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Yu Q, Liu C, Sun J, Ding M, Ding Y, Xu Y, He J, Li Q, Jin X. McWRKY43 Confers Cold Stress Tolerance in Michelia crassipes via Regulation of Flavonoid Biosynthesis. Int J Mol Sci 2024; 25:9843. [PMID: 39337331 PMCID: PMC11432407 DOI: 10.3390/ijms25189843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2024] [Revised: 09/04/2024] [Accepted: 09/08/2024] [Indexed: 09/30/2024] Open
Abstract
WRKY transcription factor (TF) plays a crucial role in plant abiotic stress response, but it is rarely reported in Michelia crassipes. Our studies have found that the transcription factor McWRKY43, a member of the IIc subgroup, is strongly upregulated under cold stress. In this study, we cloned the full length of McWRKY43 to further investigate the function of McWRKY43 in resistance to cold stress and its possible regulatory pathways in M. crassipes. Under cold stress, the seed-germination rate of transgenic tobacco was significantly higher than that of the wild type, and the flavonoid content, antioxidant enzyme activities, and proline content of transgenic tobacco seedlings were significantly increased, which promoted the expression of flavonoid pathway structural genes. In addition, the transient transformation of McWRKY43 in the M. crassipes leaves also found the accumulation of flavonoid content and the transcription level of flavonoid structural genes, especially McLDOX, were significantly increased under cold stress. Yeast one-hybrid (Y1H) assay showed that McWRKY43 could bind to McLDOX promoter, and the transcription expression of McLDOX was promoted by McWRKY43 during cold stress treatment. Overall, our results indicated that McWRKY43 is involved in flavonoid biosynthetic pathway to regulate cold stress tolerance of M. crassipes, providing a basis for molecular mechanism of stress resistance in Michelia.
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Affiliation(s)
- Qiuxiu Yu
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Caixian Liu
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Jiahui Sun
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Minghai Ding
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Yu Ding
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Yun Xu
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Jinsong He
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Qizhen Li
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
| | - Xiaoling Jin
- College of Landscape Architecture, Central South University of Forestry and Technology, Changsha 410004, China; (Q.Y.); (C.L.); (J.S.); (M.D.); (Y.D.); (Y.X.); (J.H.)
- Hunan Big Data Engineering Technology Research Center of Natural Protected Areas Landscape Resources, Changsha 410004, China
- Yuelushan Laboratory Carbon Sinks Forests Variety Innovation Center, Changsha 410004, China
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Yan X, Zhao J, Huang W, Liu C, Hao X, Gao C, Deng M, Wen J. Genome-Wide Identification of WRKY Transcription Factor Family in Chinese Rose and Response to Drought, Heat, and Salt Stress. Genes (Basel) 2024; 15:800. [PMID: 38927736 PMCID: PMC11203230 DOI: 10.3390/genes15060800] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/12/2024] [Accepted: 06/14/2024] [Indexed: 06/28/2024] Open
Abstract
The WRKY gene family is a key transcription factor family for plant development and the stress response. However, few studies have investigated the WRKY gene family in Chinese rose (Rosa chinensis). In this study, 68 RcWRKY genes were identified from the Chinese rose genome and classified into three primary groups and five subgroups based on the structural and phylogenetic characteristics. The analysis of the conserved domains, motifs, and gene structure revealed that the RcWRKY genes within the same group had the same exon-intron organization and composition. Chromosome mapping and gene duplication revealed that the RcWRKY genes were randomly dispersed across seven chromosomes. Fragment duplication and refined selection may have influenced the evolution of the WRKY gene family in Chinese rose. The cis-acting elements in the WRKY promoter region revealed that the RcWRKY genes contained numerous abiotic stress response elements. The results of qRT-PCR revealed that the expression of RcWRKY was tissue-specific, with high expression being observed under drought, heat, and salt stress. Notably, RcWRKY49's expression increased more than fivefold following salt stress, indicating that it is a crucial gene mediating the salt stress response of Chinese rose. These findings shed light on the regulatory role of RcWRKY in the growth and development of Chinese rose, and they serve as a foundation for future molecular breeding programs and gene discovery.
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Affiliation(s)
- Xinyu Yan
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Jiahui Zhao
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Wei Huang
- College of Agronomy and Life Sciences, Kunming University, Kunming 650021, China;
| | - Cheng Liu
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Xuan Hao
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Chengye Gao
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
| | - Minghua Deng
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Jinfen Wen
- Faculty of Architecture and City Planning, Kunming University of Science and Technology, Kunming 650021, China; (X.Y.); (J.Z.); (C.L.); (X.H.); (C.G.)
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Vodiasova E, Sinchenko A, Khvatkov P, Dolgov S. Genome-Wide Identification, Characterisation, and Evolution of the Transcription Factor WRKY in Grapevine ( Vitis vinifera): New View and Update. Int J Mol Sci 2024; 25:6241. [PMID: 38892428 PMCID: PMC11172563 DOI: 10.3390/ijms25116241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 05/29/2024] [Accepted: 06/03/2024] [Indexed: 06/21/2024] Open
Abstract
WRKYs are a multigenic family of transcription factors that are plant-specific and involved in the regulation of plant development and various stress response processes. However, the evolution of WRKY genes is not fully understood. This family has also been incompletely studied in grapevine, and WRKY genes have been named with different numbers in different studies, leading to great confusion. In this work, 62 Vitis vinifera WRKY genes were identified based on six genomes of different cultivars. All WRKY genes were numbered according to their chromosomal location, and a complete revision of the numbering was performed. Amino acid variability between different cultivars was assessed for the first time and was greater than 5% for some WRKYs. According to the gene structure, all WRKYs could be divided into two groups: more exons/long length and fewer exons/short length. For the first time, some chimeric WRKY genes were found in grapevine, which may play a specific role in the regulation of different processes: VvWRKY17 (an N-terminal signal peptide region followed by a non-cytoplasmic domain) and VvWRKY61 (Frigida-like domain). Five phylogenetic clades A-E were revealed and correlated with the WRKY groups (I, II, III). The evolution of WRKY was studied, and we proposed a WRKY evolution model where there were two dynamic phases of complexity and simplification in the evolution of WRKY.
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Affiliation(s)
- Ekaterina Vodiasova
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- A.O. Kovalevsky Institute of Biology of the Southern Seas of RAS, 299011 Sevastopol, Russia
| | - Anastasiya Sinchenko
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Pavel Khvatkov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
| | - Sergey Dolgov
- Federal State Funded Institution of Science “The Labor Red Banner Order Nikita Botanical Gardens—National Scientific Center of the RAS”, Nikita, 298648 Yalta, Russia; (A.S.); (P.K.); (S.D.)
- Branch of Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, 142290 Puschino, Russia
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Zhang Z, Chen C, Jiang C, Lin H, Zhao Y, Guo Y. VvWRKY5 positively regulates wounding-induced anthocyanin accumulation in grape by interplaying with VvMYBA1 and promoting jasmonic acid biosynthesis. HORTICULTURE RESEARCH 2024; 11:uhae083. [PMID: 38766531 PMCID: PMC11101322 DOI: 10.1093/hr/uhae083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/10/2024] [Indexed: 05/22/2024]
Abstract
Wounding stress induces the biosynthesis of various secondary metabolites in plants, including anthocyanin. However, the underlying molecular mechanism remains elusive. Here, we reported that a transcription factor, VvWRKY5, promotes wounding-induced anthocyanin accumulation in grape (Vitis vinifera). Biochemical and molecular analyses demonstrated that wounding stress significantly increased anthocyanin content, and VvMYBA1 plays an essential role in this process. VvWRKY5 could interact with VvMYBA1 and amplify the activation effect of VvMYBA1 on its target gene VvUFGT. The transcript level of VvWRKY5 was notably induced by wounding treatment. Moreover, our data demonstrated that VvWRKY5 could promote the synthesis of jasmonic acid (JA), a phytohormone that acts as a positive modulator in anthocyanin accumulation, by directly binding to the W-box element in the promoter of the JA biosynthesis-related gene VvLOX and enhancing its activities, and this activation was greatly enhanced by the VvWRKY5-VvMYBA1 protein complex. Collectively, our findings show that VvWRKY5 plays crucial roles in wounding-induced anthocyanin synthesis in grape and elucidates the transcriptional regulatory mechanism of wounding-induced anthocyanin accumulation.
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Affiliation(s)
- Zhen Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Cui Chen
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Changyue Jiang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Hong Lin
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yuhui Zhao
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yinshan Guo
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
- National & Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), Shenyang 110866, China
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Yang R, Huang T, Song W, An Z, Lai Z, Liu S. Identification of WRKY gene family members in amaranth based on a transcriptome database and functional analysis of AtrWRKY42-2 in betalain metabolism. FRONTIERS IN PLANT SCIENCE 2023; 14:1300522. [PMID: 38130485 PMCID: PMC10734031 DOI: 10.3389/fpls.2023.1300522] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2023] [Accepted: 11/16/2023] [Indexed: 12/23/2023]
Abstract
Introduction WRKY TFs (WRKY transcription factors) contribute to the synthesis of secondary metabolites in plants. Betalains are natural pigments that do not coexist with anthocyanins within the same plant. Amaranthus tricolor ('Suxian No.1') is an important leaf vegetable rich in betalains. However, the WRKY family members in amaranth and their roles in betalain synthesis and metabolism are still unclear. Methods To elucidate the molecular characteristics of the amaranth WRKY gene family and its role in betalain synthesis, WRKY gene family members were screened and identified using amaranth transcriptome data, and their physicochemical properties, conserved domains, phylogenetic relationships, and conserved motifs were analyzed using bioinformatics methods. Results In total, 72 WRKY family members were identified from the amaranth transcriptome. Three WRKY genes involved in betalain synthesis were screened in the phylogenetic analysis of WRKY TFs. RT-qPCR showed that the expression levels of these three genes in red amaranth 'Suxian No.1' were higher than those in green amaranth 'Suxian No.2' and also showed that the expression level of AtrWRKY42 gene short-spliced transcript AtrWRKY42-2 in Amaranth 'Suxian No.1' was higher than that of the complete sequence AtrWRKY42-1, so the short-spliced transcript AtrWRKY42-2 was mainly expressed in 'Suxian No.2' amaranth. Moreover, the total expression levels of AtrWRKY42-1 and AtrWRKY42-2 were down-regulated after GA3 treatment, so AtrWRKY42-2 was identified as a candidate gene. Therefore, the short splice variant AtrWRKY42-2 cDNA sequence, gDNA sequence, and promoter sequence of AtrWRKY42 were cloned, and the PRI 101-AN-AtrWRKY42-2-EGFP vector was constructed to evaluate subcellular localization, revealing that AtrWRKY42-2 is located in the nucleus. The overexpression vector pRI 101-AN-AtrWRKY42-2-EGFP and VIGS (virus-induced gene silencing) vector pTRV2-AtrWRKY42-2 were transferred into leaves of 'Suxian No.1' by an Agrobacterium-mediated method. The results showed that AtrWRKY42-2 overexpression could promote the expression of AtrCYP76AD1 and increase betalain synthesis. A yeast one-hybrid assay demonstrated that AtrWRKY42-2 could bind to the AtrCYP76AD1 promoter to regulate betalain synthesis. Discussion This study lays a foundation for further exploring the function of AtrWRKY42-2 in betalain metabolism.
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Affiliation(s)
| | | | | | | | | | - Shengcai Liu
- Institute of Horticultural Biotechnology, Fujian Agriculture and Forestry University, Fuzhou, Fujian, China
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Wei Y, Meng N, Wang Y, Cheng J, Duan C, Pan Q. Transcription factor VvWRKY70 inhibits both norisoprenoid and flavonol biosynthesis in grape. PLANT PHYSIOLOGY 2023; 193:2055-2070. [PMID: 37471439 DOI: 10.1093/plphys/kiad423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 06/16/2023] [Accepted: 06/21/2023] [Indexed: 07/22/2023]
Abstract
Norisoprenoids and flavonols are important secondary metabolites in grape berries (Vitis vinifera L.). The former is a class of ubiquitous flavor and fragrance compounds produced by the cleavage of carotenoids, and the latter, which is derived from the flavonoid metabolic pathway, has been proposed as a general quality marker for red grapes. However, the transcriptional regulatory mechanisms underlying norisoprenoid and flavonol production are still not fully understood. In this study, we characterized a transcription factor, VvWRKY70, as a repressor of both norisoprenoid and flavonol biosynthesis in grape berries, and its expression was downregulated by light and high-temperature treatment. Overexpressing VvWRKY70 in grape calli reduced norisoprenoid and flavonol production, particularly under light exposure or at high temperature, by repressing the expression of several related genes in the isoprenoid and flavonoid metabolic pathways. VvWRKY70 downregulated β-CAROTENE HYDROXYLASE 2 (VvBCH2) and CHALCONE SYNTHASE 3 (VvCHS3) expression based on yeast 1-hybrid analysis combined with electrophoretic mobility shift assay and chromatin immunoprecipitation-quantitative PCR. We discuss the role of VvWRKY70 in the coordinated regulatory network of isoprenoid and flavonoid metabolism. These findings provide a theoretical basis to improve flavor, color, and other comprehensive qualities of fruit crops and their processing products.
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Affiliation(s)
- Yi Wei
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing 100083, China
| | - Nan Meng
- Key Laboratory of Brewing Molecular Engineering of China Light Industry, Beijing Technology and Business University, Beijing 100048, China
| | - Yachen Wang
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing 100083, China
| | - Jing Cheng
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing 100083, China
| | - Changqing Duan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing 100083, China
| | - Qiuhong Pan
- Center for Viticulture and Enology, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
- Key Laboratory of Viticulture and Enology, Ministry of Agricultural and Rural Affairs, Beijing 100083, China
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Zheng L, Assane Hamidou A, Zhao X, Ouyang Z, Lin H, Li J, Zhang X, Luo K, Chen Y. Superoxide dismutase gene family in cassava revealed their involvement in environmental stress via genome-wide analysis. iScience 2023; 26:107801. [PMID: 37954140 PMCID: PMC10638475 DOI: 10.1016/j.isci.2023.107801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2022] [Revised: 07/29/2023] [Accepted: 08/29/2023] [Indexed: 11/14/2023] Open
Abstract
Superoxide dismutase (SOD) is a crucial metal-containing enzyme that plays a vital role in catalyzing the dismutation of superoxide anions, converting them into molecular oxygen and hydrogen peroxide, essential for enhancing plant stress tolerance. We identified 8 SOD genes (4 CSODs, 2 FSODs, and 2 MSODs) in cassava. Bioinformatics analyses provided insights into chromosomal location, phylogenetic relationships, gene structure, conserved motifs, and gene ontology annotations. MeSOD genes were classified into two groups through phylogenetic analysis, revealing evolutionary connections. Promoters of these genes harbored stress-related cis-elements. Duplication analysis indicated the functional significance of MeCSOD2/MeCSOD4 and MeMSOD1/MeMSOD2. Through qRT-PCR, MeCSOD2 responded to salt stress, MeMSOD2 to drought, and cassava bacterial blight. Silencing MeMSOD2 increased XpmCHN11 virulence, indicating MeMSOD2 is essential for cassava's defense against XpmCHN11 infection. These findings enhance our understanding of the SOD gene family's role in cassava and contribute to strategies for stress tolerance improvement.
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Affiliation(s)
- Linling Zheng
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Abdoulaye Assane Hamidou
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xuerui Zhao
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Zhiwei Ouyang
- HNU-ASU Joint International Tourism College, Hainan University, Haikou 570228, China
| | - Hongxin Lin
- Soil Fertilizer and Resources Environment Institute, Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Junyi Li
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Xiaofei Zhang
- Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali 763537, Colombia
| | - Kai Luo
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
| | - Yinhua Chen
- Sanya Nanfan Research Institute of Hainan University, School of Life Sciences, Hainan University, Sanya 572025, China
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Yu J, Zhang X, Cao J, Bai H, Wang R, Wang C, Xu Z, Li C, Liu G. Genome-Wide Identification and Characterization of WRKY Transcription Factors in Betula platyphylla Suk. and Their Responses to Abiotic Stresses. Int J Mol Sci 2023; 24:15000. [PMID: 37834448 PMCID: PMC10573109 DOI: 10.3390/ijms241915000] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/02/2023] [Accepted: 10/07/2023] [Indexed: 10/15/2023] Open
Abstract
The WRKY transcription factor (TF) family is one the largest plant-specific transcription factor families. It has been proven to play significant roles in multiple plant biological processes, especially stress response. Although many WRKY TFs have been identified in various plant species, WRKYs in white birch (Betula platyphylla Suk.) remain to be studied. Here, we identified a total of 68 BpWRKYs, which could be classified into four main groups. The basic physiochemical properties of these TFs were analyzed using bioinformatics tools, including molecular weight, isoelectric point, chromosome location, and predicted subcellular localization. Most BpWRKYs were predicted to be located in the nucleus. Synteny analysis found 17 syntenic gene pairs among BpWRKYs and 52 syntenic gene pairs between BpWRKYs and AtWRKYs. The cis-acting elements in the promoters of BpWRKYs could be enriched in multiple plant biological processes, including stress response, hormone response, growth and development, and binding sites. Tissue-specific expression analysis using qRT-PCR showed that most BpWRKYs exhibited highest expression levels in the root. After ABA, salt (NaCl), or cold treatment, different BpWRKYs showed different expression patterns at different treatment times. Furthermore, the results of the Y2H assay proved the interaction between BpWRKY17 and a cold-responsive TF, BpCBF7. By transient expression assay, BpWRKY17 and BpWRKY67 were localized in the nucleus, consistent with the previous prediction. Our study hopes to shed light for research on WRKY TFs and plant stress response.
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Affiliation(s)
- Jiajie Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Xiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Jiayu Cao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Heming Bai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Ruiqi Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Chao Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Zhiru Xu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Chunming Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
| | - Guanjun Liu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (X.Z.); (J.C.); (H.B.); (R.W.); (C.W.); (Z.X.)
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Wang Y, Li W, Qu J, Li F, Du W, Weng J. Genome-Wide Characterization of the Maize ( Zea mays L.) WRKY Transcription Factor Family and Their Responses to Ustilago maydis. Int J Mol Sci 2023; 24:14916. [PMID: 37834371 PMCID: PMC10573107 DOI: 10.3390/ijms241914916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 09/18/2023] [Accepted: 09/26/2023] [Indexed: 10/15/2023] Open
Abstract
Members of the WRKY transcription factor (TF) family are unique to plants and serve as important regulators of diverse physiological processes, including the ability of plants to manage biotic and abiotic stressors. However, the functions of specific WRKY family members in the context of maize responses to fungal pathogens remain poorly understood, particularly in response to Ustilago maydis (DC.) Corda (U. maydis), which is responsible for the devastating disease known as corn smut. A systematic bioinformatic approach was herein employed for the characterization of the maize WRKY TF family, leading to the identification of 120 ZmWRKY genes encoded on 10 chromosomes. Further structural and phylogenetic analyses of these TFs enabled their classification into seven different subgroups. Segmental duplication was established as a major driver of ZmWRKY family expansion in gene duplication analyses, while the Ka/Ks ratio suggested that these ZmWRKY genes had experienced strong purifying selection. When the transcriptional responses of these genes to pathogen inoculation were evaluated, seven U. maydis-inducible ZmWRKY genes were identified, as validated using a quantitative real-time PCR approach. All seven of these WKRY proteins were subsequently tested using a yeast one-hybrid assay approach, which revealed their ability to directly bind the ZmSWEET4b W-box element, thereby controlling the U. maydis-inducible upregulation of ZmSWEET4b. These results suggest that these WRKY TFs can control sugar transport in the context of fungal infection. Overall, these data offer novel insight into the evolution, transcriptional regulation, and functional characteristics of the maize WRKY family, providing a basis for future research aimed at exploring the mechanisms through which these TFs control host plant responses to common smut and other fungal pathogens.
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Affiliation(s)
- Yang Wang
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China;
| | - Wangshu Li
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China;
| | - Jianzhou Qu
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
| | - Fenghai Li
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
| | - Wanli Du
- Specialty Corn Institute, College of Agronomy, Shenyang Agricultural University, Dongling Street, Shenhe District, Shenyang 110866, China; (Y.W.); (J.Q.); (F.L.)
| | - Jianfeng Weng
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, Zhongguancun South Street, Haidian District, Beijing 100081, China;
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Rai GK, Mishra S, Chouhan R, Mushtaq M, Chowdhary AA, Rai PK, Kumar RR, Kumar P, Perez-Alfocea F, Colla G, Cardarelli M, Srivastava V, Gandhi SG. Plant salinity stress, sensing, and its mitigation through WRKY. FRONTIERS IN PLANT SCIENCE 2023; 14:1238507. [PMID: 37860245 PMCID: PMC10582725 DOI: 10.3389/fpls.2023.1238507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2023] [Accepted: 08/31/2023] [Indexed: 10/21/2023]
Abstract
Salinity or salt stress has deleterious effects on plant growth and development. It imposes osmotic, ionic, and secondary stresses, including oxidative stress on the plants and is responsible for the reduction of overall crop productivity and therefore challenges global food security. Plants respond to salinity, by triggering homoeostatic mechanisms that counter salt-triggered disturbances in the physiology and biochemistry of plants. This involves the activation of many signaling components such as SOS pathway, ABA pathway, and ROS and osmotic stress signaling. These biochemical responses are accompanied by transcriptional modulation of stress-responsive genes, which is mostly mediated by salt-induced transcription factor (TF) activity. Among the TFs, the multifaceted significance of WRKY proteins has been realized in many diverse avenues of plants' life including regulation of plant stress response. Therefore, in this review, we aimed to highlight the significance of salinity in a global perspective, the mechanism of salt sensing in plants, and the contribution of WRKYs in the modulation of plants' response to salinity stress. This review will be a substantial tool to investigate this problem in different perspectives, targeting WRKY and offering directions to better manage salinity stress in the field to ensure food security.
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Affiliation(s)
- Gyanendra Kumar Rai
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Sonal Mishra
- Department of Botany, School of Life Sciences, Central University of Jammu, Samba, Jammu & Kashmir, India
| | - Rekha Chouhan
- Infectious Diseases Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
| | - Muntazir Mushtaq
- School of Biotechnology, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu, India
| | - Aksar Ali Chowdhary
- Department of Botany, School of Life Sciences, Central University of Jammu, Samba, Jammu & Kashmir, India
| | - Pradeep K. Rai
- Advance Center for Horticulture Research, Udheywala, Sher-e-Kashmir University of Agricultural Sciences and Technology of Jammu, Jammu & Kashmir, India
| | - Ranjeet Ranjan Kumar
- Division of Biochemistry, Indian Council of Agricultural Research (ICAR), Indian Agricultural Research Institute, New Delhi, India
| | - Pradeep Kumar
- Division of Integrated Farming System, Central Arid Zone Research Institute, Indian Council of Agricultural Research (ICAR), Jodhpur, India
| | - Francisco Perez-Alfocea
- Department of Nutrition, Centre for Applied Soil Science and Biology of the Segura (CEBAS), of the Spanish National Research Council (CSIC), Murcia, Spain
| | - Giuseppe Colla
- Department of Agriculture and Forest Sciences, University of Tuscia, Viterbo, Italy
| | | | - Vikas Srivastava
- Department of Botany, School of Life Sciences, Central University of Jammu, Samba, Jammu & Kashmir, India
| | - Sumit G. Gandhi
- Infectious Diseases Division, Council of Scientific and Industrial Research (CSIR)-Indian Institute of Integrative Medicine (CSIR-IIIM), Jammu, India
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11
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Felipez W, Villavicencio J, Nizolli VO, Pegoraro C, da Maia L, Costa de Oliveira A. Genome-Wide Identification of Bilberry WRKY Transcription Factors: Go Wild and Duplicate. PLANTS (BASEL, SWITZERLAND) 2023; 12:3176. [PMID: 37765340 PMCID: PMC10535657 DOI: 10.3390/plants12183176] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 07/11/2023] [Accepted: 07/20/2023] [Indexed: 09/29/2023]
Abstract
WRKY transcription factor genes compose an important family of transcriptional regulators that are present in several plant species. According to previous studies, these genes can also perform important roles in bilberry (Vaccinium myrtillus L.) metabolism, making it essential to deepen our understanding of fruit ripening regulation and anthocyanin biosynthesis. In this context, the detailed characterization of these proteins will provide a comprehensive view of the functional features of VmWRKY genes in different plant organs and in response to different intensities of light. In this study, the investigation of the complete genome of the bilberry identified 76 VmWRKY genes that were evaluated and distributed in all twelve chromosomes. The proteins encoded by these genes were classified into four groups (I, II, III, and IV) based on their conserved domains and zinc finger domain types. Fifteen pairs of VmWRKY genes in segmental duplication and four pairs in tandem duplication were detected. A cis element analysis showed that all promoters of the VmWRKY genes contain at least one potential cis stress-response element. Differential expression analysis of RNA-seq data revealed that VmWRKY genes from bilberry show preferential or specific expression in samples. These findings provide an overview of the functional characterization of these proteins in bilberry.
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Affiliation(s)
- Winder Felipez
- Instituto de Agroecología y Seguridad Alimentaria, Facultad de Ciências Agrárias, Universidad San Francisco Xavier de Chuquisaca—USFX, Casilla, Correo Central, Sucre 1046, Bolivia;
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Jennifer Villavicencio
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
- Carrera de Ingeniería Agroforestal, Facultad de Ciencias Ambientales, Universidad Cientifica del Sur—UCSUR, Antigua Panamericana Sur km 19 Villa el Salvador, Lima CP 150142, Peru
| | - Valeria Oliveira Nizolli
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Camila Pegoraro
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Luciano da Maia
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
| | - Antonio Costa de Oliveira
- Plant Genomics and Breeding Center, Departamento de Fitotecnia, Faculdade de Agronomia Eliseu Maciel, Universidade Federal de Pelotas—UFPel, Pelotas CEP 96010-900, RS, Brazil; (J.V.); (V.O.N.); (L.d.M.)
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12
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Chen J, Hou S, Zhang Q, Meng J, Zhang Y, Du J, Wang C, Liang D, Guo Y. Genome-Wide Identification and Analysis of the WRKY Gene Family in Asparagus officinalis. Genes (Basel) 2023; 14:1704. [PMID: 37761844 PMCID: PMC10530708 DOI: 10.3390/genes14091704] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 09/29/2023] Open
Abstract
In recent years, the related research of the WRKY gene family has been gradually promoted, which is mainly reflected in the aspects of environmental stress and hormone response. However, to make the study of the WRKY gene family more complete, we also need to focus on the whole-genome analysis and identification of the family. In previous studies, the whole WRKY gene family of Arabidopsis, legumes and other plants has been thoroughly studied. However, since the publication of Asparagus officinalis genome-wide data, there has never been an analysis of the whole WRKY gene family. To understand more broadly the function of the WRKY gene family, the whole genome and salt stress transcriptome data of asparagus were used for comprehensive analysis in this study, including WRKY gene family identification, phylogenetic tree construction, analysis of conserved mods and gene domains, extraction of cis-acting elements, intron/exon analysis, species collinearity analysis, and WRKY expression analysis under salt stress. The results showed that a total of 70 genes were selected and randomly distributed on 10 chromosomes and one undefined chromosome. According to the functional classification of Arabidopsis thaliana, the WRKY family of asparagus was divided into 11 subgroups (C1-C9, U1, U2). It is worth considering that the distribution rules of gene-conserved motifs, gene domains and introns/exons in the same subfamily are similar, which suggests that genes in the same subfamily may regulate similar physiological processes. In this study, 11 cis-acting elements of WRKY family were selected, among which auxin, gibberellin, abscisic acid, salicylic acid and other hormone-regulated induction elements were involved. In addition, environmental stress (such as drought stress and low-temperature response) also accounted for a large proportion. Interestingly, we analyzed a total of two tandem duplicate genes and 13 segmental duplication genes, suggesting that this is related to the amplification of the WRKY gene family. Transcriptome data analysis showed that WRKY family genes could regulate plant growth and development by up-regulating and down-regulating gene expression under salt stress. Volcanic maps showed that 3 and 15 AoWRKY genes were significantly up-regulated or down-regulated in NI&NI+S and AMF&AMF+S, respectively. These results provide a new way to analyze the evolution and function of the WRKY gene family, and can provide a reference for the production and research of asparagus.
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Affiliation(s)
- Jing Chen
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Sijia Hou
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Qianqian Zhang
- Chinese Institute for Brain Research, Beijing 102206, China;
- College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianqiao Meng
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Yingying Zhang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Junhong Du
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Cong Wang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Dan Liang
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
| | - Yunqian Guo
- College of Biological Science and Technology, Center for Computational Biology, National Engineering Laboratory for Tree Breeding, Beijing Forestry University, Beijing 100083, China; (J.C.); (S.H.); (J.M.); (Y.Z.); (J.D.); (C.W.)
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing 100083, China
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13
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Li M, Zhang X, Zhang T, Bai Y, Chen C, Guo D, Guo C, Shu Y. Genome-wide analysis of the WRKY genes and their important roles during cold stress in white clover. PeerJ 2023; 11:e15610. [PMID: 37456899 PMCID: PMC10348312 DOI: 10.7717/peerj.15610] [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: 03/13/2023] [Accepted: 05/31/2023] [Indexed: 07/18/2023] Open
Abstract
Background White clover (Trifolium repens L) is a high-quality forage grass with a high protein content, but it is vulnerable to cold stress, which can negatively affect its growth and development. WRKY transcription factor is a family of plant transcription factors found mainly in higher plants and plays an important role in plant growth, development, and stress response. Although WRKY transcription factors have been studied extensively in other plants, it has been less studied in white clover. Methods and Results In the present research, we have performed a genome-wide analysis of the WRKY gene family of white clover, in total, there were 145 members of WRKY transcription factors identified in white clover. The characterization of the TrWRKY genes was detailed, including conserved motif analysis, phylogenetic analysis, and gene duplication analysis, which have provided a better understanding of the structure and evolution of the TrWRKY genes in white clover. Meanwhile, the genetic regulation network (GRN) containing TrWRKY genes was reconstructed, and Gene Ontology (GO) annotation analysis of these function genes showed they contributed to regulation of transcription process, response to wounding, and phosphorylay signal transduction system, all of which were important processes in response to abiotic stress. To determine the TrWRKY genes function under cold stress, the RNA-seq dataset was analyzed; most of TrWRKY genes were highly upregulated in response to cold stress, particularly in the early stages of cold stress. These results were validated by qRT-PCR experiment, implying they are involved in various gene regulation pathways in response to cold stress. Conclusion The results of this study provide insights that will be useful for further functional analyses of TrWRKY genes in response to biotic or abiotic stresses in white clover. These findings are likely to be useful for further research on the functions of TrWRKY genes and their role in response to cold stress, which is important to understand the molecular mechanism of cold tolerance in white clover and improve its cold tolerance.
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14
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Ma Y, Ran J, Li G, Wang M, Yang C, Wen X, Geng X, Zhang L, Li Y, Zhang Z. Revealing the Roles of the JAZ Family in Defense Signaling and the Agarwood Formation Process in Aquilaria sinensis. Int J Mol Sci 2023; 24:9872. [PMID: 37373020 DOI: 10.3390/ijms24129872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 06/04/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
Jasmonate ZIM-domain family proteins (JAZs) are repressors in the signaling cascades triggered by jasmonates (JAs). It has been proposed that JAs play essential roles in the sesquiterpene induction and agarwood formation processes in Aquilaria sinensis. However, the specific roles of JAZs in A. sinensis remain elusive. This study employed various methods, including phylogenetic analysis, real-time quantitative PCR, transcriptomic sequencing, yeast two-hybrid assay, and pull-down assay, to characterize A. sinensis JAZ family members and explore their correlations with WRKY transcription factors. The bioinformatic analysis revealed twelve putative AsJAZ proteins in five groups and sixty-four putative AsWRKY transcription factors in three groups. The AsJAZ and AsWRKY genes exhibited various tissue-specific or hormone-induced expression patterns. Some AsJAZ and AsWRKY genes were highly expressed in agarwood or significantly induced by methyl jasmonate in suspension cells. Potential relationships were proposed between AsJAZ4 and several AsWRKY transcription factors. The interaction between AsJAZ4 and AsWRKY75n was confirmed by yeast two-hybrid and pull-down assays. This study characterized the JAZ family members in A. sinensis and proposed a model of the function of the AsJAZ4/WRKY75n complex. This will advance our understanding of the roles of the AsJAZ proteins and their regulatory pathways.
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Affiliation(s)
- Yimian Ma
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Jiadong Ran
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Guoqiong Li
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Mengchen Wang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Chengmin Yang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xin Wen
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Xin Geng
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Liping Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
| | - Yuan Li
- Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zheng Zhang
- National Engineering Laboratory for Breeding of Endangered Medicinal Materials, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
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Kajla M, Roy A, Singh IK, Singh A. Regulation of the regulators: Transcription factors controlling biosynthesis of plant secondary metabolites during biotic stresses and their regulation by miRNAs. FRONTIERS IN PLANT SCIENCE 2023; 14:1126567. [PMID: 36938003 PMCID: PMC10017880 DOI: 10.3389/fpls.2023.1126567] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Accepted: 02/06/2023] [Indexed: 06/18/2023]
Abstract
Biotic stresses threaten to destabilize global food security and cause major losses to crop yield worldwide. In response to pest and pathogen attacks, plants trigger many adaptive cellular, morphological, physiological, and metabolic changes. One of the crucial stress-induced adaptive responses is the synthesis and accumulation of plant secondary metabolites (PSMs). PSMs mitigate the adverse effects of stress by maintaining the normal physiological and metabolic functioning of the plants, thereby providing stress tolerance. This differential production of PSMs is tightly orchestrated by master regulatory elements, Transcription factors (TFs) express differentially or undergo transcriptional and translational modifications during stress conditions and influence the production of PSMs. Amongst others, microRNAs, a class of small, non-coding RNA molecules that regulate gene expression post-transcriptionally, also play a vital role in controlling the expression of many such TFs. The present review summarizes the role of stress-inducible TFs in synthesizing and accumulating secondary metabolites and also highlights how miRNAs fine-tune the differential expression of various stress-responsive transcription factors during biotic stress.
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Affiliation(s)
- Mohini Kajla
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
| | - Amit Roy
- Excellent Team for Mitigation (ETM), Faculty of Forestry and Wood Sciences, Czech University of Life Sciences Prague, Prague, Czechia
| | - Indrakant K. Singh
- Department of Zoology, Deshbandhu College, University of Delhi, New Delhi, India
| | - Archana Singh
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- Jagdish Chandra Bose Center for Plant Genomics, Hansraj College, University of Delhi, Delhi, India
- Delhi School of Climate Change and Sustainability, Institution of Eminence, Maharishi Karnad Bhawan, University of Delhi, Delhi, India
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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.
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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.
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Quijada-Rivera M, Tiznado-Hernández ME, Hernández-Oñate MÁ, Vargas-Arispuro I, Astorga-Cienfuegos KR, Lazo-Javalera MF, Rivera-Domínguez M. Transcriptome assessment in 'Red Globe' grapevine zygotic embryos during the cooling and warming phase of the cryopreservation procedure. Cryobiology 2023; 110:56-68. [PMID: 36528080 DOI: 10.1016/j.cryobiol.2022.12.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Revised: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/15/2022]
Abstract
Cryopreservation has the potential for long-term germplasm storage. The metabolic pathways and gene regulation involved in cryopreservation procedures are still not well documented. Hence, the genetic expression profile was evaluated using RNA-Seq in zygotic embryos of grapevines subjected to cryopreservation by vitrification. Sequencing was performed on the Illumina NextSeq 500. The average alignment of reads was 96% against the reference genome. The expression profiles showed 229 genes differentially expressed (186 repressed and 46 induced). The main biological processes showing upregulated enrichment were related to nucleosome assembly, while downregulated processes were related to organ growth. The most highly repressed processes were associated with the organization of the cell wall and membrane components. The unnamed protein product and 17.3 kDa class II heat shock protein (HSP) were highly induced, while ATPase subunit 1 and expansin-A1 were repressed. The response to the cooling and warming process during cryopreservation probably indicates that the changes occurring in transcription may be related to epigenetics. In addition, the cell exhibits an increase in the reserve of nutrients while seeking to survive modestly using available energy and pausing the plant's development. Additionally, energy containment occurred to cope with the stress caused by the treatment where deactivation of components of the cell membrane was observed, possibly due to changes in fluidity caused by alterations in temperature.
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Affiliation(s)
- Mariana Quijada-Rivera
- Food Science Coordination, Research Center for Food and Development, Hermosillo, Sonora, 83000, Mexico
| | | | | | - Irasema Vargas-Arispuro
- Food Science Coordination, Research Center for Food and Development, Hermosillo, Sonora, 83000, Mexico
| | | | | | - Marisela Rivera-Domínguez
- Food Science Coordination, Research Center for Food and Development, Hermosillo, Sonora, 83000, Mexico.
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18
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Ren C, Fan P, Li S, Liang Z. Advances in understanding cold tolerance in grapevine. PLANT PHYSIOLOGY 2023:kiad092. [PMID: 36789447 DOI: 10.1093/plphys/kiad092] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 01/06/2023] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Grapevine (Vitis ssp.) is a deciduous perennial fruit crop, and the canes and buds of grapevine should withstand low temperatures annually during winter. However, the widely cultivated Vitis vinifera is cold-sensitive and cannot survive the severe winter in regions with extremely low temperatures, such as viticulture regions in northern China. By contrast, a few wild Vitis species like V. amurensis and V. riparia exhibit excellent freezing tolerance. However, the mechanisms underlying grapevine cold tolerance remain largely unknown. In recent years, much progress has been made in elucidating the mechanisms, owing to the advances in sequencing and molecular biotechnology. Assembly of grapevine genomes together with resequencing and transcriptome data enable researchers to conduct genomic and transcriptomic analyses in various grapevine genotypes and populations to explore genetic variations involved in cold tolerance. In addition, a number of pivotal genes have been identified and functionally characterized. In this review, we summarize recent major advances in physiological and molecular analyses of cold tolerance in grapevine and put forward questions in this field. We also discuss the strategies for improving the tolerance of grapevine to cold stress. Understanding grapevine cold tolerance will facilitate the development of grapevines for adaption to global climate change.
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Affiliation(s)
- Chong Ren
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Peige Fan
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, Key Laboratory of Plant Resource, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, PR China
- China National Botanical Garden, Beijing 100093, PR China
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19
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Zhao L, Wang B, Yang T, Yan H, Yu Q, Wang J. Genome-wide identification and analysis of the evolution and expression pattern of the HVA22 gene family in three wild species of tomatoes. PeerJ 2023; 11:e14844. [PMID: 36815985 PMCID: PMC9933743 DOI: 10.7717/peerj.14844] [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: 08/21/2022] [Accepted: 01/11/2023] [Indexed: 02/15/2023] Open
Abstract
Wild tomato germplasm is a valuable resource for improving biotic and abiotic stresses in tomato breeding. The HVA22 is widely present in eukaryotes and involved in growth and development as well as stress response, such as cold, salt, drought, and biotic stress. In the present study, we identified 45 HVA22 genes in three wild species of tomatoes. The phylogenetic relationships, gene localization to chromosomes, gene structure, gene collinearity, protein interactions, and cis-acting element prediction of all 45 HVA22 genes (14 in Solanum pennellii, 15 in S. pimpinellifolium, and 16 in S. lycopersicoides) were analyzed. The phylogenetic analysis showed that the all HVA22 proteins from the family Solanaceae were divided into three branches. The identified 45 HVA22 genes were grouped into four subfamilies, which displayed similar number of exons and expanded in a fragmentary replication manner. The distribution of HVA22 genes on the chromosomes of the three wild tomato species was also highly similar. RNA-seq and qRT-PCR revealed that HVA22 genes were expressed in different tissues and induced by drought, salt, and phytohormone treatments. These results might be useful for explaining the evolution, expression patterns, and functional divergence of HVA22 genes in Lycopersicon.
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Affiliation(s)
- LaiPeng Zhao
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science (Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang), Urumqi, Xinjiang, China,College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Baike Wang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science (Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang), Urumqi, Xinjiang, China
| | - Tao Yang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science (Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang), Urumqi, Xinjiang, China
| | - Huizhuan Yan
- College of Horticulture, Xinjiang Agricultural University, Urumqi, Xinjiang, China
| | - Qinghui Yu
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science (Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang), Urumqi, Xinjiang, China
| | - Juan Wang
- Institute of Horticultural Crops, Xinjiang Academy of Agricultural Science (Key Laboratory of Horticulture Crop Genomics Research and Genetic Improvement in Xinjiang), Urumqi, Xinjiang, China
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20
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Mu D, Chen W, Shao Y, Wilson IW, Zhao H, Luo Z, Lin X, He J, Zhang Y, Mo C, Qiu D, Tang Q. Genome-Wide Identification and Expression Analysis of WRKY Transcription Factors in Siraitia siamensis. PLANTS (BASEL, SWITZERLAND) 2023; 12:288. [PMID: 36679001 PMCID: PMC9861706 DOI: 10.3390/plants12020288] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/03/2023] [Accepted: 01/04/2023] [Indexed: 06/17/2023]
Abstract
WRKY transcription factors, as the largest gene family in higher plants, play an important role in various biological processes including growth and development, regulation of secondary metabolites, and stress response. In this study, we performed genome-wide identification and analysis of WRKY transcription factors in S. siamensis. A total of 59 SsWRKY genes were identified that were distributed on all 14 chromosomes, and these were classified into three major groups based on phylogenetic relationships. Each of these groups had similar conserved motifs and gene structures. We compared all the S. siamensis SsWRKY genes with WRKY genes identified from three diverse plant species, and the results implied that segmental duplication and tandem duplication play an important roles in the evolution processes of the WRKY gene family. Promoter region analysis revealed that SsWRKY genes included many cis-acting elements related to plant growth and development, phytohormone response, and both abiotic and biotic stress. Expression profiles originating from the transcriptome database showed expression patterns of these SsWRKY genes in four different tissues and revealed that most genes are expressed in plant roots. Fifteen SsWRKY genes with low-temperature response motifs were surveyed for their gene expression under cold stress, showing that most genes displayed continuous up-regulation during cold treatment. Our study provides a foundation for further study on the function and regulatory mechanism of the SsWRKY gene family.
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Affiliation(s)
- Detian Mu
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Wenqiang Chen
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Yingying Shao
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Iain W. Wilson
- CSIRO Agriculture and Food, Canberra, ACT 2601, Australia
| | - Huan Zhao
- School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069, China
| | - Zuliang Luo
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100193, China
| | - Xiaodong Lin
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Jialong He
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Yuan Zhang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
| | - Changming Mo
- Guangxi Crop Genetic Improvement and Biotechnology Laboaratory, Guangxi Academy of Agricultural Sciences, Nanning 530007, China
| | - Deyou Qiu
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Qi Tang
- College of Horticulture, Hunan Agricultural University, Changsha 410128, China
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21
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Saharan BS, Brar B, Duhan JS, Kumar R, Marwaha S, Rajput VD, Minkina T. Molecular and Physiological Mechanisms to Mitigate Abiotic Stress Conditions in Plants. Life (Basel) 2022; 12:1634. [PMID: 36295069 PMCID: PMC9605384 DOI: 10.3390/life12101634] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 10/14/2022] [Accepted: 10/15/2022] [Indexed: 10/03/2023] Open
Abstract
Agriculture production faces many abiotic stresses, mainly drought, salinity, low and high temperature. These abiotic stresses inhibit plants' genetic potential, which is the cause of huge reduction in crop productivity, decrease potent yields for important crop plants by more than 50% and imbalance agriculture's sustainability. They lead to changes in the physio-morphological, molecular, and biochemical nature of the plants and change plants' regular metabolism, which makes them a leading cause of losses in crop productivity. These changes in plant systems also help to mitigate abiotic stress conditions. To initiate the signal during stress conditions, sensor molecules of the plant perceive the stress signal from the outside and commence a signaling cascade to send a message and stimulate nuclear transcription factors to provoke specific gene expression. To mitigate the abiotic stress, plants contain several methods of avoidance, adaption, and acclimation. In addition to these, to manage stress conditions, plants possess several tolerance mechanisms which involve ion transporters, osmoprotectants, proteins, and other factors associated with transcriptional control, and signaling cascades are stimulated to offset abiotic stress-associated biochemical and molecular changes. Plant growth and survival depends on the ability to respond to the stress stimulus, produce the signal, and start suitable biochemical and physiological changes. Various important factors, such as the biochemical, physiological, and molecular mechanisms of plants, including the use of microbiomes and nanotechnology to combat abiotic stresses, are highlighted in this article.
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Affiliation(s)
- Baljeet Singh Saharan
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | - Basanti Brar
- Department of Microbiology, CCS Haryana Agricultural University, Hisar 125004, India
| | | | - Ravinder Kumar
- Department of Biotechnology, Ch. Devi Lal University, Sirsa 125055, India
| | - Sumnil Marwaha
- ICAR-National Research Centre on Camel, Bikaner 334001, India
| | - Vishnu D. Rajput
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia
| | - Tatiana Minkina
- Academy of Biology and Biotechnology, Southern Federal University, 344090 Rostov-on-Don, Russia
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22
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Lu J, Chen H, Yang Z, Sun S, Luo Q, Xie J, Tan J. Physiological and molecular mechanisms of the response of roots of Pinus massoniana Lamb. to low-temperature stress. FRONTIERS IN PLANT SCIENCE 2022; 13:954324. [PMID: 36247576 PMCID: PMC9554314 DOI: 10.3389/fpls.2022.954324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/02/2022] [Indexed: 06/16/2023]
Abstract
Pinus massoniana Lamb. is the timber species with the widest distribution and the largest afforestation area in China, providing a large amount of timber, turpentine and ecological products. but low temperature limits its growth and geographical distribution. Physiological and molecular studies can well explain the mechanism of P. massoniana response to low temperature. In this study, physiological and biochemical indexes, cell morphology, lignin content, gene regulatory networks, and gene expression patterns of different P. massoniana varieties (cold-tolerant and cold-sensitive) were studied from physiological, biochemical, and molecular perspectives. The results indicated that under low-temperature stress, the cold-tolerant cultivar maintained high contents of osmoregulatory substances, and the root morphology and structure remained intact. In the initial stage of low-temperature stress, the number of differentially expressed genes was 7148, and with the extension of stress time, the number of differentially expressed genes decreased to 1991. P. massoniana might direct its responses to low temperature by regulating phenylpropane metabolism, starch and sucrose metabolism, hormone signaling pathways, and transcription factors. BAM, 4CL, CCoAOMT, PRX5, WRKYs, and hormone synthesis related genes play important roles. P. massoniana cultivars may vary in response mechanisms. In this study, physiological and analytical techniques were used to study the root tip response mechanism of Masson's pine to low temperature stress. The results of this study lay a foundation for in-depth research on the molecular functions of P. massoniana under low-temperature stress conditions.
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Affiliation(s)
- Jingyu Lu
- Key Laboratory of Central South Fast-Growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning, China
| | - Hu Chen
- Key Laboratory of Central South Fast-Growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning, China
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Nanning, China
- Masson Pine Engineering Research Center of the State Forestry Administration, Nanning, China
- Masson Pine Engineering Research Center of Guangxi, Nanning, China
| | - Zhangqi Yang
- Key Laboratory of Central South Fast-Growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning, China
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Nanning, China
- Masson Pine Engineering Research Center of the State Forestry Administration, Nanning, China
- Masson Pine Engineering Research Center of Guangxi, Nanning, China
| | - Shuang Sun
- Key Laboratory of Central South Fast-Growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning, China
| | - Qunfeng Luo
- Key Laboratory of Central South Fast-Growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning, China
- Masson Pine Engineering Research Center of the State Forestry Administration, Nanning, China
| | - Junkang Xie
- Key Laboratory of Central South Fast-Growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning, China
- Guangxi Key Laboratory of Superior Timber Trees Resource Cultivation, Nanning, China
| | - Jianhui Tan
- Key Laboratory of Central South Fast-Growing Timber Cultivation of Forestry Ministry of China, Guangxi Forestry Research Institute, Nanning, China
- Masson Pine Engineering Research Center of Guangxi, Nanning, China
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23
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Chen C, Xie F, Shah K, Hua Q, Chen J, Zhang Z, Zhao J, Hu G, Qin Y. Genome-Wide Identification of WRKY Gene Family in Pitaya Reveals the Involvement of HmoWRKY42 in Betalain Biosynthesis. Int J Mol Sci 2022; 23:ijms231810568. [PMID: 36142481 PMCID: PMC9502481 DOI: 10.3390/ijms231810568] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/07/2022] [Accepted: 09/07/2022] [Indexed: 12/16/2022] Open
Abstract
The WRKY gene family is a plant-specific transcription factor (TF) that regulates many physiological processes and (a) biotic stress responses. Despite this, little is known about the molecular properties and roles of WRKY TFs in pitaya betalain biosynthesis. Here we report the identification of 70 WRKY in Hylocereus undatus, their gene structure, locations on each chromosome, systematic phylogenetic analysis, conserved motif analysis, and synteny of HuWRKY genes. HmoWRKY42 is a Group IIb WRKY protein and contains a coiled-coil motif, a WRKY domain and a C2H2 zinc-finger motif (CX5CX23HXH). Results from yeast one-hybrid and transient dual-luciferase assays showed that HmoWRKY42 was a transcriptional repressor and could repress HmocDOPA5GT1 expression by binding to its promoter. Yeast two-hybrid assays showed that HmoWRKY42 could interact with itself to form homodimers. Knocking out the coiled-coil motif of HmoWRKY42 prevented its self-interaction and prevented it from binding to the HmocDOPA5GT1 promoter. Knocking out the WRKY domain and C2H2 zinc-finger motif sequence of HmoWRKY42 also prevented it from binding to the HmocDOPA5GT1 promoter. The coiled-coil motif, the WRKY domain and the C2H2 zinc finger motif are key motifs for the binding of HmoWRKY42 to the HmocDOPA5GT1 promoter. HmoWRKY42 is localized in the nucleus and possesses trans-activation ability responsible for pitaya betalain biosynthesis by repressing the transcription of HmocDOPA5GT1. As far as we know, no reports are available on the role of HmoWRKY42 in pitaya betalain biosynthesis. The results provide an important foundation for future analyses of the regulation and functions of the HuWRKY gene family.
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24
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Baloch AA, Kakar KU, Nawaz Z, Mushtaq M, Abro A, Khan S, Latif A. Comparative genomics and evolutionary analysis of plant CNGCs. Biol Methods Protoc 2022; 7:bpac018. [PMID: 36032330 PMCID: PMC9400807 DOI: 10.1093/biomethods/bpac018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/26/2022] [Indexed: 12/04/2022] Open
Abstract
Comparative genomics and computational biology offer powerful research tools for studying evolutionary mechanisms of organisms, and the identification and characterization of conserved/distant genes and gene families. The plant CNGC gene family encodes evolutionary conserved ion channel proteins involved in important signaling pathways and biological functions. The fundamental ideas and standard procedures for genome-wide identification and evolutionary analysis of plant cyclic nucleotide-gated ion channels employing various software, tools, and online servers have been discussed. In particular, this developed method focused on practical procedures involving the comparative analysis of paralogs and orthologs of CNGC genes in different plant species at different levels including phylogenetic analysis, nomenclature and classification, gene structure, molecular protein evolution, and duplication events as mechanisms of gene family expansion and synteny.
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Affiliation(s)
- Akram Ali Baloch
- Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
| | - Kaleem U Kakar
- Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
| | - Zarqa Nawaz
- Department of Botany, University of Central Punjab, Rawalpindi, Pakistan
| | - Muhammad Mushtaq
- Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
| | - Asma Abro
- Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
| | - Samiullah Khan
- Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
| | - Abdul Latif
- Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, Pakistan
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Genome-Wide Analysis of the WRKY Gene Family in Malus domestica and the Role of MdWRKY70L in Response to Drought and Salt Stresses. Genes (Basel) 2022; 13:genes13061068. [PMID: 35741830 PMCID: PMC9222762 DOI: 10.3390/genes13061068] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/05/2023] Open
Abstract
The WRKY transcription factors are unique regulatory proteins in plants, which are important in the stress responses of plants. In this study, 113 WRKY genes were identified from the apple genome GDDH13 and a comprehensive analysis was performed, including chromosome mapping, and phylogenetic, motif and collinearity analysis. MdWRKYs are expressed in different tissues, such as seeds, flowers, stems and leaves. We analyzed seven WRKY proteins in different groups and found that all of them were localized in the nucleus. Among the 113 MdWRKYs, MdWRKY70L was induced by both drought and salt stresses. Overexpression of it in transgenic tobacco plants conferred enhanced stress tolerance to drought and salt. The malondialdehyde content and relative electrolyte leakage values were lower, while the chlorophyll content was higher in transgenic plants than in the wild-type under stressed conditions. In conclusion, this study identified the WRKY members in the apple genome GDDH13, and revealed the function of MdWRKY70L in the response to drought and salt stresses.
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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.
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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
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27
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Yao H, Yang T, Qian J, Deng X, Dong L. Genome-Wide Analysis and Exploration of WRKY Transcription Factor Family Involved in the Regulation of Shoot Branching in Petunia. Genes (Basel) 2022; 13:855. [PMID: 35627239 PMCID: PMC9141166 DOI: 10.3390/genes13050855] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 01/16/2023] Open
Abstract
The WRKY transcription factors (TFs) participate in various physiological, growth and developmental processes of plants. In our study, a total of 79 WRKY family members were identified and classified into three groups (Group I, Group IIa-e, and Group III) based on phylogenetic and conservative domain analyses. Conserved motif analysis showed that seven WRKYGQK domains changed. The promoter sequence analysis suggested that there were multiple stress- and hormone-related cis-regulatory elements in the promoter regions of PhWRKY genes. Expression patterns of PhWRKYs based on RNA-seq data revealed their diverse expression profiles in five tissues and under different treatments. Subcellular localization analysis showed that PhWRKY71 was located in the nucleus. In addition, overexpression of PhWRKY71 caused a significant increase in branch number. This indicated that PhWRKY71 played a critical role in regulating the shoot branching of Petuniahybrida. The above results lay the foundation for further revealing the functions of PhWRKY genes.
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Affiliation(s)
| | | | | | | | - Lili Dong
- College of Horticulture, Anhui Agricultural University, Hefei 230036, China; (H.Y.); (T.Y.); (J.Q.); (X.D.)
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Li W, Fu Y, Lv W, Zhao S, Feng H, Shao L, Li C, Yang J. Characterization of the early gene expression profile in Populus ussuriensis under cold stress using PacBio SMRT sequencing integrated with RNA-seq reads. TREE PHYSIOLOGY 2022; 42:646-663. [PMID: 34625806 DOI: 10.1093/treephys/tpab130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Populus ussuriensis is an important and fast-growing afforestation plant species in north-eastern China. The whole-genome sequencing of P. ussuriensis has not been completed. Also, the transcriptional network of P. ussuriensis response to cold stress remains unknown. To unravel the early response of P. ussuriensis to chilling (3 °C) stress and freezing (-3 °C) stresses at the transcriptional level, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing for P. ussuriensis. The SMRT long-read isoform sequencing led to the identification of 29,243,277 subreads and 575,481 circular consensus sequencing reads. Approximately 50,910 high-quality isoforms were generated, and 2272 simple sequence repeats and 8086 long non-coding RNAs were identified. The Ca2+ content and abscisic acid (ABA) content in P. ussuriensis were significantly increased under cold stresses, while the value in the freezing stress treatment group was significantly higher than the chilling stress treatment group. A total of 49 genes that are involved in the signal transduction pathways related to perception and transmission of cold stress signals, such as the Ca2+ signaling pathway, ABA signaling pathway and MAPK signaling cascade, were found to be differentially expressed. In addition, 158 transcription factors from 21 different families, such as MYB, WRKY and AP2/ERF, were differentially expressed during chilling and freezing treatments. Moreover, the measurement of physiological indicators and bioinformatics observations demonstrated the altered expression pattern of genes involved in reactive oxygen species balance and the sugar metabolism pathway during chilling and freezing stresses. This is the first report of the early responses of P. ussuriensis to cold stress, which lays the foundation for future studies on the regulatory mechanisms in cold-stress response. In addition the full-length reference transcriptome of P. ussuriensis deciphered could be used in future studies on P. ussuriensis.
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Affiliation(s)
- Wenlong Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Yanrui Fu
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Wanqiu Lv
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Shicheng Zhao
- School of Pharmacy, Harbin University of Commerce, No.138 Tongdajie Street, Harbin 150028, China
| | - He Feng
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Liying Shao
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Chenghao Li
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
| | - Jingli Yang
- State Key Laboratory of Forest Genetics and Tree Breeding, Northeast Forestry University, 26 Hexing Road, Harbin 150040, China
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Overexpression of CpWRKY75 from Chimonanthus praecox Promotes Flowering Time in Transgenic Arabidopsis. Genes (Basel) 2021; 13:genes13010068. [PMID: 35052409 PMCID: PMC8774968 DOI: 10.3390/genes13010068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Revised: 12/22/2021] [Accepted: 12/23/2021] [Indexed: 11/17/2022] Open
Abstract
WRKY transcription factors play critical roles in the physiological processes of plants. Although the roles of WRKYs have been characterized in some model plants, their roles in woody plants, especially wintersweet (Chimonanthus praecox), are largely unclear. In this study, a wintersweet WRKY gene named CpWRKY75 belonging to group IIc was isolated and its characteristics were identified. CpWRKY75 is a nucleus-localized protein, and exhibited no transcriptional activation activity in yeast. CpWRKY75 was highly expressed in flowers at different bloom stages. Ectopic expression of CpWRKY75 significantly promoted the flowering time of transgenic Arabidopsis (Arabidopsis thaliana), as determined by the rosette leaf number and first flower open time. The expression levels of flowering-related genes were quantified by qRT-PCR, and the results suggested that CpWRKY75 had obvious influence on the expression level of MICRORNA156C (MIR156C), SQUAMOSA PROMOTER BINDING PROTEIN-LIKE3 (SPL3) and SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 9 (SPL9), FLOWERING LOCUS T (FT), LEAFY (LFY), SUPPRESSOR OF OVEREXPRESSION OF CO 1 (SOC1), APETALA1 (AP1), CAULIFLOWER (CAL), and FRUITFULL (FUL). These results suggest that CpWRKY75 might have a flowering time regulation function, and additionally provide a new gene resource for the genetic engineering of woody flowering plants.
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Baloch AA, Raza AM, Rana SSA, Ullah S, Khan S, Zaib-un-Nisa, Zahid H, Malghani GK, Kakar KU. BrCNGC gene family in field mustard: genome-wide identification, characterization, comparative synteny, evolution and expression profiling. Sci Rep 2021; 11:24203. [PMID: 34921218 PMCID: PMC8683401 DOI: 10.1038/s41598-021-03712-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 12/03/2021] [Indexed: 12/30/2022] Open
Abstract
CNGCs are ligand-gated calcium signaling channels, which participate in important biological processes in eukaryotes. However, the CNGC gene family is not well-investigated in Brassica rapa L. (i.e., field mustard) that is economically important and evolutionary model crop. In this study, we systematically identified 29 member genes in BrCNGC gene family, and studied their physico-chemical properties. The BrCNGC family was classified into four major and two sub phylogenetic groups. These genes were randomly localized on nine chromosomes, and dispersed into three sub-genomes of B. rapa L. Both whole-genome triplication and gene duplication (i.e., segmental/tandem) events participated in the expansion of the BrCNGC family. Using in-silico bioinformatics approaches, we determined the gene structures, conserved motif compositions, protein interaction networks, and revealed that most BrCNGCs can be regulated by phosphorylation and microRNAs of diverse functionality. The differential expression patterns of BrCNGC genes in different plant tissues, and in response to different biotic, abiotic and hormonal stress types, suggest their strong role in plant growth, development and stress tolerance. Notably, BrCNGC-9, 27, 18 and 11 exhibited highest responses in terms of fold-changes against club-root pathogen Plasmodiophora brassicae, Pseudomonas syringae pv. maculicola, methyl-jasmonate, and trace elements. These results provide foundation for the selection of candidate BrCNGC genes for future breeding of field mustard.
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Affiliation(s)
- Akram Ali Baloch
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Agha Muhammad Raza
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Shahjahan Shabbir Ahmed Rana
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Saad Ullah
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Samiullah Khan
- grid.440526.10000 0004 0609 3164Department of Biotechnology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering, and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Zaib-un-Nisa
- grid.411555.10000 0001 2233 7083Department of Botany, GC University Lahore, Lahore, Pakistan
| | - Humera Zahid
- grid.413062.2Department of Zoology, University of Balochistan, Quetta, Pakistan
| | - Gohram Khan Malghani
- grid.440526.10000 0004 0609 3164Department of Environmental Sciences, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
| | - Kaleem U. Kakar
- grid.440526.10000 0004 0609 3164Department of Microbiology, Faculty of Life Sciences, Balochistan University of Information Technology, Engineering and Management Sciences (BUITEMS), Quetta, 87300 Pakistan
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Genome-Wide Identification and Analysis of the WRKY Gene Family and Cold Stress Response in Acer truncatum. Genes (Basel) 2021; 12:genes12121867. [PMID: 34946815 PMCID: PMC8701280 DOI: 10.3390/genes12121867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 11/21/2021] [Accepted: 11/23/2021] [Indexed: 11/17/2022] Open
Abstract
WRKY transcription factors constitute one of the largest gene families in plants and are involved in many biological processes, including growth and development, physiological metabolism, and the stress response. In earlier studies, the WRKY gene family of proteins has been extensively studied and analyzed in many plant species. However, information on WRKY transcription factors in Acer truncatum has not been reported. In this study, we conducted genome-wide identification and analysis of the WRKY gene family in A. truncatum, 54 WRKY genes were unevenly located on all 13 chromosomes of A. truncatum, the highest number was found in chromosomes 5. Phylogenetic relationships, gene structure, and conserved motif identification were constructed, and the results affirmed 54 AtruWRKY genes were divided into nine subgroup groups. Tissue species analysis of AtruWRKY genes revealed which were differently exhibited upregulation in flower, leaf, root, seed and stem, and the upregulation number were 23, 14, 34, 18, and 8, respectively. In addition, the WRKY genes expression in leaf under cold stress showed that more genes were significantly expressed under 0, 6 and 12 h cold stress. The results of this study provide a new insight the regulatory function of WRKY genes under abiotic and biotic stresses.
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Xiao P, Feng JW, Zhu XT, Gao J. Evolution Analyses of CAMTA Transcription Factor in Plants and Its Enhancing Effect on Cold-tolerance. FRONTIERS IN PLANT SCIENCE 2021; 12:758187. [PMID: 34790215 PMCID: PMC8591267 DOI: 10.3389/fpls.2021.758187] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 10/12/2021] [Indexed: 05/30/2023]
Abstract
The calmodulin binding transcription activator (CAMTA) is a transcription factor that is widely present in eukaryotes with conserved structure. It contributes to the response to biotic and abiotic stresses and promotes the growth and development of plants. Although previous studies have investigated the number and function of CAMTAs in some species, there is still a lack of comprehensive understanding of the evolutionary process, phylogenetic relationship, expression patterns, and functions of CAMTAs in plants. Here we identified 465 CMATA genes from 112 plants and systematically studied the origin of CAMTA family, gene expansion, functional differentiation, gene structure, and conservative motif distribution. Based on these analyses, we presented the evidence that CAMTA family was originated from chlorophyta, and we speculated that CAMTA might experience obvious structure variation during its early evolution, and that the number of CAMTA genes might gradually increase in higher plants. To reveal potential functions of CAMTA genes, we analyzed the expression patterns of 12 representative species and found significant species specificity, tissue specificity, and developmental stage specificity of CAMTAs. The results also indicated that the CAMTA genes might promote the maturation and senescence. The expression levels and regulatory networks of CAMTAs revealed that CAMTAs could enhance cold tolerance of rice by regulating carbohydrate metabolism-related genes to accumulate carbohydrates or by modulating target genes together with other transcription factors. Our study provides an insight into the molecular evolution of CAMTA family and lays a foundation for further study of related biological functions.
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Affiliation(s)
| | | | | | - Junxiang Gao
- Hubei Key Laboratory of Agricultural Bioinformatics, College of Informatics, Huazhong Agricultural University, Wuhan, China
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Li S, Wang L, Zhang Y, Zhu G, Zhu X, Xia Y, Li J, Gao X, Wang S, Zhang J, Wuyun TN, Mo W. Genome-Wide Identification and Function of Aquaporin Genes During Dormancy and Sprouting Periods of Kernel-Using Apricot ( Prunus armeniaca L.). FRONTIERS IN PLANT SCIENCE 2021; 12:690040. [PMID: 34671366 PMCID: PMC8520955 DOI: 10.3389/fpls.2021.690040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 07/27/2021] [Indexed: 06/13/2023]
Abstract
Aquaporins (AQPs) are essential channel proteins that play a major role in plant growth and development, regulate plant water homeostasis, and transport uncharged solutes across biological membranes. In this study, 33 AQP genes were systematically identified from the kernel-using apricot (Prunus armeniaca L.) genome and divided into five subfamilies based on phylogenetic analyses. A total of 14 collinear blocks containing AQP genes between P. armeniaca and Arabidopsis thaliana were identified by synteny analysis, and 30 collinear blocks were identified between P. armeniaca and P. persica. Gene structure and conserved functional motif analyses indicated that the PaAQPs exhibit a conserved exon-intron pattern and that conserved motifs are present within members of each subfamily. Physiological mechanism prediction based on the aromatic/arginine selectivity filter, Froger's positions, and three-dimensional (3D) protein model construction revealed marked differences in substrate specificity between the members of the five subfamilies of PaAQPs. Promoter analysis of the PaAQP genes for conserved regulatory elements suggested a greater abundance of cis-elements involved in light, hormone, and stress responses, which may reflect the differences in expression patterns of PaAQPs and their various functions associated with plant development and abiotic stress responses. Gene expression patterns of PaAQPs showed that PaPIP1-3, PaPIP2-1, and PaTIP1-1 were highly expressed in flower buds during the dormancy and sprouting stages of P. armeniaca. A PaAQP coexpression network showed that PaAQPs were coexpressed with 14 cold resistance genes and with 16 cold stress-associated genes. The expression pattern of 70% of the PaAQPs coexpressed with cold stress resistance genes was consistent with the four periods [Physiological dormancy (PD), ecological dormancy (ED), sprouting period (SP), and germination stage (GS)] of flower buds of P. armeniaca. Detection of the transient expression of GFP-tagged PaPIP1-1, PaPIP2-3, PaSIP1-3, PaXIP1-2, PaNIP6-1, and PaTIP1-1 revealed that the fusion proteins localized to the plasma membrane. Predictions of an A. thaliana ortholog-based protein-protein interaction network indicated that PaAQP proteins had complex relationships with the cold tolerance pathway, PaNIP6-1 could interact with WRKY6, PaTIP1-1 could interact with TSPO, and PaPIP2-1 could interact with ATHATPLC1G. Interestingly, overexpression of PaPIP1-3 and PaTIP1-1 increased the cold tolerance of and protein accumulation in yeast. Compared with wild-type plants, PaPIP1-3- and PaTIP1-1-overexpressing (OE) Arabidopsis plants exhibited greater tolerance to cold stress, as evidenced by better growth and greater antioxidative enzyme activities. Overall, our study provides insights into the interaction networks, expression patterns, and functional analysis of PaAQP genes in P. armeniaca L. and contributes to the further functional characterization of PaAQPs.
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Affiliation(s)
- Shaofeng Li
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
| | - Lin Wang
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
| | - Yaoxiang Zhang
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
| | - Gaopu Zhu
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
| | - Xuchun Zhu
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
| | - Yongxiu Xia
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
| | - Jianbo Li
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
| | - Xu Gao
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
| | - Shaoli Wang
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
| | - Jianhui Zhang
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, United States
| | - Ta-na Wuyun
- State Key Laboratory of Tree Genetics and Breeding, Non-timber Forestry Research and Development Center, Chinese Academy of Forestry, Zhengzhou, China
| | - Wenjuan Mo
- State Key Laboratory of Tree Genetics and Breeding, Experimental Center of Forestry in North China, National Permanent Scientific Research Base for Warm Temperate Zone Forestry of Jiulong Mountain in Beijing, Chinese Academy of Forestry, Beijing, China
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Bano N, Patel P, Chakrabarty D, Bag SK. Genome-wide identification, phylogeny, and expression analysis of the bHLH gene family in tobacco ( Nicotiana tabacum). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1747-1764. [PMID: 34539114 PMCID: PMC8405835 DOI: 10.1007/s12298-021-01042-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/24/2021] [Accepted: 07/27/2021] [Indexed: 05/05/2023]
Abstract
UNLABELLED The basic helix-loop-helix (bHLH) is the second-largest TF family in plants that play important roles in plant growth, development, and stress responses. In this study, a total of 100 bHLHs were identified using Hidden Markov Model profiles in the Nicotiana tabacum genome, clustered into 15 major groups (I-XV) based on their conserved domains and phylogenetic relationships. Group VIII genes were found to be the most abundant, with 27 NtbHLH members. The expansion of NtbHLHs in the genome was due to segmental and tandem duplication. The purifying selection was found to have an important role in the evolution of NtHLHs. Subsequent qRT-PCR validation of five selected genes from transcriptome data revealed that NtbHLH3.1, NtbHLH3.2, NtbHLH24, NtbHLH50, and NtbHLH59.2 have higher expressions at 12 and 24 h in comparison to 0 h (control) of chilling stress. The validated results demonstrated that NtbHLH3.2 and NtbHLH24 genes have 3 and fivefold higher expression at 12 h and 2 and threefold higher expression at 24 h than control plant, shows high sensitivity towards chilling stress. Moreover, the co-expression of positively correlated genes of NtbHLH3.2 and NtbHLH24 confirmed their functional significance in chilling stress response. Therefore, suggesting the importance of NtbHLH3.2 and NtbHLH24 genes in exerting control over the chilling stress responses in tobacco. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01042-x.
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Affiliation(s)
- Nasreen Bano
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Preeti Patel
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
| | - Debasis Chakrabarty
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
| | - Sumit Kumar Bag
- Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001 India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002 India
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Yamada Y, Nishida S, Shitan N, Sato F. Genome-Wide Profiling of WRKY Genes Involved in Benzylisoquinoline Alkaloid Biosynthesis in California Poppy ( Eschscholzia californica). FRONTIERS IN PLANT SCIENCE 2021; 12:699326. [PMID: 34220919 PMCID: PMC8248504 DOI: 10.3389/fpls.2021.699326] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/25/2021] [Indexed: 06/13/2023]
Abstract
Transcription factors of the WRKY family play pivotal roles in plant defense responses, including the biosynthesis of specialized metabolites. Based on the previous findings of WRKY proteins regulating benzylisoquinoline alkaloid (BIA) biosynthesis, such as CjWRKY1-a regulator of berberine biosynthesis in Coptis japonica-and PsWRKY1-a regulator of morphine biosynthesis in Papaver somniferum-we performed genome-wide characterization of the WRKY gene family in Eschscholzia californica (California poppy), which produces various BIAs. Fifty WRKY genes were identified by homology search and classified into three groups based on phylogenetic, gene structure, and conserved motif analyses. RNA sequencing showed that several EcWRKY genes transiently responded to methyl jasmonate, a known alkaloid inducer, and the expression patterns of these EcWRKY genes were rather similar to those of BIA biosynthetic enzyme genes. Furthermore, tissue expression profiling suggested the involvement of a few subgroup IIc EcWRKYs in the regulation of BIA biosynthesis. Transactivation analysis using luciferase reporter genes harboring the promoters of biosynthetic enzyme genes indicated little activity of subgroup IIc EcWRKYs, suggesting that the transcriptional network of BIA biosynthesis constitutes multiple members. Finally, we investigated the coexpression patterns of EcWRKYs with some transporter genes and discussed the diversified functions of WRKY genes based on a previous finding that CjWRKY1 overexpression in California poppy cells enhanced BIA secretion into the medium.
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Affiliation(s)
- Yasuyuki Yamada
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Kobe, Japan
| | - Shohei Nishida
- Department of Plant Gene and Totipotency, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
| | - Nobukazu Shitan
- Laboratory of Medicinal Cell Biology, Kobe Pharmaceutical University, Kobe, Japan
| | - Fumihiko Sato
- Department of Plant Gene and Totipotency, Division of Integrated Life Science, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
- Graduate School of Science, Osaka Prefecture University, Sakai, Japan
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Cao Z, Wu P, Gao H, Xia N, Jiang Y, Tang N, Liu G, Chen Z. Transcriptome-wide characterization of the WRKY family genes in Lonicera macranthoides and the role of LmWRKY16 in plant senescence. Genes Genomics 2021; 44:219-235. [PMID: 34110609 DOI: 10.1007/s13258-021-01118-8] [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: 02/04/2021] [Accepted: 05/31/2021] [Indexed: 11/24/2022]
Abstract
BACKGROUND Lonicera macranthoides is an important woody plant with high medicinal values widely cultivated in southern China. WRKY, one of the largest transcription factor families, participates in plant development, senescence, and stress responses. However, a comprehensive study of the WRKY family in L. macranthoides hasn't been reported previously. OBJECTIVE To establish an extensive overview of the WRKY family in L. macranthoides and identify senescence-responsive members of LmWRKYs. METHODS RNA-Seq and phylogenetic analysis were employed to identify the LmWRKYs and their evolutionary relationships. Quantitative real-time (qRT-PCR) and transgenic technology was utilized to investigate the roles of LmWRKYs in response to developmental-, cold-, and ethylene-induced senescence. RESULTS A total of 61 LmWRKY genes with a highly conserved motif WRKYGQK were identified. Phylogenetic analysis of LmWRKYs together with their orthologs from Arabidopsis classified them into three groups, with the number of 15, 39, and 7, respectively. 17 LmWRKYs were identified to be differentially expressed between young and aging leaves by RNA-Seq. Further qRT-PCR analysis showed 15 and 5 LmWRKY genes were significantly induced responding to tissue senescence in leaves and stems, respectively. What's more, five LmWRKYs, including LmWRKY4, LmWRKY5, LmWRKY6, LmWRKY11, and LmWRKY16 were dramatically upregulated under cold and ethylene treatment in both leaves and stems, indicating their involvements commonly in developmental- and stress-induced senescence. In addition, function analysis revealed LmWRKY16, a homolog of AtWRKY75, can accelerate plant senescence, as evidenced by leaf yellowing during reproductive growth in LmWRKY16-overexpressing tobaccos. CONCLUSION The results lay the foundation for molecular characterization of LmWRKYs in plant senescence.
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Affiliation(s)
- Zhengyan Cao
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.,College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, China
| | - Peiyin Wu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China.,College of Horticulture and Gardening, Yangtze University, Jingzhou, 434025, China
| | - Hongmei Gao
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Ning Xia
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Ying Jiang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Ning Tang
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China. .,Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing, 400000, China. .,Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing, 400000, China.
| | - Guohua Liu
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China
| | - Zexiong Chen
- College of Landscape Architecture and Life Science, Chongqing University of Arts and Sciences, Chongqing, 402160, China. .,Chongqing Key Laboratory of Economic Plant Biotechnology, Chongqing, 400000, China. .,Collaborative Innovation Center of Special Plant Industry in Chongqing, Chongqing, 400000, China.
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Zhao W, Li Y, Fan S, Wen T, Wang M, Zhang L, Zhao L. The transcription factor WRKY32 affects tomato fruit colour by regulating YELLOW FRUITED-TOMATO 1, a core component of ethylene signal transduction. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:4269-4282. [PMID: 33773493 DOI: 10.1093/jxb/erab113] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 03/10/2021] [Indexed: 06/12/2023]
Abstract
Fruit quality in most fleshy fruit crops is fundamentally linked to ripening-associated traits, including changes in colour. In many climacteric fruits, including tomato (Solanum lycopersicum), the phytohormone ethylene plays a key role in regulating ripening. Previous map-based cloning of YELLOW FRUITED-TOMATO 1 (YFT1) revealed that it encodes the EIN2 protein, a core component in ethylene signal transduction. A YFT1 allele with a genetic lesion was found to be down-regulated in the yft1 tomato mutant that has a yellow fruit phenotype and perturbed ethylene signalling. Based on bioinformatic analysis, yeast one hybrid assays and electrophoretic mobility shift assays, we report that transcription factor WRKY32 regulates tomato fruit colour formation. WRKY32 binds to W-box and W-box-like motifs in the regulatory region of the YFT1 promoter and induces its expression. In tomato fruits of WRKY32-RNAi generated lines, ethylene signalling was reduced, leading to a suppression in ethylene emission, a delay in chromoplast development, decreased carotenoid accumulation, and a yellow fruit phenotype. These results provide new insights into the regulatory networks that govern tomato fruit colour formation via ethylene signal transduction.
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Affiliation(s)
- Weihua Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yuhang Li
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaozhu Fan
- Branch Institute of Horticulture, Harbin Academy of Agricultural Science, Harbin, China
| | - Tengjian Wen
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Minghui Wang
- Bioinformatics Facility, Institute of Biotechnology, Cornell University, Ithaca, New York, USA
| | - Lida Zhang
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Lingxia Zhao
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- Joint Tomato Research Institute, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Plant Transcription Factors Involved in Drought and Associated Stresses. Int J Mol Sci 2021; 22:ijms22115662. [PMID: 34073446 PMCID: PMC8199153 DOI: 10.3390/ijms22115662] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 05/14/2021] [Accepted: 05/19/2021] [Indexed: 11/16/2022] Open
Abstract
Transcription factors (TFs) play a significant role in signal transduction networks spanning the perception of a stress signal and the expression of corresponding stress-responsive genes. TFs are multi-functional proteins that may simultaneously control numerous pathways during stresses in plants-this makes them powerful tools for the manipulation of regulatory and stress-responsive pathways. In recent years, the structure-function relationships of numerous plant TFs involved in drought and associated stresses have been defined, which prompted devising practical strategies for engineering plants with enhanced stress tolerance. Vast data have emerged on purposely basic leucine zipper (bZIP), WRKY, homeodomain-leucine zipper (HD-Zip), myeloblastoma (MYB), drought-response elements binding proteins/C-repeat binding factor (DREB/CBF), shine (SHN), and wax production-like (WXPL) TFs that reflect the understanding of their 3D structure and how the structure relates to function. Consequently, this information is useful in the tailored design of variant TFs that enhances our understanding of their functional states, such as oligomerization, post-translational modification patterns, protein-protein interactions, and their abilities to recognize downstream target DNA sequences. Here, we report on the progress of TFs based on their interaction pathway participation in stress-responsive networks, and pinpoint strategies and applications for crops and the impact of these strategies for improving plant stress tolerance.
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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: 23] [Impact Index Per Article: 7.7] [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.
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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.
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Wang Y, Xin H, Fan P, Zhang J, Liu Y, Dong Y, Wang Z, Yang Y, Zhang Q, Ming R, Zhong GY, Li S, Liang Z. The genome of Shanputao (Vitis amurensis) provides a new insight into cold tolerance of grapevine. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 105:1495-1506. [PMID: 33300184 DOI: 10.1111/tpj.15127] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Revised: 11/24/2020] [Accepted: 12/03/2020] [Indexed: 06/12/2023]
Abstract
Vitis amurensis (Shanputao) is the most cold tolerant Vitis species and so is of great interest to grape breeders and producers in areas with low winter temperatures. Here, we report its high-quality, chromosome-level genome assembly based on a combination of sequence data from Illumina and PacBio platforms, BioNano optical mapping and high-throughput chromosome conformation Capture (Hi-C) mapping. The 604.56-Mb genome contains 32 885 protein-coding genes. Shanputao was found to share a common ancestor with PN40024 (V. vinifera) approximately 2.17-2.91 million years ago, and gene expansion observed in Shanputao might contribute to the enhancement of cold tolerance. Transcriptome analysis revealed 17 genes involved in cold signal transduction, suggesting that there was a different response mechanism to chilling temperature and freezing conditions. Furthermore, a genome-wide association study uncovered a phosphoglycerate kinase gene that may contribute to the freezing resistance of buds in the winter. The Shanputao genome sequence not only represents a valuable resource for grape breeders, but also is important for clarifying the molecular mechanisms involved in cold tolerance.
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Affiliation(s)
- Yi Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, PR China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Peige Fan
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing, 100093, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yongbo Liu
- State Key Laboratory of Environmental Criteria and Risk Assessment, Chinese Research Academy of Environmental Sciences, 8 Dayangfang, Beijing, 100012, China
| | - Yang Dong
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, 650201, China
| | - Zemin Wang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yingzhen Yang
- US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, USA
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ray Ming
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Gan-Yuan Zhong
- US Department of Agriculture-Agricultural Research Service, Grape Genetics Research Unit, Geneva, New York, USA
| | - Shaohua Li
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, and CAS Key Laboratory of Plant Resources, Institute of Botany, Innovation Academy for Seed Design, the Chinese Academy of Science, Beijing, 100093, China
- Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China
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Wei Z, Ye J, Zhou Z, Chen G, Meng F, Liu Y. Isolation and characterization of PoWRKY, an abiotic stress-related WRKY transcription factor from Polygonatum odoratum. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1-9. [PMID: 33627958 PMCID: PMC7873195 DOI: 10.1007/s12298-020-00924-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 05/28/2023]
Abstract
WRKY transcription factors play vital roles in response to biotic and abiotic stresses in plants. As a kind of high value medicinal plant, Polygonatum odoratum has an ability to tolerate various abiotic stresses because of the special growth condition. In current study, a novel WRKY gene from P. odoratum is isolated and compared with homologous sequences from other plants. PoWRKY1 possesses two typical WRKY domains and two C2H2 zinc-finger motifs. Evolutionary analysis indicated that PoWRKY1 is most closely related to WRKY protein from Asparagus officinalis. Expression analysis showed that expression of PoWRKY1 is induced by cold and drought stresses but not salt stress. Overexpression of PoWRKY1 in Arabidopsis improved seed germination and root growth of transgenic plants during cold stress and drought. In addition, super oxide dismutase activity and proline content in transgenic plants increased under cold and drought stresses, whereas malondialdehyde levels and relative electrolyte leakage reduced under similar stress conditions. Taken together, these results showed that PoWRKY1 enhances the tolerance to cold and drought stresses. This study lays a potential foundation to understand the molecular mechanism of tolerance to abiotic stress in P. odoratum.
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Affiliation(s)
- Zhongping Wei
- Forestry Biotechnology and Analysis Test Center, Liaoning Academy of Forestry Sciences, Shenyang, 110032 China
| | - Jingfeng Ye
- Forestry Biotechnology and Analysis Test Center, Liaoning Academy of Forestry Sciences, Shenyang, 110032 China
| | - Zhiquan Zhou
- Forestry Biotechnology and Analysis Test Center, Liaoning Academy of Forestry Sciences, Shenyang, 110032 China
| | - Gang Chen
- Forestry Biotechnology and Analysis Test Center, Liaoning Academy of Forestry Sciences, Shenyang, 110032 China
| | - Fanjin Meng
- Forestry Biotechnology and Analysis Test Center, Liaoning Academy of Forestry Sciences, Shenyang, 110032 China
| | - Yifei Liu
- Forestry Biotechnology and Analysis Test Center, Liaoning Academy of Forestry Sciences, Shenyang, 110032 China
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Table Grapes during Postharvest Storage: A Review of the Mechanisms Implicated in the Beneficial Effects of Treatments Applied for Quality Retention. Int J Mol Sci 2020; 21:ijms21239320. [PMID: 33297419 PMCID: PMC7730992 DOI: 10.3390/ijms21239320] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 12/03/2020] [Accepted: 12/06/2020] [Indexed: 12/22/2022] Open
Abstract
Table grape is a fruit with increasing interest due to its attributes and nutritional compounds. During recent years, new cultivars such as those without seeds and with new flavors have reached countries around the world. For this reason, postharvest treatments that retain fruit quality need to be improved. However, little is known to date about the biochemical and molecular mechanisms related with observed quality improvements. This review aims to examine existing literature on the different mechanisms. Special attention will be placed on molecular mechanisms which activate and regulate the different postharvest treatments applied in order to improve table grape quality.
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43
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Zhang L, Wan X, Xu Y, Niyitanga S, Qi J, Zhang L. De novo assembly of transcriptome and genome-wide identification reveal GA 3 stress-responsive WRKY transcription factors involved in fiber formation in jute (Corchorus capsularis). BMC PLANT BIOLOGY 2020; 20:403. [PMID: 32867682 PMCID: PMC7460746 DOI: 10.1186/s12870-020-02617-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 08/23/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND WRKY is a group of transcription factors (TFs) that play a vital role in plant growth, development, and stress tolerance. To date, none of jute WRKY (CcWRKY) genes have been identified, even if jute (Corchorus capsularis) is one of the most important natural fiber crops in the world. Little information about the WRKY genes in jute is far from sufficient to understand the molecular mechanism of bast fiber biosynthesis. RESULTS A total of 244,489,479 clean reads were generated using Illumina paired-end sequencing. De novo assembly yielded 90,982 unigenes with an average length of 714 bp. By sequence similarity searching for known proteins, 48,896 (53.74%) unigenes were annotated. To mine the CcWRKY TFs and identify their potential function, the search for CcWRKYs against the transcriptome data of jute was performed, and a total of 43 CcWRKYs were identified in this study. The gene structure, phylogeny, conserved domain and three-dimensional structure of protein were analyzed by bioinformatics tools of GSDS2.0, MEGA7.0, DNAMAN5.0, WebLogo 3 and SWISS-MODEL respectively. Phylogenetic analysis showed that 43 CcWRKYs were divided into three groups: I, II and III, containing 9, 28, and 6 members respectively, according to the WRKY conserved domain features and the evolution analysis with Arabidopsis thaliana. Gene structure analysis indicated that the number of exons of these CcWRKYs varied from 3 to 11. Among the 43 CcWRKYs, 10, 2, 2, and 14 genes showed higher expression in leaves, stem sticks, stem barks, and roots at the vigorous vegetative growth stage, respectively. Moreover, the expression of 21 of 43 CcWRKYs was regulated significantly with secondary cell wall biosynthesis genes using FPKM and RT-qPCR by GA3 stress to a typical GA3 sensitive dwarf germplasm in comparison to an elite cultivar in jute. The Cis-element analysis showed that promoters of these 21 CcWRKYs had 1 to 4 cis-elements involved in gibberellin-responsiveness, suggesting that they might regulate the development of bast fiber in response to GA3 stress. CONCLUSIONS A total of 43 CcWRKYs were identified in jute for the first time. Analysis of phylogenetic relationship and gene structure revealed that these CcWRKYs might have a functional diversity. Expression analysis showed 21 TFs as GA3 stress responsive genes. The identification of these CcWRKYs and the characterization of their expression pattern will provide a basis for future clarification of their functions in bast fiber development in jute.
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Affiliation(s)
- Lilan Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Xuebei Wan
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
| | - Yi Xu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Sylvain Niyitanga
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Jianmin Qi
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Liwu Zhang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops / Fujian Key Laboratory for Crop Breeding by Design / College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
- Experiment Station of Ministry of Agriculture and Rural Affairs for Jute and Kenaf in Southeast China / Fujian Public Platform for Germplasm Resources of Bast Fiber Crops / Fujian International Science and Technology Cooperation Base for Genetics, Breeding and Multiple Utilization Development of Southern Economic Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002 Fujian China
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
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Li X, He L, An X, Yu K, Meng N, Duan C, Pan QH. VviWRKY40, a WRKY Transcription Factor, Regulates Glycosylated Monoterpenoid Production by VviGT14 in Grape Berry. Genes (Basel) 2020; 11:genes11050485. [PMID: 32365554 PMCID: PMC7290806 DOI: 10.3390/genes11050485] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 11/16/2022] Open
Abstract
Glycosylated volatile precursors are important, particularly in wine grape berries, as they contribute to the final aroma in wines by releasing volatile aglycones during yeast fermentation and wine storage. Previous study demonstrated that VviGT14 was functioned as a critical monoterpene glucosyltransferase in grape berry, while the transcriptional regulation mechanism of VviGT14 was still unknown. Here we identified VviWRKY40 as a binding factor of VviGT14 promoter by both DNA pull-down and yeast one-hybrid screening, followed by a series of in vitro verification. VviWRKY40 expression pattern negatively correlated with that of VviGT14 in grape berries. And the suppressor role of VviWRKY40 was further confirmed by using the dual luciferase assay with Arabidopsis protoplast and grape cell suspension system. Furthermore, the grape suspension cell ABA treatment study showed that ABA downregulated VviWRKY40 transcript level but promoted that of VviGT14, indicating that VviWRKY40 was at the downstream of ABA signal transduction network to regulate monoterpenoid glycosylation. These data extend our knowledge of transcriptional regulation of VviGT14, and provide new targets for grape breeding to alter monoterpenoid composition.
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Affiliation(s)
- Xiangyi Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.L.); (L.H.); (X.A.); (K.Y.); (N.M.); (C.D.)
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Lei He
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.L.); (L.H.); (X.A.); (K.Y.); (N.M.); (C.D.)
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Xiaohui An
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.L.); (L.H.); (X.A.); (K.Y.); (N.M.); (C.D.)
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Keji Yu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.L.); (L.H.); (X.A.); (K.Y.); (N.M.); (C.D.)
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Nan Meng
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.L.); (L.H.); (X.A.); (K.Y.); (N.M.); (C.D.)
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Changqing Duan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.L.); (L.H.); (X.A.); (K.Y.); (N.M.); (C.D.)
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
| | - Qiu-Hong Pan
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China; (X.L.); (L.H.); (X.A.); (K.Y.); (N.M.); (C.D.)
- Key Laboratory of Viticulture and Enology, Ministry of Agriculture and Rural Affairs, Beijing 100083, China
- Correspondence: ; Tel.: +86-010-62737136
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Ding W, Ouyang Q, Li Y, Shi T, Li L, Yang X, Ji K, Wang L, Yue Y. Genome-wide investigation of WRKY transcription factors in sweet osmanthus and their potential regulation of aroma synthesis. TREE PHYSIOLOGY 2020; 40:557-572. [PMID: 31860707 DOI: 10.1093/treephys/tpz129] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 08/28/2019] [Accepted: 09/17/2019] [Indexed: 05/20/2023]
Abstract
WRKY transcription factors, one of the largest transcription factor families, play important roles in regulating the synthesis of secondary metabolites. In sweet osmanthus (Osmanthus fragrans), the monoterpenes have been demonstrated as the most important volatile compounds, and the W-box, which is the cognate binding site of WRKY transcription factors, could be identified in most of the terpene-synthesis-related genes' promoters. However, the role of the WRKY family in terpene synthesis in sweet osmanthus has rarely been examined. In this study, 154 WRKY genes with conserved WRKY domain were identified and classified into three groups. The group II was further divided into five subgroups, and almost all members of IId contained a plant zinc cluster domain. Eight OfWRKYs (OfWRKY7/19/36/38/42/84/95/139) were screened from 20 OfWRKYs for their flower-specific expression patterns in different tissues. Simultaneously, the expression patterns of OfWRKYs and emission patterns of volatile compounds during the flowering process were determined and gas chromatography-mass spectrometry results showed that monoterpenes, such as linalool and ocimene, accounted for the highest proportion, contributing to the floral scent of sweet osmanthus in two cultivars. In addition, correlation analysis revealed the expression patterns of OfWRKYs (OfWRKY7/19/36/139) were each correlated with distinct monoterpenes (linalool, linalool derivatives, ocimene and ocimene derivatives). Subcellular localization analysis showed that p35S::GFP-OfWRKY7/38/95/139 were localized in the nucleus and OfWRKY139 had very strong transactivation activity. Collectively, the results indicated potential roles of OfWRKY139 and OfWRKYs with plant zinc cluster domain in regulating synthesis of aromatic compounds in sweet osmanthus, laying the foundation for use of OfWRKYs to improve the aroma of ornamental plants.
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Affiliation(s)
- Wenjie Ding
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Qixia Ouyang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Yuli Li
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Tingting Shi
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Ling Li
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Xiulian Yang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Kongshu Ji
- Key Laboratory of Forest Genetics & Biotechnology, Ministry of Education, 210037, PR China
| | - Lianggui Wang
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, PR China
| | - Yuanzheng Yue
- Key Laboratory of Landscape Architecture, Jiangsu Province, College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, PR China
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Wang X, Li J, Guo J, Qiao Q, Guo X, Ma Y. The WRKY transcription factor PlWRKY65 enhances the resistance of Paeonia lactiflora (herbaceous peony) to Alternaria tenuissima. HORTICULTURE RESEARCH 2020; 7:57. [PMID: 32284869 PMCID: PMC7113260 DOI: 10.1038/s41438-020-0267-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Revised: 02/03/2020] [Accepted: 02/07/2020] [Indexed: 05/14/2023]
Abstract
In this study, the disease resistance gene PlWRKY65 was isolated from the leaves of Paeonia lactiflora and analyzed by bioinformatics methods, and the localization of the encoded protein was explored. Quantitative real-time PCR (qRT-PCR) was also used to explore the response of this gene to Alternaria tenuissima. The results showed that the gene sequence contained multiple cis-acting elements involved in the response to hormone signaling molecules belonging to the IIe subgroup of the WRKY family, and the encoded proteins were located in the nucleus. The PlWRKY65 gene has a positive regulatory effect on A. tenuissima infection. After silencing the PlWRKY65 gene via virus-induced gene silencing (VIGS), it was found that the gene-silenced plants were more sensitive to A. tenuissima infection than the wild plants, exhibiting more severe infection symptoms and different degrees of changes in the expression of the pathogenesis-related (PR) genes. In addition, we showed that the endogenous jasmonic acid (JA) content of P. lactiflora was increased in response to A. tenuissima infection, whereas the salicylic acid (SA) content decreased. After PlWRKY65 gene silencing, the levels of the two hormones changed accordingly, indicating that PlWRKY65, acting as a disease resistance-related transcriptional activator, exerts a regulatory effect on JA and SA signals. This study lays the foundation for functional research on WRKY genes in P. lactiflora and for the discovery of candidate disease resistance genes.
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Affiliation(s)
- Xue Wang
- College of Forestry, Shandong Agricultural University, No. 61, Daizong Road, 271018 Tai’an, Shandong China
| | - Junjie Li
- College of Forestry, Shandong Agricultural University, No. 61, Daizong Road, 271018 Tai’an, Shandong China
| | - Jing Guo
- College of Forestry, Shandong Agricultural University, No. 61, Daizong Road, 271018 Tai’an, Shandong China
- Shandong Provincial Research Center of Demonstration Engineering Technology for Urban and Rural Landscapes, 271018 Tai’an, Shandong China
| | - Qian Qiao
- Shandong Institute of Pomology, 271000 Tai’an, Shandong China
| | - Xianfeng Guo
- College of Forestry, Shandong Agricultural University, No. 61, Daizong Road, 271018 Tai’an, Shandong China
- Shandong Provincial Research Center of Demonstration Engineering Technology for Urban and Rural Landscapes, 271018 Tai’an, Shandong China
| | - Yan Ma
- College of Forestry, Shandong Agricultural University, No. 61, Daizong Road, 271018 Tai’an, Shandong China
- Shandong Provincial Research Center of Demonstration Engineering Technology for Urban and Rural Landscapes, 271018 Tai’an, Shandong China
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Jian H, Xie L, Wang Y, Cao Y, Wan M, Lv D, Li J, Lu K, Xu X, Liu L. Characterization of cold stress responses in different rapeseed ecotypes based on metabolomics and transcriptomics analyses. PeerJ 2020; 8:e8704. [PMID: 32266113 PMCID: PMC7120054 DOI: 10.7717/peerj.8704] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 02/06/2020] [Indexed: 01/04/2023] Open
Abstract
The winter oilseed ecotype is more tolerant to low temperature than the spring ecotype. Transcriptome and metabolome analyses of leaf samples of five spring Brassica napus L. (B. napus) ecotype lines and five winter B. napus ecotype lines treated at 4 °C and 28 °C were performed. A total of 25,460 differentially expressed genes (DEGs) of the spring oilseed ecotype and 28,512 DEGs of the winter oilseed ecotype were identified after cold stress; there were 41 differentially expressed metabolites (DEMs) in the spring and 47 in the winter oilseed ecotypes. Moreover, more than 46.2% DEGs were commonly detected in both ecotypes, and the extent of the changes were much more pronounced in the winter than spring ecotype. By contrast, only six DEMs were detected in both the spring and winter oilseed ecotypes. Eighty-one DEMs mainly belonged to primary metabolites, including amino acids, organic acids and sugars. The large number of specific genes and metabolites emphasizes the complex regulatory mechanisms involved in the cold stress response in oilseed rape. Furthermore, these data suggest that lipid, ABA, secondary metabolism, signal transduction and transcription factors may play distinct roles in the spring and winter ecotypes in response to cold stress. Differences in gene expression and metabolite levels after cold stress treatment may have contributed to the cold tolerance of the different oilseed ecotypes.
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Affiliation(s)
- Hongju Jian
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Ling Xie
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yanhua Wang
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Yanru Cao
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Mengyuan Wan
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Dianqiu Lv
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Jiana Li
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Kun Lu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Xinfu Xu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
| | - Liezhao Liu
- College of Agronomy and Biotechnology, Southwest University, Chongqing, China
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Suksamran R, Saithong T, Thammarongtham C, Kalapanulak S. Genomic and Transcriptomic Analysis Identified Novel Putative Cassava lncRNAs Involved in Cold and Drought Stress. Genes (Basel) 2020; 11:E366. [PMID: 32231066 PMCID: PMC7230406 DOI: 10.3390/genes11040366] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 01/09/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play important roles in the regulation of complex cellular processes, including transcriptional and post-transcriptional regulation of gene expression relevant for development and stress response, among others. Compared to other important crops, there is limited knowledge of cassava lncRNAs and their roles in abiotic stress adaptation. In this study, we performed a genome-wide study of ncRNAs in cassava, integrating genomics- and transcriptomics-based approaches. In total, 56,840 putative ncRNAs were identified, and approximately half the number were verified using expression data or previously known ncRNAs. Among these were 2229 potential novel lncRNA transcripts with unmatched sequences, 250 of which were differentially expressed in cold or drought conditions, relative to controls. We showed that lncRNAs might be involved in post-transcriptional regulation of stress-induced transcription factors (TFs) such as zinc-finger, WRKY, and nuclear factor Y gene families. These findings deepened our knowledge of cassava lncRNAs and shed light on their stress-responsive roles.
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Affiliation(s)
- Rungaroon Suksamran
- Biotechnology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
| | - Treenut Saithong
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
| | - Chinae Thammarongtham
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology at King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
| | - Saowalak Kalapanulak
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
- Center for Agricultural Systems Biology, Systems Biology and Bioinformatics Research Group, Pilot Plant Development and Training Institute, King Mongkut's University of Technology Thonburi (Bang KhunThian), Bangkok 10150, Thailand
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Sun W, Ma Z, Chen H, Liu M. Genome-wide investigation of WRKY transcription factors in Tartary buckwheat ( Fagopyrum tataricum) and their potential roles in regulating growth and development. PeerJ 2020; 8:e8727. [PMID: 32185114 PMCID: PMC7060923 DOI: 10.7717/peerj.8727] [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: 08/07/2019] [Accepted: 02/10/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND The WRKY gene family plays important roles in plant biological functions and has been identified in many plant species. With the publication of the Tartary buckwheat genome, the evolutionary characteristics of the WRKY gene family can be systematically explored and the functions of Fagopyrum tataricum WRKY (FtWRKY) genes in the growth and development of this plant also can be predicted. METHODS In this study, the FtWRKY genes were identified by the BLASTP method, and HMMER, SMART, Pfam and InterPro were used to determine whether the FtWRKY genes contained conserved domains. The phylogenetic trees including FtWRKY and WRKY genes in other plants were constructed by the neighbor-joining (NJ) and maximum likelihood (ML) methods. The intron and exon structures of the FtWRKY genes were analyzed by the gene structure display server, and the motif compositions were analyzed by MEME. Chromosome location information of FtWRKY genes was obtained with gff files and sequencing files, and visualized by Circos, and the collinear relationship was analyzed by Dual synteny plotter software. The expression levels of 26 FtWRKY genes from different groups in roots, leaves, flowers, stems and fruits at the green fruit, discoloration and initial maturity stage were measured through quantitative real-time polymerase chain reaction (qRT-PCR) analysis. RESULTS A total of 76 FtWRKY genes identified from the Tartary buckwheat genome were divided into three groups. FtWRKY genes in the same group had similar gene structures and motif compositions. Despite the lack of tandem-duplicated gene pairs, there were 23 pairs of segmental-duplicated gene pairs. The synteny gene pairs of FtWRKY genes and Glycine max WRKY genes were the most. FtWRKY42 was highly expressed in roots and may perform similar functions as its homologous gene AtWRKY75, playing a role in lateral root and hairy root formation. FtWRKY9, FtWRKY42 and FtWRKY60 were highly expressed in fruits and may play an important role in fruit development. CONCLUSION We have identified several candidate FtWRKY genes that may perform critical functions in the development of Tartary buckwheat root and fruit, which need be verified through further research. Our study provides useful information on WRKY genes in regulating growth and development and establishes a foundation for screening WRKY genes to improve Tartary buckwheat quality.
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Affiliation(s)
- Wenjun Sun
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Zhaotang Ma
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Hui Chen
- College of Life Science, Sichuan Agricultural University, Ya’an, China
| | - Moyang Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
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Yu S, Kakar KU, Yang Z, Nawaz Z, Lin S, Guo Y, Ren XL, Baloch AA, Han D. Systematic study of the stress-responsive Rboh gene family in Nicotiana tabacum: Genome-wide identification, evolution and role in disease resistance. Genomics 2020; 112:1404-1418. [PMID: 31430516 DOI: 10.1016/j.ygeno.2019.08.010] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 07/12/2019] [Accepted: 08/14/2019] [Indexed: 12/26/2022]
Abstract
Plant respiratory burst oxidase homolog (Rboh) gene family encodes the key enzymatic subunits of reactive oxygen species (ROS) production pathways, and play crucial role in plant signaling, development and stress responses. In present work, twenty genes were identified in Nicotiana tabacum Rboh family (NtabRboh) and classified into four phylogenetic groups (I-IV). Fourteen NtabRboh genes were positioned on ten chromosomes (i.e., Ch1, 2, 4, 7-11, 14 and 21), and six scaffolds. Synteny and evolutionary analysis showed that most of the NtabRboh genes have evolved from the genomes of the ancestor species (N. tomentosiformis and N. sylvestris), which afterwards expanded through duplication events. The promoter regions of the NtabRboh genes contained numerous cis-acting regulatory elements for hormones, plant growth, and different biotic and abiotic factors. The NtabRbohF gene transcript comprised target sites for wounding and stress responsive microRNAs: nta-miR166a-d, g and h. The transcript abundance of NtabRboh genes in different tissues reflected their important for plant growth and organ development in tobacco. RT-qPCR-assays demonstrated that the expression of NtabRboh genes are regulated by viral and bacterial pathogens, drought, cold and cadmium stress. The expression levels NtabRbohA, B and C were significantly up-regulated in "black shank and tobacco mosaic virus-inoculated susceptible and transgenic tobacco cultivars, showing that these genes play important roles in disease resistance.
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Affiliation(s)
- Shizhou Yu
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China; College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China.
| | - Kaleem Ullah Kakar
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology and Management Sciences, Quetta 87300, Pakistan.
| | - Zhixiao Yang
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Zarqa Nawaz
- Department of Botany, University of Central Punjab, Rawalpindi, Pakistan.
| | - Shifeng Lin
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Yushuang Guo
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Xue-Liang Ren
- Molecular Genetics Key Laboratory of China Tobacco, Guizhou Academy of Tobacco Science, Guiyang 550081, China
| | - Akram Ali Baloch
- Department of Biotechnology, Faculty of Life Sciences and Informatics, Balochistan University of Information Technology and Management Sciences, Quetta 87300, Pakistan.
| | - Dejun Han
- College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China; State Key Laboratory of Crop Stress Biology for Arid Areas, Northwest A&F University, Yangling 712100, Shaanxi, People's Republic of China.
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