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Zhu H, Yang JL, Chen W. Epigenetic insights into an epimutant colorless non-ripening: from fruit ripening to stress responses. FRONTIERS IN PLANT SCIENCE 2024; 15:1440120. [PMID: 39015288 PMCID: PMC11250591 DOI: 10.3389/fpls.2024.1440120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Accepted: 06/12/2024] [Indexed: 07/18/2024]
Abstract
The epigenetic machinery has received extensive attention due to its involvement in plant growth, development, and adaptation to environmental changes. Recent studies often highlight the epigenetic regulatory network by discussing various epigenetic mutants across various plant species. However, a systemic understanding of essential epigenetic regulatory mechanisms remains limited due to a lack of representative mutants involved in multiple biological processes. Colorless Non-ripening (Cnr), a spontaneous epimutant isolated from a commercial population, was initially characterized for its role in fruit ripening regulation. Cnr fruits exhibit an immature phenotype with yellow skin, attributed to hypermethylation of the SQUAMOSA PROMOTER BINDING PROTEIN-LIKE-CNR (SlSPL-CNR) promoter, resulting in the repression of gene expression. In addition to DNA methylation, this process also involves histone modification and microRNA, integrating multiple epigenetic regulatory factors. Interestingly, knockout mutants of SlSPL-CNR display phenotypical distinctions from Cnr in fruit ripening, indicating complex genetic and epigenetic control over the non-ripening phenotype in Cnr fruits. Accumulating evidence suggests that Cnr epimutation is pleiotropic, participating in various biological processes such as Cd stress, Fe deficiency, vivipary, and cell death. Therefore, the Cnr epimutant serve as an excellent model for unveiling how epigenetic mechanisms are involved in diverse biological processes. This review paper focuses on recent research advances regarding the Cnr epimutant, delving into its complex genetic and epigenetic regulatory mechanisms, with the aim of enhancing our understanding and facilitating the development of high-quality, high-yield crops through epigenetic modification.
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Affiliation(s)
- Huihui Zhu
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Key Laboratory of Vegetable Biology, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Jian Li Yang
- Key Laboratory of Vegetable Biology, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming, China
| | - Weiwei Chen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
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2
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Ma W, Zhang P, Zhao J, Hong Y. Chinese cabbage: an emerging model for functional genomics in leafy vegetable crops. TRENDS IN PLANT SCIENCE 2023; 28:515-518. [PMID: 36914552 DOI: 10.1016/j.tplants.2023.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 02/19/2023] [Accepted: 02/21/2023] [Indexed: 05/22/2023]
Abstract
Leafy vegetable crops (LVCs) are consumed worldwide and offer essential nutrients for humans. Unlike model plant species, systematic characterisation of gene function is lacking, although whole-genome sequences (WGSs) are available for various LVCs. Several recent studies in Chinese cabbage have reported high-density mutant populations linking genotype to phenotype, providing blueprints for functional LVC genomics and beyond.
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Affiliation(s)
- Wei Ma
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Centre of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding 071000, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, UK
| | - Jianjun Zhao
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Centre of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding 071000, China.
| | - Yiguo Hong
- State Key Laboratory of North China Crop Improvement and Regulation, Key Laboratory of Vegetable Germplasm Innovation and Utilization of Hebei, Collaborative Innovation Centre of Vegetable Industry in Hebei, College of Horticulture, Hebei Agricultural University, Baoding 071000, China; Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China; Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, UK; Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, UK.
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3
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Zhang L, Yu L, Zhao Z, Li P, Tan S. Chitosan oligosaccharide as a plant immune inducer on the Passiflora spp. (passion fruit) CMV disease. FRONTIERS IN PLANT SCIENCE 2023; 14:1131766. [PMID: 36814757 PMCID: PMC9939820 DOI: 10.3389/fpls.2023.1131766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 01/25/2023] [Indexed: 06/18/2023]
Abstract
Cucumber mosaic virus (CMV), one of the main viruses, is responsible for Passiflora spp. (passion fruit) virus diseases, which negatively affect its planting, cultivation, and commercial quality. In this study, a laboratory anti-CMV activity screening model for Passiflora spp. CMV disease was first established. Then, the effects of different antiviral agents of chitosan oligosaccharide (COS), dufulin (DFL), and ningnanmycin (Ning) on CMV virulence rate in Passiflora spp. were determined. The virulence rate and anti-CMV activity in Passiflora spp. treated with COS were 50% and 45.48%, respectively, which were even better than those of DFL (66.67% and 27.30%, respectively) and Ning (83.30% and 9.17%, respectively). Field trials test results showed COS revealed better average control efficiency (47.35%) against Passiflora spp. CMV disease than those of DFL (40.93%) and Ning (33.82%), indicating that COS is effective in the control of the Passiflora spp. CMV disease. Meanwhile, the nutritional quality test results showed that COS could increase the contents of soluble solids, titratable acids, vitamin C, and soluble proteins in Passiflora spp. fruits as well as enhance the polyphenol oxidase (PPO), superoxide dismutase (SOD), and peroxidase (POD) activity in the leaves of Passiflora spp. seedlings. In addition, the combined transcriptome and proteome analysis results showed that COS mainly acted on the Brassinosteroids (BRs) cell signaling pathway, one of plant hormone signal transduction pathway, in Passiflora spp., thus activating the up-regulated expression of TCH4 and CYCD3 genes to improve the resistance to CMV disease. Therefore, our study results demonstrated that COS could be used as a potential plant immune inducer to control the Passiflora spp. CMV disease in the future.
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Affiliation(s)
- Liqun Zhang
- School of Liquor and Food Engineering, Guizhou University, Guiyang, Guizhou, China
| | - Lu Yu
- School of Liquor and Food Engineering, Guizhou University, Guiyang, Guizhou, China
| | - Zhi Zhao
- School of Liquor and Food Engineering, Guizhou University, Guiyang, Guizhou, China
| | - Pei Li
- School of Liquor and Food Engineering, Guizhou University, Guiyang, Guizhou, China
- Qiandongnan Engineering and Technology Research Center for Comprehensive Utilization of National Medicine, Kaili University, Kaili, China
| | - Shuming Tan
- School of Liquor and Food Engineering, Guizhou University, Guiyang, Guizhou, China
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4
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Segredo-Otero E, Sanjuán R. Cooperative Virus-Virus Interactions: An Evolutionary Perspective. BIODESIGN RESEARCH 2022; 2022:9819272. [PMID: 37850129 PMCID: PMC10521650 DOI: 10.34133/2022/9819272] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2022] [Accepted: 05/21/2022] [Indexed: 10/19/2023] Open
Abstract
Despite extensive evidence of virus-virus interactions, not much is known about their biological significance. Importantly, virus-virus interactions could have evolved as a form of cooperation or simply be a by-product of other processes. Here, we review and discuss different types of virus-virus interactions from the point of view of social evolution, which provides a well-established framework for interpreting the fitness costs and benefits of such traits. We also classify interactions according to their mechanisms of action and speculate on their evolutionary implications. As in any other biological system, the evolutionary stability of viral cooperation critically requires cheaters to be excluded from cooperative interactions. We discuss how cheater viruses exploit cooperative traits and how viral populations are able to counteract this maladaptive process.
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Affiliation(s)
- Ernesto Segredo-Otero
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, C/ Catedrático Agustín Escardino 9, 46980 Paterna, València, Spain
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Rössner C, Lotz D, Becker A. VIGS Goes Viral: How VIGS Transforms Our Understanding of Plant Science. ANNUAL REVIEW OF PLANT BIOLOGY 2022; 73:703-728. [PMID: 35138878 DOI: 10.1146/annurev-arplant-102820-020542] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Virus-induced gene silencing (VIGS) has developed into an indispensable approach to gene function analysis in a wide array of species, many of which are not amenable to stable genetic transformation. VIGS utilizes the posttranscriptional gene silencing (PTGS) machinery of plants to restrain viral infections systemically and is used to downregulate the plant's endogenous genes. Here, we review the molecular mechanisms of DNA- and RNA-virus-based VIGS, its inherent connection to PTGS, and what is known about the systemic spread of silencing. Recently, VIGS-based technologies have been expanded to enable not only gene silencing but also overexpression [virus-induced overexpression (VOX)], genome editing [virus-induced genome editing (VIGE)], and host-induced gene silencing (HIGS). These techniques expand the genetic toolbox for nonmodel organisms even more. Further, we illustrate the versatility of VIGS and the methods derived from it in elucidating molecular mechanisms, using tomato fruit ripening and programmed cell death as examples. Finally, we discuss challenges of and future perspectives on the use of VIGS to advance gene function analysis in nonmodel plants in the postgenomic era.
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Affiliation(s)
- Clemens Rössner
- Institute of Botany, Justus-Liebig University Gießen, Gießen, Germany;
| | - Dominik Lotz
- Institute of Botany, Justus-Liebig University Gießen, Gießen, Germany;
| | - Annette Becker
- Institute of Botany, Justus-Liebig University Gießen, Gießen, Germany;
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Zhu H, Wang J, Jiang D, Hong Y, Xu J, Zheng S, Yang J, Chen W. The miR157-SPL-CNR module acts upstream of bHLH101 to negatively regulate iron deficiency responses in tomato. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:1059-1075. [PMID: 35297168 DOI: 10.1111/jipb.13251] [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: 01/29/2022] [Accepted: 03/14/2022] [Indexed: 05/23/2023]
Abstract
Iron (Fe) homeostasis is critical for plant growth, development, and stress responses. Fe levels are tightly controlled by intricate regulatory networks in which transcription factors (TFs) play a central role. A series of basic helix-loop-helix (bHLH) TFs have been shown to contribute to Fe homeostasis, but the regulatory layers beyond bHLH TFs remain largely unclear. Here, we demonstrate that the SQUAMOSA PROMOTER-BINDING PROTEIN-LIKE (SPL) TF SlSPL-CNR negatively regulates Fe-deficiency responses in tomato (Solanum lycopersicum) roots. Fe deficiency rapidly repressed the expression of SlSPL-CNR, and Fe deficiency responses were intensified in two clustered regularly interspaced palindromic repeats (CRISPR)/CRISPR-associated protein 9-generated SlSPL-CNR knock-out lines compared to the wild-type. Comparative transcriptome analysis identified 47 Fe deficiency-responsive genes the expression of which is negatively regulated by SlSPL-CNR, one of which, SlbHLH101, helps regulate Fe uptake genes. SlSPL-CNR localizes the nucleus and interacts with the GTAC and BOX 4 (ATTAAT) motifs in the SlbHLH101 promoter to repress its expression. Inhibition of SlSPL-CNR expression in response to Fe deficiency was well correlated with the expression of the microRNA SlymiR157. SlymiR157-overexpressing tomato lines displayed enhanced Fe deficiency responses, as did SlSPL-CNR loss-of-function mutants. We propose that the SlymiR157-SlSPL-CNR module represents a novel pathway that acts upstream of SlbHLH101 to regulate Fe homeostasis in tomato roots.
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Affiliation(s)
- Huihui Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jiayi Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Dan Jiang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
| | - Jiming Xu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Shaojian Zheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Jianli Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Weiwei Chen
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310058, China
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 311121, China
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Khakhar A, Voytas DF. RNA Viral Vectors for Accelerating Plant Synthetic Biology. FRONTIERS IN PLANT SCIENCE 2021; 12:668580. [PMID: 34249040 PMCID: PMC8261061 DOI: 10.3389/fpls.2021.668580] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 05/19/2021] [Indexed: 05/03/2023]
Abstract
The tools of synthetic biology have enormous potential to help us uncover the fundamental mechanisms controlling development and metabolism in plants. However, their effective utilization typically requires transgenesis, which is plagued by long timescales and high costs. In this review we explore how transgenesis can be minimized by delivering foreign genetic material to plants with systemically mobile and persistent vectors based on RNA viruses. We examine the progress that has been made thus far and highlight the hurdles that need to be overcome and some potential strategies to do so. We conclude with a discussion of biocontainment mechanisms to ensure these vectors can be used safely as well as how these vectors might expand the accessibility of plant synthetic biology techniques. RNA vectors stand poised to revolutionize plant synthetic biology by making genetic manipulation of plants cheaper and easier to deploy, as well as by accelerating experimental timescales from years to weeks.
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Affiliation(s)
- Arjun Khakhar
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, United States
| | - Daniel F. Voytas
- Department of Genetics, Cell Biology and Development, University of Minnesota, St. Paul, MN, United States
- Center for Precision Plant Genomics, University of Minnesota, St. Paul, MN, United States
- Center for Genome Engineering, University of Minnesota, St. Paul, MN, United States
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8
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Tan Y, Bukys A, Molnár A, Hudson A. Rapid, high efficiency virus-mediated mutant complementation and gene silencing in Antirrhinum. PLANT METHODS 2020; 16:145. [PMID: 33117430 PMCID: PMC7590601 DOI: 10.1186/s13007-020-00683-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 10/07/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND Antirrhinum (snapdragon) species are models for genetic and evolutionary research but recalcitrant to genetic transformation, limiting use of transgenic methods for functional genomics. Transient gene expression from viral vectors and virus-induced gene silencing (VIGS) offer transformation-free alternatives. Here we investigate the utility of Tobacco rattle virus (TRV) for homologous gene expression in Antirrhinum and VIGS in Antirrhinum and its relative Misopates. RESULTS A. majus proved highly susceptible to systemic TRV infection. TRV carrying part of the Phytoene Desaturase (PDS) gene triggered efficient PDS silencing, visible as tissue bleaching, providing a reporter for the extent and location of VIGS. VIGS was initiated most frequently in young seedlings, persisted into inflorescences and flowers and was not significantly affected by the orientation of the homologous sequence within the TRV genome. Its utility was further demonstrated by reducing expression of two developmental regulators that act either in the protoderm of young leaf primordia or in developing flowers. The effects of co-silencing PDS and the trichome-suppressing Hairy (H) gene from the same TRV genome showed that tissue bleaching provides a useful marker for VIGS of a second target gene acting in a different cell layer. The ability of TRV-encoded H protein to complement the h mutant phenotype was also tested. TRV carrying the native H coding sequence with PDS to report infection failed to complement h mutations and triggered VIGS of H in wild-type plants. However, a sequence with 43% synonymous substitutions encoding H protein, was able to complement the h mutant phenotype when expressed without a PDS VIGS reporter. CONCLUSIONS We demonstrate an effective method for VIGS in the model genus Antirrhinum and its relative Misopates that works in vegetative and reproductive tissues. We also show that TRV can be used for complementation of a loss-of-function mutation in Antirrhinum. These methods make rapid tests of gene function possible in these species, which are difficult to transform genetically, and opens up the possibility of using additional cell biological and biochemical techniques that depend on transgene expression.
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Affiliation(s)
- Ying Tan
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF UK
- College of Life Sciences, Hunan Normal University, 136 Lushan Road, Changsha, 410006 China
| | - Alfredas Bukys
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Attila Molnár
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF UK
| | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Max Born Crescent, Edinburgh, EH9 3BF UK
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Yao M, Chen W, Kong J, Zhang X, Shi N, Zhong S, Ma P, Gallusci P, Jackson S, Liu Y, Hong Y. METHYLTRANSFERASE1 and Ripening Modulate Vivipary during Tomato Fruit Development. PLANT PHYSIOLOGY 2020; 183:1883-1897. [PMID: 32503901 PMCID: PMC7401104 DOI: 10.1104/pp.20.00499] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 05/26/2020] [Indexed: 05/04/2023]
Abstract
Vivipary, wherein seeds germinate prior to dispersal while still associated with the maternal plant, is an adaptation to extreme environments. It is normally inhibited by the establishment of dormancy. The genetic framework of vivipary has been well studied; however, the role of epigenetics in vivipary remains unknown. Here, we report that silencing of METHYLTRANSFERASE1 (SlMET1) promoted precocious seed germination and seedling growth within the tomato (Solanum lycopersicum) epimutant Colorless non-ripening (Cnr) fruits. This was associated with decreases in abscisic acid concentration and levels of mRNA encoding 9-cis-epoxycarotenoid-dioxygenase (SlNCED), which is involved in abscisic acid biosynthesis. Differentially methylated regions were identified in promoters of differentially expressed genes, including SlNCED SlNCED knockdown also induced viviparous seedling growth in Cnr fruits. Strikingly, Cnr ripening reversion suppressed vivipary. Moreover, neither SlMET1/SlNCED-virus-induced gene silencing nor transgenic SlMET1-RNA interference produced vivipary in wild-type tomatoes; the latter affected leaf architecture, arrested flowering, and repressed seed development. Thus, a dual pathway in ripening and SlMET1-mediated epigenetics coordinates the blockage of seed vivipary.
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Affiliation(s)
- Mengqin Yao
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Junhua Kong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Xinlian Zhang
- Division of Biostatistics and Bioinformatics, University of California, San Diego, California 92093
- Department of Statistics, University of Georgia, Athens, Georgia 30602
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Ping Ma
- Department of Statistics, University of Georgia, Athens, Georgia 30602
| | - Philippe Gallusci
- UMR EGFV, Bordeaux Sciences Agro, INRA, Université de Bordeaux, 210 Chemin de Leysotte, CS 50008, 33882 Villenave d'Ornon, France
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick CV4 7AL, United Kingdom
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester WR2 6AJ, United Kingdom
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Zhang X, Kang L, Zhang Q, Meng Q, Pan Y, Yu Z, Shi N, Jackson S, Zhang X, Wang H, Tor M, Hong Y. An RNAi suppressor activates in planta virus-mediated gene editing. Funct Integr Genomics 2020; 20:471-477. [PMID: 31848794 DOI: 10.1007/s10142-019-00730-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Revised: 10/10/2019] [Accepted: 11/05/2019] [Indexed: 11/30/2022]
Abstract
RNA-guided CRISPR/Cas9 technology has been developed for gene/genome editing (GE) in organisms across kingdoms. However, in planta delivery of the two core GE components, Cas9 and small guide RNA (sgRNA), often involves time-consuming and labor-intensive production of transgenic plants. Here we show that Foxtail mosaic virus, a monocot- and dicot-infecting potexvirus, can simultaneously express Cas9, sgRNA, and an RNAi suppressor to efficiently induce GE in Nicotiana benthamiana through a transgenic plant-free manner.
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Affiliation(s)
- Xian Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Lihua Kang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qi Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qiqi Meng
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Yafei Pan
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, 92093, USA
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Mahmut Tor
- Department of Biology, School of Science and the Environment, Worcester-Hangzhou Joint Molecular Plant Health Laboratory, University of Worcester, Worcester, WR2 6AJ, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.
- Department of Biology, School of Science and the Environment, Worcester-Hangzhou Joint Molecular Plant Health Laboratory, University of Worcester, Worcester, WR2 6AJ, UK.
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11
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Yuan C, Li H, Qin C, Zhang X, Chen Q, Zhang P, Xu X, He M, Zhang X, Tör M, Xue D, Wang H, Jackson S, He Y, Liu Y, Shi N, Hong Y. Foxtail mosaic virus-induced flowering assays in monocot crops. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:3012-3023. [PMID: 32061090 DOI: 10.1093/jxb/eraa080] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2019] [Accepted: 02/11/2020] [Indexed: 05/04/2023]
Abstract
Virus-induced flowering (VIF) exploits RNA or DNA viruses to express flowering time genes to induce flowering in plants. Such plant virus-based tools have recently attracted widespread attention for their fundamental and applied uses in flowering physiology and in accelerating breeding in dicotyledonous crops and woody fruit-trees. We now extend this technology to a monocot grass and a cereal crop. Using a Foxtail mosaic virus (FoMV)-based VIF system, dubbed FoMViF, we showed that expression of florigenic Flowering Locus T (FT) genes can promote early flowering and spikelet development in proso millet, a C4 grass species with potential as a nutritional food and biofuel resource, and in non-vernalized C3 wheat, a major food crop worldwide. Floral and spikelet/grain induction in the two monocot plants was caused by the virally expressed untagged or FLAG-tagged FT orthologs, and the florigenic activity of rice Hd3a was more pronounced than its dicotyledonous counterparts in proso millet. The FoMViF system is easy to use and its efficacy to induce flowering and early spikelet/grain production is high. In addition to proso millet and wheat, we envisage that FoMViF will be also applicable to many economically important monocotyledonous food and biofuel crops.
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Affiliation(s)
- Chen Yuan
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Hongmei Li
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Qianqian Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaorui Xu
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Meiling He
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Dawei Xue
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Stephen Jackson
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Yuehui He
- Shanghai Center for Plant Stress Biology, Center for Excellence in Molecular Plant Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Yule Liu
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
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12
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Lai T, Wang X, Ye B, Jin M, Chen W, Wang Y, Zhou Y, Blanks AM, Gu M, Zhang P, Zhang X, Li C, Wang H, Liu Y, Gallusci P, Tör M, Hong Y. Molecular and functional characterization of the SBP-box transcription factor SPL-CNR in tomato fruit ripening and cell death. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:2995-3011. [PMID: 32016417 PMCID: PMC7260717 DOI: 10.1093/jxb/eraa067] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Accepted: 02/01/2020] [Indexed: 05/19/2023]
Abstract
SlSPL-CNR, an SBP-box transcription factor (TF) gene residing at the epimutant Colourless non-ripening (Cnr) locus, is involved in tomato ripening. This epimutant provides a unique model to investigate the (epi)genetic basis of fruit ripening. Here we report that SlSPL-CNR is a nucleus-localized protein with a distinct monopartite nuclear localization signal (NLS). It consists of four consecutive residues ' 30KRKR33' at the N-terminus of the protein. Mutation of the NLS abolishes SlSPL-CNR's ability to localize in the nucleus. SlSPL-CNR comprises two zinc-finger motifs (ZFMs) within the C-terminal SBP-box domain. Both ZFMs contribute to zinc-binding activity. SlSPL-CNR can induce cell death in tomato and tobacco, dependent on its nuclear localization. However, the two ZFMs have differential impacts on SlSPL-CNR's induction of severe necrosis or mild necrotic ringspot. NLS and ZFM mutants cannot complement Cnr fruits to ripen. SlSPL-CNR interacts with SlSnRK1. Virus-induced SlSnRK1 silencing leads to reduction in expression of ripening-related genes and inhibits ripening in tomato. We conclude that SlSPL-CNR is a multifunctional protein that consists of a distinct monopartite NLS, binds to zinc, and interacts with SlSnRK1 to affect cell death and tomato fruit ripening.
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Affiliation(s)
- Tongfei Lai
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xiaohong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Bishun Ye
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Mingfei Jin
- School of Life Sciences, East China Normal University, Shanghai, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Ying Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yingying Zhou
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Andrew M Blanks
- Cell and Developmental Biology, Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, UK
| | - Mei Gu
- The Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Xinlian Zhang
- Department of Family Medicine and Public Health, Division of Biostatistics & Bioinformatics, University of California San Diego, La Jolla, CA, USA
| | - Chunyang Li
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Philippe Gallusci
- Laboratory of Grape Ecophysiology and Functional Biology, Bordeaux University, INRA, Bordeaux Science Agro, Villenave d’Ornon, France
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, China
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Coventry, UK
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, School of Science and the Environment, University of Worcester, Worcester, UK
- Correspondence: , or
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Zhang T, Liu P, Zhong K, Zhang F, Xu M, He L, Jin P, Chen J, Yang J. Wheat Yellow Mosaic Virus NIb Interacting with Host Light Induced Protein (LIP) Facilitates Its Infection through Perturbing the Abscisic Acid Pathway in Wheat. BIOLOGY 2019; 8:biology8040080. [PMID: 31652738 PMCID: PMC6955802 DOI: 10.3390/biology8040080] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 10/10/2019] [Accepted: 10/22/2019] [Indexed: 11/17/2022]
Abstract
Positive-sense RNA viruses have a small genome with very limited coding capacity and are highly reliant on host factors to fulfill their infection. However, few host factors have been identified to participate in wheat yellow mosaic virus (WYMV) infection. Here, we demonstrate that wheat (Triticum aestivum) light-induced protein (TaLIP) interacts with the WYMV nuclear inclusion b protein (NIb). A bimolecular fluorescence complementation (BIFC) assay displayed that the subcellular distribution patterns of TaLIP were altered by NIb in Nicotiana benthamiana. Transcription of TaLIP was significantly decreased by WYMV infection and TaLIP-silencing wheat plants displayed more susceptibility to WYMV in comparison with the control plants, suggesting that knockdown of TaLIP impaired host resistance. Moreover, the transcription level of TaLIP was induced by exogenous abscisic acid (ABA) stimuli in wheat, while knockdown of TaLIP significantly repressed the expression of ABA-related genes such as wheat abscisic acid insensitive 5 (TaABI5), abscisic acid insensitive 8 (TaABI8), pyrabatin resistance 1-Llike (TaPYL1), and pyrabatin resistance 3-Llike (TaPYL3). Collectively, our results suggest that the interaction of NIb with TaLIP facilitated the virus infection possibly by disturbing the ABA signaling pathway in wheat.
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Affiliation(s)
- Tianye Zhang
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 310021, China.
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Peng Liu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Kaili Zhong
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Fan Zhang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Miaoze Xu
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Long He
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Peng Jin
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Jianping Chen
- School of Forestry and Biotechnology, Zhejiang Agriculture and Forestry University, Hangzhou 310021, China.
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
| | - Jian Yang
- State Key Laboratory for Quality and Safety of Agro-products, Institute of Plant Virology, Ningbo University, Ningbo 315211, China.
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Zhou D, Shen Y, Zhou P, Fatima M, Lin J, Yue J, Zhang X, Chen LY, Ming R. Papaya CpbHLH1/2 regulate carotenoid biosynthesis-related genes during papaya fruit ripening. HORTICULTURE RESEARCH 2019; 6:80. [PMID: 31263564 PMCID: PMC6588581 DOI: 10.1038/s41438-019-0162-2] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/22/2019] [Accepted: 04/26/2019] [Indexed: 05/03/2023]
Abstract
The ripening of papaya is a physiological and metabolic process associated with accumulation of carotenoids, alternation of flesh color and flavor, which depending on genotype and external factors such as light and hormone. Transcription factors regulating carotenoid biosynthesis have not been analyzed during papaya fruit ripening. RNA-Seq experiments were implemented using different ripening stages of papaya fruit from two papaya varieties. Cis-elements in lycopene β-cyclase genes (CpCYC-B and CpLCY-B) were identified, and followed by genome-wide analysis to identify transcription factors binding to these cis-elements, resulting in the identification of CpbHLH1 and CpbHLH2, two bHLH genes. The expressions of CpbHLH1/2 were changed during fruit development, coupled with transcript increase of carotenoid biosynthesis-related genes including CpCYC-B, CpLCY-B, CpPDS2, CpZDS, CpLCY-E, and CpCHY-B. Yeast one-hybrid (Y1H) and transient expression assay revealed that CpbHLH1/2 could bind to the promoters of CpCYC-B and CpLCY-B, and regulate their transcriptions. In response to strong light, the results of elevated expression of carotenoid biosynthesis-related genes and the changed expression of CpbHLH1/2 indicated that CpbHLH1/2 were involved in light-mediated mechanisms of regulating critical genes in the carotenoid biosynthesis pathway. Collectively, our findings demonstrated several TF family members participating in the regulation of carotenoid genes and proved that CpbHLH1 and CpbHLH2 individually regulated the transcription of lycopene β-cyclase genes (CpCYC-B and CpLCY-B). This study yielded novel findings on regulatory mechanism of carotenoid biosynthesis during papaya fruit ripening.
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Affiliation(s)
- Dong Zhou
- College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Yanhong Shen
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
| | - Ping Zhou
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Mahpara Fatima
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Jishan Lin
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Jingjing Yue
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Xingtan Zhang
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Li-Yu Chen
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
| | - Ray Ming
- FAFU and UIUC-SIB Joint Center for Genomics and Biotechnology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Genetics, Breeding and Multiple Utilization of Crops, Ministry of Education, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002 China
- Department of Plant Biology, University of Illinois at Urbana-Champaign, Urbana, IL 61801 USA
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Rothan C, Diouf I, Causse M. Trait discovery and editing in tomato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:73-90. [PMID: 30417464 DOI: 10.1111/tpj.14152] [Citation(s) in RCA: 61] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Revised: 10/08/2018] [Accepted: 10/30/2018] [Indexed: 06/09/2023]
Abstract
Tomato (Solanum lycopersicum), which is used for both processing and fresh markets, is a major crop species that is the top ranked vegetable produced over the world. Tomato is also a model species for research in genetics, fruit development and disease resistance. Genetic resources available in public repositories comprise the 12 wild related species and thousands of landraces, modern cultivars and mutants. In addition, high quality genome sequences are available for cultivated tomato and for several wild relatives, hundreds of accessions have been sequenced, and databases gathering sequence data together with genetic and phenotypic data are accessible to the tomato community. Major breeding goals are productivity, resistance to biotic and abiotic stresses, and fruit sensorial and nutritional quality. New traits, including resistance to various biotic and abiotic stresses and root architecture, are increasingly being studied. Several major mutations and quantitative trait loci (QTLs) underlying traits of interest in tomato have been uncovered to date and, thanks to new populations and advances in sequencing technologies, the pace of trait discovery has considerably accelerated. In recent years, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing (GE) already proved its remarkable efficiency in tomato for engineering favorable alleles and for creating new genetic diversity by gene disruption, gene replacement, and precise base editing. Here, we provide insight into the major tomato traits and underlying causal genetic variations discovered so far and review the existing genetic resources and most recent strategies for trait discovery in tomato. Furthermore, we explore the opportunities offered by CRISPR/Cas9 and their exploitation for trait editing in tomato.
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Affiliation(s)
- Christophe Rothan
- INRA and University of Bordeaux, UMR 1332 Biologie du Fruit et Pathologie, F-33140, Villenave d'Ornon, France
| | - Isidore Diouf
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
| | - Mathilde Causse
- INRA, UR1052, Génétique et Amélioration des Fruits et Légumes, CS60094, F-84143, Montfavet, France
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16
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Zhan Y, Qu Y, Zhu L, Shen C, Feng X, Yu C. Transcriptome analysis of tomato (Solanum lycopersicum L.) shoots reveals a crosstalk between auxin and strigolactone. PLoS One 2018; 13:e0201124. [PMID: 30044859 PMCID: PMC6059464 DOI: 10.1371/journal.pone.0201124] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2018] [Accepted: 07/09/2018] [Indexed: 11/22/2022] Open
Abstract
Auxin and strigolactone (SL) are two important phytohormones involved in shoot branching and morphology. Tomato (Solanum lycopersicum L.), a member of the Solanaceae family, is one of the most popular food crops with high economic value in the world. To seek a better understanding of the responses to exogenous hormones, transcriptome analyses of the tomato shoots treated with exogenous auxin and SL, separately or together, were performed. A total of 2326, 260 and 1379 differential expressed genes (DEGs) were identified under the IAA, GR24 and IAA+GR24 treatments, respectively. Network analysis pointed out two enriched interaction clusters, including “ethylene biosynthesis” and “photosynthesis”. Several ethylene biosynthesis and metabolism-related genes were up-regulated under both IAA and IAA+GR24 treatments, suggesting their involvement in the regulation of ethylene biosynthesis. Besides, auxin-SLs-triggered the expression of several CAB genes may lead to systemic increases in the induction of photosynthesis. Several auxin-activated metabolic pathways could be reduced by the GR24 treatment, indicated that the crosstalk between auxin and SLs may be involved in the metabolic regulation of tomato. Further analysis showed that SLs affect the responses of tomato shoots to auxin by inducing the expression of a series of auxin downstream genes. On the other hand, auxin regulated the biosynthesis of SLs by affecting the genes in the “Carotenoid biosynthesis” pathway. Our data will give us an opportunity to reveal the crosstalk between auxin and SLs in the shoots of tomato.
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Affiliation(s)
- Yihua Zhan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yinchao Qu
- Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Longjing Zhu
- Wenzhou Vocational College of Science and Technology, Wenzhou, Zhejiang, China
| | - Chenjia Shen
- College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, China
| | - Xuping Feng
- College of Life Sciences, China Jiliang University, Hangzhou, People’s Republic of China
- * E-mail: (XF); (CY)
| | - Chenliang Yu
- Vegetable Research Institute, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
- * E-mail: (XF); (CY)
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17
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Liu K, Yuan C, Li H, Chen K, Lu L, Shen C, Zheng X. A qualitative proteome-wide lysine crotonylation profiling of papaya (Carica papaya L.). Sci Rep 2018; 8:8230. [PMID: 29844531 PMCID: PMC5974297 DOI: 10.1038/s41598-018-26676-y] [Citation(s) in RCA: 41] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2018] [Accepted: 05/17/2018] [Indexed: 02/06/2023] Open
Abstract
Lysine crotonylation of histone proteins is a recently-identified post-translational modification with multiple cellular functions. However, no information about lysine crotonylation of non-histone proteins in fruit cells is available. Using high-resolution LC-MS/MS coupled with highly sensitive immune-affinity antibody analysis, a global crotonylation proteome analysis of papaya fruit (Carica papaya L.) was performed. In total, 2,120 proteins with 5,995 lysine crotonylation sites were discovered, among which eight conserved motifs were identified. Bioinformatic analysis linked crotonylated proteins to multiple metabolic pathways, including biosynthesis of antibiotics, carbon metabolism, biosynthesis of amino acids, and glycolysis. particularly, 40 crotonylated enzymes involved in various pathways of amino acid metabolism were identified, suggesting a potential conserved function for crotonylation in the regulation of amino acid metabolism. Numerous crotonylation sites were identified in proteins involved in the hormone signaling and cell wall-related pathways. Our comprehensive crotonylation proteome indicated diverse functions for lysine crotonylation in papaya.
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Affiliation(s)
- Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China. .,College of Bioscience and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
| | - Changchun Yuan
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Haili Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Kunyan Chen
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Lishi Lu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xiaolin Zheng
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China.
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18
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Liu K, Yuan C, Li H, Chen K, Lu L, Shen C, Zheng X. A qualitative proteome-wide lysine crotonylation profiling of papaya (Carica papaya L.). Sci Rep 2018. [PMID: 29844531 DOI: 10.1038/s41598018-26676-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2023] Open
Abstract
Lysine crotonylation of histone proteins is a recently-identified post-translational modification with multiple cellular functions. However, no information about lysine crotonylation of non-histone proteins in fruit cells is available. Using high-resolution LC-MS/MS coupled with highly sensitive immune-affinity antibody analysis, a global crotonylation proteome analysis of papaya fruit (Carica papaya L.) was performed. In total, 2,120 proteins with 5,995 lysine crotonylation sites were discovered, among which eight conserved motifs were identified. Bioinformatic analysis linked crotonylated proteins to multiple metabolic pathways, including biosynthesis of antibiotics, carbon metabolism, biosynthesis of amino acids, and glycolysis. particularly, 40 crotonylated enzymes involved in various pathways of amino acid metabolism were identified, suggesting a potential conserved function for crotonylation in the regulation of amino acid metabolism. Numerous crotonylation sites were identified in proteins involved in the hormone signaling and cell wall-related pathways. Our comprehensive crotonylation proteome indicated diverse functions for lysine crotonylation in papaya.
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Affiliation(s)
- Kaidong Liu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China.
- College of Bioscience and Technology, Hunan Agricultural University, Changsha, Hunan, 410128, China.
| | - Changchun Yuan
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Haili Li
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Kunyan Chen
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Lishi Lu
- Life Science and Technology School, Lingnan Normal University, Zhanjiang, Guangdong, 524048, China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xiaolin Zheng
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, 310035, China.
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19
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Zhou S, Hong Q, Li Y, Li Q, Wang M. Autophagy contributes to regulate the ROS levels and PCD progress in TMV-infected tomatoes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 269:12-19. [PMID: 29606209 DOI: 10.1016/j.plantsci.2017.11.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Revised: 10/10/2017] [Accepted: 11/01/2017] [Indexed: 06/08/2023]
Abstract
Programmed cell death (PCD) and autophagy are both important means for plants to resist pathogen. It is also the main biological reaction of plant immunity. In previous studies, we found that TMV local-infection on tomato leaves not only caused the PCD process in the distal root tissues, but also induced autophagy in root-tip cells. However, the reasons for these biological phenomena are unclear. In order to get deeper insight, the role of a putative inducible factor reactive oxidative species (ROS) was investigated. The situ staining and subcellular localization analysis showed that the ROS level in the root tissue of TMV infected plants was significantly promoted. TEM observation showed that the intracellular ROS was excreted into the cell wall and intercellular layer. At the same time, the results of western blot and qRT-PCR showed that the expression of autophagy related protein Atg8 and genes (Atg5, Atg7 and Atg10) were increased. However, in the subsequent DPI inhibition experiments we found that the accumulation of ROS in infected plant root-tip tissues was inhibited and the autophagy in the root-tip cells also decreased. When 3-methyladenine (3-MA) was used to inhibit autophagy, there was no significant change in the ROS level in the apical tissue, while the systemic PCD process of the root-tip cells was elevated. Taken together, these results indicate that local TMV inoculation on the leaves induced the root-tip cells producing and releasing a lot of ROS into the extracellular matrix for defense against pathogen invasion. Meanwhile, ROS acted as a signaling substance and triggered autophagy in root-tip cells, in order to eliminate excessive intracellular ROS oxidative damage and maintain cell survival.
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Affiliation(s)
- Shumin Zhou
- Lab of Plant Cell Biology, Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qiang Hong
- Lab of Plant Cell Biology, Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Yang Li
- Lab of Plant Cell Biology, Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Qi Li
- Lab of Plant Cell Biology, Shanghai Key Laboratory of Bio-Energy Crops, School of Life Sciences, Shanghai University, Shanghai 200444, China
| | - Mao Wang
- College of Biology, China Agricultural University, Beijing 100094, China.
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Chen W, Yu Z, Kong J, Wang H, Li Y, Zhao M, Wang X, Zheng Q, Shi N, Zhang P, Zhong S, Hunter P, Tör M, Hong Y. Comparative WGBS identifies genes that influence non-ripe phenotype in tomato epimutant Colourless non-ripening. SCIENCE CHINA. LIFE SCIENCES 2018; 61:244-252. [PMID: 29288427 DOI: 10.1007/s11427-017-9206-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 10/21/2017] [Indexed: 01/02/2023]
Abstract
Whole-genome bisulfite sequencing (WGBS) allows single-base resolution and genome-wide profiling of DNA methylation in plants and animals. This technology provides a powerful tool to identify genes that are potentially controlled by dynamic changes of DNA methylation and demethylation. However, naturally occurring epimutants are rare and genes under epigenetic regulation as well as their biological relevances are often difficult to define. In tomato, fruit development and ripening are a complex process that involves epigenetic control. We have taken the advantage of the tomato epimutant Colourless non-ripening (Cnr) and performed comparative mining of the WGBS datasets for the Cnr and SlCMT3-silenced Cnr fruits. We compared DNA methylation profiles for the promoter sequences of approximately 5,000 bp immediately upstream of the coding region of a list of 20 genes. Differentially methylated regions were found for some of these genes. Virus-induced gene silencing (VIGS) of differentially methylated gene SlDET1 or SlPDS resulted in unusual brown pigmentation in Cnr fruits. These results suggest that comparative WGBS coupled with VIGS can be used to identify genes that may contribute to the colourless unripe phenotype of fruit in the Cnr epimutant.
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Affiliation(s)
- Weiwei Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Junhua Kong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Hui Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Yichen Li
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Mei Zhao
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Xiaohong Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Qianqian Zheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Paul Hunter
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK
| | - Mahmut Tör
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, Warwick, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China.
- Warwick-Hangzhou Joint RNA Signaling Laboratory, School of Life Sciences, University of Warwick, Warwick, CV4 7AL, UK.
- Worcester-Hangzhou Joint Molecular Plant Health Laboratory, Institute of Science and the Environment, University of Worcester, WR2 6AJ, Warwick, UK.
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21
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Qin C, Chen W, Shen J, Cheng L, Akande F, Zhang K, Yuan C, Li C, Zhang P, Shi N, Cheng Q, Liu Y, Jackson S, Hong Y. A Virus-Induced Assay for Functional Dissection and Analysis of Monocot and Dicot Flowering Time Genes. PLANT PHYSIOLOGY 2017; 174:875-885. [PMID: 28400493 PMCID: PMC5462034 DOI: 10.1104/pp.17.00392] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 04/07/2017] [Indexed: 05/20/2023]
Abstract
Virus-induced flowering (VIF) uses virus vectors to express Flowering Locus T (FT) to induce flowering in plants. This approach has recently attracted wide interest for its practical applications in accelerating breeding in crops and woody fruit trees. However, the insight into VIF and its potential as a powerful tool for dissecting florigenic proteins remained to be elucidated. Here, we describe the mechanism and further applications of Potato virus X (PVX)-based VIF in the short-day Nicotiana tabacum cultivar Maryland Mammoth. Ectopic delivery of Arabidopsis (Arabidopsis thaliana) AtFT by PVX/AtFT did not induce the expression of the endogenous FT ortholog NtFT4; however, it was sufficient to trigger flowering in Maryland Mammoth plants grown under noninductive long-day conditions. Infected tobacco plants developed no systemic symptoms, and the PVX-based VIF did not cause transgenerational flowering. We showed that the PVX-based VIF is a much more rapid method to examine the impacts of single amino acid mutations on AtFT for floral induction than making individual transgenic Arabidopsis lines for each mutation. We also used the PVX-based VIF to demonstrate that adding a His- or FLAG-tag to the N or C terminus of AtFT could affect its florigenic activity and that this system can be applied to assay the function of FT genes from heterologous species, including tomato (Solanum lycopersicum) SFT and rice (Oryza sativa) Hd3a Thus, the PVX-based VIF represents a simple and efficient system to identify individual amino acids that are essential for FT-mediated floral induction and to test the ability of mono- and dicotyledonous FT genes and FT fusion proteins to induce flowering.
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Affiliation(s)
- Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Jiajia Shen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Linming Cheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Femi Akande
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Ke Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Chen Yuan
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Chunyang Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Qi Cheng
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Yule Liu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Stephen Jackson
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.)
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.)
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China (C.Q., W.C., J.S., L.C., K.Z., C.Y., P.Z., N.S., Y.H.);
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China (Q.C.);
- Centre for Plant Biology and MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing 100084, China (Y.L.); and
- Warwick-Hangzhou RNA Signaling Joint Laboratory, School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK (F.A, C.L., S.J., Y.H.)
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22
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Kumar V, Irfan M, Ghosh S, Chakraborty N, Chakraborty S, Datta A. Fruit ripening mutants reveal cell metabolism and redox state during ripening. PROTOPLASMA 2016; 253:581-94. [PMID: 26008650 DOI: 10.1007/s00709-015-0836-z] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 05/17/2015] [Indexed: 05/18/2023]
Abstract
Ripening which leads to fruit senescence is an inimitable process characterized by vivid changes in color, texture, flavor, and aroma of the fleshy fruits. Our understanding of the mechanisms underlying the regulation of fruit ripening and senescence is far from complete. Molecular and biochemical studies on tomato (Solanum lycopersicum) ripening mutants such as ripening inhibitor (rin), nonripening (nor), and never ripe (Nr) have been useful in our understanding of fruit development and ripening. The MADS-box transcription factor RIN, a global regulator of fruit ripening, is vital for the broad aspects of ripening, in both ethylene-dependent and independent manners. Here, we have carried out microarray analysis to study the expression profiles of tomato genes during ripening of wild type and rin mutant fruits. Analysis of the differentially expressed genes revealed the role of RIN in regulation of several molecular and biochemical events during fruit ripening including fruit specialized metabolism and cellular redox state. The role of reactive oxygen species (ROS) during fruit ripening and senescence was further examined by determining the changes in ROS level during ripening of wild type and mutant fruits and by analyzing expression profiles of the genes involved in maintaining cellular redox state. Taken together, our findings suggest an important role of ROS during fruit ripening and senescence, and therefore, modulation of ROS level during ripening could be useful in achieving desired fruit quality.
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Affiliation(s)
- Vinay Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Mohammad Irfan
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Sumit Ghosh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Niranjan Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Subhra Chakraborty
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, 110067, India.
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23
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Chen W, Kong J, Qin C, Yu S, Tan J, Chen YR, Wu C, Wang H, Shi Y, Li C, Li B, Zhang P, Wang Y, Lai T, Yu Z, Zhang X, Shi N, Wang H, Osman T, Liu Y, Manning K, Jackson S, Rolin D, Zhong S, Seymour GB, Gallusci P, Hong Y. Requirement of CHROMOMETHYLASE3 for somatic inheritance of the spontaneous tomato epimutation Colourless non-ripening. Sci Rep 2015; 5:9192. [PMID: 25778911 PMCID: PMC4361866 DOI: 10.1038/srep09192] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Accepted: 02/23/2015] [Indexed: 11/09/2022] Open
Abstract
Naturally-occurring epimutants are rare and have mainly been described in plants. However how these mutants maintain their epigenetic marks and how they are inherited remain unknown. Here we report that CHROMOMETHYLASE3 (SlCMT3) and other methyltransferases are required for maintenance of a spontaneous epimutation and its cognate Colourless non-ripening (Cnr) phenotype in tomato. We screened a series of DNA methylation-related genes that could rescue the hypermethylated Cnr mutant. Silencing of the developmentally-regulated SlCMT3 gene results in increased expression of LeSPL-CNR, the gene encodes the SBP-box transcription factor residing at the Cnr locus and triggers Cnr fruits to ripen normally. Expression of other key ripening-genes was also up-regulated. Targeted and whole-genome bisulfite sequencing showed that the induced ripening of Cnr fruits is associated with reduction of methylation at CHG sites in a 286-bp region of the LeSPL-CNR promoter, and a decrease of DNA methylation in differentially-methylated regions associated with the LeMADS-RIN binding sites. Our results indicate that there is likely a concerted effect of different methyltransferases at the Cnr locus and the plant-specific SlCMT3 is essential for sustaining Cnr epi-allele. Maintenance of DNA methylation dynamics is critical for the somatic stability of Cnr epimutation and for the inheritance of tomato non-ripening phenotype.
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Affiliation(s)
- Weiwei Chen
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Junhua Kong
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Qin
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Sheng Yu
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Jinjuan Tan
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Yun-ru Chen
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Chaoqun Wu
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Hui Wang
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Yan Shi
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Chunyang Li
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Bin Li
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Ying Wang
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Tongfei Lai
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xian Zhang
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Nongnong Shi
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Toba Osman
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Kenneth Manning
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Stephen Jackson
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Dominique Rolin
- UMR Fruit Biology and Pathology, Bordeaux University, INRA, Villenave d′Ornon 33883, France
| | - Silin Zhong
- State Key Laboratory of Agrobiotechnology, School of Life Sciences, The Chinese University of Hong Kong, Hong Kong
| | - Graham B. Seymour
- Plant and Crop Science Division, School of Biosciences, University of Nottingham, Loughborough, Leics LE12 5RD, UK
| | - Philippe Gallusci
- UMR Fruit Biology and Pathology, Bordeaux University, INRA, Villenave d′Ornon 33883, France
| | - Yiguo Hong
- Research Centre for Plant RNA Signalling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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24
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Chen W, Kong J, Lai T, Manning K, Wu C, Wang Y, Qin C, Li B, Yu Z, Zhang X, He M, Zhang P, Gu M, Yang X, Mahammed A, Li C, Osman T, Shi N, Wang H, Jackson S, Liu Y, Gallusci P, Hong Y. Tuning LeSPL-CNR expression by SlymiR157 affects tomato fruit ripening. Sci Rep 2015; 5:7852. [PMID: 25597857 PMCID: PMC4297963 DOI: 10.1038/srep07852] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Accepted: 12/16/2014] [Indexed: 01/25/2023] Open
Abstract
In plants, microRNAs (miRNAs) play essential roles in growth, development, yield, stress response and interactions with pathogens. However no miRNA has been experimentally documented to be functionally involved in fruit ripening although many miRNAs have been profiled in fruits. Here we show that SlymiR157 and SlymiR156 differentially modulate ripening and softening in tomato (Solanum lycopersicum). SlymiR157 is expressed and developmentally regulated in normal tomato fruits and in those of the Colourless non-ripening (Cnr) epimutant. It regulates expression of the key ripening gene LeSPL-CNR in a likely dose-dependent manner through miRNA-induced mRNA degradation and translation repression. Viral delivery of either pre-SlymiR157 or mature SlymiR157 results in delayed ripening. Furthermore, qRT-PCR profiling of key ripening regulatory genes indicates that the SlymiR157-target LeSPL-CNR may affect expression of LeMADS-RIN, LeHB1, SlAP2a and SlTAGL1. However SlymiR156 does not affect the onset of ripening, but it impacts fruit softening after the red ripe stage. Our findings reveal that working together with a ripening network of transcription factors, SlymiR157 and SlymiR156 form a critical additional layer of regulatory control over the fruit ripening process in tomato.
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Affiliation(s)
- Weiwei Chen
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Junhua Kong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Tongfei Lai
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Kenneth Manning
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Chaoqun Wu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Ying Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Bin Li
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Zhiming Yu
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Xian Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Meiling He
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Mei Gu
- Clinical Sciences Research Institute, University of Warwick, Coventry CV2 2DX, UK
| | - Xin Yang
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Atef Mahammed
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Department of Botany, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Chunyang Li
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Toba Osman
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
- Department of Botany, Faculty of Agriculture, Fayoum University, Fayoum 63514, Egypt
| | - Nongnong Shi
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Huizhong Wang
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
| | - Stephen Jackson
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
| | - Yule Liu
- MOE Key Laboratory of Bioinformatics, Centre for Plant Biology, School of Life Sciences, Tsinghua University, Beijing 100084, China
| | - Philippe Gallusci
- UMR Fruit Biology and Pathology, University of Bordeaux, INRA, Villenave d'Ornon 33883, France
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 310036, China
- School of Life Sciences, University of Warwick, Coventry CV4 7AL, UK
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25
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Ansari MW, Tuteja N. Post-harvest quality risks by stress/ethylene: management to mitigate. PROTOPLASMA 2015; 252:21-32. [PMID: 25091877 DOI: 10.1007/s00709-014-0678-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2014] [Accepted: 07/07/2014] [Indexed: 05/10/2023]
Abstract
Fresh produce, in actual fact, is exposed to multiple stresses through entire post-harvest phase such as handling, storage and distribution. The biotic stresses are associated with various post-harvest diseases leading to massive produce loss. Abiotic stresses such as drought, heat and chilling cause cell weakening, membrane leakage, flavour loss, surface pitting, internal browning, textural changes, softening and mealiness of post-harvest produce. A burst in 'stress ethylene' formation makes post-harvest produce to be at high risk for over-ripening, decay, deterioration, pathogen attack and physiological disorders. The mutation study of genes and receptors involved in ethylene signal transduction shows reduced sensitivity to bind ethylene resulting in delayed ripening and longer shelf life of produce. This review is aimed to highlight the various detrimental effects of stress/ethylene on quality of post-harvest produce, primarily fruits, with special emphasize to its subsequent practical management involving the 'omics' tools. The outcome of the literature appraised herein will help us to understand the physiological and molecular bases of stress/ethylene which sustain fruit quality at post-harvest phase.
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Affiliation(s)
- Mohammad W Ansari
- Plant Molecular Biology Group, International Centre for Genetic Engineering and Biotechnology, Aruna Asaf Ali Marg, New Delhi, 110067, India
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Gerszberg A, Hnatuszko-Konka K, Kowalczyk T. In vitro regeneration of eight cultivars of Brassica oleracea var. capitata. IN VITRO CELLULAR & DEVELOPMENTAL BIOLOGY. PLANT : JOURNAL OF THE TISSUE CULTURE ASSOCIATION 2015; 51:80-87. [PMID: 25774081 DOI: 10.1007/s11240-014-0664-4] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 09/08/2014] [Indexed: 05/22/2023]
Abstract
Eight cultivars of Brassica oleracea var. capitata and two types of explant (hypocotyl and cotyledon) were tested for their potential to regenerate under in vitro conditions. Hypocotyl and cotyledon explants from 10-d-old seedlings were subcultured onto different callus induction media based on Murashige and Skoog (MS) basal medium supplemented with 1% sucrose and different concentrations and combinations of plant growth regulators. Hypocotyl explants were found to be more suitable for callus induction and organogenesis than cotyledon explants for all cultivars tested. In terms of regeneration, the cv. 'Amager' was significantly more responsive than the other cultivars tested and produced the highest number of shoots/buds per explant. Moreover, among five types of media tested, MS + 8.88 μM 6-benzyloaminopurine (BAP) + 0.53 μM α-naphthylacetic acid (NAA) was most effective for shoot regeneration. Rooting was achieved within 10-15 d on all the rooting media, but MS medium containing 5.37 μM NAA produced the maximum number of strong and healthy roots. Plantlets (95%) were subsequently established in the greenhouse, and no phenotypic variations were observed among regenerated plants. This plant regeneration protocol could be suitable for a wide range of cabbage cultivars.
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Affiliation(s)
- Aneta Gerszberg
- Department of Genetics Plant Molecular Biology and Biotechnology, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
| | - Katarzyna Hnatuszko-Konka
- Department of Genetics Plant Molecular Biology and Biotechnology, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
| | - Tomasz Kowalczyk
- Department of Genetics Plant Molecular Biology and Biotechnology, University of Lodz, Banacha Street 12/16, 90-237 Lodz, Poland
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Wang Y, Wang W, Cai J, Zhang Y, Qin G, Tian S. Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. Genome Biol 2014; 15:548. [PMID: 25464976 DOI: 10.1186/preaccept-3895766441330481] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Indexed: 05/20/2023] Open
Abstract
BACKGROUND Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. RESULTS Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening. CONCLUSIONS Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
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Wang Y, Wang W, Cai J, Zhang Y, Qin G, Tian S. Tomato nuclear proteome reveals the involvement of specific E2 ubiquitin-conjugating enzymes in fruit ripening. Genome Biol 2014; 15:548. [PMID: 25464976 PMCID: PMC4269173 DOI: 10.1186/s13059-014-0548-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 11/18/2014] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND Fruits are unique to flowering plants and play a central role in seed maturation and dispersal. Molecular dissection of fruit ripening has received considerable interest because of the biological and dietary significance of fruit. To better understand the regulatory mechanisms underlying fruit ripening, we report here the first comprehensive analysis of the nuclear proteome in tomato fruits. RESULTS Nuclear proteins were isolated from tomatoes in different stages of ripening, and subjected to iTRAQ (isobaric tags for relative and absolute quantification) analysis. We show that the proteins whose abundances change during ripening stages are involved in various cellular processes. We additionally evaluate changes in the nuclear proteome in the ripening-deficient mutant, ripening-inhibitor (rin), carrying a mutation in the transcription factor RIN. A set of proteins were identified and particular attention was paid to SlUBC32 and PSMD2, the components of ubiquitin-proteasome pathway. Through chromatin immunoprecipitation and gel mobility shift assays, we provide evidence that RIN directly binds to the promoters of SlUBC32 and PSMD2. Moreover, loss of RIN function affects protein ubiquitination in nuclei. SlUBC32 encodes an E2 ubiquitin-conjugating enzyme and a genome-wide survey of the E2 gene family in tomatoes identified five more E2s as direct targets of RIN. Virus-induced gene silencing assays show that two E2s are involved in the regulation of fruit ripening. CONCLUSIONS Our results uncover a novel function of protein ubiquitination, identifying specific E2s as regulators of fruit ripening. These findings contribute to the unraveling of the gene regulatory networks that control fruit ripening.
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Affiliation(s)
- Yuying Wang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
| | - Weihao Wang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Jianghua Cai
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Yanrui Zhang
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
| | - Guozheng Qin
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
| | - Shiping Tian
- />Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, No.20 Nanxincun, Xiangshan, Haidian District, Beijing, 100093 China
- />The Graduate University of the Chinese Academy of Sciences, Yuquanlu, Beijing, 100049 China
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Kong J, Chen W, Shen J, Qin C, Lai T, Zhang P, Wang Y, Wu C, Yang X, Hong Y. Virus-induced gene complementation in tomato. PLANT SIGNALING & BEHAVIOR 2013; 8:e27142. [PMID: 24305652 PMCID: PMC4091552 DOI: 10.4161/psb.27142] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Accepted: 11/10/2013] [Indexed: 05/20/2023]
Abstract
Virus-induced gene complementation (VIGC), a plant virus technology based on Potato virus X for transient overexpression of endogenous genes complemented tomato mutants, resulting in non-ripening fruits to ripen. This efficient "gain-of-function" approach involves no stable transformation, and reveals a fruit-specific transcriptional network that may exist among key transcription factors in modulating tomato ripening. Thus, VIGC represents a novel and feasible strategy for gene functional analysis in plants.
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Affiliation(s)
- Jinhua Kong
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Jiajia Shen
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Cheng Qin
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Tongfei Lai
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Pengcheng Zhang
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Ying Wang
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Chaoqun Wu
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
| | - Xin Yang
- School of Life Sciences; University of Warwick; Coventry, UK
| | - Yiguo Hong
- Research Centre for Plant RNA Signaling; College of Life and Environmental Sciences; Hangzhou Normal University; Hangzhou, PR China
- School of Life Sciences; University of Warwick; Coventry, UK
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Fujisawa M, Nakano T, Shima Y, Ito Y. A large-scale identification of direct targets of the tomato MADS box transcription factor RIPENING INHIBITOR reveals the regulation of fruit ripening. THE PLANT CELL 2013; 25:371-86. [PMID: 23386264 PMCID: PMC3608766 DOI: 10.1105/tpc.112.108118] [Citation(s) in RCA: 249] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Revised: 01/10/2013] [Accepted: 01/22/2013] [Indexed: 05/18/2023]
Abstract
The fruit ripening developmental program is specific to plants bearing fleshy fruits and dramatically changes fruit characteristics, including color, aroma, and texture. The tomato (Solanum lycopersicum) MADS box transcription factor RIPENING INHIBITOR (RIN), one of the earliest acting ripening regulators, is required for both ethylene-dependent and -independent ripening regulatory pathways. Recent studies have identified two dozen direct RIN targets, but many more RIN targets remain to be identified. Here, we report the large-scale identification of direct RIN targets by chromatin immunoprecipitation coupled with DNA microarray analysis (ChIP-chip) targeting the predicted promoters of tomato genes. Our combined ChIP-chip and transcriptome analysis identified 241 direct RIN target genes that contain a RIN binding site and exhibit RIN-dependent positive or negative regulation during fruit ripening, suggesting that RIN has both activator and repressor roles. Examination of the predicted functions of RIN targets revealed that RIN participates in the regulation of lycopene accumulation, ethylene production, chlorophyll degradation, and many other physiological processes. Analysis of the effect of ethylene using 1-methylcyclopropene revealed that the positively regulated subset of RIN targets includes ethylene-sensitive and -insensitive transcription factors. Intriguingly, ethylene is involved in the upregulation of RIN expression during ripening. These results suggest that tomato fruit ripening is regulated by the interaction between RIN and ethylene signaling.
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