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Liu M, Zeng J, Li T, Li Y, Jiang Y, Duan X, Jiang G. Transcription factor NOR and CNR synergistically regulate tomato fruit ripening and carotenoid biosynthesis. MOLECULAR HORTICULTURE 2024; 4:27. [PMID: 38978069 PMCID: PMC11232299 DOI: 10.1186/s43897-024-00103-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2024] [Accepted: 06/13/2024] [Indexed: 07/10/2024]
Affiliation(s)
- Mengting Liu
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden , Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jing Zeng
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden , Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ting Li
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden , Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ying Li
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden , Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yueming Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden , Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuewu Duan
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden , Chinese Academy of Sciences, Guangzhou, 510650, China
- South China National Botanical Garden, Guangzhou, 510650, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Guoxiang Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China, Botanical Garden , Chinese Academy of Sciences, Guangzhou, 510650, China.
- South China National Botanical Garden, Guangzhou, 510650, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Santo Domingo M, Orduña L, Navarro D, Mayobre C, Santiago A, Valverde L, Alexiou KG, Matus JT, Pujol M, Garcia-Mas J. The ethylene-responsive transcription factor ERF024 is a novel regulator of climacteric fruit ripening in melon. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38900073 DOI: 10.1111/tpj.16889] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 05/21/2024] [Accepted: 06/06/2024] [Indexed: 06/21/2024]
Abstract
Fruit ripening is an essential developmental stage in Angiosperms triggered by hormonal signals such as ethylene, a major player in climacteric ripening. Melon is a unique crop showing both climacteric and non-climacteric cultivars, offering an ideal model for dissecting the genetic mechanisms underpinning this process. The major quantitative trait locus ETHQV8.1 was previously identified as a key regulator of melon fruit ripening. Here, we narrowed down ETHQV8.1 to a precise genomic region containing a single gene, the transcription factor CmERF024. Functional validation using CRISPR/Cas9 knock-out plants unequivocally identified CmERF024 as the causal gene governing ETHQV8.1. The erf024 mutants exhibited suppression of ethylene production, leading to a significant delay and attenuation of fruit ripening. Integrative multi-omic analyses encompassing RNA-seq, DAP-seq, and DNase-seq revealed the association of CmERF024 with chromatin accessibility and gene expression dynamics throughout fruit ripening. Our data suggest CmERF024 as a novel regulator of climacteric fruit ripening in melon.
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Affiliation(s)
- Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - David Navarro
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Carlos Mayobre
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Laura Valverde
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Konstantinos G Alexiou
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain
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3
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Silva GCB, Camillo LR, Santos DB, Amorim MS, Gonçalves LP, Barbosa ACO, Rocha Junior DS, Alcântara GM, Costa MGC. Identification of DEMETER-like DNA demethylase gene family in citrus and their role in drought stress-adaptive responses. Comput Biol Chem 2024; 112:108128. [PMID: 38905900 DOI: 10.1016/j.compbiolchem.2024.108128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 05/17/2024] [Accepted: 06/10/2024] [Indexed: 06/23/2024]
Abstract
DEMETER-Like DNA demethylases (DMLs) are epigenetic regulators of many developmental and biological processes in plants. No comprehensive information about the DML gene family in citrus is available to date. Here, a total of three DML genes in the genomes of Citrus sinensis (named CsDML1-3) and C. clementina (named CcDML1-3) were identified and analyzed. They encode hydrophilic and relatively large proteins, with prediction of nuclear localization, containing the conserved domains and motifs typical of plant DMLs. Protein interaction network analysis suggested that they interact primarily with proteins related to the maintenance of DNA methylation and remodeling of chromatin. Analysis of their promoter regions led to the identification of several cis-acting regulatory elements involved in stress response, including drought, heat and cold stresses. The presence of several miRNA targets and potential phosphorylation sites suggest that their expression is also regulated at post-transcriptional and post-translational levels. RNA-Seq data and quantitative real-time PCR analysis showed a low and drought-regulated gene expression of the citrus DMLs in different plant tissues. CsDML1 and CsDML3 were also differentially regulated by deficit irrigation in fruits at different developmental stages, with a positive and significant correlation found between CsDML1 and PHYTOENE SYNTHASE (PSY) and between CsDML3 and ATP CITRATE LYASEs (ACLs) and ZETA-CAROTENE DESATURASE (ZDS) gene expression. These results indicate that the citrus DMLs are potentially functional enzymes involved in developmental processes and drought stress-adaptive responses, providing a useful reference for further investigation of their functions and applications on the citrus improvement.
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Affiliation(s)
- Gláucia C B Silva
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Luciana R Camillo
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Dalma B Santos
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Maurício S Amorim
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Luana P Gonçalves
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Ana C O Barbosa
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Dílson S Rocha Junior
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Grazielle M Alcântara
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil
| | - Marcio G C Costa
- Centro de Biotecnologia e Genética, Departamento de Ciências Biológicas, Universidade Estadual de Santa Cruz, Rodovia Jorge Amado km 16, Ilhéus, BA 45662-900, Brazil.
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Ezura K, Lu Y, Suzuki Y, Mitsuda N, Ariizumi T. Class II knotted-like homeodomain protein SlKN5 with BEL1-like homeodomain proteins suppresses fruit greening in tomato fruit. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 118:2037-2054. [PMID: 38577750 DOI: 10.1111/tpj.16727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 04/06/2024]
Abstract
Knotted1-like homeodomain (KNOX) proteins are essential in regulating plant organ differentiation. Land plants, including tomato (Solanum lycopersicum), have two classes of the KNOX protein family, namely, class I (KNOX I) and class II KNOX (KNOX II). While tomato KNOX I proteins are known to stimulate chloroplast development in fruit, affecting fruit coloration, the role of KNOX II proteins in this context remains unclear. In this study, we employ CRISPR/Cas9 to generate knockout mutants of the KNOX II member, SlKN5. These mutants display increased leaf complexity, a phenotype commonly associated with reduced KNOX II activity, as well as enhanced accumulation of chloroplasts and chlorophylls in smaller cells within young, unripe fruit. RNA-seq data analyses indicate that SlKN5 suppresses the transcriptions of genes involved in chloroplast biogenesis, chlorophyll biosynthesis, and gibberellin catabolism. Furthermore, protein-protein interaction assays reveal that SlKN5 physically interacts with three transcriptional repressors from the BLH1-clade of BEL1-like homeodomain (BLH) protein family, SlBLH4, SlBLH5, and SlBLH7, with SlBLH7 showing the strongest interaction. CRISPR/Cas9-mediated knockout of these SlBLH genes confirmed their overlapping roles in suppressing chloroplast biogenesis, chlorophyll biosynthesis, and lycopene cyclization. Transient assays further demonstrate that the SlKN5-SlBLH7 interaction enhances binding capacity to regulatory regions of key chloroplast- and chlorophyll-related genes, including SlAPRR2-like1, SlCAB-1C, and SlGUN4. Collectively, our findings elucidate that the KNOX II SlKN5-SlBLH regulatory modules serve to inhibit fruit greening and subsequently promote lycopene accumulation, thereby fine-tuning the color transition from immature green fruit to mature red fruit.
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Affiliation(s)
- Kentaro Ezura
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
- Japan Society for Promotion of Science (JSPS), Kojimachi, Tokyo, 102-0083, Japan
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Yu Lu
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, 277-8562, Japan
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, Ibaraki, 305-8566, Japan
| | - Tohru Ariizumi
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, 305-8572, Japan
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Daware A, Mohanty JK, Narnoliya L, Singh A, Rathore D, Thakro V, Francis A, Singh NP, Francis P, Tripathi S, Chattopadhyay D, Parida SK. Uncovering DNA methylation landscapes to decipher evolutionary footprints of phenotypic diversity in chickpea. DNA Res 2024; 31:dsae013. [PMID: 38702947 PMCID: PMC11149376 DOI: 10.1093/dnares/dsae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2024] [Accepted: 05/02/2024] [Indexed: 05/06/2024] Open
Abstract
Genetic diversity and environmental factors are long believed to be the dominant contributors to phenotypic diversity in crop plants. However, it has been recently established that, besides genetic variation, epigenetic variation, especially variation in DNA methylation, plays a significant role in determining phenotypic diversity in crop plants. Therefore, assessing DNA methylation diversity in crop plants becomes vital, especially in the case of crops like chickpea, which has a narrow genetic base. Thus, in the present study, we employed whole-genome bisulfite sequencing to assess DNA methylation diversity in wild and cultivated (desi and kabuli) chickpea. This revealed extensive DNA methylation diversity in both wild and cultivated chickpea. Interestingly, the methylation diversity was found to be significantly higher than genetic diversity, suggesting its potential role in providing vital phenotypic diversity for the evolution and domestication of the Cicer gene pool. The phylogeny based on DNA methylation variation also indicates a potential complementary role of DNA methylation variation in addition to DNA sequence variation in shaping chickpea evolution. Besides, the study also identified diverse epi-alleles of many previously known genes of agronomic importance. The Cicer MethVarMap database developed in this study enables researchers to readily visualize methylation variation within the genes and genomic regions of their interest (http://223.31.159.7/cicer/public/). Therefore, epigenetic variation like DNA methylation variation can potentially explain the paradox of high phenotypic diversity despite the narrow genetic base in chickpea and can potentially be employed for crop improvement.
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Affiliation(s)
- Anurag Daware
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Jitendra K Mohanty
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Laxmi Narnoliya
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Akansha Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Deepanshi Rathore
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Virevol Thakro
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Aleena Francis
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Nagendra Pratap Singh
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Philip Francis
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Shailesh Tripathi
- Indian Institute of Pulses Research (IIPR), Uttar Pradesh, Kanpur 208024, India
| | - Debasis Chattopadhyay
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
| | - Swarup K Parida
- National Institute of Plant Genome Research (NIPGR), Aruna Asaf Ali Marg, New Delhi 110067, India
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Shi Z, Zhao W, Li C, Tan W, Zhu Y, Han Y, Ai P, Li Z, Wang Z. Overexpression of the Chrysanthemum lavandulifolium ROS1 gene promotes flowering in Arabidopsis thaliana by reducing the methylation level of CONSTANS. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112019. [PMID: 38346563 DOI: 10.1016/j.plantsci.2024.112019] [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: 11/30/2023] [Revised: 01/27/2024] [Accepted: 01/31/2024] [Indexed: 02/24/2024]
Abstract
DNA demethylation is involved in the regulation of flowering in plants, yet the underlying molecular mechanisms remain largely unexplored. The RELEASE OF SILENCING 1 (ROS1) gene, encoding a DNA demethyltransferase, plays key roles in many developmental processes. In this study, the ROS1 gene was isolated from Chrysanthemum lavandulifolium, where it was strongly expressed in the leaves, buds and flowers. Overexpression of the ClROS1 gene caused an early flowering phenotype in Arabidopsis thaliana. RNA-seq analysis of the transgenic plants revealed that differentially expressed genes (DEGs) were significantly enriched in the circadian rhythm pathway and that the positive regulator of flowering, CONSTANS (CO), was up-regulated. Additionally, whole-genome bisulphite sequencing (WGBS), PCR following methylation-dependent digestion with the enzyme McrBC, and bisulfite sequencing PCR (BSP) confirmed that the methylation level of the AtCO promoter was reduced, specifically in CG context. Overall, our results demonstrated that ClROS1 accelerates flowering by reducing the methylation level of the AtCO promoter. These findings clarify the epigenetic mechanism by which ClROS1-mediated DNA demethylation regulates flowering.
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Affiliation(s)
- Zhongya Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Chenran Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Wenchao Tan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Yifei Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Yanchao Han
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, Henan, China.
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Nie WF, Mao Y, Xing E, Liu R. Actin-related protein ARP4 and ARP6 antagonistically regulate DNA demethylase ROS1 in plants. PLANT PHYSIOLOGY 2024; 195:279-282. [PMID: 38319641 DOI: 10.1093/plphys/kiae058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/30/2024] [Accepted: 01/30/2024] [Indexed: 02/07/2024]
Affiliation(s)
- Wen-Feng Nie
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products, Ministry of Agriculture and Rural Affairs Key Laboratory of Vegetable Legumes Germplasm Enhancement and Molecular Breeding in Southern China, Institute of Vegetables, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
| | - Yueying Mao
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Enjie Xing
- Department of Horticulture, College of Horticulture and Landscape Architecture, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Ruie Liu
- Department of Plant Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
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Yang X, Bai Z, He Y, Wang N, Sun L, Li Y, Yin Z, Wang X, Zhang B, Han M, Lu X, Chen X, Wang D, Wang J, Wang S, Guo L, Chen C, Feng K, Ye W. Genome-wide characterization of DNA methyltransferase family genes implies GhDMT6 improving tolerance of salt and drought on cotton. BMC PLANT BIOLOGY 2024; 24:312. [PMID: 38649800 PMCID: PMC11036760 DOI: 10.1186/s12870-024-04985-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2023] [Accepted: 04/03/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND DNA methylation is an important epigenetic mode of genomic DNA modification and plays a vital role in maintaining epigenetic content and regulating gene expression. Cytosine-5 DNA methyltransferase (C5-MTase) are the key enzymes in the process of DNA methylation. However, there is no systematic analysis of the C5-MTase in cotton so far, and the function of DNMT2 genes has not been studied. METHODS In this study, the whole genome of cotton C5-MTase coding genes was identified and analyzed using a bioinformatics method based on information from the cotton genome, and the function of GhDMT6 was further validated by VIGS experiments and subcellular localization analysis. RESULTS 33 C5-MTases were identified from three cotton genomes, and were divided into four subfamilies by systematic evolutionary analysis. After the protein domain alignment of C5-MTases in cotton, 6 highly conserved motifs were found in the C-terminus of 33 proteins involved in methylation modification, which indicated that C5-MTases had a basic catalytic methylation function. These proteins were divided into four classes based on the N-terminal difference, of which DNMT2 lacks the N-terminal regulatory domain. The expression of C5-MTases in different parts of cotton was different under different stress treatments, which indicated the functional diversity of cotton C5-MTase gene family. Among the C5-MTases, the GhDMT6 had a obvious up-regulated expression. After silencing GhDMT6 with VIGS, the phenotype of cotton seedlings under different stress treatments showed a significant difference. Compared with cotton seedlings that did not silence GhDMT6, cotton seedlings silencing GhDMT6 showed significant stress resistance. CONCLUSION The results show that C5-MTases plays an important role in cotton stress response, which is beneficial to further explore the function of DNMT2 subfamily genes.
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Affiliation(s)
- Xiaomin Yang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
- Cash Crop Research Institute of Jiangxi Province, Jiujiang, Jiangxi, 332105, China
| | - Zhigang Bai
- Cash Crop Research Institute of Jiangxi Province, Jiujiang, Jiangxi, 332105, China
| | - Yunxin He
- Hunan Institute of Cotton Science, Changde, Hunan, 415101, China
| | - Ning Wang
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, 730070, China
| | - Liangqing Sun
- Cash Crop Research Institute of Jiangxi Province, Jiujiang, Jiangxi, 332105, China
| | - Yongqi Li
- Cash Crop Research Institute of Jiangxi Province, Jiujiang, Jiangxi, 332105, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Xiaoge Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Binglei Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China
| | - Keyun Feng
- Institute of Crop Sciences, Gansu Academy of Agricultural Sciences, Lanzhou, Gansu, 730070, China.
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Research Base, State Key Laboratory of Cotton Bio-breeding and Integrated Utilization, School of Agricultural Sciences, Zhengzhou University, Anyang, Henan, 455000, China.
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9
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Xiong J, Liu Y, Wu P, Bian Z, Li B, Zhang Y, Zhu B. Identification and virus-induced gene silencing (VIGS) analysis of methyltransferase affecting tomato (Solanum lycopersicum) fruit ripening. PLANTA 2024; 259:109. [PMID: 38558186 DOI: 10.1007/s00425-024-04384-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 03/09/2024] [Indexed: 04/04/2024]
Abstract
MAIN CONCLUSION Six methyltransferase genes affecting tomato fruit ripening were identified through genome-wide screening, VIGS assay, and expression pattern analysis. The data provide the basis for understanding new mechanisms of methyltransferases. Fruit ripening is a critical stage for the formation of edible quality and seed maturation, which is finely modulated by kinds of factors, including genetic regulators, hormones, external signals, etc. Methyltransferases (MTases), important genetic regulators, play vital roles in plant development through epigenetic regulation, post-translational modification, or other mechanisms. However, the regulatory functions of numerous MTases except DNA methylation in fruit ripening remain limited so far. Here, six MTases, which act on different types of substrates, were identified to affect tomato fruit ripening. First, 35 MTase genes with relatively high expression at breaker (Br) stage of tomato fruit were screened from the tomato MTase gene database encompassing 421 genes totally. Thereafter, six MTase genes were identified as potential regulators of fruit ripening via virus-induced gene silencing (VIGS), including four genes with a positive regulatory role and two genes with a negative regulatory role, respectively. The expression of these six MTase genes exhibited diverse patterns during the fruit ripening process, and responded to various external ripening-related factors, including ethylene, 1-methylcyclopropene (1-MCP), temperature, and light exposure. These results help to further elaborate the biological mechanisms of MTase genes in tomato fruit ripening and enrich the understanding of the regulatory mechanisms of fruit ripening involving MTases, despite of DNA MTases.
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Affiliation(s)
- Jiaxin Xiong
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Ye Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Peiwen Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Zheng Bian
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Bowen Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Yifan Zhang
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, 100083, People's Republic of China.
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10
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Cao X, Li X, Su Y, Zhang C, Wei C, Chen K, Grierson D, Zhang B. Transcription factor PpNAC1 and DNA demethylase PpDML1 synergistically regulate peach fruit ripening. PLANT PHYSIOLOGY 2024; 194:2049-2068. [PMID: 37992120 DOI: 10.1093/plphys/kiad627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Revised: 10/26/2023] [Accepted: 10/27/2023] [Indexed: 11/24/2023]
Abstract
Fruit ripening is accompanied by dramatic changes in color, texture, and flavor and is regulated by transcription factors (TFs) and epigenetic factors. However, the detailed regulatory mechanism remains unclear. Gene expression patterns suggest that PpNAC1 (NAM/ATAF1/2/CUC) TF plays a major role in peach (Prunus persica) fruit ripening. DNA affinity purification (DAP)-seq combined with transactivation tests demonstrated that PpNAC1 can directly activate the expression of multiple ripening-related genes, including ACC synthase1 (PpACS1) and ACC oxidase1 (PpACO1) involved in ethylene biosynthesis, pectinesterase1 (PpPME1), pectate lyase1 (PpPL1), and polygalacturonase1 (PpPG1) related to cell wall modification, and lipase1 (PpLIP1), fatty acid desaturase (PpFAD3-1), and alcohol acyltransferase1 (PpAAT1) involved in volatiles synthesis. Overexpression of PpNAC1 in the tomato (Solanum lycopersicum) nor (nonripening) mutant restored fruit ripening, and its transient overexpression in peach fruit induced target gene expression, supporting a positive role of PpNAC1 in fruit ripening. The enhanced transcript levels of PpNAC1 and its target genes were associated with decreases in their promoter mCG methylation during ripening. Declining DNA methylation was negatively associated with increased transcripts of DNA demethylase1 (PpDML1), whose promoter is recognized and activated by PpNAC1. We propose that decreased methylation of the promoter region of PpNAC1 leads to a subsequent decrease in DNA methylation levels and enhanced transcription of ripening-related genes. These results indicate that positive feedback between PpNAC1 and PpDML1 plays an important role in directly regulating expression of multiple genes required for peach ripening and quality formation.
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Affiliation(s)
- Xiangmei Cao
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xinzhao Li
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yike Su
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chi Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Chunyan Wei
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Desheng Middle Road No. 298, Hangzhou, Zhejiang Province 310021, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Donald Grierson
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Plant and Crop Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, Leicestershire LE12 5RD, UK
| | - Bo Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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11
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Pereira L. And yet another transcription factor-the complex world of fruit ripening. PLANT PHYSIOLOGY 2024; 194:2185-2187. [PMID: 38173334 PMCID: PMC10980389 DOI: 10.1093/plphys/kiad673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/12/2023] [Accepted: 12/13/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Lara Pereira
- Assistant Features Editor, Plant Physiology, American Society of Plant Biologists
- Ecology and Evolutionary Biology, School of Biosciences, University of Sheffield, Sheffield S10 2TN, UK
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12
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Jiang G, Li Z, Ding X, Zhou Y, Lai H, Jiang Y, Duan X. WUSCHEL-related homeobox transcription factor SlWOX13 regulates tomato fruit ripening. PLANT PHYSIOLOGY 2024; 194:2322-2337. [PMID: 37995308 DOI: 10.1093/plphys/kiad623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/27/2023] [Accepted: 10/27/2023] [Indexed: 11/25/2023]
Abstract
Fruit ripening is a complex, genetically programmed process involving the action of critical transcription factors (TFs). Despite the established importance of WUSCHEL-related homeobox (WOX) TFs in plant development, the involvement of WOX and its underlying mechanism in the regulation of fruit ripening remain unclear. Here, we demonstrate that SlWOX13 regulates fruit ripening in tomato (Solanum lycopersicum). Overexpression of SlWOX13 accelerates fruit ripening, whereas loss-of-function mutation in SlWOX13 delays this process. Moreover, ethylene synthesis and carotenoid accumulation are significantly inhibited in slwox13 mutant fruit but accelerated in SlWOX13 transgenic fruit. Integrated analyses of RNA-seq and chromatin immunoprecipitation (ChIP)-seq identified 422 direct targets of SlWOX13, of which 243 genes are negatively regulated and 179 are positively regulated by SlWOX13. Electrophoretic mobility shift assay, RT-qPCR, dual-luciferase reporter assay, and ChIP-qPCR analyses demonstrated that SlWOX13 directly activates the expression of several genes involved in ethylene synthesis and signaling and carotenoid biosynthesis. Furthermore, SlWOX13 modulates tomato fruit ripening through key ripening-related TFs, such as RIPENING INHIBITOR (RIN), NON-RIPENING (NOR), and NAM, ATAF1, 2, and CUC2 4 (NAC4). Consequently, these effects promote fruit ripening. Taken together, these results demonstrate that SlWOX13 positively regulates tomato fruit ripening via both ethylene synthesis and signaling and by transcriptional regulation of key ripening-related TFs.
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Affiliation(s)
- Guoxiang Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhiwei Li
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiaochun Ding
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Yijie Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
| | - Hongmei Lai
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yueming Jiang
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuewu Duan
- State Key Laboratory of Plant Diversity and Specialty Crops & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
- South China National Botanical Garden, Guangzhou 510650, China
- University of Chinese Academy of Sciences, Beijing 100049, China
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13
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Zhong S, Zhu H, Li W, Wu D, Miao Y, Dong B, Wang Y, Xiao Z, Fang Q, Deng J, Zhao H. DNA methylome analysis reveals novel insights into active hypomethylated regulatory mechanisms of temperature-dependent flower opening in Osmanthus fragrans. HORTICULTURE RESEARCH 2024; 11:uhae010. [PMID: 38464472 PMCID: PMC10923647 DOI: 10.1093/hr/uhae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2023] [Accepted: 01/01/2024] [Indexed: 03/12/2024]
Abstract
Short-term ambient low temperature (ALT) stimulation is necessary for Osmanthus fragrans to facilitate continued flower opening after floral bud development reaches maturity. DNA methylation, a vital epigenetic modification, regulates various biological processes in response to temperature fluctuations. However, its role in temperature-driven flower opening remains elusive. In this study, we identified the pivotal timeframe during which O. fragrans promptly detected temperature cues. Using whole-genome bisulfite sequencing, we explored global DNA hypomethylation during this phase, with the most significant changes occurring in CHH sequence contexts. Auxin transport inhibitor (TIBA) application revealed that ALT-induced endogenous auxin accumulation promoted peduncle elongation. In our mRNA-seq analysis, we discovered that the differentially expressed genes (DEGs) with hypo-differentially methylated regions (hypo-DMRs) were mainly enriched in auxin and temperature response, RNA processing, and carbohydrate and lipid metabolism. Transcripts of three DNA demethylase genes (OfROS1a, OfDML3, OfDME) showed upregulation. Furthermore, all DNA methylase genes, except OfCMT2b, also displayed increased expression, specifically with two of them, OfCMT3a and OfCMT1, being associated with hypo-DMRs. Promoter assays showed that OfROS1a, with promoters containing low-temperature- and auxin-responsive elements, were activated by ALT and exogenous IAA at low concentrations but inhibited at high concentrations. Overexpression of OfROS1 reduced endogenous auxin levels but enhanced the expression of genes related to auxin response and spliceosome in petunia. Furthermore, OfROS1 promoted sucrose synthesis in petunia corollas. Our data characterized the rapid response of active DNA hypomethylation to ALT and suggested a possible epiregulation of temperature-dependent flower opening in O. fragrans. This study revealed the pivotal role of DNA hypomethylation in O. fragrans during the ALT-responsive phase before flower opening, involving dynamic DNA demethylation, auxin signaling modulation, and a potential feedback loop between hypomethylation and methylation.
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Affiliation(s)
- Shiwei Zhong
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
| | - Huijun Zhu
- Zhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Key Laboratory of National Forestry and Grassland Administration on Germplasm Innovation and Utilization for Southern Garden Plants, School of Landscape and Architecture, Zhejiang A&F University, Hangzhou, Zhejiang 311300, China
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14
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Yu H, Zhang C, Lu C, Wang Y, Ge C, Huang G, Wang H. The lemon genome and DNA methylome unveil epigenetic regulation of citric acid biosynthesis during fruit development. HORTICULTURE RESEARCH 2024; 11:uhae005. [PMID: 38464476 PMCID: PMC10923643 DOI: 10.1093/hr/uhae005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 12/30/2023] [Indexed: 03/12/2024]
Abstract
Citric acid gives lemons their unique flavor, which impacts their sensory traits and market value. However, the intricate process of citric acid accumulation during lemon fruit growth remains incompletely understood. Here, we achieved a chromosomal-level genome assembly for the 'Xiangshui' lemon variety, spanning 364.85 Mb across nine chromosomes. This assembly revealed 27 945 genes and 51.37% repetitive sequences, tracing the divergence from citron 2.85 million years ago. DNA methylome analysis of lemon fruits across different developmental stages revealed significant variations in DNA methylation. We observed decreased CG and CHG methylation but increased CHH methylation. Notably, the expression of RdDM pathway-related genes increased with fruit development, suggesting a connection with elevated CHH methylation, which is potentially influenced by the canonical RdDM pathway. Furthermore, we observed that elevated CHH DNA methylation within promoters significantly influenced the expression of key genes, critically contributing to vital biological processes, such as citric acid accumulation. In particular, the pivotal gene phosphoenolpyruvate carboxykinase (ClPEPCK), which regulates the tricarboxylic acid cycle, was strikingly upregulated during fruit development, concomitant with increased CHH methylation in its promoter region. Other essential genes associated with citric acid accumulation, such as the MYB transcription factor (ClPH1/4/5) and ANTHOCYANIN 1 (ClAN1), were strongly correlated with DNA methylation levels. These results strongly indicate that DNA methylation crucially orchestrates the metabolic synthesis of citric acid. In conclusion, our study revealed dynamic changes in DNA methylation during lemon fruit development, underscoring the significant role of DNA methylation in controlling the citric acid metabolic pathway.
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Affiliation(s)
- Hang Yu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Chao Zhang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Chuang Lu
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Yana Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Congcong Ge
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
| | - Guixiang Huang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning 530004, China
| | - Haifeng Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, Guangxi 530004, China
- Key Laboratory of Crop Cultivation and Physiology, Education Department of Guangxi Zhuang Autonomous Region, Guangxi University, Nanning 530004, China
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15
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Feng S, Jiang X, Huang Z, Li F, Wang R, Yuan X, Sun Z, Tan H, Zhong L, Li S, Cheng Y, Bao M, Qiao H, Song Q, Wang J, Zhang F. DNA methylation remodeled amino acids biosynthesis regulates flower senescence in carnation (Dianthus caryophyllus). THE NEW PHYTOLOGIST 2024; 241:1605-1620. [PMID: 38179647 DOI: 10.1111/nph.19499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 11/20/2023] [Indexed: 01/06/2024]
Abstract
Dynamic DNA methylation regulatory networks are involved in many biological processes. However, how DNA methylation patterns change during flower senescence and their relevance with gene expression and related molecular mechanism remain largely unknown. Here, we used whole genome bisulfite sequencing to reveal a significant increase of DNA methylation in the promoter region of genes during natural and ethylene-induced flower senescence in carnation (Dianthus caryophyllus L.), which was correlated with decreased expression of DNA demethylase gene DcROS1. Silencing of DcROS1 accelerated while overexpression of DcROS1 delayed carnation flower senescence. Moreover, among the hypermethylated differentially expressed genes during flower senescence, we identified two amino acid biosynthesis genes, DcCARA and DcDHAD, with increased DNA methylation and reduced expression in DcROS1 silenced petals, and decreased DNA methylation and increased expression in DcROS1 overexpression petals, accompanied by decreased or increased amino acids content. Silencing of DcCARA and DcDHAD accelerates carnation flower senescence. We further showed that adding corresponding amino acids could largely rescue the senescence phenotype of DcROS1, DcCARA and DcDHAD silenced plants. Our study not only demonstrates an essential role of DcROS1-mediated remodeling of DNA methylation in flower senescence but also unravels a novel epigenetic regulatory mechanism underlying DNA methylation and amino acid biosynthesis during flower senescence.
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Affiliation(s)
- Shan Feng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyu Jiang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhiheng Huang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Fan Li
- Yunnan Seed Laboratory, Kunming, 650200, China
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, 650200, China
| | - Ruiming Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Xinyi Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng Sun
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hualiang Tan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Linlin Zhong
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Shenchong Li
- Yunnan Seed Laboratory, Kunming, 650200, China
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, 650200, China
| | - Yunjiang Cheng
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Manzhu Bao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
| | - Hong Qiao
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Qingxin Song
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jihua Wang
- Yunnan Seed Laboratory, Kunming, 650200, China
- Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Kunming, 650200, China
| | - Fan Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan, 430070, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
- National R&D Center for Citrus Postharvest Technology, Huazhong Agricultural University, Wuhan, 430070, China
- Yunnan Seed Laboratory, Kunming, 650200, China
- The Institute of Flowers Research, Huazhong Agricultural University, Wuhan, 430070, China
- Key Laboratory of Huazhong Urban Agriculture, Ministry of Agriculture and Rural Affairs, Huazhong Agricultural University, Wuhan, 430070, China
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16
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Seem K, Kaur S, Kumar S, Mohapatra T. Epigenome editing for targeted DNA (de)methylation: a new perspective in modulating gene expression. Crit Rev Biochem Mol Biol 2024; 59:69-98. [PMID: 38440883 DOI: 10.1080/10409238.2024.2320659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 02/15/2024] [Indexed: 03/06/2024]
Abstract
Traditionally, it has been believed that inheritance is driven as phenotypic variations resulting from changes in DNA sequence. However, this paradigm has been challenged and redefined in the contemporary era of epigenetics. The changes in DNA methylation, histone modification, non-coding RNA biogenesis, and chromatin remodeling play crucial roles in genomic functions and regulation of gene expression. More importantly, some of these changes are inherited to the next generations as a part of epigenetic memory and play significant roles in gene expression. The sum total of all changes in DNA bases, histone proteins, and ncRNA biogenesis constitutes the epigenome. Continuous progress in deciphering epigenetic regulations and the existence of heritable epigenetic/epiallelic variations associated with trait of interest enables to deploy epigenome editing tools to modulate gene expression. DNA methylation marks can be utilized in epigenome editing for the manipulation of gene expression. Initially, genome/epigenome editing technologies relied on zinc-finger protein or transcriptional activator-like effector protein. However, the discovery of clustered regulatory interspaced short palindromic repeats CRISPR)/deadCRISPR-associated protein 9 (dCas9) enabled epigenome editing to be more specific/efficient for targeted DNA (de)methylation. One of the major concerns has been the off-target effects, wherein epigenome editing may unintentionally modify gene/regulatory element which may cause unintended change/harmful effects. Moreover, epigenome editing of germline cell raises several ethical/safety issues. This review focuses on the recent developments in epigenome editing tools/techniques, technological limitations, and future perspectives of this emerging technology in therapeutics for human diseases as well as plant improvement to achieve sustainable developmental goals.
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Affiliation(s)
- Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Trilochan Mohapatra
- Protection of Plant Varieties and Farmers' Rights Authority, New Delhi, India
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17
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Zhang Y, Zhong J, Munawar A, Cai Y, He W, Zhang Y, Guo H, Gao Y, Zhu Z, Zhou W. Knocking down a DNA demethylase gene affects potato plant defense against a specialist insect herbivore. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:483-499. [PMID: 37781866 DOI: 10.1093/jxb/erad387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 09/29/2023] [Indexed: 10/03/2023]
Abstract
DNA demethylase (DML) is involved in plant development and responses to biotic and abiotic stresses; however, its role in plant-herbivore interaction remains elusive. Here, we found that herbivory by the potato tuber moth, Phthorimaea operculella, rapidly induced the genome-wide DNA methylation and accumulation of DML gene transcripts in potato plants. Herbivory induction of DML transcripts was suppressed in jasmonate-deficient plants, whereas exogenous application of methyl jasmonate (MeJA) improved DML transcripts, indicating that the induction of DML transcripts by herbivory is associated with jasmonate signaling. Moreover, P. operculella larvae grew heavier on DML gene (StDML2) knockdown plants than on wild-type plants, and the decreased biosynthesis of jasmonates in the former may be responsible for this difference, since the larvae feeding on these two genotypes supplemented with MeJA showed similar growth. In addition, P. operculella adult moths preferred to oviposit on StDML2 knockdown plants than on wild-type plants, which was associated with the reduced emission of β-caryophyllene in the former. In addition, supplementing β-caryophyllene to these two genotypes further disrupted moths' oviposit choice preference for them. Interestingly, in StDML2 knockdown plants, hypermethylation was found at the promoter regions for the key genes StAOS and StAOC in the jasmonate biosynthetic pathway, as well as for the key gene StTPS12 in β-caryophyllene production. Our findings suggest that knocking down StDML2 can affect herbivore defense via jasmonate signaling and defense compound production in potato plants.
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Affiliation(s)
- Yadong Zhang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Jian Zhong
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Asim Munawar
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yajie Cai
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Wenjing He
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Yixin Zhang
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
| | - Han Guo
- Department of Economic Plants and Biotechnology, Yunnan Key Laboratory for Wild Plant Resources, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming 650201, China
| | - Yulin Gao
- State Key Laboratory for Biology of Plant Disease and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zengrong Zhu
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
| | - Wenwu Zhou
- State Key Laboratory of Rice Biology, Ministry of Agricultural and Rural Affairs Key Laboratory of Molecular Biology of Crop Pathogens and Insect Pests, Institute of Insect Sciences, Zhejiang University, Hangzhou 310058, China
- Hainan Institute, Zhejiang University, Sanya 572000, China
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18
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Jin W, Yan W, Ma M, Hasi A, Che G. Genome-wide identification and expression analysis of the JMJ-C gene family in melon (Cucumis melo L.) reveals their potential role in fruit development. BMC Genomics 2023; 24:771. [PMID: 38093236 PMCID: PMC10720240 DOI: 10.1186/s12864-023-09868-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Proteins with the jumonji (JMJ)-C domain belong to the histone demethylase family and contribute to reverse histone methylation. Although JMJ-C family genes have an essential role in regulating plant growth and development, the characterization of the JMJ-C family genes in melon has not been uncovered. RESULTS In this study, a total of 17 JMJ-C proteins were identified in melon (Cucumis melo L.). CmJMJs were categorized into five subfamilies based on the specific conserved domain: KDM4/JHDM3, KDM5/JARID1, JMJD6, KDM3/JHDM2, and JMJ-C domain-only. The chromosome localization analyses showed that 17 CmJMJs were distributed on nine chromosomes. Cis-acting element analyses of the 17 CmJMJ genes showed numerous hormone, light, and stress response elements distributed in the promoter region. Covariance analysis revealed one pair of replicated fragments (CmJMJ3a and CmJMJ3b) in 17 CmJMJ genes. We investigated the expression profile of 17 CmJMJ genes in different lateral organs and four developmental stages of fruit by RNA-seq transcriptome analysis and RT-qPCR. The results revealed that most CmJMJ genes were prominently expressed in female flowers, ovaries, and developing fruits, suggesting their active role in melon fruit development. Subcellular localization showed that the fruit-related CmJMJ5a protein is specifically localized in the cell nucleus. CONCLUSIONS This study provides a comprehensive understanding of the gene structure, classification, and evolution of JMJ-C in melon and supports the clarification of the JMJ-C functions in further research.
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Affiliation(s)
- Wuyun Jin
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Wei Yan
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Ming Ma
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Agula Hasi
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
| | - Gen Che
- Key Laboratory of Herbage & Endemic Crop Biology, Ministry of Education, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China.
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19
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Zhou L, Gao G, Li X, Wang W, Tian S, Qin G. The pivotal ripening gene SlDML2 participates in regulating disease resistance in tomato. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2291-2306. [PMID: 37466912 PMCID: PMC10579708 DOI: 10.1111/pbi.14130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Revised: 06/14/2023] [Accepted: 07/06/2023] [Indexed: 07/20/2023]
Abstract
Fruit ripening and disease resistance are two essential biological processes for quality formation and maintenance. DNA methylation, in the form of 5-methylcytosine (5mC), has been elucidated to modulate fruit ripening, but its role in regulating fruit disease resistance remains poorly understood. In this study, we show that mutation of SlDML2, the DNA demethylase gene essential for fruit ripening, affects multiple developmental processes of tomato besides fruit ripening, including seed germination, leaf length and width and flower branching. Intriguingly, loss of SlDML2 function decreased the resistance of tomato fruits against the necrotrophic fungal pathogen Botrytis cinerea. Comparative transcriptomic analysis revealed an obvious transcriptome reprogramming caused by SlDML2 mutation during B. cinerea invasion. Among the thousands of differentially expressed genes, SlβCA3 encoding a β-carbonic anhydrase and SlFAD3 encoding a ω-3 fatty acid desaturase were demonstrated to be transcriptionally activated by SlDML2-mediated DNA demethylation and positively regulate tomato resistance to B. cinerea probably in the same genetic pathway with SlDML2. We further show that the pericarp tissue surrounding B. cinerea infection exhibited a delay in ripening with singnificant decrease in expression of ripening genes that are targeted by SlDML2 and increase in expression of SlβCA3 and SlFAD3. Taken together, our results uncover an essential layer of gene regulation mediated by DNA methylation upon B. cinerea infection and raise the possible that the DNA demethylase gene SlDML2, as a multifunctional gene, participates in modulating the trade-off between fruit ripening and disease resistance.
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Affiliation(s)
- Leilei Zhou
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Guangtong Gao
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Xiaojing Li
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Weihao Wang
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
| | - Shiping Tian
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
| | - Guozheng Qin
- Key Laboratory of Plant Resources, Institute of BotanyChinese Academy of SciencesBeijingChina
- China National Botanical GardenBeijingChina
- University of Chinese Academy of SciencesBeijingChina
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20
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Pujol M, Garcia-Mas J. Regulation of climacteric fruit ripening in melon: recent advances and future challenges. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6224-6236. [PMID: 37399085 DOI: 10.1093/jxb/erad256] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Fruit ripening is a complex and highly regulated process where tomato and strawberry have been the model species classically used for studying climacteric and non-climacteric fleshy fruit ripening types, respectively. Melon has emerged as an alternative ripening model because climacteric and non-climacteric cultivars exist, which makes it possible to dissect the regulation of ripening using a genetic approach. Several quantitative trait loci that regulate climacteric fruit ripening have been identified to date, and their combination in both climacteric and non-climacteric genetic backgrounds resulted in lines with different ripening behaviors, demonstrating that the climacteric intensity can be genetically modulated. This review discusses our current knowledge of the physiological changes observed during melon climacteric fruit ripening such as ethylene production, fruit abscission, chlorophyll degradation, firmness, and aroma, as well as their complex genetic control. From pioneer experiments in which ethylene biosynthesis was silenced, to the recent genetic edition of ripening regulators, current data suggest that the climacteric response is determined by the interaction of several loci under quantitative inheritance. The exploitation of the rich genetic diversity of melon will enable the discovery of additional genes involved in the regulation of the climacteric response, ultimately leading to breeding aromatic melon fruits with extended shelf life.
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Affiliation(s)
- Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
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21
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Zhang Y, Huang D, Miao Y. Epigenetic control of plant senescence and cell death and its application in crop improvement. FRONTIERS IN PLANT SCIENCE 2023; 14:1258487. [PMID: 37965008 PMCID: PMC10642554 DOI: 10.3389/fpls.2023.1258487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 10/16/2023] [Indexed: 11/16/2023]
Abstract
Plant senescence is the last stage of plant development and a type of programmed cell death, occurring at a predictable time and cell. It involves the functional conversion from nutrient assimilation to nutrient remobilization, which substantially impacts plant architecture and plant biomass, crop quality, and horticultural ornamental traits. In past two decades, DNA damage was believed to be a main reason for cell senescence. Increasing evidence suggests that the alteration of epigenetic information is a contributing factor to cell senescence in organisms. In this review, we summarize the current research progresses of epigenetic and epitranscriptional mechanism involved in cell senescence of plant, at the regulatory level of DNA methylation, histone methylation and acetylation, chromatin remodeling, non-coding RNAs and RNA methylation. Furthermore, we discuss their molecular genetic manipulation and potential application in agriculture for crop improvement. Finally we point out the prospects of future research topics.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dongmei Huang
- Department of Biochemistry and Molecular Biology, Xiamen Medical College, Xiamen, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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22
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Liu P, Liu R, Xu Y, Zhang C, Niu Q, Lang Z. DNA cytosine methylation dynamics and functional roles in horticultural crops. HORTICULTURE RESEARCH 2023; 10:uhad170. [PMID: 38025976 PMCID: PMC10660380 DOI: 10.1093/hr/uhad170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 08/20/2023] [Indexed: 12/01/2023]
Abstract
Methylation of cytosine is a conserved epigenetic modification that maintains the dynamic balance of methylation in plants under the regulation of methyltransferases and demethylases. In recent years, the study of DNA methylation in regulating the growth and development of plants and animals has become a key area of research. This review describes the regulatory mechanisms of DNA cytosine methylation in plants. It summarizes studies on epigenetic modifications of DNA methylation in fruit ripening, development, senescence, plant height, organ size, and under biotic and abiotic stresses in horticultural crops. The review provides a theoretical basis for understanding the mechanisms of DNA methylation and their relevance to breeding, genetic improvement, research, innovation, and exploitation of new cultivars of horticultural crops.
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Affiliation(s)
- Peipei Liu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Ruie Liu
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Yaping Xu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 201602, China
| | - Caixi Zhang
- School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Qingfeng Niu
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Zhaobo Lang
- Institute of Advanced Biotechnology, School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
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23
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Grin IR, Petrova DV, Endutkin AV, Ma C, Yu B, Li H, Zharkov DO. Base Excision DNA Repair in Plants: Arabidopsis and Beyond. Int J Mol Sci 2023; 24:14746. [PMID: 37834194 PMCID: PMC10573277 DOI: 10.3390/ijms241914746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/27/2023] [Accepted: 09/27/2023] [Indexed: 10/15/2023] Open
Abstract
Base excision DNA repair (BER) is a key pathway safeguarding the genome of all living organisms from damage caused by both intrinsic and environmental factors. Most present knowledge about BER comes from studies of human cells, E. coli, and yeast. Plants may be under an even heavier DNA damage threat from abiotic stress, reactive oxygen species leaking from the photosynthetic system, and reactive secondary metabolites. In general, BER in plant species is similar to that in humans and model organisms, but several important details are specific to plants. Here, we review the current state of knowledge about BER in plants, with special attention paid to its unique features, such as the existence of active epigenetic demethylation based on the BER machinery, the unexplained diversity of alkylation damage repair enzymes, and the differences in the processing of abasic sites that appear either spontaneously or are generated as BER intermediates. Understanding the biochemistry of plant DNA repair, especially in species other than the Arabidopsis model, is important for future efforts to develop new crop varieties.
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Affiliation(s)
- Inga R. Grin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
| | - Daria V. Petrova
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Anton V. Endutkin
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
| | - Chunquan Ma
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Bing Yu
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Haiying Li
- Engineering Research Center of Agricultural Microbiology Technology, Ministry of Education, Harbin 150080, China; (C.M.); (B.Y.); (H.L.)
- Heilongjiang Provincial Key Laboratory of Plant Genetic Engineering and Biological Fermentation Engineering for Cold Region, Harbin 150080, China
- School of Life Sciences, Heilongjiang University, Harbin 150080, China
| | - Dmitry O. Zharkov
- Siberian Branch of the Russian Academy of Sciences Institute of Chemical Biology and Fundamental Medicine, 8 Lavrentieva Ave., Novosibirsk 630090, Russia; (D.V.P.); (A.V.E.)
- Department of Natural Sciences, Novosibirsk State University, 2 Pirogova St., Novosibirsk 630090, Russia
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24
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Ming Y, Jiang L, Ji D. Epigenetic regulation in tomato fruit ripening. FRONTIERS IN PLANT SCIENCE 2023; 14:1269090. [PMID: 37780524 PMCID: PMC10539587 DOI: 10.3389/fpls.2023.1269090] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2023] [Accepted: 08/31/2023] [Indexed: 10/03/2023]
Abstract
Fruit ripening is a crucial stage in quality development, influenced by a diverse array of internal and external factors. Among these factors, epigenetic regulation holds significant importance and has garnered substantial research attention in recent years. Here, this review aims to discuss the breakthrough in epigenetic regulation of tomato (Solanum lycopersicum) fruit ripening, including DNA methylation, N6-Methyladenosine mRNA modification, histone demethylation/deacetylation, and non-coding RNA. Through this brief review, we seek to enhance our understanding of the regulatory mechanisms governing tomato fruit ripening, while providing fresh insights for the precise modulation of these mechanisms.
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Affiliation(s)
| | - Libo Jiang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
| | - Dongchao Ji
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo, China
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25
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Wang L, Li T, Liu N, Liu X. Identification of tomato AHL gene families and functional analysis their roles in fruit development and abiotic stress response. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 202:107931. [PMID: 37557017 DOI: 10.1016/j.plaphy.2023.107931] [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: 05/02/2023] [Revised: 07/31/2023] [Accepted: 08/01/2023] [Indexed: 08/11/2023]
Abstract
The AT-HOOK MOTIF CONTAINING NUCLEAR LOCALIZED (AHL) transcription factors play important roles in regulating plant development and stress response. However, the AHL family genes have not been identified in tomato (Solanum lycopersicum) and their biological functions have not been elucidated. In this work, the gene families encoding AHLs were identified in tomato genome, and their physical and chemical characteristics, subcellular localization, gene expression profiles during fruit development and upon abiotic stimulus were investigated. Overall, a total of 18 AHL members were identified in tomato genome, phylogenetic analysis classified these SlAHL members into two clades, clade A (SlAHL1-8) and clade B (SlAHL9-18). Six clade A SlAHLs were detected to be subcellular localized in the nucleus. The transcripts of the representative clade A SlAHLs predominantly accumulated 10 days post anthesis (dpa) in tomato fruits, revealing an involvement of these SlAHLs in early fruit development. Furthermore, compared with clade B members, the transcripts of the clade A SlAHLs were more responsive to heat, drought, cold and salt stresses, suggesting that these SlAHLs may play major roles in response to abiotic stresses. Moreover, overexpression of SlAHL1 and SlAHL7 in Arabidopsis increased the sensitivity to ABA during seed germination and seedling stages. Overexpression of SlAHL1 inhibited seed germination while increased primary root elongation upon salt and drought stresses. Together, our work suggested that the clade A SlAHL genes may play an important role in response to abiotic stresses, which paving the way for future functional analysis of AHL genes in tomato and other Solanaceae species.
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Affiliation(s)
- Liyuan Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Tingting Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Nan Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, 510650, China
| | - Xuncheng Liu
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, Chinese Academy of Sciences, Guangzhou, 510650, China.
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26
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Li Y, Shi Y, Li Y, Lu J, Sun Y, Zhang Y, Chen W, Yang X, Grierson D, Lang Z, Jiang G, Chen K. DNA methylation mediated by RdDM pathway and demethylation affects furanone accumulation through regulation of QUINONE OXIDOREDUCTASE in strawberry. HORTICULTURE RESEARCH 2023; 10:uhad131. [PMID: 37560014 PMCID: PMC10407599 DOI: 10.1093/hr/uhad131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 06/19/2023] [Indexed: 08/11/2023]
Abstract
Recently, increasing evidence suggests that DNA methylation plays a crucial role in fruit ripening. However, the role of DNA methylation in regulating specific traits, such as flavor, remains unclear. Here, we report a role of DNA methylation in affecting furanone biosynthesis in strawberry. Strawberry quinone oxidoreductase (FaQR) is a key enzyme in furanone biosynthesis. There are four FaQR homologs in strawberry cultivar 'Yuexin', and one of them, FaQR3, contributes ~50% of FaQR transcripts, indicating a major role of FaQR3 in furanone biosynthesis. Through characterization of levels of DNA methylation and FaQR3 transcript and furanone contents during fruit ripening and after the application of DNA methylation inhibitor, we found that the DNA methylation level of the FaQR3 promoter was negatively correlated with FaQR3 expression and furanone accumulation, suggesting that DNA methylation may be involved in furanone biosynthesis through adjusting FaQR3 expression, and responded to different temperatures consistently. In addition, transient expression of a gene in the RNA-directed DNA methylation (RdDM) pathway, FaAGO4, and enrichment analysis of the 24-nucleotide siRNAs suggested that DNA methylation in the FaQR3 promoter is mediated by the RdDM pathway. Transient RNA interference (RNAi) of FaDML indicated that the demethylation pathway may be involved in regulating furanone accumulation. These findings provide new insights into the role of DNA methylation and demethylation in affecting flavor quality in strawberry during fruit ripening.
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Affiliation(s)
- Yunduan Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yanna Shi
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yichen Li
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Jiao Lu
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yunfan Sun
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Yuanyuan Zhang
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Wenbo Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
| | - Xiaofang Yang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Donald Grierson
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough LE12 5RD, United Kingdom
| | - Zhaobo Lang
- Institute of Advanced Biotechnology and School of Life Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Guihua Jiang
- Institute of Horticulture, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, Zhejiang, China
| | - Kunsong Chen
- College of Agriculture & Biotechnology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
- The State Agriculture Ministry Laboratory of Horticultural Plant Growth, Development and Quality Improvement, Zhejiang University, Zijingang Campus, Hangzhou 310058, China
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Liu Y, Wu P, Li B, Wang W, Zhu B. Phosphoribosyltransferases and Their Roles in Plant Development and Abiotic Stress Response. Int J Mol Sci 2023; 24:11828. [PMID: 37511586 PMCID: PMC10380321 DOI: 10.3390/ijms241411828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 07/19/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
Glycosylation is a widespread glycosyl modification that regulates gene expression and metabolite bioactivity in all life processes of plants. Phosphoribosylation is a special glycosyl modification catalyzed by phosphoribosyltransferase (PRTase), which functions as a key step in the biosynthesis pathway of purine and pyrimidine nucleotides, histidine, tryptophan, and coenzyme NAD(P)+ to control the production of these essential metabolites. Studies in the past decades have reported that PRTases are indispensable for plant survival and thriving, whereas the complicated physiological role of PRTases in plant life and their crosstalk is not well understood. Here, we comprehensively overview and critically discuss the recent findings on PRTases, including their classification, as well as the function and crosstalk in regulating plant development, abiotic stress response, and the balance of growth and stress responses. This review aims to increase the understanding of the role of plant PRTase and also contribute to future research on the trade-off between plant growth and stress response.
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Affiliation(s)
- Ye Liu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Peiwen Wu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Bowen Li
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
| | - Weihao Wang
- Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Benzhong Zhu
- College of Food Science and Nutritional Engineering, China Agricultural University, Beijing 100083, China
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Ji Y, Wang A. Recent advances in epigenetic triggering of climacteric fruit ripening. PLANT PHYSIOLOGY 2023; 192:1711-1717. [PMID: 37002826 PMCID: PMC10315304 DOI: 10.1093/plphys/kiad206] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 03/03/2023] [Accepted: 03/18/2023] [Indexed: 06/19/2023]
Abstract
During ripening, fleshy fruits undergo irreversible changes in color, texture, sugar content, aroma, and flavor to appeal to seed-dispersal vectors. The onset of climacteric fruit ripening is accompanied by an ethylene burst. Understanding the factors triggering this ethylene burst is important for manipulating climacteric fruit ripening. Here, we review the current understanding and recent insights into the possible factors triggering climacteric fruit ripening: DNA methylation and histone modification, including methylation and acetylation. Understanding the initiation factors of fruit ripening is important for exploring and accurately regulating the mechanisms of fruit ripening. Lastly, we discuss the potential mechanisms responsible for climacteric fruit ripening.
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Affiliation(s)
- Yinglin Ji
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province), Key Laboratory of Protected Horticulture (Ministry of Education), National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Aide Wang
- Key Laboratory of Fruit Postharvest Biology (Liaoning Province), Key Laboratory of Protected Horticulture (Ministry of Education), National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology (Liaoning), College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
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29
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Li J, Li C, Deng Y, Wei H, Lu S. Characteristics of Salvia miltiorrhiza methylome and the regulatory mechanism of DNA methylation in tanshinone biosynthesis. HORTICULTURE RESEARCH 2023; 10:uhad114. [PMID: 37577393 PMCID: PMC10419789 DOI: 10.1093/hr/uhad114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Accepted: 05/21/2023] [Indexed: 08/15/2023]
Abstract
Salvia miltiorrhiza is a model medicinal plant with significant economic and medicinal value. Its roots produce a group of diterpenoid lipophilic bioactive components, termed tanshinones. Biosynthesis and regulation of tanshinones has attracted widespread interest. However, the methylome of S. miltiorrhiza has not been analysed and the regulatory mechanism of DNA methylation in tanshinone production is largely unknown. Here we report single-base resolution DNA methylomes from roots and leaves. Comparative analysis revealed differential methylation patterns for CG, CHG, and CHH contexts and the association between DNA methylation and the expression of genes and small RNAs. Lowly methylated genes always had higher expression levels and 24-nucleotide sRNAs could be key players in the RdDM pathway in S. miltiorrhiza. DNA methylation variation analysis showed that CHH methylation contributed mostly to the difference. Go enrichment analysis showed that diterpenoid biosynthetic process was significantly enriched for genes with downstream overlapping with hypoCHHDMR in July_root when comparing with those in March_root. Tanshinone biosynthesis-related enzyme genes, such as DXS2, CMK, IDI1, HMGR2, DXR, MDS, CYP76AH1, 2OGD25, and CYP71D373, were less CHH methylated in gene promoters or downstream regions in roots collected in July than those collected in March. Consistently, gene expression was up-regulated in S. miltiorrhiza roots collected in July compared with March and the treatment of DNA methylation inhibitor 5-azacytidine significantly promoted tanshinone production. It suggests that DNA methylation plays a significant regulatory role in tanshinone biosynthesis in S. miltiorrhiza through changing the levels of CHH methylation in promoters or downstreams of key enzyme genes.
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Affiliation(s)
- Jiang Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Caili Li
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Yuxing Deng
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
| | - Hairong Wei
- College of Forest Resources and Environmental Science, Michigan Technological University, Houghton, MI 49931, USA
| | - Shanfa Lu
- Key Lab of Chinese Medicine Resources Conservation, State Administration of Traditional Chinese Medicine of the People' s Republic of China, Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Engineering Research Center of Chinese Medicine Resource, Ministry of Education, Beijing 100193, China
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30
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Zeng J, Jiang G, Liang H, Yan H, Kong X, Duan X, Li Z. Histone demethylase MaJMJ15 is involved in the regulation of postharvest banana fruit ripening. Food Chem 2023; 407:135102. [PMID: 36495744 DOI: 10.1016/j.foodchem.2022.135102] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 11/05/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022]
Abstract
Histone methylation plays important roles in plant development. However, the role of histone methylation in fruit ripening remains unclear. Here, a total of 16 Jumonji domain-containing proteins (JMJs) were identified from banana genome. During fruit ripening, expression of MaJMJ15 was significantly upregulated. Exogenous ethylene accelerated the upregulation whereas 1-methylcyclopropene delayed the process, suggesting that MaJMJ15 positively regulates banana fruit ripening. MaJMJ15 is an H3K27me3 site-specific demethylase. Transient overexpression of MaJMJ15 promoted banana fruit ripening. Moreover, the global H3K27me3 was decreased by MaJMJ15. Furthermore, MaJMJ15 directly targeted several key ripening-related genes (RRGs) in banana including NAC transcription factor 1/2 (MaNAC1/2), 1-aminocyclopropane-1-carboxylate synthase 1 (MaACS1), 1-aminocyclopropane-1-carboxylate oxidase 1 (MaACO1) and expansin 2 (MaEXP2), removed H3K27me3 from their chromatin, and activated their expression. Our data suggest that MaJMJ15 is an H3K27me3 demethylase, which is involved in the regulation of banana fruit ripening by activating expression of key RRGs via removal of H3K27me3.
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Affiliation(s)
- Jing Zeng
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guoxiang Jiang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanzhi Liang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Huiling Yan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiangjin Kong
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xuewu Duan
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; Center of Economic Botany, Core Botanical Gardens, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China; Agro-food Science and Technology Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China.
| | - Zhiwei Li
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement & Guangdong Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China; University of Chinese Academy of Sciences, Beijing 100049, China.
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31
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Sharma N, Shivran M, Singh N, Dubey AK, Singh SK, Sharma N, Gupta R, Vittal H, Singh BP, Sevanthi AM, Singh NK. Differential gene expression associated with flower development of mango (Mangifera indica L.) varieties with different shelf-life. Gene Expr Patterns 2023; 47:119301. [PMID: 36526239 DOI: 10.1016/j.gep.2022.119301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 11/22/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022]
Abstract
Mango (Mangifera indica L.) is one of the most important commercial fruit crop grown in many parts of the world. Major challenges affecting mango trade are short shelf-life, high susceptibility to chilling injury, post-harvest diseases and consumer demand for improved fruit quality. The objective of the present study was to reveal the key regulators present in bud and flower tissues during flower development stage, associated with fruit development and affect the shelf-life of the mango fruit. RNA-sequencing of contrasting genotypes having short and long shelf-life, was carried out. Comparative differential expression pathway studies of long shelf-life (Totapuri) and short shelf-life (Bombay Green) mango genotypes revealed a total of 177 highly differentially expressed genes. Out of 177 total genes, 101 genes from endoplasmic reticulum pathway and very few from gibberellins (3) and jasmonic acid (1) pathway were identified. Genes from endoplasmic reticulum pathway like hsp 90, SRC2, DFRA, CHS, BG3 and ASPG1 mainly up regulated in Bombay Green. Uniprotein B9R8D3 also shows up regulation in Bombay Green. Ethylene insensitive pathway gene EIL1 up regulated in Bombay Green. Gene CAD1 from phenylpropanoid pathway mainly up regulated in Bombay Green. A total of 4 SSRs and 227 SNPs were mined from these pathways specific to the shelf-life. Molecular studies of endoplasmic reticulum, phenylpropanoid, ethylene, polygalacturonase and hormone pathways at the time of bud and flower formation revealed key regulators that determine the shelf-life of mango fruit.
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Affiliation(s)
- Nimisha Sharma
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
| | - Mukesh Shivran
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Narendra Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Anil Kumar Dubey
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sanjay Kumar Singh
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Neha Sharma
- IILM Academy of Higher Learning, College of Engineering and Technology Greater, Noida, Uttar Pradesh, 201310, India
| | - Ruchi Gupta
- NGB Diagnostics Private Limited, Noida, UP, 201301, India
| | - Hatkari Vittal
- Division of Fruits and Horticultural Technology, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
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32
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Hayashi K, Alseekh S, Fernie AR. Genetic and epigenetic control of the plant metabolome. Proteomics 2023:e2200104. [PMID: 36781168 DOI: 10.1002/pmic.202200104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 02/06/2023] [Accepted: 02/07/2023] [Indexed: 02/15/2023]
Abstract
Plant metabolites are mainly produced through chemical reactions catalysed by enzymes encoded in the genome. Mutations in enzyme-encoding or transcription factor-encoding genes can alter the metabolome by changing the enzyme's catalytic activity or abundance, respectively. Insertion of transposable elements into non-coding regions has also been reported to affect transcription and ultimately metabolite content. In addition to genetic mutations, transgenerational epigenetic variations have also been found to affect metabolic content by controlling the transcription of metabolism-related genes. However, the majority of cases reported so far, in which epigenetic mechanisms are associated with metabolism, are non-transgenerational, and are triggered by developmental signals or environmental stress. Although, accumulating research has provided evidence of strong genetic control of the metabolome, epigenetic control has been largely untouched. Here, we provide a review of the genetic and epigenetic control of metabolism with a focus on epigenetics. We discuss both transgenerational and non-transgenerational epigenetic marks regulating metabolism as well as prospects of the field of metabolic control where intricate interactions between genetics and epigenetics are involved.
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Affiliation(s)
- Koki Hayashi
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Potsdam-Golm, Germany.,Center for Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
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33
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Ma Z, Ma L, Zhou J. Applications of CRISPR/Cas genome editing in economically important fruit crops: recent advances and future directions. MOLECULAR HORTICULTURE 2023; 3:1. [PMID: 37789479 PMCID: PMC10515014 DOI: 10.1186/s43897-023-00049-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2022] [Accepted: 01/10/2023] [Indexed: 10/05/2023]
Abstract
Fruit crops, consist of climacteric and non-climacteric fruits, are the major sources of nutrients and fiber for human diet. Since 2013, CRISPR/Cas (Clustered Regularly Interspersed Short Palindromic Repeats and CRISPR-Associated Protein) genome editing system has been widely employed in different plants, leading to unprecedented progress in the genetic improvement of many agronomically important fruit crops. Here, we summarize latest advancements in CRISPR/Cas genome editing of fruit crops, including efforts to decipher the mechanisms behind plant development and plant immunity, We also highlight the potential challenges and improvements in the application of genome editing tools to fruit crops, including optimizing the expression of CRISPR/Cas cassette, improving the delivery efficiency of CRISPR/Cas reagents, increasing the specificity of genome editing, and optimizing the transformation and regeneration system. In addition, we propose the perspectives on the application of genome editing in crop breeding especially in fruit crops and highlight the potential challenges. It is worth noting that efforts to manipulate fruit crops with genome editing systems are urgently needed for fruit crops breeding and demonstration.
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Affiliation(s)
- Zhimin Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Lijing Ma
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China
| | - Junhui Zhou
- Peking University Institute of Advanced Agricultural Sciences, Weifang, 261000, Shandong, China.
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Zheng G, Hu S, Cheng S, Wang L, Kan L, Wang Z, Xu Q, Liu Z, Kang C. Factor of DNA methylation 1 affects woodland strawberry plant stature and organ size via DNA methylation. PLANT PHYSIOLOGY 2023; 191:335-351. [PMID: 36200851 PMCID: PMC9806633 DOI: 10.1093/plphys/kiac462] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 09/18/2022] [Indexed: 06/16/2023]
Abstract
RNA-directed DNA methylation (RdDM) is an epigenetic process that directs silencing to specific genomic regions and loci. The biological functions of RdDM are not well studied in horticultural plants. Here, we isolated the ethyl methane-sulfonate-induced mutant reduced organ size (ros) producing small leaves, flowers, and fruits in woodland strawberry (Fragaria vesca) due to reduced cell numbers compared with that in the wild-type (WT). The candidate mutation causes a premature stop codon in FvH4_6g28780, which shares high similarity to Arabidopsis (Arabidopsis thaliana) Factor of DNA Methylation1 (FDM1) encoding an RdDM pathway component and was named FveFDM1. Consistently, the fvefdm1CR mutants generated by CRISPR/Cas9 also produced smaller organs. Overexpressing FveFDM1 in an Arabidopsis fdm1-1 fdm2-1 double mutant restored DNA methylation at the RdDM target loci. FveFDM1 acts in a protein complex with its homolog Involved in De Novo 2 (FveIDN2). Furthermore, whole-genome bisulfite sequencing revealed that DNA methylation, especially in the CHH context, was remarkably reduced throughout the genome in fvefdm1. Common and specific differentially expressed genes were identified in different tissues of fvefdm1 compared to in WT tissues. DNA methylation and expression levels of several gibberellic acid (GA) biosynthesis and cell cycle genes were validated. Moreover, the contents of GA and auxin were substantially reduced in the young leaves of fvefdm1 compared to in the WT. However, exogenous application of GA and auxin could not recover the organ size of fvefdm1. In addition, expression levels of FveFDM1, FveIDN2, Nuclear RNA Polymerase D1 (FveNRPD1), Domains Rearranged Methylase 2 (FveDRM2), and cell cycle genes were greatly induced by GA treatment. Overall, our work demonstrated the critical roles of FveFDM1 in plant growth and development via RdDM-mediated DNA methylation in horticultural crops.
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Affiliation(s)
- Guanghui Zheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- College of Horticulture, Anhui Agricultural University, Hefei 230036, China
| | - Shaoqiang Hu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Simin Cheng
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Liyang Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Lijun Kan
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
| | - Zhengming Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Qiang Xu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Zhongchi Liu
- Department of Cell Biology and Molecular Genetics, University of Maryland, Mary land 20742, USA
| | - Chunying Kang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
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Zhou T, Li R, Yu Q, Wang J, Pan J, Lai T. Proteomic Changes in Response to Colorless nonripening Mutation during Tomato Fruit Ripening. PLANTS (BASEL, SWITZERLAND) 2022; 11:3570. [PMID: 36559681 PMCID: PMC9782875 DOI: 10.3390/plants11243570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 12/09/2022] [Accepted: 12/14/2022] [Indexed: 06/17/2023]
Abstract
SlSPL-CNR is a multifunctional transcription factor gene that plays important roles in regulating tomato fruit ripening. However, the molecular basis of SlSPL-CNR in the regulatory networks is not exactly clear. In the present study, the biochemical characteristics and expression levels of genes involved in ethylene biosynthesis in Colorless nonripening (Cnr) natural mutant were determined. The proteomic changes during the ripening stage were also uncovered by isobaric tags for relative and absolute quantitation (iTRAQ)-based quantitative proteomic analysis. Results indicated that both the lycopene content and soluble solid content (SSC) in Cnr fruit were lower than those in wild-type AC fruit. Meanwhile, pH, flavonoid content, and chlorophyll content were higher in Cnr fruit. Expressions of genes involved in ethylene biosynthesis were also downregulated or delayed in Cnr fruit. Furthermore, 1024 and 1234 differentially expressed proteins (DEPs) were respectively identified for the breaker and 10 days postbreaker stages. Among them, a total of 512 proteins were differentially expressed at both stages. In addition, the functions of DEPs were classified by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Results would lay the groundwork for wider explorations of the regulatory mechanism of SlSPL-CNR on tomato fruit ripening.
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Shang JY, Cai XW, Su YN, Zhang ZC, Wang X, Zhao N, He XJ. Arabidopsis Trithorax histone methyltransferases are redundant in regulating development and DNA methylation. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2438-2454. [PMID: 36354145 DOI: 10.1111/jipb.13406] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Accepted: 11/09/2022] [Indexed: 06/16/2023]
Abstract
Although the Trithorax histone methyltransferases ATX1-5 are known to regulate development and stress responses by catalyzing histone H3K4 methylation in Arabidopsis thaliana, it is unknown whether and how these histone methyltransferases affect DNA methylation. Here, we found that the redundant ATX1-5 proteins are not only required for plant development and viability but also for the regulation of DNA methylation. The expression and H3K4me3 levels of both RNA-directed DNA methylation (RdDM) genes (NRPE1, DCL3, IDN2, and IDP2) and active DNA demethylation genes (ROS1, DML2, and DML3) were downregulated in the atx1/2/4/5 mutant. Consistent with the facts that the active DNA demethylation pathway mediates DNA demethylation mainly at CG and CHG sites, and that the RdDM pathway mediates DNA methylation mainly at CHH sites, whole-genome DNA methylation analyses showed that hyper-CG and CHG DMRs in atx1/2/4/5 significantly overlapped with those in the DNA demethylation pathway mutant ros1 dml2 dml3 (rdd), and that hypo-CHH DMRs in atx1/2/4/5 significantly overlapped with those in the RdDM mutant nrpe1, suggesting that the ATX paralogues function redundantly to regulate DNA methylation by promoting H3K4me3 levels and expression levels of both RdDM genes and active DNA demethylation genes. Given that the ATX proteins function as catalytic subunits of COMPASS histone methyltransferase complexes, we also demonstrated that the COMPASS complex components function as a whole to regulate DNA methylation. This study reveals a previously uncharacterized mechanism underlying the regulation of DNA methylation.
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Affiliation(s)
- Ji-Yun Shang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xue-Wei Cai
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Yin-Na Su
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Zhao-Chen Zhang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin Wang
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Nan Zhao
- National Institute of Biological Sciences, Beijing, 102206, China
| | - Xin-Jian He
- National Institute of Biological Sciences, Beijing, 102206, China
- Tsinghua Institute of Multidisciplinary Biomedical Research, Tsinghua University, Beijing, 100084, China
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Zhang H, Gong Z, Zhu JK. Active DNA demethylation in plants: 20 years of discovery and beyond. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2217-2239. [PMID: 36478523 DOI: 10.1111/jipb.13423] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Maintaining proper DNA methylation levels in the genome requires active demethylation of DNA. However, removing the methyl group from a modified cytosine is chemically difficult and therefore, the underlying mechanism of demethylation had remained unclear for many years. The discovery of the first eukaryotic DNA demethylase, Arabidopsis thaliana REPRESSOR OF SILENCING 1 (ROS1), led to elucidation of the 5-methylcytosine base excision repair mechanism of active DNA demethylation. In the 20 years since ROS1 was discovered, our understanding of this active DNA demethylation pathway, as well as its regulation and biological functions in plants, has greatly expanded. These exciting developments have laid the groundwork for further dissecting the regulatory mechanisms of active DNA demethylation, with potential applications in epigenome editing to facilitate crop breeding and gene therapy.
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Affiliation(s)
- Heng Zhang
- State Key Laboratory of Molecular Plant Genetics, Shanghai Centre for Plant Stress Biology, Centre for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhizhong Gong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing, 100193, China
- School of Life Sciences, Institute of Life Science and Green Development, Hebei University, Baoding, 071002, China
| | - Jian-Kang Zhu
- School of Life Sciences, Institute of Advanced Biotechnology, Southern University of Science and Technology, Shenzhen, 518055, China
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Lu Y, Wang H, Liu Z, Zhang T, Li Z, Cao L, Wu S, Liu Y, Yu S, Zhang Q, Zheng Z. A naturally-occurring phenomenon of flower color change during flower development in Xanthoceras sorbifolium. FRONTIERS IN PLANT SCIENCE 2022; 13:1072185. [PMID: 36457525 PMCID: PMC9706096 DOI: 10.3389/fpls.2022.1072185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 10/31/2022] [Indexed: 06/17/2023]
Abstract
Xanthoceras sorbifolium (yellowhorn) is originated in China and is a unique tree in northern China. Yellowhorn is very popular because of the gradual color change of its flower at different flower developmental stages. During flowering development, the color at the base of yellowhorn flower petals gradually changes from yellow to purple. The mechanism of this miraculous phenomenon is still unclear. Here we show that anthocyanin accumulation during flowering development is the main reason for this color change. RT-PCR results show that the expression level of a variety of anthocyanin biosynthesis genes changes in different flower developmental stages. Realtime results show that the expression changes of these anthocyanin biosynthesis genes are positively regulated by a cluster of R2R3-MYB transcription factor genes, XsMYB113s. Furthermore, the DNA methylation analysis showed that CHH methylation status on the transposon element near the XsMYB113-1 influence its transcript level during flowering development. Our results suggest that dynamic epigenetic regulation of the XsMYB113-1 leads to the accumulation of anthocyanins during yellowhorn flower color change. These findings reemphasize the role of epigenetic regulation in flower development and provide a foundation for further studies of epigenetic regulation in long-lived woody perennials.
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Affiliation(s)
- Yanan Lu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Hanhui Wang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Zhi Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Tianxu Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Zongjian Li
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Li Cao
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Siyao Wu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Yueying Liu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Song Yu
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
| | - Qingzhu Zhang
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
- College of Life Science, Northeast Forestry University, Harbin, China
| | - Zhimin Zheng
- State Key Laboratory of Tree Genetics and Breeding, College of Forestry, Northeast Forestry University, Harbin, China
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Varotto S, Krugman T, Aiese Cigliano R, Kashkush K, Kondić-Špika A, Aravanopoulos FA, Pradillo M, Consiglio F, Aversano R, Pecinka A, Miladinović D. Exploitation of epigenetic variation of crop wild relatives for crop improvement and agrobiodiversity preservation. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2022; 135:3987-4003. [PMID: 35678824 PMCID: PMC9729329 DOI: 10.1007/s00122-022-04122-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/04/2022] [Indexed: 05/05/2023]
Abstract
Crop wild relatives (CWRs) are recognized as the best potential source of traits for crop improvement. However, successful crop improvement using CWR relies on identifying variation in genes controlling desired traits in plant germplasms and subsequently incorporating them into cultivars. Epigenetic diversity may provide an additional layer of variation within CWR and can contribute novel epialleles for key traits for crop improvement. There is emerging evidence that epigenetic variants of functional and/or agronomic importance exist in CWR gene pools. This provides a rationale for the conservation of epigenotypes of interest, thus contributing to agrobiodiversity preservation through conservation and (epi)genetic monitoring. Concepts and techniques of classical and modern breeding should consider integrating recent progress in epigenetics, initially by identifying their association with phenotypic variations and then by assessing their heritability and stability in subsequent generations. New tools available for epigenomic analysis offer the opportunity to capture epigenetic variation and integrate it into advanced (epi)breeding programmes. Advances in -omics have provided new insights into the sources and inheritance of epigenetic variation and enabled the efficient introduction of epi-traits from CWR into crops using epigenetic molecular markers, such as epiQTLs.
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Affiliation(s)
- Serena Varotto
- Department of Agronomy Animal Food Natural Resources and Environment, University of Padova, Viale dell'Università, 16 35020, Legnaro, Italy.
| | - Tamar Krugman
- Institute of Evolution, University of Haifa, Abba Khoushy Ave 199, 3498838, Haifa, Israel
| | | | - Khalil Kashkush
- Department of Life Sciences, Ben-Gurion University, Beersheba, 84105, Israel
| | - Ankica Kondić-Špika
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
| | - Fillipos A Aravanopoulos
- Faculty of Agriculture, Forest Science & Natural Environment, Aristotle University of Thessaloniki, Thessaloniki, GR54006, Greece
| | - Monica Pradillo
- Department of Genetics, Physiology and Microbiology, Faculty of Biology, Complutense University of Madrid, 28040, Madrid, Spain
| | - Federica Consiglio
- Institute of Biosciences and Bioresources, National Research Council (CNR), Via Università 133, 80055, Portici, Italy
| | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples Federico II, Via Università 100, 80055, Portici, Italy
| | - Ales Pecinka
- Institute of Experimental Botany, Centre of the Region Haná for Biotechnological and Agricultural Research, Czech Acad Sci, Šlechtitelů 31, 779 00, Olomouc, Czech Republic
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, Maksima Gorkog 30, 21000, Novi Sad, Serbia
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Guo S, Zheng Y, Meng D, Zhao X, Sang Z, Tan J, Deng Z, Lang Z, Zhang B, Wang Q, Bouzayen M, Zuo J. DNA and coding/non-coding RNA methylation analysis provide insights into tomato fruit ripening. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:399-413. [PMID: 36004545 DOI: 10.1111/tpj.15951] [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: 06/13/2022] [Revised: 08/03/2022] [Accepted: 08/14/2022] [Indexed: 06/15/2023]
Abstract
Ripening is the last, irreversible developmental stage during which fruit become palatable, thus promoting seed dispersal by frugivory. In Alisa Craig fruit, mRNAs with increasing m5C levels, such as STPK and WRKY 40, were identified as being involved in response to biotic and abiotic stresses. Furthermore, two mRNAs involved in cell wall metabolism, PG and EXP-B1, also presented increased m5C levels. In the Nr mutant, several m5C-modified mRNAs involved in fruit ripening, including those encoding WRKY and MADS-box proteins, were found. Targets of long non-coding RNAs and circular RNAs with different m5C sites were also found; these targets included 2-alkenal reductase, soluble starch synthase 1, WRKY, MADS-box, and F-box/ketch-repeat protein SKIP11. A combined analysis of changes in 5mC methylation and mRNA revealed many differentially expressed genes with differentially methylated regions encoding transcription factors and key enzymes related to ethylene biosynthesis and signal transduction; these included ERF084, EIN3, AP2/ERF, ACO5, ACS7, EIN3/4, EBF1, MADS-box, AP2/ERF, and ETR1. Taken together, our findings contribute to the global understanding of the mechanisms underlying fruit ripening, thereby providing new information for both fruit and post-harvest behavior.
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Affiliation(s)
- Susu Guo
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Yanyan Zheng
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Demei Meng
- State Key Laboratory of Food Nutrition and Safety, College of Food Science and Engineering, Tianjin University of Science & Technology, Tianjin, 300457, China
| | - Xiaoyan Zhao
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Zhaoze Sang
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Jinjuan Tan
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhiping Deng
- Institute of Virology and Biotechnology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bo Zhang
- College of Agriculture & Biotechnology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Qing Wang
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Mondher Bouzayen
- Laboratory Genomics and Biotechnology of Fruits, INRA, Toulouse INP, University of Toulouse, Castanet-Tolosan, France
| | - Jinhua Zuo
- Institute of Agri-food Processing and Nutrition, Key Laboratory of Vegetable Postharvest Processing of Ministry of Agriculture and Rural Areas, Beijing Key Laboratory of Fruits and Vegetable Storage and Processing, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
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Bhatia G, Prall W, Sharma B, Gregory BD. Covalent RNA modifications and their budding crosstalk with plant epigenetic processes. CURRENT OPINION IN PLANT BIOLOGY 2022; 69:102287. [PMID: 35988352 DOI: 10.1016/j.pbi.2022.102287] [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: 04/11/2022] [Revised: 06/29/2022] [Accepted: 07/15/2022] [Indexed: 06/15/2023]
Abstract
Our recent cognizance of diverse RNA classes undergoing dynamic covalent chemical modifications (or epitranscriptomic marks) in plants has provided fresh insight into the underlying molecular mechanisms of gene expression regulation. Comparatively, epigenetic marks comprising heritable modifications of DNA and histones have been extensively studied in plants and their impact on plant gene expression is quite established. Based on our growing knowledge of the plant epitranscriptome and epigenome, it is logical to explore how the two regulatory layers intermingle to intricately determine gene expression levels underlying key biological processes such as development and response to stress. Herein, we focus on the emerging evidence of crosstalk between the plant epitranscriptome with epigenetic regulation involving DNA modification, histone modification, and non-coding RNAs.
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Affiliation(s)
- Garima Bhatia
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Wil Prall
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Bishwas Sharma
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA
| | - Brian D Gregory
- Department of Biology, University of Pennsylvania, School of Arts and Sciences, Philadelphia, PA 19104, USA.
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Tonosaki K, Fujimoto R, Dennis ES, Raboy V, Osabe K. Will epigenetics be a key player in crop breeding? FRONTIERS IN PLANT SCIENCE 2022; 13:958350. [PMID: 36247549 PMCID: PMC9562705 DOI: 10.3389/fpls.2022.958350] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Accepted: 09/12/2022] [Indexed: 06/16/2023]
Abstract
If food and feed production are to keep up with world demand in the face of climate change, continued progress in understanding and utilizing both genetic and epigenetic sources of crop variation is necessary. Progress in plant breeding has traditionally been thought to be due to selection for spontaneous DNA sequence mutations that impart desirable phenotypes. These spontaneous mutations can expand phenotypic diversity, from which breeders can select agronomically useful traits. However, it has become clear that phenotypic diversity can be generated even when the genome sequence is unaltered. Epigenetic gene regulation is a mechanism by which genome expression is regulated without altering the DNA sequence. With the development of high throughput DNA sequencers, it has become possible to analyze the epigenetic state of the whole genome, which is termed the epigenome. These techniques enable us to identify spontaneous epigenetic mutations (epimutations) with high throughput and identify the epimutations that lead to increased phenotypic diversity. These epimutations can create new phenotypes and the causative epimutations can be inherited over generations. There is evidence of selected agronomic traits being conditioned by heritable epimutations, and breeders may have historically selected for epiallele-conditioned agronomic traits. These results imply that not only DNA sequence diversity, but the diversity of epigenetic states can contribute to increased phenotypic diversity. However, since the modes of induction and transmission of epialleles and their stability differ from that of genetic alleles, the importance of inheritance as classically defined also differs. For example, there may be a difference between the types of epigenetic inheritance important to crop breeding and crop production. The former may depend more on longer-term inheritance whereas the latter may simply take advantage of shorter-term phenomena. With the advances in our understanding of epigenetics, epigenetics may bring new perspectives for crop improvement, such as the use of epigenetic variation or epigenome editing in breeding. In this review, we will introduce the role of epigenetic variation in plant breeding, largely focusing on DNA methylation, and conclude by asking to what extent new knowledge of epigenetics in crop breeding has led to documented cases of its successful use.
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Affiliation(s)
- Kaoru Tonosaki
- Kihara Institute for Biological Research, Yokohama City University, Yokohama, Japan
| | - Ryo Fujimoto
- Graduate School of Agricultural Science, Kobe University, Kobe, Japan
| | - Elizabeth S. Dennis
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Canberra, ACT, Australia
- School of Life Sciences, Faculty of Science, University of Technology Sydney, Ultimo, NSW, Australia
| | - Victor Raboy
- Independent Researcher Portland, Portland, OR, United States
| | - Kenji Osabe
- Institute of Scientific and Industrial Research (SANKEN), Osaka University, Osaka, Japan
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Junaid A, Singh NK, Gaikwad K. Evolutionary fates of gene-body methylation and its divergent association with gene expression in pigeonpea. THE PLANT GENOME 2022; 15:e20207. [PMID: 35790083 DOI: 10.1002/tpg2.20207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 05/07/2021] [Indexed: 06/15/2023]
Abstract
Pigeonpea (Cajanus cajan L. Huth) is an agronomically important legume cultivated worldwide. In this study, we extensively analyzed gene-body methylation (GbM) patterns in pigeonpea. We found a bimodal distribution of CG and CHG methylation patterns. GbM features- slow evolution rate and increased length remained conserved. Genes with moderate CG body methylation showed highest expression where as highly-methylated genes showed lowest expression. Transposable element (TE)-related genes were methylated in multiple contexts and hence classified as C-methylated genes. A low expression among C-methylated genes was associated with transposons insertion in gene-body and upstream regulatory regions. The CG methylation patterns were found to be conserved in orthologs compared with non-CG methylation. By comparing methylation patterns between differentially methylated regions (DMRs) of the three genotypes, we found that variably methylated marks are less likely to target evolutionary conserved sequences. Finally, our analysis showed enrichment of nitrogen-related genes in GbM orthologs of legumes, which could be promising candidates for generating epialleles for crop improvement.
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Affiliation(s)
- Alim Junaid
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Nagendra Kumar Singh
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
| | - Kishor Gaikwad
- National Institute of Plant Biotechnology, Pusa Campus, New Delhi, 110012, India
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Gao Y, Lin Y, Xu M, Bian H, Zhang C, Wang J, Wang H, Xu Y, Niu Q, Zuo J, Fu DQ, Pan Y, Chen K, Klee H, Lang Z, Zhang B. The role and interaction between transcription factor NAC-NOR and DNA demethylase SlDML2 in the biosynthesis of tomato fruit flavor volatiles. THE NEW PHYTOLOGIST 2022; 235:1913-1926. [PMID: 35686614 DOI: 10.1111/nph.18301] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 05/22/2022] [Indexed: 06/15/2023]
Abstract
Flavor-imparting volatile chemicals accumulate as fruits ripen, making major contributions to taste. The NAC transcription factor nonripening (NAC-NOR) and DNA demethylase 2 (SlDML2) are essential for tomato fruit ripening, but details of the potential roles and the relationship between these two regulators in the synthesis of volatiles are lacking. Here, we show substantial reductions in fatty acid and carotenoid-derived volatiles in tomato slnor and sldml2 mutants. An unexpected finding is the redundancy and divergence in volatile profiles, biosynthetic gene expression, and DNA methylation in slnor and sldml2 mutants relative to wild-type tomato fruit. Reduced transcript levels are accompanied by hypermethylation of promoters, including the NAC-NOR target gene lipoxygenase (SlLOXC) that is involved in fatty acid-derived volatile synthesis. Interestingly, NAC-NOR activates SlDML2 expression by directly binding to its promoter both in vitro and in vivo. Meanwhile, reduced NAC-NOR expression in the sldml2 mutant is accompanied by hypermethylation of its promoter. These results reveal a relationship between SlDML2-mediated DNA demethylation and NAC-NOR during tomato fruit ripening. In addition to providing new insights into the metabolic modulation of flavor volatiles, the outcome of our study contributes to understanding the genetics and control of fruit ripening and quality attributes in tomato.
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Affiliation(s)
- Ying Gao
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yujing Lin
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Min Xu
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Hanxiao Bian
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Chi Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Jingyu Wang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Hanqing Wang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Yaping Xu
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Qingfeng Niu
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Jinhua Zuo
- Institute of Agri-food Processing and Nutrition, Beijing Academy of Agricultural and Forestry Sciences, Beijing, 100097, China
| | - Da-Qi Fu
- Laboratory of Fruit Biology, College of Food Science & Nutritional Engineering, China Agricultural University, Beijing, 100083, China
| | - Yu Pan
- Key Laboratory of Horticulture Science for Southern Mountainous Regions, Ministry of Education, Southwest University, Chongqing, 400715, China
| | - Kunsong Chen
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
| | - Harry Klee
- Horticultural Sciences, Genetic Institute, University of Florida, Gainesville, FL, 32611, USA
| | - Zhaobo Lang
- Shanghai Center for Plant Stress Biology, and National Key Laboratory of Plant Molecular Genetics, Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Bo Zhang
- Laboratory of Fruit Quality Biology/Zhejiang Provincial Key Laboratory of Horticultural Plant Integrative Biology, Zhejiang University, Zijingang Campus, Hangzhou, 310058, China
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Kong J, Garcia V, Zehraoui E, Stammitti L, Hilbert G, Renaud C, Maury S, Delaunay A, Cluzet S, Lecourieux F, Lecourieux D, Teyssier E, Gallusci P. Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells. Genes (Basel) 2022; 13:genes13071256. [PMID: 35886036 PMCID: PMC9316115 DOI: 10.3390/genes13071256] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 02/01/2023] Open
Abstract
Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. In this model, zebularine increased anthocyanin accumulation in the light, and induced its production in the dark. To unravel the underlying mechanisms, cell transcriptome, metabolic content, and DNA methylation were analyzed. The up-regulation of stress-related genes, as well as a decrease in cell viability, revealed that zebularine affected cell integrity. Concomitantly, the global DNA methylation level was only slightly decreased in the light and not modified in the dark. However, locus-specific analyses demonstrated a decrease in DNA methylation at a few selected loci, including a CACTA DNA transposon and a small region upstream from the UFGT gene, coding for the UDP glucose:flavonoid-3-O-glucosyltransferase, known to be critical for anthocyanin biosynthesis. Moreover, this decrease was correlated with an increase in UFGT expression and in anthocyanin content. In conclusion, our data suggest that UFGT expression could be regulated through DNA methylation in Gamay Teinturier, although the functional link between changes in DNA methylation and UFGT transcription still needs to be demonstrated.
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Affiliation(s)
- Junhua Kong
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Virginie Garcia
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Enric Zehraoui
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Linda Stammitti
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Ghislaine Hilbert
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Christel Renaud
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Stéphane Maury
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Alain Delaunay
- INRAe, EA1207 USC1328 Laboratoire de Biologie des Ligneux et des Grandes Cultures, Université d’Orléans, 45067 Orléans, France; (S.M.); (A.D.)
| | - Stéphanie Cluzet
- Unité de Recherche Oenologie, Faculté des Sciences Pharmaceutiques, University Bordeaux, EA4577, USC 1366 INRA, Equipe Molécules d’Intérêt Biologique (GESVAB), ISVV, CEDEX, 33882 Villenave d’Ornon, France;
| | - Fatma Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - David Lecourieux
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
| | - Emeline Teyssier
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
- Correspondence: ; Tel.: +33-5-5757-5928
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, 210 Chemin de Leysotte—33140 Villenave d’Ornon, France; (J.K.); (V.G.); (E.Z.); (L.S.); (G.H.); (C.R.); (F.L.); (D.L.); (P.G.)
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Petrova DV, Permyakova NV, Grin IR, Zharkov DO. Characterization of demethylating DNA glycosylase ROS1 from Nicotiana tabacum L. Vavilovskii Zhurnal Genet Selektsii 2022; 26:341-348. [PMID: 35860677 PMCID: PMC9257373 DOI: 10.18699/vjgb-22-41] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/24/2022] [Accepted: 04/06/2022] [Indexed: 11/19/2022] Open
Abstract
One of the main mechanisms of epigenetic regulation in higher eukaryotes is based on the methylation of cytosine at the C5 position with the formation of 5-methylcytosine (mC), which is further recognized by regulatory proteins. In mammals, methylation mainly occurs in CG dinucleotides, while in plants it targets CG, CHG, and CHH sequences (H is any base but G). Correct maintenance of the DNA methylation status is based on the balance of methylation, passive demethylation, and active demethylation. While in mammals active demethylation is based on targeted regulated damage to mC in DNA followed by the action of repair enzymes, demethylation in plants is performed by specialized DNA glycosylases that hydrolyze the N-glycosidic bond of mC nucleotides. The genome of the model plant Arabidopsis thaliana encodes four paralogous proteins, two of which, DEMETER (DME) and REPRESSOR OF SILENCING 1 (ROS1), possess 5-methylcytosine-DNA glycosylase activity and are necessary for the regulation of development, response to infections and abiotic stress and silencing of transgenes and mobile elements. Homologues of DME and ROS1 are present in all plant groups; however, outside A. thaliana, they are poorly studied. Here we report the properties of a recombinant fragment of the ROS1 protein from Nicotiana tabacum (NtROS1), which contains all main structural domains required for catalytic activity. Using homologous modeling, we have constructed a structural model of NtROS1, which revealed folding characteristic of DNA glycosylases of the helix– hairpin–helix structural superfamily. The recombinant NtROS1 protein was able to remove mC bases from DNA, and the enzyme activity was barely affected by the methylation status of CG dinucleotides in the opposite strand. The enzyme removed 5-hydroxymethylcytosine (hmC) from DNA with a lower efficiency, showing minimal activity in the presence of mC in the opposite strand. Expression of the NtROS1 gene in cultured human cells resulted in a global decrease in the level of genomic DNA methylation. In general, it can be said that the NtROS1 protein and other homologues of DME and ROS1 represent a promising scaffold for engineering enzymes to analyze the status of epigenetic methylation and to control gene activity.
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Affiliation(s)
- D. V. Petrova
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - N. V. Permyakova
- Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences
| | - I. R. Grin
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences
| | - D. O. Zharkov
- Institute of Chemical Biology and Fundamental Medicine of the Siberian Branch of the Russian Academy of Sciences; Novosibirsk State University
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Pecrix Y, Sallet E, Moreau S, Bouchez O, Carrere S, Gouzy J, Jardinaud MF, Gamas P. DNA demethylation and hypermethylation are both required for late nodule development in Medicago. NATURE PLANTS 2022; 8:741-749. [PMID: 35817824 DOI: 10.1038/s41477-022-01188-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/30/2022] [Indexed: 06/15/2023]
Abstract
Plant epigenetic regulations are involved in transposable element silencing, developmental processes and responses to the environment1-7. They often involve modifications of DNA methylation, particularly through the DEMETER (DME) demethylase family and RNA-dependent DNA methylation (RdDM)8. Root nodules host rhizobia that can fix atmospheric nitrogen for the plant's benefit in nitrogen-poor soils. The development of indeterminate nodules, as in Medicago truncatula, involves successive waves of gene activation9-12, control of which raises interesting questions. Using laser capture microdissection (LCM) coupled to RNA-sequencing (SYMbiMICS data11), we previously identified 4,309 genes (termed NDD) activated in the nodule differentiation and nitrogen fixation zones, 36% of which belong to co-regulated genomic regions dubbed symbiotic islands13. We found MtDME to be upregulated in the differentiation zone and required for nodule development, and we identified 474 differentially methylated regions hypomethylated in the nodule by analysing ~2% of the genome4. Here, we coupled LCM and whole-genome bisulfite sequencing for a comprehensive view of DNA methylation, integrated with gene expression at the tissue level. Furthermore, using CRISPR-Cas9 mutagenesis of MtDRM2, we showed the importance of RdDM for CHH hypermethylation and nodule development. We thus proposed a model of DNA methylation dynamics during nodule development.
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Affiliation(s)
- Y Pecrix
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
- CIRAD, UMR PVBMT, Saint-Pierre, La Réunion, France
| | - E Sallet
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - S Moreau
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - O Bouchez
- INRAE, US1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - S Carrere
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - J Gouzy
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - M-F Jardinaud
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France
| | - P Gamas
- LIPME, Université de Toulouse, INRAE, CNRS, Castanet-Tolosan, France.
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Giordano A, Santo Domingo M, Quadrana L, Pujol M, Martín-Hernández AM, Garcia-Mas J. CRISPR/Cas9 gene editing uncovers the roles of CONSTITUTIVE TRIPLE RESPONSE 1 and REPRESSOR OF SILENCING 1 in melon fruit ripening and epigenetic regulation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4022-4033. [PMID: 35394503 DOI: 10.1093/jxb/erac148] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 04/06/2022] [Indexed: 05/14/2023]
Abstract
Melon (Cucumis melo) has emerged as an alternative model to tomato for studying fruit ripening due to the coexistence of climacteric and non-climacteric varieties. Previous characterization of a major quantitative trait locus (QTL), ETHQV8.1, that is able to trigger climacteric ripening in a non-climacteric background resulted in the identification of a negative regulator of ripening CTR1-like (MELO3C024518) and a putative DNA demethylase ROS1 (MELO3C024516) that is the orthologue of DML2, a DNA demethylase that regulates fruit ripening in tomato. To understand the role of these genes in climacteric ripening, in this study we generated homozygous CRISPR knockout mutants of CTR1-like and ROS1 in a climacteric genetic background. The climacteric behavior was altered in both loss-of-function mutants in two growing seasons with an earlier ethylene production profile being observed compared to the climacteric wild type, suggesting a role of both genes in climacteric ripening in melon. Single-cytosine methylome analyses of the ROS1-knockout mutant revealed changes in DNA methylation in the promoter regions of the key ripening genes such as ACS1, ETR1, and ACO1, and in transcription factors associated with ripening including NAC-NOR, RIN, and CNR, suggesting the importance of ROS1-mediated DNA demethylation for triggering fruit ripening in melon.
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Affiliation(s)
- Andrea Giordano
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Miguel Santo Domingo
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Leandro Quadrana
- Institut de Biologie de l'Ecole Normale Supérieure, Paris, France
| | - Marta Pujol
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Ana Montserrat Martín-Hernández
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
| | - Jordi Garcia-Mas
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
- Institut de Recerca i Tecnologia Agroalimentàries (IRTA), Edifici CRAG, Campus UAB, 08193 Bellaterra, Barcelona, Spain
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Martínez-Rivas FJ, Blanco-Portales R, Molina-Hidalgo FJ, Caballero JL, Perez de Souza L, Alseekh S, Fernie AR, Muñoz-Blanco J, Rodríguez-Franco A. Azacytidine arrests ripening in cultivated strawberry (Fragaria × ananassa) by repressing key genes and altering hormone contents. BMC PLANT BIOLOGY 2022; 22:278. [PMID: 35672704 PMCID: PMC9172142 DOI: 10.1186/s12870-022-03670-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 05/31/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND Strawberry ripening involves a number of irreversible biochemical reactions that cause sensory changes through accumulation of sugars, acids and other compounds responsible for fruit color and flavor. The process, which is strongly dependent on methylation marks in other fruits such as tomatoes and oranges, is highly controlled and coordinated in strawberry. RESULTS Repeated injections of the hypomethylating compound 5-azacytidine (AZA) into green and unripe Fragaria × ananassa receptacles fully arrested the ripening of the fruit. The process, however, was reversible since treated fruit parts reached full maturity within a few days after AZA treatment was stopped. Transcriptomic analyses showed that key genes responsible for the biosynthesis of anthocyanins, phenylpropanoids, and hormones such as abscisic acid (ABA) were affected by the AZA treatment. In fact, AZA downregulated genes associated with ABA biosynthetic genes but upregulated genes associated with its degradation. AZA treatment additionally downregulated a number of essential transcription factors associated with the regulation and control of ripening. Metabolic analyses revealed a marked imbalance in hormone levels, with treated parts accumulating auxins, gibberellins and ABA degradation products, as well as metabolites associated with unripe fruits. CONCLUSIONS AZA completely halted strawberry ripening by altering the hormone balance, and the expression of genes involves in hormone biosynthesis and degradation processes. These results contradict those previously obtained in other climacteric and fleshly fruits, where AZA led to premature ripening. In any case, our results suggests that the strawberry ripening process is governed by methylation marks.
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Affiliation(s)
- Félix Juan Martínez-Rivas
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain.
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany.
| | - Rosario Blanco-Portales
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Francisco Javier Molina-Hidalgo
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - José Luis Caballero
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain
| | - Leonardo Perez de Souza
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, 4000, Plovdiv, Bulgaria
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, Ruski Blvd. 139, 4000, Plovdiv, Bulgaria
| | - Juan Muñoz-Blanco
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain.
| | - Antonio Rodríguez-Franco
- Department of Biochemistry and Molecular Biology, University of Cordoba, Edificio Severo Ochoa, Campus de Rabanales, E-14014, Córdoba, Spain.
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Kumari P, Khan S, Wani IA, Gupta R, Verma S, Alam P, Alaklabi A. Unravelling the Role of Epigenetic Modifications in Development and Reproduction of Angiosperms: A Critical Appraisal. Front Genet 2022; 13:819941. [PMID: 35664328 PMCID: PMC9157814 DOI: 10.3389/fgene.2022.819941] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Accepted: 02/14/2022] [Indexed: 12/28/2022] Open
Abstract
Epigenetics are the heritable changes in gene expression patterns which occur without altering DNA sequence. These changes are reversible and do not change the sequence of the DNA but can alter the way in which the DNA sequences are read. Epigenetic modifications are induced by DNA methylation, histone modification, and RNA-mediated mechanisms which alter the gene expression, primarily at the transcriptional level. Such alterations do control genome activity through transcriptional silencing of transposable elements thereby contributing toward genome stability. Plants being sessile in nature are highly susceptible to the extremes of changing environmental conditions. This increases the likelihood of epigenetic modifications within the composite network of genes that affect the developmental changes of a plant species. Genetic and epigenetic reprogramming enhances the growth and development, imparts phenotypic plasticity, and also ensures flowering under stress conditions without changing the genotype for several generations. Epigenetic modifications hold an immense significance during the development of male and female gametophytes, fertilization, embryogenesis, fruit formation, and seed germination. In this review, we focus on the mechanism of epigenetic modifications and their dynamic role in maintaining the genomic integrity during plant development and reproduction.
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Affiliation(s)
- Priyanka Kumari
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Sajid Khan
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Ishfaq Ahmad Wani
- Conservation and Molecular Biology Lab., Department of Botany, Baba Ghulam Shah Badshah University, Rajouri, India
| | - Renu Gupta
- Division of Soil Sciences & Agricultural Chemistry, Faculty of Agriculture Sher e Kashmir University of Agricultural Sciences and Technology, Chatha, India
| | - Susheel Verma
- Department of Botany, University of Jammu, Jammu, India
- *Correspondence: Susheel Verma,
| | - Pravej Alam
- Department of Biology, College of Science and Humanities, Prince Sattam bin Abdulaziz University (PSAU), Alkharj, Saudi Arabia
| | - Abdullah Alaklabi
- Department of Biology, College of Science, University of Bisha, Bisha, Saudi Arabia
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