1
|
Goyal P, Devi R, Verma B, Hussain S, Arora P, Tabassum R, Gupta S. WRKY transcription factors: evolution, regulation, and functional diversity in plants. PROTOPLASMA 2023; 260:331-348. [PMID: 35829836 DOI: 10.1007/s00709-022-01794-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 07/04/2022] [Indexed: 06/15/2023]
Abstract
The recent advancements in sequencing technologies and informatic tools promoted a paradigm shift to decipher the hidden biological mysteries and transformed the biological issues into digital data to express both qualitative and quantitative forms. The transcriptomic approach, in particular, has added new dimensions to the versatile essence of plant genomics through the large and deep transcripts generated in the process. This has enabled the mining of super families from the sequenced plants, both model and non-model, understanding their ancestry, diversity, and evolution. The elucidation of the crystal structure of the WRKY proteins and recent advancement in computational prediction through homology modeling and molecular dynamic simulation has provided an insight into the DNA-protein complex formation, stability, and interaction, thereby giving a new dimension in understanding the WRKY regulation. The present review summarizes the functional aspects of the high volume of sequence data of WRKY transcription factors studied from different species, till date. The review focuses on the dynamics of structural classification and lineage in light of the recent information. Additionally, a comparative analysis approach was incorporated to understand the functions of the identified WRKY transcription factors subjected to abiotic (heat, cold, salinity, senescence, dark, wounding, UV, and carbon starvation) stresses as revealed through various sets of studies on different plant species. The review will be instrumental in understanding the events of evolution and the importance of WRKY TFs under the threat of climate change, considering the new scientific evidences to propose a fresh perspective.
Collapse
Affiliation(s)
- Pooja Goyal
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Registered from Guru Nanak Dev University, Amritsar, India
| | - Ritu Devi
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Bhawana Verma
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Shahnawaz Hussain
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Palak Arora
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
| | - Rubeena Tabassum
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India
- CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, 180001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Suphla Gupta
- Plant Science & Agrotechnology, CSIR-Indian Institute of Integrative Medicine, Canal Road, Jammu, Jammu & Kashmir, 180001, India.
- Faculty, Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
| |
Collapse
|
2
|
Astigueta FH, Baigorria AH, García MN, Delfosse VC, González SA, Pérez de la Torre MC, Moschen S, Lia VV, Heinz RA, Fernández P, Trupkin SA. Characterization and expression analysis of WRKY genes during leaf and corolla senescence of Petunia hybrida plants. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2022; 28:1765-1784. [PMID: 36387973 PMCID: PMC9636358 DOI: 10.1007/s12298-022-01243-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 10/14/2022] [Accepted: 10/17/2022] [Indexed: 06/16/2023]
Abstract
Several families of transcription factors (TFs) control the progression of senescence. Many key TFs belonging to the WRKY family have been described to play crucial roles in the regulation of leaf senescence, mainly in Arabidopsis thaliana. However, little is known about senescence-associated WRKY members in floricultural species. Delay of senescence in leaves and petals of Petunia hybrida, a worldwide ornamental crop are highly appreciated traits. In this work, starting from 28 differentially expressed WRKY genes of A. thaliana during the progression of leaf senescence, we identified the orthologous in P. hybrida and explored the expression profiles of 20 PhWRKY genes during the progression of natural (age-related) leaf and corolla senescence as well as in the corollas of flowers undergoing pollination-induced senescence. Simultaneous visualization showed consistent and similar expression profiles of PhWRKYs during natural leaf and corolla senescence, although weak expression changes were observed during pollination-induced senescence. Comparable expression trends between PhWRKYs and the corresponding genes of A. thaliana were observed during leaf senescence, although more divergence was found in petals of pollinated petunia flowers. Integration of expression data with phylogenetics, conserved motif and cis-regulatory element analyses were used to establish a list of candidates that could regulate more than one senescence process. Our results suggest that several members of the WRKY family of TFs are tightly linked to the regulation of senescence in P. hybrida. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-022-01243-y.
Collapse
Affiliation(s)
- Francisco H. Astigueta
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Amilcar H. Baigorria
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Martín N. García
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Verónica C. Delfosse
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
| | - Sergio A. González
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
| | - Mariana C. Pérez de la Torre
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Sebastián Moschen
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto Nacional de Tecnología Agropecuaria, Estación Experimental Agropecuaria Famaillá, 4142 Tucumán, Argentina
| | - Verónica V. Lia
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
- Facultad de Ciencias Exactas Y Naturales, Universidad de Buenos Aires, 1428 Buenos Aires, Argentina
| | - Ruth A. Heinz
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Paula Fernández
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Escuela de Ciencia Y Tecnología, Universidad Nacional de San Martín, 1650 San Martín, Buenos Aires Argentina
- Instituto de Agrobiotecnología y Biología Molecular (INTA-CONICET), Centro de Investigaciones en Ciencias Agronómicas Y Veterinarias, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| | - Santiago A. Trupkin
- Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Autónoma de
Buenos Aires, 1425 Buenos Aires, Argentina
- Instituto de Floricultura, Centro de Investigación de Recursos Naturales, Instituto Nacional de Tecnología Agropecuaria, 1686 Hurlingham, Buenos Aires Argentina
| |
Collapse
|
3
|
Fei J, Wang YS, Cheng H, Su YB, Zhong YJ, Zheng L. The Kandelia obovata transcription factor KoWRKY40 enhances cold tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2022; 22:274. [PMID: 35659253 PMCID: PMC9166612 DOI: 10.1186/s12870-022-03661-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 05/27/2022] [Indexed: 05/16/2023]
Abstract
BACKGROUND WRKY transcription factors play key roles in plant development processes and stress response. Kandelia obovata is the most cold-resistant species of mangrove plants, which are the important contributors to coastal marine environment. However, there is little known about the WRKY genes in K. obovata. RESULTS In this study, a WRKY transcription factor gene, named KoWRKY40, was identified from mangrove plant K. obovata. The full-length cDNA of KoWRKY40 gene was 1420 nucleotide bases, which encoded 318 amino acids. The KoWRKY40 protein contained a typical WRKY domain and a C2H2 zinc-finger motif, which were common signatures to group II of WRKY family. The three-dimensional (3D) model of KoWRKY40 was formed by one α-helix and five β-strands. Evolutionary analysis revealed that KoWRKY40 has the closest homology with a WRKY protein from another mangrove plant Bruguiera gymnorhiza. The KoWRKY40 protein was verified to be exclusively located in nucleus of tobacco epidermis cells. Gene expression analysis demonstrated that KoWRKY40 was induced highly in the roots and leaves, but lowly in stems in K. obovata under cold stress. Overexpression of KoWRKY40 in Arabidopsis significantly enhanced the fresh weight, root length, and lateral root number of the transgenic lines under cold stress. KoWRKY40 transgenic Arabidopsis exhibited higher proline content, SOD, POD, and CAT activities, and lower MDA content, and H2O2 content than wild-type Arabidopsis under cold stress condition. Cold stress affected the expression of genes related to proline biosynthesis, antioxidant system, and the ICE-CBF-COR signaling pathway, including AtP5CS1, AtPRODH1, AtMnSOD, AtPOD, AtCAT1, AtCBF1, AtCBF2, AtICE1, AtCOR47 in KoWRKY40 transgenic Arabidopsis plants. CONCLUSION These results demonstrated that KoWRKY40 conferred cold tolerance in transgenic Arabidopsis by regulating plant growth, osmotic balance, the antioxidant system, and ICE-CBF-COR signaling pathway. The study indicates that KoWRKY40 is an important regulator involved in the cold stress response in plants.
Collapse
Affiliation(s)
- Jiao Fei
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - You-Shao Wang
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Hao Cheng
- State Key Laboratory of Tropical Oceanography, South China Sea Institute of Oceanology, Chinese Academy of Sciences, Guangzhou, 510301 China
- Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou), Guangzhou, 511458 China
- Innovation Academy of South China Sea Ecology and Environmental Engineering, Chinese Academy of Sciences, Guangzhou, 510301 China
| | - Yu-Bin Su
- Department of Cell Biology & Institute of Biomedicine, National Engineering Research Center of Genetic Medicine, MOE Key Laboratory of Tumor Molecular Biology, Guangdong Provincial Key Laboratory of Bioengineering Medicine, College of Life Science and Technology, Jinan University, Guangzhou, 510632 China
| | - Yong-Jia Zhong
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Lei Zheng
- Root Biology Center, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| |
Collapse
|
4
|
Matos MKDS, Benko-Iseppon AM, Bezerra-Neto JP, Ferreira-Neto JRC, Wang Y, Liu H, Pandolfi V, Amorim LLB, Willadino L, do Vale Amorim TC, Kido EA, Vianello RP, Timko MP, Brasileiro-Vidal AC. The WRKY transcription factor family in cowpea: Genomic characterization and transcriptomic profiling under root dehydration. Gene X 2022; 823:146377. [PMID: 35231571 DOI: 10.1016/j.gene.2022.146377] [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: 09/09/2021] [Revised: 01/06/2022] [Accepted: 02/24/2022] [Indexed: 11/25/2022] Open
Abstract
Cowpea [Vigna unguiculata (L.) Walp.] is one of the most tolerant legume crops to drought and salt stresses. WRKY transcription factor (TF) family members stand out among plant transcriptional regulators related to abiotic stress tolerance. However, little information is currently available on the expression of the cowpea WRKY gene family (VuWRKY) in response to water deficit. Thus, we analyzed genomic and transcriptomic data from cowpea to identify VuWRKY members and characterize their structure and transcriptional response under root dehydration stress. Ninety-two complete VuWRKY genes were found in the cowpea genome based on their domain characteristics. They were clustered into three groups: I (15 members), II (58), and III (16), while three genes were unclassified. Domain analysis of the encoded proteins identified four major variants of the conserved heptapeptide motif WRKYGQK. In silico analysis of VuWRKY gene promoters identified eight candidate binding motifs of cis-regulatory elements, regulated mainly by six TF families associated with abiotic stress responses. Ninety-seven VuWRKY modulated splicing variants associated with 55 VuWRKY genes were identified via RNA-Seq analysis available at the Cowpea Genomics Consortium (CpGC) database. qPCR analyses showed that 22 genes are induced under root dehydration, with VuWRKY18, 21, and 75 exhibiting the most significant induction levels. Given their central role in activating signal transduction cascades in abiotic stress response, the data provide a foundation for the targeted modification of specific VuWRKY family members to improve drought tolerance in this important climate-resilient legume in the developing world and beyond.
Collapse
Affiliation(s)
- Mitalle Karen da Silva Matos
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Ana Maria Benko-Iseppon
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - João Pacifico Bezerra-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - José Ribamar Costa Ferreira-Neto
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Yu Wang
- Department of Biology, University of Virginia, Charlottesville, VA, USA; Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Hai Liu
- Department of Biology, University of Virginia, Charlottesville, VA, USA
| | - Valesca Pandolfi
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Lidiane Lindinalva Barbosa Amorim
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Lilia Willadino
- Laboratório de Cultura de Tecidos Vegetais, Departamento de Biologia, Universidade Federal Rural de Pernambuco, Recife, Brazil
| | - Thialisson Caaci do Vale Amorim
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Ederson Akio Kido
- Laboratório de Genética Molecular, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil
| | - Rosana Pereira Vianello
- Laboratório de Biotecnologia, Empresa Brasileira de Pesquisa Agropecuária, Centro Nacional de Pesquisa de Arroz e Feijão, Goiânia, Brazil
| | - Michael P Timko
- Department of Biology, University of Virginia, Charlottesville, VA, USA.
| | - Ana Christina Brasileiro-Vidal
- Laboratório de Genética e Biotecnologia Vegetal, Departamento de Genética, Centro de Biociências, Universidade Federal de Pernambuco, Recife, Brazil.
| |
Collapse
|
5
|
Wang C, Hao X, Wang Y, Maoz I, Zhou W, Zhou Z, Kai G. Identification of WRKY transcription factors involved in regulating the biosynthesis of the anti-cancer drug camptothecin in Ophiorrhiza pumila. HORTICULTURE RESEARCH 2022; 9:uhac099. [PMID: 35795387 PMCID: PMC9250654 DOI: 10.1093/hr/uhac099] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/15/2022] [Indexed: 05/13/2023]
Abstract
Camptothecin is a chemotherapeutic drug widely used to treat various cancers. Ophiorrhiza pumila is an ideal plant model for the study of camptothecin production, with various advantages for studying camptothecin biosynthesis and regulation. The DNA-binding WRKY transcription factors have a key regulatory role in secondary metabolite biosynthesis in plants. However, little is currently known about their involvement in camptothecin biosynthesis in O. pumila. We identified 46 OpWRKY genes unevenly distributed on the 11 chromosomes of O. pumila. Phylogenetic and multiple sequence alignment analyses divided the OpWRKY proteins into three subfamilies. Based on spatial expression and co-expression, we targeted the candidate gene OpWRKY6. Overexpression of OpWRKY6 significantly reduced the accumulation of camptothecin compared with the control. Conversely, camptothecin accumulation increased in OpWRKY6 knockout lines. Further biochemical assays showed that OpWRKY6 negatively regulates camptothecin biosynthesis from both the iridoid and shikimate pathways by directly downregulating the gene expression of OpGES, Op10HGO, Op7DLH, and OpTDC. Our data provide direct evidence for the involvement of WRKYs in the regulation of camptothecin biosynthesis and offer valuable information for enriching the production of camptothecin in plant systems.
Collapse
Affiliation(s)
| | - Xiaolong Hao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, The Third Affiliated Hospital, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Yao Wang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, The Third Affiliated Hospital, School of Pharmaceutical Sciences, Zhejiang Chinese Medical University, Hangzhou, Zhejiang, 310053, China
| | - Itay Maoz
- Department of Postharvest Science, ARO, The Volcani Center, HaMaccabim Rd 68, POB 15159, Rishon LeZion, 7528809, Israel
| | - Wei Zhou
- Corresponding authors. E-mail: , ,
| | | | | |
Collapse
|
6
|
Wang C, Hao X, Wang Y, Shi M, Zhou ZG, Kai G. Genome-Wide Identification and Comparative Analysis of the Teosinte Branched 1/Cycloidea/Proliferating Cell Factors 1/2 Transcription Factors Related to Anti-cancer Drug Camptothecin Biosynthesis in Ophiorrhiza pumila. FRONTIERS IN PLANT SCIENCE 2021; 12:746648. [PMID: 34691124 PMCID: PMC8529195 DOI: 10.3389/fpls.2021.746648] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 09/09/2021] [Indexed: 05/27/2023]
Abstract
Ophiorrhiza pumila (O. pumila; Op) is a medicinal herbaceous plant, which can accumulate camptothecin (CPT). CPT and its derivatives are widely used as chemotherapeutic drugs for treating malignant tumors. Its biosynthesis pathway has been attracted significant attention. Teosinte branched 1/cycloidea/proliferating cell factors 1/2 (TCP) transcription factors (TFs) regulate a variety of physiological processes, while TCP TFs are involved in the regulation of CPT biosynthesis remain unclear. In this study, a systematic analysis of the TCP TFs family in O. pumila was performed. A total of 16 O. pumila TCP (OpTCP) genes were identified and categorized into two subgroups based on their phylogenetic relationships with those in Arabidopsis thaliana. Tissue-specific expression patterns revealed that nine OpTCP genes showed the highest expression levels in leaves, while the other seven OpTCPs showed a higher expression level in the stems. Co-expression, phylogeny analysis, and dual-luciferase (Dual-LUC) assay revealed that OpTCP15 potentially plays important role in CPT and its precursor biosynthesis. In addition, the subcellular localization experiment of candidate OpTCP genes showed that they are all localized in the nucleus. Our study lays a foundation for further functional characterization of the candidate OpTCP genes involved in CPT biosynthesis regulation and provides new strategies for increasing CPT production.
Collapse
Affiliation(s)
- Can Wang
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, China
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Xiaolong Hao
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Yao Wang
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Min Shi
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| | - Zhi-Gang Zhou
- Key Laboratory of Exploration and Utilization of Aquatic Genetic Resources Conferred by Ministry of Education, Shanghai Ocean University, Shanghai, China
| | - Guoyin Kai
- Laboratory for Core Technology of TCM Quality Improvement and Transformation, School of Pharmaceutical Sciences, The Third Affiliated Hospital, Zhejiang Chinese Medical University, Hangzhou, China
| |
Collapse
|
7
|
Liu R, Song J, Liu S, Chen C, Zhang S, Wang J, Xiao Y, Cao B, Lei J, Zhu Z. Genome-wide identification of the Capsicum bHLH transcription factor family: discovery of a candidate regulator involved in the regulation of species-specific bioactive metabolites. BMC PLANT BIOLOGY 2021; 21:262. [PMID: 34098881 PMCID: PMC8183072 DOI: 10.1186/s12870-021-03004-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 05/04/2021] [Indexed: 05/26/2023]
Abstract
BACKGROUND The basic helix-loop-helix (bHLH) transcription factors (TFs) serve crucial roles in regulating plant growth and development and typically participate in biological processes by interacting with other TFs. Capsorubin and capsaicinoids are found only in Capsicum, which has high nutritional and economic value. However, whether bHLH family genes regulate capsorubin and capsaicinoid biosynthesis and participate in these processes by interacting with other TFs remains unknown. RESULTS In this study, a total of 107 CabHLHs were identified from the Capsicum annuum genome. Phylogenetic tree analysis revealed that these CabHLH proteins were classified into 15 groups by comparing the CabHLH proteins with Arabidopsis thaliana bHLH proteins. The analysis showed that the expression profiles of CabHLH009, CabHLH032, CabHLH048, CabHLH095 and CabHLH100 found in clusters C1, C2, and C3 were similar to the profile of carotenoid biosynthesis in pericarp, including zeaxanthin, lutein and capsorubin, whereas the expression profiles of CabHLH007, CabHLH009, CabHLH026, CabHLH063 and CabHLH086 found in clusters L5, L6 and L9 were consistent with the profile of capsaicinoid accumulation in the placenta. Moreover, CabHLH007, CabHLH009, CabHLH026 and CabHLH086 also might be involved in temperature-mediated capsaicinoid biosynthesis. Yeast two-hybrid (Y2H) assays demonstrated that CabHLH007, CabHLH009, CabHLH026, CabHLH063 and CabHLH086 could interact with MYB31, a master regulator of capsaicinoid biosynthesis. CONCLUSIONS The comprehensive and systematic analysis of CabHLH TFs provides useful information that contributes to further investigation of CabHLHs in carotenoid and capsaicinoid biosynthesis.
Collapse
Affiliation(s)
- Renjian Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
| | - Jiali Song
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
| | - Shaoqun Liu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642 China
| | - Changming Chen
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642 China
| | - Shuanglin Zhang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
| | - Juntao Wang
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
| | - Yanhui Xiao
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005 China
| | - Bihao Cao
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642 China
| | - Jianjun Lei
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642 China
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, 512005 China
| | - Zhangsheng Zhu
- Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (South China), College of Horticulture, Ministry of Agriculture and Rural Affairs, South China Agricultural University, Guangzhou, 510642 Guangdong China
- Lingnan Guangdong Laboratory of Modern Agriculture, Guangzhou, 510642 China
- Department of Biology, Peking University-Southern University of Science and Technology Joint Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| |
Collapse
|
8
|
Kan J, Gao G, He Q, Gao Q, Jiang C, Ahmar S, Liu J, Zhang J, Yang P. Genome-Wide Characterization of WRKY Transcription Factors Revealed Gene Duplication and Diversification in Populations of Wild to Domesticated Barley. Int J Mol Sci 2021; 22:5354. [PMID: 34069581 PMCID: PMC8160967 DOI: 10.3390/ijms22105354] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Revised: 05/16/2021] [Accepted: 05/17/2021] [Indexed: 12/19/2022] Open
Abstract
The WRKY transcription factors (WRKYs) are known for their crucial roles in biotic and abiotic stress responses, and developmental and physiological processes. In barley, early studies revealed their importance, whereas their diversity at the population scale remains hardly estimated. In this study, 98 HsWRKYs and 103 HvWRKYs have been identified from the reference genome of wild and cultivated barley, respectively. The tandem duplication and segmental duplication events from the cultivated barley were observed. By taking advantage of early released exome-captured sequencing datasets in 90 wild barley accessions and 137 landraces, the diversity analysis uncovered synonymous and non-synonymous variants instead of loss-of-function mutations that had occurred at all WRKYs. For majority of WRKYs, the haplotype and nucleotide diversity both decreased in cultivated barley relative to the wild population. Five WRKYs were detected to have undergone selection, among which haplotypes of WRKY9 were enriched, correlating with the geographic collection sites. Collectively, profiting from the state-of-the-art barley genomic resources, this work represented the characterization and diversity of barley WRKY transcription factors, shedding light on future deciphering of their roles in barley domestication and adaptation.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | - Ping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100081, China; (J.K.); (G.G.); (Q.H.); (Q.G.); (C.J.); (S.A.); (J.L.); (J.Z.)
| |
Collapse
|
9
|
Qu R, Cao Y, Tang X, Sun L, Wei L, Wang K. Identification and expression analysis of the WRKY gene family in Isatis indigotica. Gene 2021; 783:145561. [PMID: 33705810 DOI: 10.1016/j.gene.2021.145561] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 01/14/2021] [Accepted: 03/01/2021] [Indexed: 12/16/2022]
Abstract
The WRKY proteins, which represent one of the largest families of transcriptional regulators in plants, play pivotal roles in regulating multiple processes of growth and development, particularly in diverse stress responses. Isatis indigotica is widely used in Traditional Chinese Medicine and is famous for its use as a dye for the color indigo. However, reports of the WRKY gene family in I. indigotica are limited. In this study, 64 IiWRKY genes encoding proteins with the complete WRKY domain were identified from genome of I. indigotica. Based on their structure and phylogenetic relationships of this gene family in I. indigotica, the IiWRKY genes were classified into three groups: Group I (n = 13), Group II (n = 35) and Group III (n = 16). Sequence alignment revealed that IiWRKY proteins harbored two variants, WRKYRQK and WRKYGKK, of the highly conserved WRKYGQK motif. The number of exons in IiWRKY genes varied from two to 14, with most of IiWRKY genes containing three exons. Investigation of gene duplication demonstrated that 10 and 14 IiWRKY genes were incorporated in tandem and segmental duplication events, respectively. Finally, the expression profiles derived from transcriptome data and quantitative real-time PCR analysis showed distinct expression patterns of these IiWRKY gene in five different organs or in response to four abiotic stresses. Taken together, our results will contribute to functional analysis of IiWRKY genes, and also provide a basis for further clarification of the molecular mechanism of stress responses in this important herb.
Collapse
Affiliation(s)
- Renjun Qu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Yiwen Cao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Xiaoqing Tang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Liqiong Sun
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Lian Wei
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kangcai Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| |
Collapse
|
10
|
Baillo EH, Hanif MS, Guo Y, Zhang Z, Xu P, Algam SA. Genome-wide Identification of WRKY transcription factor family members in sorghum (Sorghum bicolor (L.) moench). PLoS One 2020; 15:e0236651. [PMID: 32804948 PMCID: PMC7430707 DOI: 10.1371/journal.pone.0236651] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 07/10/2020] [Indexed: 12/26/2022] Open
Abstract
WRKY transcription factors regulate diverse biological processes in plants, including abiotic and biotic stress responses, and constitute one of the largest transcription factor families in higher plants. Although the past decade has seen significant progress towards identifying and functionally characterizing WRKY genes in diverse species, little is known about the WRKY family in sorghum (Sorghum bicolor (L.) moench). Here we report the comprehensive identification of 94 putative WRKY transcription factors (SbWRKYs). The SbWRKYs were divided into three groups (I, II, and III), with those in group II further classified into five subgroups (IIa–IIe), based on their conserved domains and zinc finger motif types. WRKYs from the model plant Arabidopsis (Arabidopsis thaliana) were used for the phylogenetic analysis of all SbWRKY genes. Motif analysis showed that all SbWRKYs contained either one or two WRKY domains and that SbWRKYs within the same group had similar motif compositions. SbWRKY genes were located on all 10 sorghum chromosomes, and some gene clusters and two tandem duplications were detected. SbWRKY gene structure analysis showed that they contained 0–7 introns, with most SbWRKY genes consisting of two introns and three exons. Gene ontology (GO) annotation functionally categorized SbWRKYs under cellular components, molecular functions and biological processes. A cis-element analysis showed that all SbWRKYs contain at least one stress response-related cis-element. We exploited publicly available microarray datasets to analyze the expression profiles of 78 SbWRKY genes at different growth stages and in different tissues. The induction of SbWRKYs by different abiotic stresses hinted at their potential involvement in stress responses. qRT-PCR analysis revealed different expression patterns for SbWRKYs during drought stress. Functionally characterized WRKY genes in Arabidopsis and other species will provide clues for the functional characterization of putative orthologs in sorghum. Thus, the present study delivers a solid foundation for future functional studies of SbWRKY genes and their roles in the response to critical stresses such as drought.
Collapse
Affiliation(s)
- Elamin Hafiz Baillo
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- Agricultural Research Corporation (ARC), Ministry of Agriculture, Wad Madani, Gezira, Sudan
- * E-mail: ,
| | - Muhammad Sajid Hanif
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yinghui Guo
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhengbin Zhang
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
- * E-mail: ,
| | - Ping Xu
- Center for Agricultural Resources Research, Key Laboratory of Agricultural Water Resources, Hebei Laboratory of Agricultural Water Saving, Institute of Genetics and Developmental Biology, University of Chinese Academy of Sciences, Shijiazhuang, Hebei, China
- University of Chinese Academy of Sciences, Beijing, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, China
| | - Soad Ali Algam
- Faculty of Agriculture, University of Khartoum, Khartoum, Sudan
| |
Collapse
|
11
|
Tolosa LN, Zhang Z. The Role of Major Transcription Factors in Solanaceous Food Crops under Different Stress Conditions: Current and Future Perspectives. PLANTS 2020; 9:plants9010056. [PMID: 31906447 PMCID: PMC7020414 DOI: 10.3390/plants9010056] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/09/2019] [Accepted: 12/21/2019] [Indexed: 01/08/2023]
Abstract
Plant growth, development, and productivity are adversely affected by environmental stresses such as drought (osmotic stress), soil salinity, cold, oxidative stress, irradiation, and diverse diseases. These impacts are of increasing concern in light of climate change. Noticeably, plants have developed their adaptive mechanism to respond to environmental stresses by transcriptional activation of stress-responsive genes. Among the known transcription factors, DoF, WRKY, MYB, NAC, bZIP, ERF, ARF and HSF are those widely associated with abiotic and biotic stress response in plants. Genome-wide identification and characterization analyses of these transcription factors have been almost completed in major solanaceous food crops, emphasizing these transcription factor families which have much potential for the improvement of yield, stress tolerance, reducing marginal land and increase the water use efficiency of solanaceous crops in arid and semi-arid areas where plant demand more water. Most importantly, transcription factors are proteins that play a key role in improving crop yield under water-deficient areas and a place where the severity of pathogen is very high to withstand the ongoing climate change. Therefore, this review highlights the role of major transcription factors in solanaceous crops, current and future perspectives in improving the crop traits towards abiotic and biotic stress tolerance and beyond. We have tried to accentuate the importance of using genome editing molecular technologies like CRISPR/Cas9, Virus-induced gene silencing and some other methods to improve the plant potential in giving yield under unfavorable environmental conditions.
Collapse
Affiliation(s)
- Lemessa Negasa Tolosa
- Key Laboratory of Agricultural Water Resources, Hebie Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Shijiazhuang 050021, China;
- University of Chinese Academy Sciences, Beijing 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences CAS, Beijing 100101, China
| | - Zhengbin Zhang
- Key Laboratory of Agricultural Water Resources, Hebie Laboratory of Agricultural Water Saving, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Shijiazhuang 050021, China;
- University of Chinese Academy Sciences, Beijing 100049, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences CAS, Beijing 100101, China
- Correspondence:
| |
Collapse
|
12
|
Cheng Y, Ahammed GJ, Yao Z, Ye Q, Ruan M, Wang R, Li Z, Zhou G, Wan H. Comparative Genomic Analysis Reveals Extensive Genetic Variations of WRKYs in Solanaceae and Functional Variations of CaWRKYs in Pepper. Front Genet 2019; 10:492. [PMID: 31191610 PMCID: PMC6546733 DOI: 10.3389/fgene.2019.00492] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 05/06/2019] [Indexed: 01/15/2023] Open
Abstract
As a conserved protein family, WRKY has been shown to be involved in multiple biological processes in plants. However, the mechanism of functional diversity for WRKYs in pepper has not been well elucidated. Here, a total of 223 WRKY members from solanaceae crops including pepper, tomato and potato, were analyzed using comparative genomics. A tremendous genetic variation among WRKY members of different solanaceous plants or groups was demonstrated by the comparison of some WRKY features, including number/size, group constitution, gene structure, and domain composition. The phylogenetic analysis showed that except for the known WRKY groups (I, IIa/b/c/d/e and III), two extra WRKY subgroups specifically existed in solanaceous plants, which were named group IIf and group IIg in this study, and their genetic variations were also revealed by the characteristics of some group IIf and IIg WRKYs. Except for the extensive genetic variations, certain degrees of conservatism for solanaceae WRKYs were also revealed. Moreover, the variant zinc-finger structure (CX4,7CX22-24HXC) in group III of solanaceae WRKYs was identified. Expression profiles of CaWRKY genes suggested their potential roles in pepper development and stress responses, and demonstrated a functional division pattern for pepper CaWRKYs. Furthermore, functional analysis using virus induced gene silencing (VIGS) revealed critical roles of two CaWRKYs (CaWRKY45 and CaWRKY58) in plant responses to disease and drought, respectively. This study provides a solid foundation for further dissection of the evolutionary and functional diversity of solanaceae WRKYs in crop plants.
Collapse
Affiliation(s)
- Yuan Cheng
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Golam Jalal Ahammed
- College of Forestry, Henan University of Science and Technology, Luoyang, China
| | - Zhuping Yao
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Qingjing Ye
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Meiying Ruan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Rongqing Wang
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhimiao Li
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Guozhi Zhou
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Hongjian Wan
- State Key Laboratory Breeding Base for Zhejiang Sustainable Pest and Disease Control, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
13
|
Structural and functional dissection of differentially expressed tomato WRKY transcripts in host defense response against the vascular wilt pathogen (Fusarium oxysporum f. sp. lycopersici). PLoS One 2018; 13:e0193922. [PMID: 29709017 PMCID: PMC5927432 DOI: 10.1371/journal.pone.0193922] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Accepted: 02/21/2018] [Indexed: 11/24/2022] Open
Abstract
The WRKY transcription factors have indispensable role in plant growth, development and defense responses. The differential expression of WRKY genes following the stress conditions has been well demonstrated. We investigated the temporal and tissue-specific (root and leaf tissues) differential expression of plant defense-related WRKY genes, following the infection of Fusarium oxysporum f. sp. lycopersici (Fol) in tomato. The genome-wide computational analysis revealed that during the Fol infection in tomato, 16 different members of WRKY gene superfamily were found to be involved, of which only three WRKYs (SolyWRKY4, SolyWRKY33, and SolyWRKY37) were shown to have clear-cut differential gene expression. The quantitative real time PCR (qRT-PCR) studies revealed different gene expression profile changes in tomato root and leaf tissues. In root tissues, infected with Fol, an increased expression for SolyWRKY33 (2.76 fold) followed by SolyWRKY37 (1.93 fold) gene was found at 24 hrs which further increased at 48 hrs (5.0 fold). In contrast, the leaf tissues, the expression was more pronounced at an earlier stage of infection (24 hrs). However, in both cases, we found repression of SolyWRKY4 gene, which further decreased at an increased time interval. The biochemical defense programming against Fol pathogenesis was characterized by the highest accumulation of H2O2 (at 48 hrs) and enhanced lignification. The functional diversity across the characterized WRKYs was explored through motif scanning using MEME suite, and the WRKYs specific gene regulation was assessed through the DNA protein docking studies The functional WRKY domain modeled had β sheets like topology with coil and turns. The DNA-protein interaction results revealed the importance of core residues (Tyr, Arg, and Lys) in a feasible WRKY-W-box DNA interaction. The protein interaction network analysis revealed that the SolyWRKY33 could interact with other proteins, such as mitogen-activated protein kinase 5 (MAPK), sigma factor binding protein1 (SIB1) and with other WRKY members including WRKY70, WRKY1, and WRKY40, to respond various biotic and abiotic stresses. The STRING results were further validated through Predicted Tomato Interactome Resource (PTIR) database. The CELLO2GO web server revealed the functional gene ontology annotation and protein subcellular localization, which predicted that SolyWRKY33 is involved in amelioration of biological stress (39.3%) and other metabolic processes (39.3%). The protein (SolyWRKY33) most probably located inside the nucleus (91.3%) with having transcription factor binding activity. We conclude that the defense response following the Fol challenge was accompanied by differential expression of the SolyWRKY4(↓), SolyWRKY33(↑) and SolyWRKY37(↑) transcripts. The biochemical changes are occupied by elicitation of H2O2 generation and accumulation and enhanced lignified tissues.
Collapse
|
14
|
Zhang C, Wang D, Yang C, Kong N, Shi Z, Zhao P, Nan Y, Nie T, Wang R, Ma H, Chen Q. Genome-wide identification of the potato WRKY transcription factor family. PLoS One 2017; 12:e0181573. [PMID: 28727761 PMCID: PMC5519183 DOI: 10.1371/journal.pone.0181573] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 07/03/2017] [Indexed: 12/05/2022] Open
Abstract
WRKY transcription factors play pivotal roles in regulation of stress responses. This study identified 79 WRKY genes in potato (Solanum tuberosum). Based on multiple sequence alignment and phylogenetic relationships, WRKY genes were classified into three major groups. The majority of WRKY genes belonged to Group II (52 StWRKYs), Group III had 14 and Group I consisted of 13. The phylogenetic tree further classified Group II into five sub-groups. All StWRKY genes except StWRKY79 were mapped on potato chromosomes, with eight tandem duplication gene pairs and seven segmental duplication gene pairs found from StWRKY family genes. The expression analysis of 22 StWRKYs showed their differential expression levels under various stress conditions. Cis-element prediction showed that a large number of elements related to drought, heat and salicylic acid were present in the promotor regions of StWRKY genes. The expression analysis indicated that seven StWRKYs seemed to respond to stress (heat, drought and salinity) and salicylic acid treatment. These genes are candidates for abiotic stress signaling for further research.
Collapse
Affiliation(s)
- Chao Zhang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Dongdong Wang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Chenghui Yang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Nana Kong
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Zheng Shi
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Peng Zhao
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Yunyou Nan
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Tengkun Nie
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Ruoqiu Wang
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
| | - Haoli Ma
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail: (HM); (QC)
| | - Qin Chen
- Department of Agronomy, State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A & F University, Yangling, Shaanxi, China
- * E-mail: (HM); (QC)
| |
Collapse
|