, APA and EFTu-GTP were the most stable reference genes in the leaves, and the RCD1 and NLI2 genes were highly stable in the roots. Under 10% PEG-6000 stress, NLI1 and NLI2 were highly stable in the leaves, and RCD1 and PPIL3 were the most stable in the roots. Overall, RCD1 and NLI2 were the most stable reference genes in organs under normal conditions and across all samples. The most and least stable reference genes were validated by assessing their appropriateness for normalization via WRKY genes.
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Affiliation(s)
- Xiujie Yin
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Taotao He
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Kun Yi
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yihang Zhao
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yao Hu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Jiaxue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Xiaomeng Zhang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lingdong Meng
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Lina Wang
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Haoyue Liu
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Yonggang Li
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China
| | - Guowen Cui
- College of Animal Science and Technology, Northeast Agricultural University, No. 600 Changjiang Street, Xiangfang District, Harbin City, Heilongjiang, China.
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13
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Nehela Y, Killiny N. The unknown soldier in citrus plants: polyamines-based defensive mechanisms against biotic and abiotic stresses and their relationship with other stress-associated metabolites. PLANT SIGNALING & BEHAVIOR 2020; 15:1761080. [PMID: 32408848 PMCID: PMC8570725 DOI: 10.1080/15592324.2020.1761080] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 04/20/2020] [Accepted: 04/21/2020] [Indexed: 05/07/2023]
Abstract
Citrus plants are challenged by a broad diversity of abiotic and biotic stresses, which definitely alter their growth, development, and productivity. In order to survive the various stressful conditions, citrus plants relay on multi-layered adaptive strategies, among which is the accumulation of stress-associated metabolites that play vital and complex roles in citrus defensive responses. These metabolites included amino acids, organic acids, fatty acids, phytohormones, polyamines (PAs), and other secondary metabolites. However, the contribution of PAs pathways in citrus defense responses is poorly understood. In this review article, we will discuss the recent metabolic, genetic, and molecular evidence illustrating the potential roles of PAs in citrus defensive responses against biotic and abiotic stressors. We believe that PAs-based defensive role, against biotic and abiotic stress in citrus, is involving the interaction with other stress-associated metabolites, particularly phytohormones. The knowledge gained so far about PAs-based defensive responses in citrus underpins our need for further genetic manipulation of PAs biosynthetic genes to produce transgenic citrus plants with modulated PAs content that may enhance the tolerance of citrus plants against stressful conditions. In addition, it provides valuable information for the potential use of PAs or their synthetic analogs and their emergence as a promising approach to practical applications in citriculture to enhance stress tolerance in citrus plants.
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Affiliation(s)
- Yasser Nehela
- Citrus Research and Education Center and Department of Plant Pathology, IFAS, University of Florida, Lake Alfred, FL, USA
| | - Nabil Killiny
- Citrus Research and Education Center and Department of Plant Pathology, IFAS, University of Florida, Lake Alfred, FL, USA
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14
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Acid Soil Improvement Enhances Disease Tolerance in Citrus Infected by Candidatus Liberibacter asiaticus. Int J Mol Sci 2020; 21:ijms21103614. [PMID: 32443846 PMCID: PMC7279377 DOI: 10.3390/ijms21103614] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/13/2020] [Accepted: 05/15/2020] [Indexed: 11/20/2022] Open
Abstract
Huanglongbing (HLB) is a devastating citrus disease that has caused massive economic losses to the citrus industry worldwide. The disease is endemic in most citrus-producing areas of southern China, especially in the sweet orange orchards where soil acidification has intensified. In this work, we used lime as soil pH amendment to optimize soil pH and enhance the endurance capacity of citrus against Candidatus Liberibacter asiaticus (CLas). The results showed that regulation of soil acidity is effective to reduce the occurrence of new infections and mitigate disease severity in the presence of HLB disease. We also studied the associated molecular mechanism and found that acid soil improvement can (i) increase the root metabolic activity and up-regulate the expression of ion transporter-related genes in HLB-infected roots, (ii) alleviate the physiological disorders of sieve tube blockage of HLB-infected leaves, (iii) strengthen the citrus immune response by increasing the expression of genes involved in SAR and activating the salicylic acid signal pathway, (iv) up-regulate 55 proteins related to stress/defence response and secondary metabolism. This study contributes to a better understanding of the correlation between environment factors and HLB disease outbreaks and also suggests that acid soil improvement is of potential value for the management of HLB disease in southern China.
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15
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Zhang J, Yang E, He Q, Lin M, Zhou W, Pian R, Chen X. Genome-wide analysis of the WRKY gene family in drumstick ( Moringa oleifera Lam.). PeerJ 2019; 7:e7063. [PMID: 31218125 PMCID: PMC6563795 DOI: 10.7717/peerj.7063] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 05/02/2019] [Indexed: 11/30/2022] Open
Abstract
WRKY proteins belong to one of the largest families of transcription factors. They have important functions in plant growth and development, signal transduction and stress responses. However, little information is available regarding the WRKY family in drumstick (Moringa oleifera Lam.). In the present study, we identified 54 MoWRKY genes in this species using genomic data. On the basis of structural features of the proteins they encode, the MoWRKY genes were classified into three main groups, with the second group being further divided into five subgroups. Phylogenetic trees constructed from the sequences of WRKY domains and overall amino acid compositions derived from drumstick and Arabidopsis were similar; the results indicated that the WRKY domain was the main evolutionary unit of WRKY genes. Gene structure and conserved motif analysis showed that genes with similar structures and proteins with similar motif compositions were usually clustered in the same class. Selective pressure analysis indicated that although neutral evolution and positive selection have happened in several MoWRKY genes, most have evolved under strong purifying selection. Moreover, different subgroups had evolved at different rates. The levels of expression of MoWRKY genes in response to five different abiotic stresses (salt, heat, drought, H2O2, cold) were evaluated by reverse transcription polymerase chain reaction (RT-PCR) and quantitative RT-PCR (qRT-PCR), with the results indicating that these genes had different expression levels and that some may be involved in abiotic stress responses. Our results will provide a foundation for cloning genes with specific functions for use in further research and applications.
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Affiliation(s)
- Junjie Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Endian Yang
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Qian He
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Mengfei Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Wei Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Ruiqi Pian
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
| | - Xiaoyang Chen
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources (South China Agricultural University), Guangzhou, China
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, Guangzhou, China
- Guangdong Province Research Center of Woody Forage Engineering Technology, Guangzhou, China
- College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, China
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16
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Finatto T, Viana VE, Woyann LG, Busanello C, da Maia LC, de Oliveira AC. Can WRKY transcription factors help plants to overcome environmental challenges? Genet Mol Biol 2018; 41:533-544. [PMID: 30235398 PMCID: PMC6136380 DOI: 10.1590/1678-4685-gmb-2017-0232] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
WRKY transcription factors (TFs) are responsible for the regulation of genes responsive to many plant growth and developmental cues, as well as to biotic and abiotic stresses. The modulation of gene expression by WRKY proteins primarily occurs by DNA binding at specific cis-regulatory elements, the W-box elements, which are short sequences located in the promoter region of certain genes. In addition, their action can occur through interaction with other TFs and the cellular transcription machinery. The current genome sequences available reveal a relatively large number of WRKY genes, reaching hundreds of copies. Recently, functional genomics studies in model plants have enabled the identification of function and mechanism of action of several WRKY TFs in plants. This review addresses the more recent studies in plants regarding the function of WRKY TFs in both model and crop plants for coping with environmental challenges, including a wide variety of abiotic and biotic stresses.
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Affiliation(s)
- Taciane Finatto
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Vívian Ebeling Viana
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Leomar Guilherme Woyann
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Carlos Busanello
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Luciano Carlos da Maia
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
| | - Antonio Costa de Oliveira
- Centro de Genômica e Fitomelhoramento, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas, Pelotas, RS, Brazil
- Programa de Pós-Graduação em Biotecnologia, Centro de Desenvolvimento Tecnologico, Universidade Federal de Pelotas, Pelotas, RS, Brazil
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17
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Zhang M, Chen Y, Nie L, Jin X, Liao W, Zhao S, Fu C, Yu L. Transcriptome-wide identification and screening of WRKY factors involved in the regulation of taxol biosynthesis in Taxus chinensis. Sci Rep 2018; 8:5197. [PMID: 29581461 PMCID: PMC5980082 DOI: 10.1038/s41598-018-23558-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/13/2018] [Indexed: 11/12/2022] Open
Abstract
WRKY, a plant-specific transcription factor family, plays important roles in pathogen defense, abiotic cues, phytohormone signaling, and regulation of plant secondary metabolism. However, little is known about the roles, functions, and mechanisms of WRKY in taxane biosynthesis in Taxus spp. In this study, 61 transcripts were identified from Taxus chinensis transcriptome datasets by using hidden Markov model search. All of these transcripts encoded proteins containing WRKY domains, which were designated as TcWRKY1–61. After phylogenetic analysis of the WRKY domains of TcWRKYs and AtWRKYs, 16, 8, 10, 14, 5, 7, and 1 TcWRKYs were cladded into Group I, IIa–IIe, and III, respectively. Then, six representative TcWRKYs were selected to classify their effects on taxol biosynthesis. After MeJA (methyl jasmonate acid) and SA (salicylic acid) treatments, all of the six TcWRKYs were upregulated by MeJA treatment. TcWRKY44 (IId) and TcWRKY47 (IIa) were upregulated, whereas TcWRKY8 (IIc), TcWRKY20 (III), TcWRKY26 (I), TcWRKY41 (IIe), and TcWRKY52 (IIb) were downregulated by SA treatment. Overexpression experiments showed that the six selected TcWRKYs exerted different effects on taxol biosynthesis. In specific, TcWRKY8 and TcWRKY47 significantly improved the expression levels of taxol-biosynthesis-related genes. Transcriptome-wide identification of WRKY factors in Taxus not only enhances our understanding of plant WRKY factors but also identifies candidate regulators of taxol biosynthesis.
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Affiliation(s)
- Meng Zhang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Ying Chen
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Lin Nie
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Xiaofei Jin
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Weifang Liao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Shengying Zhao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Chunhua Fu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China. .,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China.
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.,Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
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Zhang M, Chen Y, Nie L, Jin X, Liao W, Zhao S, Fu C, Yu L. Transcriptome-wide identification and screening of WRKY factors involved in the regulation of taxol biosynthesis in Taxus chinensis. Sci Rep 2018; 8:5197. [PMID: 29581461 DOI: 10.1038/s41598-018-23558-23551] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2017] [Accepted: 03/13/2018] [Indexed: 05/26/2023] Open
Abstract
WRKY, a plant-specific transcription factor family, plays important roles in pathogen defense, abiotic cues, phytohormone signaling, and regulation of plant secondary metabolism. However, little is known about the roles, functions, and mechanisms of WRKY in taxane biosynthesis in Taxus spp. In this study, 61 transcripts were identified from Taxus chinensis transcriptome datasets by using hidden Markov model search. All of these transcripts encoded proteins containing WRKY domains, which were designated as TcWRKY1-61. After phylogenetic analysis of the WRKY domains of TcWRKYs and AtWRKYs, 16, 8, 10, 14, 5, 7, and 1 TcWRKYs were cladded into Group I, IIa-IIe, and III, respectively. Then, six representative TcWRKYs were selected to classify their effects on taxol biosynthesis. After MeJA (methyl jasmonate acid) and SA (salicylic acid) treatments, all of the six TcWRKYs were upregulated by MeJA treatment. TcWRKY44 (IId) and TcWRKY47 (IIa) were upregulated, whereas TcWRKY8 (IIc), TcWRKY20 (III), TcWRKY26 (I), TcWRKY41 (IIe), and TcWRKY52 (IIb) were downregulated by SA treatment. Overexpression experiments showed that the six selected TcWRKYs exerted different effects on taxol biosynthesis. In specific, TcWRKY8 and TcWRKY47 significantly improved the expression levels of taxol-biosynthesis-related genes. Transcriptome-wide identification of WRKY factors in Taxus not only enhances our understanding of plant WRKY factors but also identifies candidate regulators of taxol biosynthesis.
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Affiliation(s)
- Meng Zhang
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Ying Chen
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Lin Nie
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Xiaofei Jin
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Weifang Liao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Shengying Zhao
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Chunhua Fu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China.
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China.
| | - Longjiang Yu
- Institute of Resource Biology and Biotechnology, Department of Biotechnology, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, Hubei, P. R. China
- Key Laboratory of Molecular Biophysics Ministry of Education, College of Life Science and Technology, Huazhong University of Science and Technology, No.1037 Luoyu Road, Wuhan, 430074, P. R. China
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Genome-wide identification and characterization of the WRKY gene family in potato ( Solanum tuberosum ). BIOCHEM SYST ECOL 2017. [DOI: 10.1016/j.bse.2017.02.010] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Khodadadi E, Mehrabi AA, Najafi A, Rastad S, Masoudi-Nejad A. Systems biology study of transcriptional and post-transcriptional co-regulatory network sheds light on key regulators involved in important biological processes in Citrus sinensis. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2017; 23:331-342. [PMID: 28461722 PMCID: PMC5391350 DOI: 10.1007/s12298-017-0416-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 12/25/2016] [Accepted: 01/17/2017] [Indexed: 05/08/2023]
Abstract
Transcriptional and post-transcriptional regulators including transcription regulator, transcription factor and miRNA are the main endogenous molecular elements which control complex cellular mechanisms such as development, growth and response to biotic and abiotic stresses in a coordinated manner in plants. Utilizing the most recent information on such relationships in a plant species, obtained from high-throughput experimental technologies and advanced computational tools, we can reconstruct its co-regulatory network which consequently sheds light on key regulators involved in its important biological processes. In this article, combined systems biology approaches such as mining the literatures, various databases and network reconstruction, analysis, and visualization tools were employed to infer and visualize the coregulatory relationships between miRNAs and transcriptional regulators in Citrus sinensis. Using computationally and experimentally verified miRNA-target interactions and constructed co-expression networks on array-based data, 10 coregulatory networks and 10 corresponding subgraphs include FFL motifs were obtained for 10 distinct tissues/conditions. Then PPI subnetworks were extracted for transcripts/genes included in mentioned subgraphs in order to the functional analysis of extracted coregulatory circuits. These proposed coregulatory connections shed light on precisely identifying C. sinensis metabolic pathways key switches, which are demanded for ultimate goals such as genome editing.
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Affiliation(s)
- Ehsan Khodadadi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Ilam, Ilam, Iran
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Ashraf Mehrabi
- Department of Agronomy and Plant Breeding, Faculty of Agriculture, University of Ilam, Ilam, Iran
| | - Ali Najafi
- Department of Molecular Biology, Medical University of Baqiyatalah, Tehran, Iran
| | - Saber Rastad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Masoudi-Nejad
- Laboratory of Systems Biology and Bioinformatics (LBB), Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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