1
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Gupta M, Dwivedi V, Kumar S, Patel A, Niazi P, Yadav VK. Lead toxicity in plants: mechanistic insights into toxicity, physiological responses of plants and mitigation strategies. PLANT SIGNALING & BEHAVIOR 2024; 19:2365576. [PMID: 38899525 PMCID: PMC11195469 DOI: 10.1080/15592324.2024.2365576] [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: 02/28/2024] [Accepted: 06/04/2024] [Indexed: 06/21/2024]
Abstract
Soil toxicity is a major environmental issue that leads to numerous harmful effects on plants and human beings. Every year a huge amount of Pb is dumped into the environment either from natural sources or anthropogenically. Being a heavy metal it is highly toxic and non-biodegradable but remains in the environment for a long time. It is considered a neurotoxic and exerts harmful effects on living beings. In the present review article, investigators have emphasized the side effects of Pb on the plants. Further, the authors have focused on the various sources of Pb in the environment. Investigators have emphasized the various responses including molecular, biochemical, and morphological of plants to the toxic levels of Pb. Further emphasis was given to the effect of elevated levels of Pb on the microbial population in the rhizospheres. Further, emphasized the various remediation strategies for the Pb removal from the soil and water sources.
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Affiliation(s)
- Minoti Gupta
- Department of Biotechnology, University Institute of Biotechnology, Chandigarh University, Chandigarh, Punjab, India
| | - Vinay Dwivedi
- Amity Institute of Biotechnology, Amity University, Gwalior, Madhya Pradesh, India
| | - Swatantar Kumar
- Department of Biotechnology Engineering and Food Technology, Chandigarh University, Chandigarh, Punjab, India
| | - Ashish Patel
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
| | - Parwiz Niazi
- Department of Biology, Faculty of Education, Kandahar University, Kandahar, Afghanistan
- Department of Plant Protection, Faculty of Agriculture, EGE University, İzmir, Turkey
| | - Virendra Kumar Yadav
- Department of Life Sciences, Hemchandracharya North Gujarat University, Patan, Gujarat, India
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2
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Sun M, Qiao HX, Yang T, Zhao P, Zhao JH, Luo JM, Liu FF, Xiong AS. DcMYB62, a transcription factor from carrot, enhanced cadmium tolerance of Arabidopsis by inducing the accumulation of carotenoids and hydrogen sulfide. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 216:109114. [PMID: 39250846 DOI: 10.1016/j.plaphy.2024.109114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2024] [Revised: 09/01/2024] [Accepted: 09/07/2024] [Indexed: 09/11/2024]
Abstract
Cadmium (Cd) is a significant heavy metal contaminant within the environment, carrying a notable level of toxicity that presents a substantial hazard to both plant and human. Carrot (Daucus carota), a significant root vegetable crop globally, have evolved multiple transcriptional regulatory mechanisms to cope with Cd stress, with a crucial involvement of the myeloblastosis (MYB) transcription factor. In this study, the DcMYB62 gene encoding 288 amino acids, localized in the nucleus and demonstrated transcription activation property, was isolated from carrot (cv. 'Kuroda'). There was a positive relationship observed between the levels of DcMYB62 expression and the accumulation patterns of carotenoids in two distinct carrot cultivars. Further investigation revealed that the expression of DcMYB62 improved Cd tolerance of Arabidopsis by increasing seed germination rate, root length, and overall survival rate. The levels of carotenoids in DcMYB62 transgenic Arabidopsis surpassed those in wild type, accompanied by elevated expression levels of 15-cis-phytoene desaturase, zeta-carotene desaturase, and carotenoid isomerase. Meanwhile, the heterologous expression of DcMYB62 promoted the biosynthesis of abscisic acid (ABA) and hydrogen sulfide (H2S), which in turn suppressed the formation of hydrogen peroxide and superoxide anion, while also stimulating stomatal closure. Furthermore, the heterologous expression of DcMYB62 increased the transcription of genes associated with heavy metal resistance in Arabidopsis, notably nicotianamine synthase. Overall, this study contributes to understanding how DcMYB62 promote Cd stress resistance of plants by regulating the biosynthesis pathways of carotenoids, ABA, and H2S, which offers valuable insights into the regulatory mechanism connecting DcMYBs with Cd stress response of carrot.
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Affiliation(s)
- Miao Sun
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China; State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Huan-Xuan Qiao
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Tao Yang
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Peng Zhao
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Jun-Hao Zhao
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Jia-Ming Luo
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Fang-Fang Liu
- College of Marine and Biological Engineering, Yancheng Teachers University, Yancheng, Jiangsu 224002, China
| | - Ai-Sheng Xiong
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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Mansoor S, Hamid S, Tuan TT, Park JE, Chung YS. Advance computational tools for multiomics data learning. Biotechnol Adv 2024:108447. [PMID: 39251098 DOI: 10.1016/j.biotechadv.2024.108447] [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: 05/19/2024] [Revised: 09/01/2024] [Accepted: 09/05/2024] [Indexed: 09/11/2024]
Abstract
The burgeoning field of bioinformatics has seen a surge in computational tools tailored for omics data analysis driven by the heterogeneous and high-dimensional nature of omics data. In biomedical and plant science research multi-omics data has become pivotal for predictive analytics in the era of big data necessitating sophisticated computational methodologies. This review explores a diverse array of computational approaches which play crucial roles in processing, normalizing, integrating, and analyzing omics data. Notable methods such similarity-based methods, network-based approaches, correlation-based methods, Bayesian methods, fusion-based methods and multivariate techniques among others are discussed in detail, each offering unique functionalities to address the complexities of multi-omics data. Furthermore, this review underscores the significance of computational tools in advancing our understanding of data and their transformative impact on research.
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Affiliation(s)
- Sheikh Mansoor
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea
| | - Saira Hamid
- Watson Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Thai Thanh Tuan
- Watson Crick Centre for Molecular Medicine, Islamic University of Science and Technology, Awantipora, Pulwama, J&K, India
| | - Jong Eun Park
- Department of Animal Biotechnology, College of Applied Life Science, Jeju National University, Jeju, Jeju-do, Republic of Korea.
| | - Yong Suk Chung
- Department of Plant Resources and Environment, Jeju National University, 63243, Republic of Korea.
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Zhang C, Xiong AT, Ren MY, Zhao YY, Huang MJ, Huang LC, Zhang Z, Wang Y, Zheng QQ, Fan J, Guan JJ, Yang ZN. An epigenetically mediated double negative cascade from EFD to HB21 regulates anther development. Nat Commun 2024; 15:7796. [PMID: 39242635 PMCID: PMC11379828 DOI: 10.1038/s41467-024-52114-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/27/2024] [Indexed: 09/09/2024] Open
Abstract
Epigenetic modifications are crucial for plant development. EFD (Exine Formation Defect) encodes a SAM-dependent methyltransferase that is essential for the pollen wall pattern formation and male fertility in Arabidopsis. In this study, we find that the expression of DRM2, a de novo DNA methyltransferase in plants, complements for the defects in efd, suggesting its potential de novo DNA methyltransferase activity. Genetic analysis indicates that EFD functions through HB21, as the knockout of HB21 fully restores fertility in efd mutants. DNA methylation and histone modification analyses reveal that EFD represses the transcription of HB21 through epigenetic mechanisms. Additionally, we demonstrate that HB21 directly represses the expression of genes crucial for pollen formation and anther dehiscence, including CalS5, RPG1/SWEET8, CYP703A2 and NST2. Collectively, our findings unveil a double negative regulatory cascade mediated by epigenetic modifications that coordinates anther development, offering insights into the epigenetic regulation of this process.
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Affiliation(s)
- Cheng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Ao-Tong Xiong
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Meng-Yi Ren
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yan-Yun Zhao
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Min-Jia Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Long-Cheng Huang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zheng Zhang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Yun Wang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Quan-Quan Zheng
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jing Fan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Jing-Jing Guan
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China
| | - Zhong-Nan Yang
- Shanghai Key Laboratory of Plant Molecular Sciences, College of Life Sciences, Shanghai Normal University, Shanghai, China.
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Shilpa, Thakur R, Prasad P. Epigenetic regulation of abiotic stress responses in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130661. [PMID: 38885816 DOI: 10.1016/j.bbagen.2024.130661] [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: 08/24/2023] [Revised: 02/15/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Plants face a wide array of challenges in their environment, both from living organisms (biotic stresses) and non-living factors (abiotic stresses). Among the major abiotic stressors affecting crop plants, variations in temperature, water availability, salinity, and cold pose significant threats to crop yield and the quality of produce. Plants possess remarkable adaptability and resilience, and they employ a range of genetic and epigenetic mechanisms to respond and cope with abiotic stresses. A few crucial set of epigenetic mechanisms that support plants in their battle against these stresses includes DNA methylation and histone modifications. These mechanisms play a pivotal role in enabling plants to endure and thrive under challenging environmental conditions. The mechanisms of different epigenetic mechanisms in responding to the abiotic stresses vary. Each plant species and type of stress may trigger distinct epigenetic responses, highlighting the complexity of the plant's ability to adapt under stress conditions. This review focuses on the paramount importance of epigenetics in enhancing a plant's ability to survive and excel under various abiotic stresses. It highlights recent advancements in our understanding of the epigenetic mechanisms that contribute to abiotic stress tolerance in plants. This growing knowledge is pivotal for shaping future efforts aimed at mitigating the impact of abiotic stresses on diverse crop plants.
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Affiliation(s)
- Shilpa
- Department of Biotechnology, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
| | - Rajnikant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India
| | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India.
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6
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Chen S, Han J, Wu S, Guo S, Tang Y, Zheng Y, Hu L, Zhang X, Zhang P, Zhang H, Ren G, Gao S. From non-coding RNAs to histone modification: The epigenetic mechanisms in tomato fruit ripening and quality regulation. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 215:109070. [PMID: 39191041 DOI: 10.1016/j.plaphy.2024.109070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/28/2024] [Accepted: 08/22/2024] [Indexed: 08/29/2024]
Abstract
Ripening is one of the most important stages of fruit development and determines the fruit quality. Various factors play a role in this process, with epigenetic mechanisms emerging as important players. Epigenetic regulation encompasses DNA methylation, histone modifications and variants, chromatin remodeling, RNA modifications, and non-coding RNAs. Over the past decade, studies using tomato as a model have made considerable progress in understanding the impact of epigenetic regulation on fleshy fruit ripening and quality. In this paper, we provide an overview of recent advancements in the epigenetic regulation of tomato fruit ripening and quality regulation, focusing on three main mechanisms: DNA/RNA modifications, non-coding RNAs, and histone modifications. Furthermore, we highlight the unresolved issues and challenges within this research field, offering perspectives for future investigations to drive agricultural innovation.
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Affiliation(s)
- Shengbo Chen
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Jiazhen Han
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shu Wu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Shangjing Guo
- Qingdao Agricultural University, Qingdao, 266109, China
| | - Yufei Tang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Yujing Zheng
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Lei Hu
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Xingxing Zhang
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China
| | - Peng Zhang
- Zhejiang Academy of Agricultural Sciences, Hangzhou, 310021, China
| | | | - Guodong Ren
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Plant Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Shuai Gao
- The Key Laboratory of Quality and Safety Control for Subtropical Fruit and Vege-table, Ministry of Agriculture and Rural Affairs, College of Horticultural Science, Zhejiang A&F University, Hangzhou, 311300, China.
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7
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Liu N, Hu Z, Zhang L, Yang Q, Deng L, Terzaghi W, Hua W, Yan M, Liu J, Zheng M. BAPID suppresses the inhibition of BRM on Di19-PR module in response to drought. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 39166483 DOI: 10.1111/tpj.16984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Revised: 07/26/2024] [Accepted: 08/05/2024] [Indexed: 08/23/2024]
Abstract
Drought is one of the most important abiotic stresses, and seriously threatens plant development and productivity. Increasing evidence indicates that chromatin remodelers are pivotal for plant drought response. However, molecular mechanisms of chromatin remodelers-mediated plant drought responses remain obscure. In this study, we found a novel interactor of BRM called BRM-associated protein involved in drought response (BAPID), which interacted with SWI/SNF chromatin remodeler BRM and drought-induced transcription factor Di19. Our findings demonstrated that BAPID acted as a positive drought regulator since drought tolerance was increased in BAPID-overexpressing plants, but decreased in BAPID-deficient plants, and physically bound to PR1, PR2, and PR5 promoters to mediate expression of PR genes to defend against dehydration stress. Genetic approaches demonstrated that BRM acted epistatically to BAPID and Di19 in drought response in Arabidopsis. Furthermore, the BAPID protein-inhibited interaction between BRM and Di19, and suppressed the inhibition of BRM on the Di19-PR module by mediating the H3K27me3 deposition at PR loci, thus changing nucleosome accessibility of Di19 and activating transcription of PR genes in response to drought. Our results shed light on the molecular mechanism whereby the BAPID-BRM-Di19-PRs pathway mediates plant drought responses. We provide data improving our understanding of chromatin remodeler-mediated plant drought regulation network.
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Affiliation(s)
- Nian Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Zhiyong Hu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Liang Zhang
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - Qian Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Yuelushan Laboratory, Changsha, 410125, China
| | - Linbin Deng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania, USA
| | - Wei Hua
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Mingli Yan
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Yuelushan Laboratory, Changsha, 410125, China
| | - Jing Liu
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
- Hubei Hongshan Laboratory, Wuhan, 430070, China
| | - Ming Zheng
- Oil Crops Research Institute of the Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Oil Crops, Ministry of Agriculture and Rural Affairs, Wuhan, 430062, China
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8
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Zheng S, Zhao W, Liu Z, Geng Z, Li Q, Liu B, Li B, Bai J. Establishment and Maintenance of Heat-Stress Memory in Plants. Int J Mol Sci 2024; 25:8976. [PMID: 39201662 PMCID: PMC11354667 DOI: 10.3390/ijms25168976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/02/2024] Open
Abstract
Among the rich repertoire of strategies that allow plants to adapt to high-temperature stress is heat-stress memory. The mechanisms underlying the establishment and maintenance of heat-stress memory are poorly understood, although the chromatin opening state appears to be an important structural basis for maintaining heat-stress memory. The chromatin opening state is influenced by epigenetic modifications, making DNA and histone modifications important entry points for understanding heat-shock memory. Current research suggests that traditional heat-stress signaling pathway components might be involved in chromatin opening, thereby promoting the establishment of heat-stress memory in plants. In this review, we discuss the relationship between chromatin structure-based maintenance and the establishment of heat-stress memory. We also discuss the association between traditional heat-stress signals and epigenetic modifications. Finally, we discuss potential research ideas for exploring plant adaptation to high-temperature stress in the future.
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Affiliation(s)
- Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Weishuang Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zimeng Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ziyue Geng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiang Li
- Dryland Farming Institute of Hebei Academy of Agricultural and Forestry Science, Key Laboratory of Crop Drought Tolerance Research of Hebei Province, Hengshui 053000, China
| | - Binhui Liu
- Dryland Farming Institute of Hebei Academy of Agricultural and Forestry Science, Key Laboratory of Crop Drought Tolerance Research of Hebei Province, Hengshui 053000, China
| | - Bing Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Jiaoteng Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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9
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Talarico E, Zambelli A, Araniti F, Greco E, Chiappetta A, Bruno L. Unravelling the Epigenetic Code: DNA Methylation in Plants and Its Role in Stress Response. EPIGENOMES 2024; 8:30. [PMID: 39189256 PMCID: PMC11348131 DOI: 10.3390/epigenomes8030030] [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: 05/31/2024] [Revised: 07/31/2024] [Accepted: 08/06/2024] [Indexed: 08/28/2024] Open
Abstract
Environmental stress significantly affects plant growth, development, and survival. Plants respond to stressors such as temperature fluctuations, water scarcity, nutrient deficiencies, and pathogen attacks through intricate molecular and physiological adaptations. Epigenetic mechanisms are crucial in regulating gene expression in response to environmental stress. This review explores the current understanding of epigenetic modifications, including DNA methylation, and their roles in modulating gene expression patterns under environmental stress conditions. The dynamic nature of epigenetic modifications, their crosstalk with stress-responsive pathways, and their potential implications for plant adaptation and crop improvement are highlighted in the face of changing environmental conditions.
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Affiliation(s)
- Emanuela Talarico
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Alice Zambelli
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy; (A.Z.); (F.A.)
| | - Fabrizio Araniti
- Department of Agricultural and Environmental Sciences—Production, Landscape, Agroenergy, University of Milan, 20133 Milan, Italy; (A.Z.); (F.A.)
| | - Eleonora Greco
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Adriana Chiappetta
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
| | - Leonardo Bruno
- Department of Biology, Ecology and Earth Sciences (DiBEST), University of Calabria, 87036 Rende, Italy; (E.T.); (E.G.); (A.C.)
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10
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Zeng R, Zhang X, Song G, Lv Q, Li M, Fu D, Zhang Z, Gao L, Zhang S, Yang X, Tian F, Yang S, Shi Y. Genetic variation in the aquaporin TONOPLAST INTRINSIC PROTEIN 4;3 modulates maize cold tolerance. PLANT BIOTECHNOLOGY JOURNAL 2024. [PMID: 39024420 DOI: 10.1111/pbi.14426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 06/18/2024] [Accepted: 06/25/2024] [Indexed: 07/20/2024]
Abstract
Cold stress is a major abiotic stress that threatens maize (Zea mays L.) production worldwide. Understanding the molecular mechanisms underlying cold tolerance is crucial for breeding resilient maize varieties. Tonoplast intrinsic proteins (TIPs) are a subfamily of aquaporins in plants. Here, we report that TIP family proteins are involved in maize cold tolerance. The expression of most TIP genes was responsive to cold stress. Overexpressing TIP2;1, TIP3;2 or TIP4;3 reduced the cold tolerance of maize seedlings, while loss-of-function mutants of TIP4;3 exhibited enhanced cold tolerance. Candidate gene-based association analysis revealed that a 328-bp transposon insertion in the promoter region of TIP4;3 was strongly associated with maize cold tolerance. This transposon insertion conferred cold tolerance by repressing TIP4;3 expression through increased methylation of its promoter region. Moreover, TIP4;3 was found to suppress stomatal closure and facilitate reactive oxygen species (ROS) accumulation under cold stress, thereby inhibiting the expression of cold-responsive genes, including DEHYDRATION-RESPONSIVE ELEMENT BINDING FACTOR 1 (DREB1) genes and a subset of peroxidase genes, ultimately attenuating maize cold tolerance. This study thus elucidates the mechanism underlying TIP-mediated cold tolerance and identifies a favourable TIP4;3 allele as a potential genetic resource for breeding cold-tolerant maize varieties.
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Affiliation(s)
- Rong Zeng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Xiaoyan Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Guangshu Song
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun, China
| | - Qingxue Lv
- Jilin Academy of Agricultural Sciences (Northeast Agricultural Research Center of China), Changchun, China
| | - Minze Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Diyi Fu
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Zhuo Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Lei Gao
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Shuaisong Zhang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Xiaohong Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Feng Tian
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
- National Maize Improvement Center, Frontiers Science Center for Molecular Design Breeding, Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China
| | - Shuhua Yang
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
| | - Yiting Shi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, Frontiers Science Center for Molecular Design Breeding, Center for Crop Functional Genomics and Molecular Breeding, China Agricultural University, Beijing, China
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11
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Kelemen A, Garda T, Kónya Z, Erdődi F, Ujlaky-Nagy L, Juhász GP, Freytag C, M-Hamvas M, Máthé C. Treatments with Diquat Reveal the Relationship between Protein Phosphatases (PP2A) and Oxidative Stress during Mitosis in Arabidopsis thaliana Root Meristems. PLANTS (BASEL, SWITZERLAND) 2024; 13:1896. [PMID: 39065423 PMCID: PMC11279869 DOI: 10.3390/plants13141896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 07/02/2024] [Accepted: 07/05/2024] [Indexed: 07/28/2024]
Abstract
Reversible protein phosphorylation regulates various cellular mechanisms in eukaryotes by altering the conformation, activity, localization, and stability of substrate proteins. In Arabidopsis thaliana root meristems, histone post-translational modifications are crucial for proper cell division, and they are also involved in oxidative stress signaling. To investigate the link between reactive oxygen species (ROS) and mitosis, we treated various Arabidopsis genotypes, including wild-types and mutants showing dysfunctional PP2A, with the ROS-inducing herbicide diquat (DQ). Studying the c3c4 double catalytic subunit mutant and fass regulatory subunit mutants of PP2A provided insights into phosphorylation-dependent mitotic processes. DQ treatment reduced mitotic activity in all genotypes and caused early mitotic arrest in PP2A mutants, likely due to oxidative stress-induced damage to essential mitotic processes. DQ had a minimal effect on reversible histone H3 phosphorylation in wild-type plants but significantly decreased phospho-histone H3 levels in PP2A mutants. Following drug treatment, the phosphatase activity decreased only in the stronger phenotype mutant plants (fass-5 and c3c4). Our findings demonstrate that (i) the studied PP2A loss-of-function mutants are more sensitive to increased intracellular ROS and (ii) DQ has indirect altering effects of mitotic activities and histone H3 phosphorylation. All these findings underscore the importance of PP2A in stress responses.
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Affiliation(s)
- Adrienn Kelemen
- Plant Cell and Developmental Biology Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (T.G.); (G.P.J.); (C.F.); (M.M.-H.)
| | - Tamás Garda
- Plant Cell and Developmental Biology Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (T.G.); (G.P.J.); (C.F.); (M.M.-H.)
| | - Zoltán Kónya
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (Z.K.); (F.E.)
| | - Ferenc Erdődi
- Department of Medical Chemistry, Faculty of Medicine, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (Z.K.); (F.E.)
| | - László Ujlaky-Nagy
- Department of Biophysics and Cell Biology, Faculty of Medicine, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary;
| | - Gabriella Petra Juhász
- Plant Cell and Developmental Biology Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (T.G.); (G.P.J.); (C.F.); (M.M.-H.)
| | - Csongor Freytag
- Plant Cell and Developmental Biology Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (T.G.); (G.P.J.); (C.F.); (M.M.-H.)
- “One Health” Institute, Faculty of Health Science, University of Debrecen, Nagyerdei Blvd. 98, 4032 Debrecen, Hungary
| | - Márta M-Hamvas
- Plant Cell and Developmental Biology Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (T.G.); (G.P.J.); (C.F.); (M.M.-H.)
| | - Csaba Máthé
- Plant Cell and Developmental Biology Research Group, Department of Botany, Faculty of Science and Technology, University of Debrecen, Egyetem sq. 1, 4032 Debrecen, Hungary; (T.G.); (G.P.J.); (C.F.); (M.M.-H.)
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12
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Lundell S, Biligetu B. Differential gene expression of salt-tolerant alfalfa in response to salinity and inoculation by Ensifer meliloti. BMC PLANT BIOLOGY 2024; 24:633. [PMID: 38971752 PMCID: PMC11227210 DOI: 10.1186/s12870-024-05337-5] [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: 03/07/2024] [Accepted: 06/25/2024] [Indexed: 07/08/2024]
Abstract
BACKGROUND Alfalfa (Medicago sativa L.) experiences many negative effects under salinity stress, which may be mediated by recurrent selection. Salt-tolerant alfalfa may display unique adaptations in association with rhizobium under salt stress. RESULTS To elucidate inoculation effects on salt-tolerant alfalfa under salt stress, this study leveraged a salt-tolerant alfalfa population selected through two cycles of recurrent selection under high salt stress. After experiencing 120-day salt stress, mRNA was extracted from 8 random genotypes either grown in 0 or 8 dS/m salt stress with or without inoculation by Ensifer meliloti. Results showed 320 and 176 differentially expressed genes (DEGs) modulated in response to salinity stress or inoculation x salinity stress, respectively. Notable results in plants under 8 dS/m stress included upregulation of a key gene involved in the Target of Rapamycin (TOR) signaling pathway with a concomitant decrease in expression of the SNrK pathway. Inoculation of salt-stressed plants stimulated increased transcription of a sulfate-uptake gene as well as upregulation of the Lysine-27-trimethyltransferase (EZH2), Histone 3 (H3), and argonaute (AGO, a component of miRISC silencing complexes) genes related to epigenetic and post-transcriptional gene control. CONCLUSIONS Salt-tolerant alfalfa may benefit from improved activity of TOR and decreased activity of SNrK1 in salt stress, while inoculation by rhizobiumstimulates production of sulfate uptake- and other unique genes.
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Affiliation(s)
- Seth Lundell
- Department of Plant Sciences, College of Agriculture and Bio-Resources, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N5A8, Canada
| | - Bill Biligetu
- Department of Plant Sciences, College of Agriculture and Bio-Resources, University of Saskatchewan, 51 Campus Dr., Saskatoon, SK, S7N5A8, Canada.
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13
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Zetzsche J, Fallet M. To live or let die? Epigenetic adaptations to climate change-a review. ENVIRONMENTAL EPIGENETICS 2024; 10:dvae009. [PMID: 39139701 PMCID: PMC11321362 DOI: 10.1093/eep/dvae009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/05/2024] [Accepted: 07/03/2024] [Indexed: 08/15/2024]
Abstract
Anthropogenic activities are responsible for a wide array of environmental disturbances that threaten biodiversity. Climate change, encompassing temperature increases, ocean acidification, increased salinity, droughts, and floods caused by frequent extreme weather events, represents one of the most significant environmental alterations. These drastic challenges pose ecological constraints, with over a million species expected to disappear in the coming years. Therefore, organisms must adapt or face potential extinctions. Adaptations can occur not only through genetic changes but also through non-genetic mechanisms, which often confer faster acclimatization and wider variability ranges than their genetic counterparts. Among these non-genetic mechanisms are epigenetics defined as the study of molecules and mechanisms that can perpetuate alternative gene activity states in the context of the same DNA sequence. Epigenetics has received increased attention in the past decades, as epigenetic mechanisms are sensitive to a wide array of environmental cues, and epimutations spread faster through populations than genetic mutations. Epimutations can be neutral, deleterious, or adaptative and can be transmitted to subsequent generations, making them crucial factors in both long- and short-term responses to environmental fluctuations, such as climate change. In this review, we compile existing evidence of epigenetic involvement in acclimatization and adaptation to climate change and discuss derived perspectives and remaining challenges in the field of environmental epigenetics. Graphical Abstract.
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Affiliation(s)
- Jonas Zetzsche
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
| | - Manon Fallet
- Man-Technology-Environment Research Centre (MTM), School of Science and Technology, Örebro University, Örebro 70182, Sweden
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14
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Chen C, Zhang Z, Lei Y, Chen W, Zhang Z, Dai H. The transcription factor MdERF023 negatively regulates salt tolerance by modulating ABA signaling and Na +/H + transport in apple. PLANT CELL REPORTS 2024; 43:187. [PMID: 38958739 DOI: 10.1007/s00299-024-03272-1] [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: 05/06/2024] [Accepted: 06/24/2024] [Indexed: 07/04/2024]
Abstract
KEY MESSAGE MdERF023 is a transcription factor that can reduce salt tolerance by inhibiting ABA signaling and Na+/H+ homeostasis. Salt stress is one of the principal environmental stresses limiting the growth and productivity of apple (Malus × domestica). The APETALA2/ethylene response factor (AP2/ERF) family plays key roles in plant growth and various stress responses; however, the regulatory mechanism involved has not been fully elucidated. In the present study, we identified an AP2/ERF transcription factor (TF), MdERF023, which plays a negative role in apple salt tolerance. Stable overexpression of MdERF023 in apple plants and calli significantly decreased salt tolerance. Biochemical and molecular analyses revealed that MdERF023 directly binds to the promoter of MdMYB44-like, a positive modulator of ABA signaling-mediated salt tolerance, and suppresses its transcription. In addition, MdERF023 downregulated the transcription of MdSOS2 and MdAKT1, thereby reducing the Na+ expulsion, K+ absorption, and salt tolerance of apple plants. Taken together, these results suggest that MdERF023 reduces apple salt tolerance by inhibiting ABA signaling and ion transport, and that it could be used as a potential target for breeding new varieties of salt-tolerant apple plants via genetic engineering.
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Affiliation(s)
- Cui Chen
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhen Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Yingying Lei
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Wenjun Chen
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Zhihong Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China
| | - Hongyan Dai
- College of Horticulture, Shenyang Agricultural University, Shenyang, 110866, China.
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15
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Ren F, Huang J, Yang Y. Unveiling the impact of microplastics and nanoplastics on vascular plants: A cellular metabolomic and transcriptomic review. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 279:116490. [PMID: 38795417 DOI: 10.1016/j.ecoenv.2024.116490] [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: 04/07/2023] [Revised: 05/03/2024] [Accepted: 05/19/2024] [Indexed: 05/28/2024]
Abstract
With increasing plastic manufacture and consumption, microplastics/nanoplastics (MP/NP) pollution has become one of the world's pressing global environmental issues, which poses significant threats to ecosystems and human health. In recent years, sharp increasing researches have confirmed that MP/NP had direct or indirect effects on vegetative growth and sexual process of vascular plant. But the potential mechanisms remain ambiguous. MP/NP particles can be adsorbed and/or absorbed by plant roots or leaves and thus cause diverse effects on plant. This holistic review aims to discuss the direct effects of MP/NP on vascular plant, with special emphasis on the changes of metabolic and molecular levels. MP/NP can alter substance and energy metabolism, as well as shifts in gene expression patterns. Key aspects affected by MP/NP stress include carbon and nitrogen metabolism, amino acids biosynthesis and plant hormone signal transduction, expression of stress related genes, carbon and nitrogen metabolism related genes, as well as those involved in pathogen defense. Additionally, the review provides updated insights into the growth and physiological responses of plants exposed to MP/NP, encompassing phenomena such as seed/spore germination, photosynthesis, oxidative stress, cytotoxicity, and genotoxicity. By examining the direct impact of MP/NP from both physiological and molecular perspectives, this review sets the stage for future investigations into the complex interactions between plants and plastic pollutants.
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Affiliation(s)
- Fugang Ren
- Hospital of Chengdu University of Traditional Chinese Medicine, Chengdu 610072, China; College of Medical Technology, Chengdu University of Traditional Chinese Medicine, Chengdu 611137, China; Chongqing Key Laboratory of Sichuan-Chongqing Co-construction for Diagnosis and Treatment of Infectious Diseases Integrated Traditional Chinese and Western Medicine, China
| | - Jing Huang
- Department of Vocal Performance, Sichuan Conservatory of Music, Chengdu 610021, China
| | - Yongqing Yang
- College of Life Sciences, Chongqing Normal University, Chongqing 401331, China.
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16
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Yu G, Zhang B, Chen Q, Huang Z, Zhang B, Wang K, Han J. Dynamic DNA methylation modifications in the cold stress response of cassava. Genomics 2024; 116:110871. [PMID: 38806102 DOI: 10.1016/j.ygeno.2024.110871] [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: 03/09/2024] [Revised: 05/21/2024] [Accepted: 05/25/2024] [Indexed: 05/30/2024]
Abstract
Cassava, a crucial tropical crop, faces challenges from cold stress, necessitating an exploration of its molecular response. Here, we investigated the role of DNA methylation in moderating the response to moderate cold stress (10 °C) in cassava. Using whole-genome bisulfite sequencing, we examined DNA methylation patterns in leaf blades and petioles under control conditions, 5 h, and 48 h of cold stress. Tissue-specific responses were observed, with leaf blades exhibiting subtle changes, while petioles displayed a pronounced decrease in methylation levels under cold stress. We identified cold stress-induced differentially methylated regions (DMRs) that demonstrated both tissue and treatment specificity. Importantly, these DMRs were enriched in genes with altered expression, implying functional relevance. The cold-response transcription factor ERF105 associated with DMRs emerged as a significant and conserved regulator across tissues and treatments. Furthermore, we investigated DNA methylation dynamics in transposable elements, emphasizing the sensitivity of MITEs with bHLH binding motifs to cold stress. These findings provide insights into the epigenetic regulation of response to cold stress in cassava, contributing to an understanding of the molecular mechanisms underlying stress adaptation in this tropical plant.
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Affiliation(s)
- Guangrun Yu
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Baowang Zhang
- Qingdao Smart Rural Development Service Center, Qingdao 266000, China
| | - Qi Chen
- School of Life Sciences, Nantong University, Nantong 226019, China; Xinglin College, Nantong University, Qidong 226236, China
| | - Zequan Huang
- Xinglin College, Nantong University, Qidong 226236, China
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong 226019, China.
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong 226019, China.
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17
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Zhu H, Wang J, Huang R, Yang Z, Fan W, Huang L, Yang J, Chen W. Epigenetic modification of a pectin methylesterase gene activates apoplastic iron reutilization in tomato roots. PLANT PHYSIOLOGY 2024; 195:2339-2353. [PMID: 38506490 DOI: 10.1093/plphys/kiae167] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2024] [Revised: 02/06/2024] [Accepted: 02/17/2024] [Indexed: 03/21/2024]
Abstract
Iron (Fe) distribution and reutilization are crucial for maintaining Fe homeostasis in plants. Here, we demonstrate that the tomato (Solanum lycopersicum) Colorless nonripening (Cnr) epimutant exhibits increased Fe retention in cell wall pectin due to an increase in pectin methylesterase (PME) activity. This ultimately leads to Fe deficiency responses even under Fe-sufficient conditions when compared to the wild type (WT). Whole-genome bisulfite sequencing revealed that modifications to cell wall-related genes, especially CG hypermethylation in the intron region of PECTIN METHYLESTERASE53 (SlPME53), are involved in the Cnr response to Fe deficiency. When this intron hypermethylation of SlPME53 was artificially induced in WT, we found that elevated SlPME53 expression was accompanied by increased PME activity and increased pectin-Fe retention. The manipulation of SlPME53, either through overexpression in WT or knockdown in Cnr, influenced levels of pectin methylesterification and accumulation of apoplast Fe in roots. Moreover, CG hypermethylation mediated by METHYLTRANSFERASE1 (SlMET1) increased SlPME53 transcript abundance, resulting in greater PME activity and higher Fe retention in cell wall pectin. Therefore, we conclude that the Cnr mutation epigenetically modulates SlPME53 expression by SlMET1-mediated CG hypermethylation, and thus the capacity of the apoplastic Fe pool, creating opportunities for genetic improvement of crop mineral nutrition.
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Affiliation(s)
- Huihui Zhu
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jiayi Wang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
- State Key Laboratory of Plant Physiology and Biochemistry, Institute of Plant Biology, College of Life Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ru'nan Huang
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
| | - Zheng'an Yang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Wei Fan
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Li Huang
- Laboratory of Cell & Molecular Biology, Institute of Vegetable Science, Zhejiang University, Hangzhou 310058, China
| | - Jianli Yang
- Key Laboratory of Vegetable Biology of Yunnan Province, College of Landscape and Horticulture, Yunnan Agricultural University, Kunming 650201, China
| | - Weiwei Chen
- Research Centre for Plant RNA Signaling and Zhejiang Provincial Key Laboratory for Genetic Improvement and Quality Control of Medicinal Plants, College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou 311121, China
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18
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Wang L, Li C, Luo K. Biosynthesis and metabolic engineering of isoflavonoids in model plants and crops: a review. FRONTIERS IN PLANT SCIENCE 2024; 15:1384091. [PMID: 38984160 PMCID: PMC11231381 DOI: 10.3389/fpls.2024.1384091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Accepted: 06/10/2024] [Indexed: 07/11/2024]
Abstract
Isoflavonoids, the major secondary metabolites within the flavonoid biosynthetic pathway, play important roles in plant defense and exhibit free radical scavenging properties in mammals. Recent advancements in understanding the synthesis, transport, and regulation of isoflavonoids have identified their biosynthetic pathways as promising targets for metabolic engineering, offering potential benefits such as enhanced plant resistance, improved biomass, and restoration of soil fertility. This review provides an overview of recent breakthroughs in isoflavonoid biosynthesis, encompassing key enzymes in the biosynthetic pathway, transporters influencing their subcellular localization, molecular mechanisms regulating the metabolic pathway (including transcriptional and post-transcriptional regulation, as well as epigenetic modifications). Metabolic engineering strategies aimed at boosting isoflavonoid content in both leguminous and non-leguminous plants. Additionally, we discuss emerging technologies and resources for precise isoflavonoid regulation. This comprehensive review primarily focuses on model plants and crops, offering insights for more effective and sustainable metabolic engineering approaches to enhance nutritional quality and stress tolerance.
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Affiliation(s)
- Lijun Wang
- School of Life Science and Engineering, Southwest University of Science and Technology, Mianyang, China
| | - Chaofeng Li
- Maize Research Institute, Southwest University, Chongqing, China
- Engineering Research Center of South Upland Agriculture, Ministry of Education, Chongqing, China
| | - Keming Luo
- Chongqing Key Laboratory of Plant Resource Conservation and Germplasm Innovation, Integrative Science Center of Germplasm Creation in Western China (Chongqing) Science City, School of Life Sciences, Southwest University, Chongqing, China
- Key Laboratory of Eco-environments of Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University, Chongqing, China
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19
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Li Z, Zhai X, Zhang L, Yang Y, Zhu H, Lü H, Xiong E, Chu S, Zhang X, Zhang D, Hu D. Genome-Wide Identification of the Whirly Gene Family and Its Potential Function in Low Phosphate Stress in Soybean ( Glycine max). Genes (Basel) 2024; 15:833. [PMID: 39062612 PMCID: PMC11275625 DOI: 10.3390/genes15070833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 06/21/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024] Open
Abstract
The Whirly (WHY) gene family, functioning as transcription factors, plays an essential role in the regulation of plant metabolic responses, which has been demonstrated across multiple species. However, the WHY gene family and its functions in soybean remains unclear. In this paper, we conducted genome-wide screening and identification to characterize the WHY gene family. Seven WHY members were identified and randomly distributed across six chromosomes. The phylogenetic evolutionary tree of WHY genes in soybean and other species was divided into five clades. An in-depth analysis revealed that segmental duplications significantly contributed to the expansion of GmWHYs, and the GmWHY gene members may have experienced evolutionary pressure for purifying selection in soybeans. The analysis of promoter Cis-elements in GmWHYs suggested their potential significance in addressing diverse stress conditions. The expression patterns of GmWHYs exhibited tissue-specific variations throughout the different stages of soybean development. Additionally, six GmWHY genes exhibited different responses to low phosphate stress. These findings will provide a theoretical basis and valuable reference for the future exploration of WHY gene function.
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Affiliation(s)
- Zhimin Li
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Xuhao Zhai
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Lina Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Yifei Yang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Hongqing Zhu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Haiyan Lü
- College of Information and Management Science, Henan Agricultural University, Zhengzhou 450046, China;
| | - Erhui Xiong
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Shanshan Chu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Xingguo Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Dan Zhang
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
| | - Dandan Hu
- Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, China; (Z.L.); (X.Z.); (L.Z.); (Y.Y.); (H.Z.); (E.X.); (S.C.); (X.Z.); (D.Z.)
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20
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Liu L, Wang W, Lu X, Zhang T, Wu J, Fang Y, Ma L, Pu Y, Yang G, Wang W, Sun W. Methyl-Sensitive Amplification Polymorphism (MSAP) Analysis Provides Insights into the DNA Methylation Changes Underlying Adaptation to Low Temperature of Brassica rapa L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1748. [PMID: 38999588 PMCID: PMC11244143 DOI: 10.3390/plants13131748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/06/2024] [Accepted: 06/21/2024] [Indexed: 07/14/2024]
Abstract
BACKGROUND DNA methylation can change rapidly to regulate the expression of stress-responsive genes. Previous studies have shown that there are significant differences in the cold resistance of winter rapeseed (Brassica rapa L.) after being domesticated in different selection environments; however, little is known about the epigenetic regulatory mechanisms of its cold resistance formation. METHODS Four winter rapeseed materials ('CT-2360', 'MXW-1', '2018-FJT', and 'DT-7') domesticated in different environments were selected to analyze the DNA methylation level and pattern changes under low temperature using methylation-sensitive amplified polymorphism technology with 60 primer pairs. RESULTS A total of 18 pairs of primers with good polymorphism were screened, and 1426 clear bands were amplified, with 594 methylation sites, accounting for 41.65% of the total amplified bands. The total methylation ratios of the four materials were reduced after low-temperature treatment, in which the DNA methylation level of 'CT-2360' was higher than that of the other three materials; the analysis of methylation patterns revealed that the degree of demethylation was higher than that of methylation in 'MXW-1', '2018-FJT', and 'DT-7', which were 22.99%, 19.77%, and 24.35%, respectively, and that the methylation events in 'CT-2360' were predominantly dominant at 22.95%. Fifty-three polymorphic methylated DNA fragments were randomly selected and further analyzed, and twenty-nine of the cloned fragments were homologous to genes with known functions. The candidate genes VQ22 and LOC103871127 verified the existence of different expressive patterns before and after low-temperature treatment. CONCLUSIONS Our work implies the critical role of DNA methylation in the formation of cold resistance in winter rapeseed. These results provide a comprehensive insight into the adaptation epigenetic regulatory mechanism of Brassica rapa L. to low temperature, and the identified differentially methylated genes can also be used as important genetic resources for the multilateral breeding of winter-resistant varieties.
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Affiliation(s)
- Lijun Liu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wanpeng Wang
- Zhangye Academy of Agricultural Sciences, Zhangye 734000, China
| | - Xiaoming Lu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Tianyu Zhang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Junyan Wu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yan Fang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Li Ma
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Yuanyuan Pu
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Gang Yang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wangtian Wang
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
| | - Wancang Sun
- State Key Laboratory of Aridland Crop Science, College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China
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Chengatt AP, Sarath NG, A M S, Sebastian DP, George S. 6-Benzylaminopurine mediated augmentation of cadmium phytostabilization potential in Strobilanthes alternata. INTERNATIONAL JOURNAL OF PHYTOREMEDIATION 2024:1-21. [PMID: 38836518 DOI: 10.1080/15226514.2024.2360573] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
This study unveiled the cadmium phytoremediation potential and its augmentation using 6-Benzylaminopurine in Strobilanthes alternata. Cadmium stress was provided by applying 250 mg/kg cadmium chloride in soil and 25 ppm of 6-BAP (25 ml) was administered to the plants as foliar spray. The results revealed high bioconcentration factor (BCF) (18.82 ± 0.54) and low translocation factor (TF) values (0.055 ± 0.002) for the plant based on which we strongly recommend S. alternata as a promising candidate for Cd phytoremediation. The phytostabilization potential of the plant was further enhanced by applying 6-BAP, which augmented its BCF to 22.09 ± 0.64 and reduced the TF to 0.038 ± 0.001. Cd toxicity caused a reduction of plant growth parameters, root volume, adaxial-abaxial stomatal indices, relative water content, tolerance index, moisture content, membrane stability index, and xylem vessel diameter in S. alternata. However, Cd + 6-BAP treated plants exhibited an increase of the same compared to Cd-treated plants. FTIR analysis of Cd + 6-BAP treated plants revealed increased deposition of hemicellulose, causing enhanced retention of Cd in the root xylem walls, which is largely responsible for increased phytostabilization of Cd. Therefore, 6-BAP application in S. alternata can be exploited to restore Cd-contaminated areas effectively.
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Affiliation(s)
- Akshaya Prakash Chengatt
- Department of Botany, St. Joseph's College (Autonomous) Devagiri, Kozhikode, Affiliated to University of Calicut, Kerala, India
| | - Nair G Sarath
- Department of Botany, Mar Athanasius College (Autonomous), Kothamangalam, Kerala, India
| | - Shackira A M
- Department of Botany, Sir Syed College, Kannur University, Kannur, Kerala, India
| | - Delse Parekkattil Sebastian
- Department of Botany, St. Joseph's College (Autonomous) Devagiri, Kozhikode, Affiliated to University of Calicut, Kerala, India
| | - Satheesh George
- Department of Botany, St. Joseph's College (Autonomous) Devagiri, Kozhikode, Affiliated to University of Calicut, Kerala, India
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22
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Yu S, Zhu J, Yin Y, Zhang X, Dai Y, Xing Y, Cheng X, Zhang A, Li C, Zhu Y, Ruan Y, Dong X, Fan J. Dynamic transcriptome profiling revealed a key gene ZmJMJ20 and pathways associated with cadmium stress in maize. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2024; 277:116352. [PMID: 38663195 DOI: 10.1016/j.ecoenv.2024.116352] [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: 10/17/2023] [Revised: 03/26/2024] [Accepted: 04/17/2024] [Indexed: 06/06/2024]
Abstract
Cadmium (Cd) pollution in soil poses a global concern due to its serious impacts on human health and ecological security. In plants, tremendous efforts have been made to identify some key genes and pathways in Cd stress responses. However, studies on the roles of epigenetic factors in response to Cd stress were still limited. In the study, we first gain insight into the gene expression dynamics for maize seedlings under 0 h, 12 h, and 72 h Cd stress. As a result, six distinct groups of genes were identified by hierarchical clustering and principal component analysis. The key pathways associated with 12 h Cd stress were protein modifications including protein ubiquitination, signal transduction by protein phosphorylation, and histone modification. Whereas, under 72 h stress, main pathways were involved in biological processes including phenylalanine metabolism, response to oxygen-containing compounds and metal ions. Then to be noted, one of the most highly expressed genes at 12 h under Cd treatment is annotated as histone demethylases (ZmJMJ20). The evolutionary tree analysis and domain analysis showed that ZmJMJ20 belonged to the JmjC-only subfamily of the Jumonji-C (JmjC) family, and ZmJMJ20 was conserved in rice and Arabidopsis. After 72 h of Cd treatment, the zmjmj20 mutant created by EMS treatment manifested less severe chlorosis/leaf yellowing symptoms compared with wild-type plants, and there was no significant difference in Fv/Fm and φPSII value before and after Cd treatment. Moreover, the expression levels of several photosynthesis-related down-regulated genes in EMS mutant plants were dramatically increased compared with those in wild-type plants at 12 h under Cd treatment. Our results suggested that ZmJMJ20 plays an important role in the Cd tolerance response pathway and will facilitate the development of cultivars with improved Cd stress tolerance.
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Affiliation(s)
- Shuai Yu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Jialun Zhu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Yanzhe Yin
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Xiaoyu Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Yuxin Dai
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Yupeng Xing
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Xipeng Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Ao Zhang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Cong Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Yanshu Zhu
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Yanye Ruan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China
| | - Xiaomei Dong
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China.
| | - Jinjuan Fan
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang, Liaoning 110866, China; Shenyang City Key Laboratory of Maize Genomic Selection Breeding, Shenyang, Liaoning 110866, China.
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23
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Balard A, Baltazar-Soares M, Eizaguirre C, Heckwolf MJ. An epigenetic toolbox for conservation biologists. Evol Appl 2024; 17:e13699. [PMID: 38832081 PMCID: PMC11146150 DOI: 10.1111/eva.13699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 06/05/2024] Open
Abstract
Ongoing climatic shifts and increasing anthropogenic pressures demand an efficient delineation of conservation units and accurate predictions of populations' resilience and adaptive potential. Molecular tools involving DNA sequencing are nowadays routinely used for these purposes. Yet, most of the existing tools focusing on sequence-level information have shortcomings in detecting signals of short-term ecological relevance. Epigenetic modifications carry valuable information to better link individuals, populations, and species to their environment. Here, we discuss a series of epigenetic monitoring tools that can be directly applied to various conservation contexts, complementing already existing molecular monitoring frameworks. Focusing on DNA sequence-based methods (e.g. DNA methylation, for which the applications are readily available), we demonstrate how (a) the identification of epi-biomarkers associated with age or infection can facilitate the determination of an individual's health status in wild populations; (b) whole epigenome analyses can identify signatures of selection linked to environmental conditions and facilitate estimating the adaptive potential of populations; and (c) epi-eDNA (epigenetic environmental DNA), an epigenetic-based conservation tool, presents a non-invasive sampling method to monitor biological information beyond the mere presence of individuals. Overall, our framework refines conservation strategies, ensuring a comprehensive understanding of species' adaptive potential and persistence on ecologically relevant timescales.
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Affiliation(s)
- Alice Balard
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | | | - Christophe Eizaguirre
- School of Biological and Behavioural Sciences Queen Mary University of London London UK
| | - Melanie J Heckwolf
- Department of Ecology Leibniz Centre for Tropical Marine Research Bremen Germany
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24
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Hou J, Xiao H, Yao P, Ma X, Shi Q, Yang J, Hou H, Li L. Unveiling the mechanism of broad-spectrum blast resistance in rice: The collaborative role of transcription factor OsGRAS30 and histone deacetylase OsHDAC1. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1740-1756. [PMID: 38294722 PMCID: PMC11123394 DOI: 10.1111/pbi.14299] [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: 08/31/2023] [Revised: 11/15/2023] [Accepted: 01/16/2024] [Indexed: 02/01/2024]
Abstract
Rice blast, caused by Magnaporthe oryzae, significantly impacts grain yield, necessitating the identification of broad-spectrum resistance genes and their functional mechanisms for disease-resistant crop breeding. Here, we report that rice with knockdown OsHDAC1 gene expression displays enhanced broad-spectrum blast resistance without effects on plant height and tiller numbers compared to wild-type rice, while rice overexpressing OsHDAC1 is more susceptible to M. oryzae. We identify a novel blast resistance transcription factor, OsGRAS30, which genetically acts upstream of OsHDAC1 and interacts with OsHDAC1 to suppress its enzymatic activity. This inhibition increases the histone H3K27ac level, thereby boosting broad-spectrum blast resistance. Integrating genome-wide mapping of OsHDAC1 and H3K27ac targets with RNA sequencing analysis unveils how OsHDAC1 mediates the expression of OsSSI2, OsF3H, OsRLR1 and OsRGA5 to regulate blast resistance. Our findings reveal that the OsGRAS30-OsHDAC1 module is critical to rice blast control. Therefore, targeting either OsHDAC1 or OsGRAS30 offers a promising approach for enhancing crop blast resistance.
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Affiliation(s)
- Jiaqi Hou
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Huangzhuo Xiao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Peng Yao
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Xiaoci Ma
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Qipeng Shi
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Jin Yang
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Haoli Hou
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
| | - Lijia Li
- State Key Laboratory of Hybrid Rice, College of Life SciencesWuhan UniversityWuhanChina
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25
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Guo W, Li X, Yang T, Huang C, Zhao B, Wang P. Identification and expression of the Di19 gene family in response to abiotic stress in common bean ( Phaseolus vulgaris L.). Front Genet 2024; 15:1401011. [PMID: 38873116 PMCID: PMC11169598 DOI: 10.3389/fgene.2024.1401011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2024] [Accepted: 05/08/2024] [Indexed: 06/15/2024] Open
Abstract
Drought-induced 19 (Di19) protein plays critical biological functions in response to adversity as well as in plant growth and development. Exploring the role and mechanism of Di19 in abiotic stress responses is of great significance for improving plant tolerance. In this study, six Di19 genes were identified in the common bean (Phaseolus vulgaris L.), which were mainly derived from segmental duplications. These genes share conserved exon/intron structures and were classified into three subfamilies based on their phylogenetic relationships. The composition and arrangement of conserved motifs were consistent with their phylogenetic relationships. Many hormone- and stress-responsive elements were distributed in the promoters region of PvDi19 genes. Variations in histidine residues in the Cys2/His2 (C2H2) zinc-finger domains resulted in an atypical tertiary structure of PvDi19-5. Gene expression analysis showed rapid induction of PvDi19-1 in roots by 10% PEG treatment, and PvDi19-2 in leaves by 20% PEG treatment, respectively. Most PvDi19s exhibited insensitivity to saline-alkali stress, except for PvDi19-6, which was notably induced during later stages of treatment. The most common bean Di19 genes were inhibited or not regulated by cadmium stress, but the expression of PvDi19-6 in roots was significantly upregulated when subjected to lower concentrations of cadmium (5 mmol). Moreover, Di19s exhibited greater sensitivity to severe cold stress (6°C). These findings enhance our understanding of the role of PvDi19s in common bean abiotic stress responses and provide a basis for future genetic enhancements in common bean stress tolerance.
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Affiliation(s)
- Wei Guo
- Department of Basic Sciences, Shanxi Agricultural University, Taigu, China
| | - Xinhui Li
- Shanxi Houji Laboratory, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Tao Yang
- Shanxi Houji Laboratory, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Chunguo Huang
- Shanxi Houji Laboratory, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Bo Zhao
- Shanxi Houji Laboratory, College of Agriculture, Shanxi Agricultural University, Taigu, China
| | - Peng Wang
- Shanxi Houji Laboratory, College of Agriculture, Shanxi Agricultural University, Taigu, China
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26
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da Paschoa RP, Pinto VB, Pereira JP, Cavatte PC, Garbin ML, Godinho T, Xavier LR, Carrijo TT, Silveira V. Proteomic and physiological signatures of altitude adaptation in a Myrsine coriacea population under common garden conditions. J Proteomics 2024; 299:105156. [PMID: 38467267 DOI: 10.1016/j.jprot.2024.105156] [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: 12/23/2023] [Revised: 02/20/2024] [Accepted: 03/06/2024] [Indexed: 03/13/2024]
Abstract
Plants exhibit phenotypic plasticity in response to environmental variations, which can lead to stable genetic and physiological adaptations if exposure to specific conditions is prolonged. Myrsine coriacea demonstrates this through its ability to thrive in diverse environments. The objective of the article is to investigate potential differences in protein accumulation and physiological responses of M. coriacea by cultivating plants from seeds collected from four populations at different altitudes in a common garden experiment. Additionally, we aim to evaluate whether these differences exhibit genetic fixation. Through integrated physiological and proteomic analyses, we identified 170 differentially accumulated proteins and observed significant physiological differences among the populations. The high-altitude population (POP1) exhibited a unique proteomic profile with significant down-regulation of proteins involved in carbon fixation and energy metabolism, suggesting a potential reduction in photosynthetic efficiency. Physiological analyses showed lower leaf nitrogen content, net CO2 assimilation rate, specific leaf area, and relative growth rate in stem height for POP1, alongside higher leaf carbon isotopic composition (δ13C) and leaf carbon (C) content. These findings provide insight into the complex interplay between proteomic and physiological adaptations in M. coriacea and underscore the importance of local adaptations. SIGNIFICANCE: We investigate the adaptive responses of M. coriacea, a shrub with a broad phenotypic range, by cultivating plants from seeds collected at four different altitudes in a common garden experiment. These findings provide insight into the complex interplay between proteomic and physiological adaptations in M. coriacea and underscore the importance of local adaptations in the face of climate change. This study contributes to advancing our understanding of the influence of altitude-specific selection pressures on the molecular biology and physiology of plants in natural populations. Our findings provide valuable insights that enhance our ability to predict and comprehend how plants respond to climate change.
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Affiliation(s)
- Roberta Pena da Paschoa
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil
| | | | - Jéssica Priscilla Pereira
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Paulo Cezar Cavatte
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Mário Luís Garbin
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil
| | - Tiago Godinho
- Reserva Natural Vale, Rodovia BR 101, km 122 s/n Zona Rural, Linhares, ES 29900-111, Brazil
| | - Lucas Rodrigues Xavier
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil
| | - Tatiana Tavares Carrijo
- Universidade Federal do Espírito Santo, Centro de Ciências Exatas, Naturais e da Saúde, Depto. Biologia, Lab. Botânica, Alto Universitário, Guararema, Alegre, ES, Brazil.
| | - Vanildo Silveira
- Laboratório de Biotecnologia, Centro de Biociências e Biotecnologia (CBB), Universidade Estadual do Norte Fluminense Darcy Ribeiro (UENF), Av. Alberto Lamego, 2000, Campos dos Goytacazes, RJ 28013-602, Brazil; Unidade de Biologia Integrativa, Setor de Genômica e Proteômica, UENF, Brazil.
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27
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Javed T, Wang W, Yang B, Shen L, Sun T, Gao SJ, Zhang S. Pathogenesis related-1 proteins in plant defense: regulation and functional diversity. Crit Rev Biotechnol 2024:1-9. [PMID: 38719539 DOI: 10.1080/07388551.2024.2344583] [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: 01/22/2024] [Accepted: 03/20/2024] [Indexed: 05/14/2024]
Abstract
Climate change-related environmental stresses can negatively impact crop productivity and pose a threat to sustainable agriculture. Plants have a remarkable innate ability to detect a broad array of environmental cues, including stresses that trigger stress-induced regulatory networks and signaling pathways. Transcriptional activation of plant pathogenesis related-1 (PR-1) proteins was first identified as an integral component of systemic acquired resistance in response to stress. Consistent with their central role in immune defense, overexpression of PR-1s in diverse plant species is frequently used as a marker for salicylic acid (SA)-mediated defense responses. Recent advances demonstrated how virulence effectors, SA signaling cascades, and epigenetic modifications modulate PR-1 expression in response to environmental stresses. We and others showed that transcriptional regulatory networks involving PR-1s could be used to improve plant resilience to stress. Together, the results of these studies have re-energized the field and provided long-awaited insights into a possible function of PR-1s under extreme environmental stress.
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Affiliation(s)
- Talha Javed
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Wenzhi Wang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
| | - Benpeng Yang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Linbo Shen
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - Tingting Sun
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
| | - San-Ji Gao
- National Engineering Research Center for Sugarcane, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shuzhen Zhang
- National Key Laboratory for Tropical Crop Breeding, Institute of Tropical Bioscience and Biotechnology, Chinese Academy of Tropical Agricultural Sciences, Haikou, China
- Sanya Research Institute, Chinese Academy of Tropical Agricultural Sciences, Sanya, China
- Hainan Yazhou Bay Seed Lab, Sanya, China
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28
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Marques I, Hu H. Molecular Insight of Plants Response to Drought Stress: Perspectives and New Insights towards Food Security. Int J Mol Sci 2024; 25:4988. [PMID: 38732211 PMCID: PMC11084910 DOI: 10.3390/ijms25094988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2024] [Revised: 04/28/2024] [Accepted: 04/29/2024] [Indexed: 05/13/2024] Open
Abstract
In the face of climate-induced challenges, understanding the intricate molecular mechanisms underlying drought tolerance in plants has become imperative [...].
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Affiliation(s)
- Isabel Marques
- Forest Research Centre, Associate Laboratory TERRA, School of Agriculture, University of Lisbon, 1349-017 Lisbon, Portugal
| | - Honghong Hu
- Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
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29
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Wani AK, Khan Z, Sena S, Akhtar N, Alreshdi MA, Yadav KK, Alkahtani AM, Wani AW, Rahayu F, Tafakresnanto C, Latifah E, Hariyono B, Arifin Z, Eltayeb LB. Carbon nanotubes in plant dynamics: Unravelling multifaceted roles and phytotoxic implications. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 210:108628. [PMID: 38636256 DOI: 10.1016/j.plaphy.2024.108628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 03/19/2024] [Accepted: 04/10/2024] [Indexed: 04/20/2024]
Abstract
Carbon nanotubes (CNTs) have emerged as a promising frontier in plant science owing to their unique physicochemical properties and versatile applications. CNTs enhance stress tolerance by improving water dynamics and nutrient uptake and activating defence mechanisms against abiotic and biotic stresses. They can be taken up by roots and translocated within the plant, impacting water retention, nutrient assimilation, and photosynthesis. CNTs have shown promise in modulating plant-microbe interactions, influencing symbiotic relationships and mitigating the detrimental effects of phytopathogens. CNTs have demonstrated the ability to modulate gene expression in plants, offering a powerful tool for targeted genetic modifications. The integration of CNTs as sensing elements in plants has opened new avenues for real-time monitoring of environmental conditions and early detection of stress-induced changes. In the realm of agrochemicals, CNTs have been explored for their potential as carriers for targeted delivery of nutrients, pesticides, and other bioactive compounds. CNTs have the potential to demonstrate phytotoxic effects, detrimentally influencing both the growth and developmental processes of plants. Phytotoxicity is characterized by induction of oxidative stress, impairment of cellular integrity, disruption of photosynthetic processes, perturbation of nutrient homeostasis, and alterations in gene expression. This review aims to provide a comprehensive overview of the current state of knowledge regarding the multifaceted roles of CNTs in plant physiology, emphasizing their potential applications and addressing the existing challenges in translating this knowledge into sustainable agricultural practices.
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Affiliation(s)
- Atif Khurshid Wani
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, 144411, Punjab, India.
| | - Zehra Khan
- Department of Biology, College of Science, Jazan University, 45142 Jazan, Saudi Arabia
| | - Saikat Sena
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, 144411, Punjab, India
| | - Nahid Akhtar
- School of Bioengineering and Biosciences, Lovely Professional University, Jalandhar, 144411, Punjab, India
| | | | - Krishna Kumar Yadav
- Faculty of Science and Technology, Madhyanchal Professional University, Ratibad, Bhopal, 4620044, India; Environmental and Atmospheric Sciences Research Group, Scientific Research Center, Al-Ayen University, Thi-Qar, Nasiriyah, 64001, Iraq
| | - Abdullah M Alkahtani
- Department of Microbiology & Clinical Parasitology College of Medicine, King Khalid University, Abha, Saudi Arabia
| | - Ab Waheed Wani
- Department of Horticulture, School of Agriculture, Lovely Professional University, Jalandhar, 144411, Punjab, India
| | - Farida Rahayu
- Research Center for Genetic Engineering, National Research and Innovation Agency, Bogor, 16911, Indonesia
| | - Chendy Tafakresnanto
- Research Center for Food Crops, Research Organization for Agriculture and Food, National Research Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Evy Latifah
- Research Center for Horticulture, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Budi Hariyono
- Research Center for Estate Crops, Research Organization for Agriculture and Food, National Research Innovation Agenc (BRIN), Bogor, 16911, Indonesia
| | - Zainal Arifin
- Research Center for Horticulture, Research Organization for Agriculture and Food, National Research and Innovation Agency (BRIN), Bogor, 16911, Indonesia
| | - Lienda Bashier Eltayeb
- Department of Medical Laboratory Sciences, College of Applied Sciences, Prince Sattam Bin AbdulAziz University-Al-Kharj, 11942, Riyadh, Saudi Arabia
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Sun Y, Wang X, Di Y, Li J, Li K, Wei H, Zhang F, Su Z. Systematic Analysis of DNA Demethylase Gene Families in Foxtail Millet ( Setaria italica L.) and Their Expression Variations after Abiotic Stresses. Int J Mol Sci 2024; 25:4464. [PMID: 38674049 PMCID: PMC11050331 DOI: 10.3390/ijms25084464] [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: 03/12/2024] [Revised: 04/15/2024] [Accepted: 04/17/2024] [Indexed: 04/28/2024] Open
Abstract
DNA methylation is a highly conserved epigenetic modification involved in many biological processes, including growth and development, stress response, and secondary metabolism. DNA demethylase (DNA-deMTase) genes have been identified in some plant species; however, there are no reports on the identification and analysis of DNA-deMTase genes in Foxtail millet (Setaria italica L.). In this study, seven DNA-deMTases were identified in S. italica. These DNA-deMTase genes were divided into four subfamilies (DML5, DML4, DML3, and ROS1) by phylogenetic and gene structure analysis. Further analysis shows that the physical and chemical properties of these DNA-deMTases proteins are similar, contain the typical conserved domains of ENCO3c and are located in the nucleus. Furthermore, multiple cis-acting elements were observed in DNA-deMTases, including light responsiveness, phytohormone responsiveness, stress responsiveness, and elements related to plant growth and development. The DNA-deMTase genes are expressed in all tissues detected with certain tissue specificity. Then, we investigated the abundance of DNA-deMTase transcripts under abiotic stresses (cold, drought, salt, ABA, and MeJA). The results showed that different genes of DNA-deMTases were involved in the regulation of different abiotic stresses. In total, our findings will provide a basis for the roles of DNA-deMTase in response to abiotic stress.
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Affiliation(s)
- Yingying Sun
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Xin Wang
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Yunfei Di
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Jinxiu Li
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Keyu Li
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Huanhuan Wei
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Fan Zhang
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
| | - Zhenxia Su
- College of Life Sciences, Shanxi University, Taiyuan 030006, China; (Y.S.); (X.W.); (Y.D.); (J.L.); (K.L.); (H.W.); (F.Z.)
- Xinghuacun College (Shanxi Institute of Brewing Technology and Industry), Shanxi University, Taiyuan 030006, China
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Bakala HS, Devi J, Singh G, Singh I. Drought and heat stress: insights into tolerance mechanisms and breeding strategies for pigeonpea improvement. PLANTA 2024; 259:123. [PMID: 38622376 DOI: 10.1007/s00425-024-04401-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Accepted: 03/29/2024] [Indexed: 04/17/2024]
Abstract
MAIN CONCLUSION Pigeonpea has potential to foster sustainable agriculture and resilience in evolving climate change; understanding bio-physiological and molecular mechanisms of heat and drought stress tolerance is imperative to developing resilience cultivars. Pigeonpea is an important legume crop that has potential resilience in the face of evolving climate scenarios. However, compared to other legumes, there has been limited research on abiotic stress tolerance in pigeonpea, particularly towards drought stress (DS) and heat stress (HS). To address this gap, this review delves into the genetic, physiological, and molecular mechanisms that govern pigeonpea's response to DS and HS. It emphasizes the need to understand how this crop combats these stresses and exhibits different types of tolerance and adaptation mechanisms through component traits. The current article provides a comprehensive overview of the complex interplay of factors contributing to the resilience of pigeonpea under adverse environmental conditions. Furthermore, the review synthesizes information on major breeding techniques, encompassing both conventional methods and modern molecular omics-assisted tools and techniques. It highlights the potential of genomics and phenomics tools and their pivotal role in enhancing adaptability and resilience in pigeonpea. Despite the progress made in genomics, phenomics and big data analytics, the complexity of drought and heat tolerance in pigeonpea necessitate continuous exploration at multi-omic levels. High-throughput phenotyping (HTP) is crucial for gaining insights into perplexed interactions among genotype, environment, and management practices (GxExM). Thus, integration of advanced technologies in breeding programs is critical for developing pigeonpea varieties that can withstand the challenges posed by climate change. This review is expected to serve as a valuable resource for researchers, providing a deeper understanding of the mechanisms underlying abiotic stress tolerance in pigeonpea and offering insights into modern breeding strategies that can contribute to the development of resilient varieties suited for changing environmental conditions.
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Affiliation(s)
- Harmeet Singh Bakala
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Jomika Devi
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
| | - Gurjeet Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India.
- Texas A&M University, AgriLife Research Center, Beaumont, TX, 77713, USA.
| | - Inderjit Singh
- Department of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, Punjab, 141004, India
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Doddavarapu B, Lata C, Shah JM. Epigenetic regulation influenced by soil microbiota and nutrients: Paving road to epigenome editing in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130580. [PMID: 38325761 DOI: 10.1016/j.bbagen.2024.130580] [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: 06/16/2023] [Revised: 12/25/2023] [Accepted: 02/02/2024] [Indexed: 02/09/2024]
Abstract
Soil is a complex ecosystem that houses microbes and nutrients that are necessary for plant development. Edaphic properties of the soil and environmental conditions influence microbial growth and nutrient accessibility. Various environmental stimuli largely affect the soil microbes and ionic balance, in turn influencing plants. Soil microflora helps decompose organic matter and is involved in mineral uptake. The combination of soil microbes and mineral nutrients notably affects plant growth. Recent advancements have enabled a deeper understanding of plant genetic/molecular regulators. Deficiencies/sufficiencies of soil minerals and microbes also alter plant gene regulation. Gene regulation mediated by epigenetic mechanisms comprises conformational alterations in chromatin structure, DNA/histone modifications, or involvement of small RNAs. Epigenetic regulation is unique due to its potential to inherit without involving alteration of the DNA sequence. Thus, the compilation study of heritable epigenetic changes driven by nutrient imbalances and soil microbes would facilitate understanding this molecular phenomenon in plants. This information can aid in epigenome editing, which has recently emerged as a promising technology for plant non-transgenic/non-mutagenic modification. Potential epigenetic marks induced by biotic and abiotic stresses in plants could be explored as target sites for epigenome editing. This review discusses novel ways of epigenome editing to create epigenome edited plants with desirable and heritable phenotypes. As plants are sessile and in constant exposure to the soil microbiome and nutrients, epigenetic changes induced by these factors could provide more effective, stable and a sustainable molecular solution for crop improvement.
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Affiliation(s)
- Bhavya Doddavarapu
- Department of Plant Science, Central University of Kerala, Kerala, India
| | - Charu Lata
- Inclusive Health & Traditional Knowledge Studies Division, CSIR- National Institute of Science Communication and Policy Research, New Delhi, India
| | - Jasmine M Shah
- Department of Plant Science, Central University of Kerala, Kerala, India.
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Usai G, Fambrini M, Pugliesi C, Simoni S. Exploring the patterns of evolution: Core thoughts and focus on the saltational model. Biosystems 2024; 238:105181. [PMID: 38479653 DOI: 10.1016/j.biosystems.2024.105181] [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: 12/07/2023] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/18/2024]
Abstract
The Modern Synthesis, a pillar in biological thought, united Darwin's species origin concepts with Mendel's laws of character heredity, providing a comprehensive understanding of evolution within species. Highlighting phenotypic variation and natural selection, it elucidated the environment's role as a selective force, shaping populations over time. This framework integrated additional mechanisms, including genetic drift, random mutations, and gene flow, predicting their cumulative effects on microevolution and the emergence of new species. Beyond the Modern Synthesis, the Extended Evolutionary Synthesis expands perspectives by recognizing the role of developmental plasticity, non-genetic inheritance, and epigenetics. We suggest that these aspects coexist in the plant evolutionary process; in this context, we focus on the saltational model, emphasizing how saltation events, such as dichotomous saltation, chromosomal mutations, epigenetic phenomena, and polyploidy, contribute to rapid evolutionary changes. The saltational model proposes that certain evolutionary changes, such as the rise of new species, may result suddenly from single macromutations rather than from gradual changes in DNA sequences and allele frequencies within a species over time. These events, observed in domesticated and wild higher plants, provide well-defined mechanistic bases, revealing their profound impact on plant diversity and rapid evolutionary events. Notably, next-generation sequencing exposes the likely crucial role of allopolyploidy and autopolyploidy (saltational events) in generating new plant species, each characterized by distinct chromosomal complements. In conclusion, through this review, we offer a thorough exploration of the ongoing dissertation on the saltational model, elucidating its implications for our understanding of plant evolutionary processes and paving the way for continued research in this intriguing field.
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Affiliation(s)
- Gabriele Usai
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Marco Fambrini
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
| | - Claudio Pugliesi
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy.
| | - Samuel Simoni
- Department of Agriculture, Food and Environment (DAFE), University of Pisa, Via del Borghetto 80, 56124, Pisa, Italy
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Naderi S, Maali-Amiri R, Sadeghi L, Hamidi A. Physio-biochemical and DNA methylation analysis of the defense response network of wheat to drought stress. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 209:108516. [PMID: 38537384 DOI: 10.1016/j.plaphy.2024.108516] [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: 12/11/2023] [Revised: 03/03/2024] [Accepted: 03/08/2024] [Indexed: 04/06/2024]
Abstract
In the present work, physio-biochemical and DNA methylation analysis were conducted in wheat (Triticum aestivum L.) cultivars "Bolani" (drought-tolerant) and "Sistan" (drought-sensitive) during drought treatments: well-watered (at 90% field capacity (FC)), mild stress (at 50% FC, and severe stress (at 25% FC). During severe stress, O2•- and H2O2 content in cultivar Sistan showed significant increase (by 1.3 and 2.5-fold, respectively) relative to cultivar Bolani. In Bolani, the increased levels of radical scavenging activity (by 32%), glycine betaine (GB) (by 11.44%), proline (4-fold), abscisic acid (by 63.76%), and more stability of relative water content (RWC) (2-fold) were observed against drought-induced oxidative stress. Methylation level significantly decreased from 70.26% to 60.64% in Bolani and from 69.06% to 59.85% in Sistan during stress, and higher decreased tendency was related to CG and CHG in Bolani but CG in Sistan under severe stress. Methylation patterns showed that the highest polymorphism in Bolani was mainly as CG. As the intensity of stress increased, the enhanced physio-biochemical responses of Bolani cultivar were accompanied by a more decrease in the number of unchanged bands. According to heat map analysis, the highest difference (84.38%) in methylation patterns was observed between control and severe stress. Multivariate analysis using principal component analysis (PCA) showed a cultivar-specific methylation during stress and that methylation changes between cultivars are much higher than that of within a cultivar. Higher methylation to demethylation in Bolani (30.06 vs. 22.12%) compared to that of cultivar Sistan (23.21 vs. 30.15%) indicated more demethylation did not induce tolerance responses in Sistan. Sequencing differentially methylated fragments along with qRT-PCR analysis showed the efficient role of various DNA fragments, including demethylated fragments such as phosphoenol pyruvate carboxylase (PEPC), beta-glucosidase (BGlu), glycosyltransferase (GT), glutathione S-transferase (GST) and lysine demethylase (LSD) genes and methylated fragments like ubiquitin E2 enzyme genes in the development of drought tolerance. These results suggested the specific roles of DNA methylation in development of drought tolerance in wheat landrace.
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Affiliation(s)
- Salehe Naderi
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran
| | - Reza Maali-Amiri
- Department of Agronomy and Plant Breeding, College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-77871, Iran.
| | - Leila Sadeghi
- Seed and Plant Certification and Registration Research Institute, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31368-63111, Karaj, Iran
| | - Aidin Hamidi
- Seed and Plant Certification and Registration Research Institute, Agricultural Research, Education and Extension Organization (AREEO), P.O. Box 31368-63111, Karaj, Iran
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Miloro F, Kis A, Havelda Z, Dalmadi Á. Barley AGO4 proteins show overlapping functionality with distinct small RNA-binding properties in heterologous complementation. PLANT CELL REPORTS 2024; 43:96. [PMID: 38480545 PMCID: PMC10937801 DOI: 10.1007/s00299-024-03177-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/15/2024] [Indexed: 03/17/2024]
Abstract
KEY MESSAGE Barley AGO4 proteins complement expressional changes of epigenetically regulated genes in Arabidopsis ago4-3 mutant and show a distinct affinity for the 5' terminal nucleotide of small RNAs, demonstrating functional conservation and divergence. The function of Argonaute 4 (AGO4) in Arabidopsis thaliana has been extensively characterized; however, its role in monocots, which have large genomes abundantly supplemented with transposable elements (TEs), remains elusive. The study of barley AGO4 proteins can provide insights into the conserved aspects of RNA-directed DNA methylation (RdDM) and could also have further applications in the field of epigenetics or crop improvement. Bioinformatic analysis of RNA sequencing data identified two active AGO4 genes in barley, HvAGO4a and HvAGO4b. These genes function similar to AtAGO4 in an Arabidopsis heterologous complementation system, primarily binding to 24-nucleotide long small RNAs (sRNAs) and triggering methylation at specific target loci. Like AtAGO4, HvAGO4B exhibits a preference for binding sRNAs with 5' adenine residue, while also accepting 5' guanine, uracil, and cytosine residues. In contrast, HvAGO4A selectively binds only sRNAs with a 5' adenine residue. The diverse binding capacity of barley AGO4 proteins is reflected in TE-derived sRNAs and in their varying abundance. Both barley AGO4 proteins effectively restore the levels of extrachromosomal DNA and transcript abundancy of the heat-activated ONSEN retrotransposon to those observed in wild-type Arabidopsis plants. Our study provides insight into the distinct binding specificities and involvement in TE regulation of barley AGO4 proteins in Arabidopsis by heterologous complementation.
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Affiliation(s)
- Fabio Miloro
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - András Kis
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
| | - Zoltán Havelda
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary
| | - Ágnes Dalmadi
- Hungarian University of Agriculture and Life Sciences (MATE), Institute of Genetics and Biotechnology, Gödöllő, Hungary.
- Agribiotechnology and Precision Breeding for Food Security National Laboratory, Plant Biotechnology Section, Gödöllő, Hungary.
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Yang L, Xu L, Guo J, Li A, Qi H, Wang J, Song S. SNAC1-OsERF103-OsSDG705 module mediates drought response in rice. THE NEW PHYTOLOGIST 2024; 241:2480-2494. [PMID: 38296835 DOI: 10.1111/nph.19552] [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: 10/08/2023] [Accepted: 01/02/2024] [Indexed: 02/02/2024]
Abstract
Drought stress profoundly hampers both plant growth and crop yield. To combat this, plants have evolved intricate transcriptional regulation mechanisms as a pivotal strategy. Through a genetic screening with rice genome-scale mutagenesis pool under drought stress, we identified an APETALA2/Ethylene Responsive Factor, namely OsERF103, positively responds to drought tolerance in rice. Combining chromatin immunoprecipitation sequencing and RNA sequencing analyses, we pinpointed c. 1000 genes directly influenced by OsERF103. Further results revealed that OsERF103 interacts with Stress-responsive NAC1 (SNAC1), a positive regulator of drought tolerance in rice, to synergistically regulate the expression of key drought-related genes, such as OsbZIP23. Moreover, we found that OsERF103 recruits a Su(var)3-9,enhancer of zeste and trithorax-domain group protein 705, which encodes a histone 3 lysine 4 (H3K4)-specific methyltransferase to specifically affect the deposition of H3K4me3 at loci like OsbZIP23 and other genes linked to dehydration responses. Additionally, the natural alleles of OsERF103 are selected during the domestication of both indica and japonica rice varieties and exhibit significant geographic distribution. Collectively, our findings have unfurled a comprehensive mechanistic framework underlying the OsERF103-mediated cascade regulation of drought response. This discovery not only enhances our understanding of drought signaling but also presents a promising avenue for the genetic improvement of drought-tolerant rice cultivars.
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Affiliation(s)
- Lijia Yang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Liang Xu
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiazhuo Guo
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Aipeng Li
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Haoyue Qi
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Jiaxuan Wang
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
| | - Shiyong Song
- State Key Laboratory of Rice Biology and Breeding, Zhejiang Provincial Key Laboratory of Crop Genetic Resources, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, 310058, China
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Kashyap S, Agarwala N, Sunkar R. Understanding plant stress memory traits can provide a way for sustainable agriculture. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 340:111954. [PMID: 38092267 DOI: 10.1016/j.plantsci.2023.111954] [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: 07/26/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 01/01/2024]
Abstract
Being sessile, plants encounter various biotic and abiotic threats in their life cycle. To minimize the damages caused by such threats, plants have acquired sophisticated response mechanisms. One major such response includes memorizing the encountered stimuli in the form of a metabolite, hormone, protein, or epigenetic marks. All of these individually as well as together, facilitate effective transcriptional and post-transcriptional responses upon encountering the stress episode for a second time during the life cycle and in some instances even in the future generations. This review attempts to highlight the recent advances in the area of plant memory. A detailed understanding of plant memory has the potential to offer solutions for developing climate-resilient crops for sustainable agriculture.
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Affiliation(s)
- Sampurna Kashyap
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India
| | - Niraj Agarwala
- Department of Botany, Gauhati University, Gopinath Bordoloi Nagar, Jalukbari, Guwahati, Assam, 781014, India.
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK, United States
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Bhoite R, Han Y, Chaitanya AK, Varshney RK, Sharma DL. Genomic approaches to enhance adaptive plasticity to cope with soil constraints amidst climate change in wheat. THE PLANT GENOME 2024; 17:e20358. [PMID: 37265088 DOI: 10.1002/tpg2.20358] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/09/2023] [Accepted: 05/09/2023] [Indexed: 06/03/2023]
Abstract
Climate change is varying the availability of resources, soil physicochemical properties, and rainfall events, which collectively determines soil physical and chemical properties. Soil constraints-acidity (pH < 6), salinity (pH ≤ 8.5), sodicity, and dispersion (pH > 8.5)-are major causes of wheat yield loss in arid and semiarid cropping systems. To cope with changing environments, plants employ adaptive strategies such as phenotypic plasticity, a key multifaceted trait, to promote shifts in phenotypes. Adaptive strategies for constrained soils are complex, determined by key functional traits and genotype × environment × management interactions. The understanding of the molecular basis of stress tolerance is particularly challenging for plasticity traits. Advances in sequencing and high-throughput genomics technologies have identified functional alleles in gene-rich regions, haplotypes, candidate genes, mechanisms, and in silico gene expression profiles at various growth developmental stages. Our review focuses on favorable alleles for enhanced gene expression, quantitative trait loci, and epigenetic regulation of plant responses to soil constraints, including heavy metal stress and nutrient limitations. A strategy is then described for quantitative traits in wheat by investigating significant alleles and functional characterization of variants, followed by gene validation using advanced genomic tools, and marker development for molecular breeding and genome editing. Moreover, the review highlights the progress of gene editing in wheat, multiplex gene editing, and novel alleles for smart control of gene expression. Application of these advanced genomic technologies to enhance plasticity traits along with soil management practices will be an effective tool to build yield, stability, and sustainability on constrained soils in the face of climate change.
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Affiliation(s)
- Roopali Bhoite
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, Western Australia, Australia
| | - Yong Han
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Alamuru Krishna Chaitanya
- Grains Genetics Portfolio, University of Southern Queensland, Centre for Crop Health, Toowoomba, Queensland, Australia
| | - Rajeev K Varshney
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
| | - Darshan Lal Sharma
- Department of Primary Industries and Regional Development, South Perth, Western Australia, Australia
- Centre for Crop & Food Innovation, State Agricultural Biotechnology Centre, Murdoch University, Perth, Western Australia, Australia
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Soliman ERS. Preserving the adaptive salt stress response activity of a tissue-specific promoter with modulating activity. J Genet Eng Biotechnol 2024; 22:100354. [PMID: 38494266 PMCID: PMC10941203 DOI: 10.1016/j.jgeb.2024.100354] [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: 11/29/2023] [Accepted: 01/17/2024] [Indexed: 03/19/2024]
Abstract
BACKGROUND The Arabidopsis "Redox Responsive Transcription Factor1" (RRTF1) promoter is transiently activated by salt stress in roots over 6 h period, followed by an adaptation phase during which its activity returns to baseline levels, even if the salt stress is prolonged. This enables the short-term production of genes that, while initially advantageous to the plant, will have long-term detrimental effects if expressed at high levels indefinitely. RESULTS In this paper, we demonstrate that the RRTF1 promoter salt adaption response is a dominant feature of the promoter, that cannot be overwritten by a strong enhancer. While maintaining the transient activation profile of the RRTF1 promoter, linking it to the 35S enhancer results in a significant boost of salt stress induction in roots. CONCLUSION The RRTF1 promoter's enhanced and still adaptable activity could become a useful tool in plant biotechnology.
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Affiliation(s)
- Elham R S Soliman
- Cytogenetics and Molecular Genetics Unit, Botany and Microbiology Department, Faculty of Science, Helwan University, Helwan, Egypt.
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Rahman A, Yadav NS, Byeon B, Ilnytskyy Y, Kovalchuk I. Genomic and Epigenomic Changes in the Progeny of Cold-Stressed Arabidopsis thaliana Plants. Int J Mol Sci 2024; 25:2795. [PMID: 38474042 DOI: 10.3390/ijms25052795] [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: 12/20/2023] [Revised: 02/20/2024] [Accepted: 02/25/2024] [Indexed: 03/14/2024] Open
Abstract
Plants are continuously exposed to various environmental stresses. Because they can not escape stress, they have to develop mechanisms of remembering stress exposures somatically and passing it to the progeny. We studied the Arabidopsis thaliana ecotype Columbia plants exposed to cold stress for 25 continuous generations. Our study revealed that multigenerational exposure to cold stress resulted in the changes in the genome and epigenome (DNA methylation) across generations. Main changes in the progeny were due to the high frequency of genetic mutations rather than epigenetic changes; the difference was primarily in single nucleotide substitutions and deletions. The progeny of cold-stressed plants exhibited the higher rate of missense non-synonymous mutations as compared to the progeny of control plants. At the same time, epigenetic changes were more common in the CHG (C = cytosine, H = cytosine, adenine or thymine, G = guanine) and CHH contexts and favored hypomethylation. There was an increase in the frequency of C to T (thymine) transitions at the CHH positions in the progeny of cold stressed plants; because this type of mutations is often due to the deamination of the methylated cytosines, it can be hypothesized that environment-induced changes in methylation contribute to mutagenesis and may be to microevolution processes and that RNA-dependent DNA methylation plays a crucial role. Our work supports the existence of heritable stress response in plants and demonstrates that genetic changes prevail.
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Affiliation(s)
- Ashif Rahman
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Narendra Singh Yadav
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Boseon Byeon
- Biomedical and Health Informatics, Computer Science Department, State University of New York, 2 S Clinton St, Syracuse, NY 13202, USA
| | - Yaroslav Ilnytskyy
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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Zhang X, Li Z, Zhao C, Chen T, Wang X, Sun X, Zhao X, Lu X, Xu G. Leveraging Unidentified Metabolic Features for Key Pathway Discovery: Chemical Classification-driven Network Analysis in Untargeted Metabolomics. Anal Chem 2024; 96:3409-3418. [PMID: 38354311 DOI: 10.1021/acs.analchem.3c04591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024]
Abstract
Untargeted metabolomics using liquid chromatography-electrospray ionization-high-resolution tandem mass spectrometry (UPLC-ESI-MS/MS) provides comprehensive insights into the dynamic changes of metabolites in biological systems. However, numerous unidentified metabolic features limit its utilization. In this study, a novel approach, the Chemical Classification-driven Molecular Network (CCMN), was proposed to unveil key metabolic pathways by leveraging hidden information within unidentified metabolic features. The method was demonstrated by using the herbivore-induced metabolic response in corn silk as a case study. Untargeted metabolomics analysis using UPLC-MS/MS was performed on wild corn silk and two genetically modified lines (pre- and postinsect treatment). Global annotation initially identified 256 (ESI-) and 327 (ESI+) metabolites. MS/MS-based classifications predicted 1939 (ESI-) and 1985 (ESI+) metabolic features into the chemical classes. CCMNs were then constructed using metabolic features shared classes, which facilitated the structure- or class annotation for completely unknown metabolic features. Next, 844/713 significantly decreased and 1593/1378 increased metabolites in ESI-/ESI+ modes were defined in response to insect herbivory, respectively. Method validation on a spiked maize sample demonstrated an overall class prediction accuracy rate of 95.7%. Potential key pathways were prescreened by a hypergeometric test using both structure- and class-annotated differential metabolites. Subsequently, CCMN was used to deeply amend and uncover the pathway metabolites deeply. Finally, 8 key pathways were defined, including phenylpropanoid (C6-C3), flavonoid, octadecanoid, diterpenoid, lignan, steroid, amino acid/small peptide, and monoterpenoid. This study highlights the effectiveness of leveraging unidentified metabolic features. CCMN-based key pathway analysis reduced the bias in conventional pathway enrichment analysis. It provides valuable insights into complex biological processes.
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Affiliation(s)
- Xiuqiong Zhang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Zaifang Li
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Chunxia Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Tiantian Chen
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xinxin Wang
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xiaoshan Sun
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xinjie Zhao
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Xin Lu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
| | - Guowang Xu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, P. R. China
- University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Liaoning Province Key Laboratory of Metabolomics, Dalian 116023, P. R. China
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Zhang G, Ren N, Huang L, Shen T, Chen Y, Yang Y, Huang X, Jiang M. Basic helix-loop-helix transcription factor OsbHLH110 positively regulates abscisic acid biosynthesis and salinity tolerance in rice. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 207:108423. [PMID: 38373370 DOI: 10.1016/j.plaphy.2024.108423] [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: 09/21/2023] [Revised: 01/16/2024] [Accepted: 02/03/2024] [Indexed: 02/21/2024]
Abstract
Salinity is a significant abiotic stress factor affecting plant growth, consequently reducing crop yield. Abscisic acid (ABA), a well-known phytohormone, is crucial in conferring resistance to abiotic stress, thus, understanding the mechanisms underlying ABA biosynthesis is crucial. In rice (Oryza sativa L.), OsABA2, a short-chain dehydrogenase protein, has a pivotal role in modulating ABA biosynthesis and salt tolerance by undergoing phosphorylation at Ser197 through mitogen-activated protein kinase OsMPK1. However, the interaction between OsABA2 and other proteins in regulating ABA biosynthesis remains unclear. We employed OsABA2 as a bait in yeast two-hybrid screening: a basic helix-loop-helix transcription factor interacting with OsABA2, named OsbHLH110, was identified. Our results showed that firefly luciferase complementary imaging, pull-down, and co-immunoprecipitation assays validated the interaction between OsbHLH110 and OsABA2, affirming their interaction in vivo and in vitro. Moreover, the expression of OsbHLH110 significantly increases in response to salt and ABA treatments. Additionally, OsbHLH110 can directly bind to the G-box element in the OsABA2 promoter. This binding enhances luciferase activity controlled by the OsABA2 promoter, thereby increasing the expression of the OsABA2 gene and content of the OsABA2 protein, resulting in an increase in ABA content. OsABA2 enhanced the interaction between OsbHLH110 and OsABA2 promoter. This collaborative effect enhanced the regulation of ABA biosynthesis. Subsequent genetic analysis demonstrated that OsbHLH110 improved the tolerance of rice to salt stress.
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Affiliation(s)
- Gang Zhang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China; Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Ning Ren
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liping Huang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China; Internationgal Research Center for Enviromental Membrane Biology, Foshan University, Foshan, 528000, China.
| | - Tao Shen
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yao Chen
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yi Yang
- Shandong Key Laboratory of Biophysics, Institute of Biophysics, Dezhou University, Dezhou, 253023, China
| | - Xingxiu Huang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mingyi Jiang
- College of Life Sciences, National Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
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Shoaib N, Pan K, Mughal N, Raza A, Liu L, Zhang J, Wu X, Sun X, Zhang L, Pan Z. Potential of UV-B radiation in drought stress resilience: A multidimensional approach to plant adaptation and future implications. PLANT, CELL & ENVIRONMENT 2024; 47:387-407. [PMID: 38058262 DOI: 10.1111/pce.14774] [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: 08/16/2023] [Revised: 10/28/2023] [Accepted: 11/10/2023] [Indexed: 12/08/2023]
Abstract
The escalating impact of climate change and ultraviolet (UV) radiation is subjecting plants to unique combinations of UV-B and drought stress. These combined stressors could have additive, synergistic, or antagonistic effects, but the precise nature of these impacts remains uncertain, hampering our ability to predict plant adaptations approach towards stressors. Our analysis of various studies shows that UV-B or drought conditions detrimentally influence plant growth and health metrics by the enhanced generation of reactive oxygen species causing damage to lipids, proteins, carbohydrates and DNA. Further reducing biomass accumulation, plant height, photosynthetic efficiency, leaf area, and water transpiration, while enhancing stress-related symptoms. In response to UV-B radiation and drought stress, plants exhibit a notable up-regulation of specific acclimation-associated metabolites, including proline, flavonoids, anthocyanins, unsaturated fatty acids, and antioxidants. These metabolites play a pivotal role in conferring protection against environmental stresses. Their biosynthesis and functional roles are potentially modulated by signalling molecules such as hydrogen peroxide, abscisic acid, jasmonic acid, salicylic acid, and ethylene, all of which have associated genetic markers that further elucidate their involvement in stress response pathways. In comparison to single stress, the combination of UV-B and drought induces the plant defence responses and growth retardation which are less-than-additive. This sub-additive response, consistent across different study environments, suggests the possibility of a cross-resistance mechanism. Our outlines imply that the adverse effects of increased drought and UV-B could potentially be mitigated by cross-talk between UV-B and drought regimes utilizing a multidimensional approach. This crucial insight could contribute significantly to refining our understanding of stress tolerance in the face of ongoing global climate change.
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Affiliation(s)
- Noman Shoaib
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Kaiwen Pan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Nishbah Mughal
- Engineering Research Centre for Crop Strip Intercropping System, Key Laboratory of Crop Ecophysiology and Farming System in Southwest China (Ministry of Agriculture), College of Agronomy, Sichuan Agricultural University, Chengdu, China
| | - Ali Raza
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Liling Liu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Juan Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Xiaogang Wu
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Xiaoming Sun
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Lin Zhang
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Zhifen Pan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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Wang J, Liang Y, Gong Z, Zheng J, Li Z, Zhou G, Xu Y, Li X. Genomic and epigenomic insights into the mechanism of cold response in upland cotton (Gossypium hirsutum). PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108206. [PMID: 38029617 DOI: 10.1016/j.plaphy.2023.108206] [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: 08/16/2023] [Revised: 11/15/2023] [Accepted: 11/16/2023] [Indexed: 12/01/2023]
Abstract
Functional genome research, including gene transcriptional and posttranslational modifications of histones, can benefit greatly from a high-quality genome assembly. Histone modification plays a significant role in modulating the responses to abiotic stress in plants. However, there are limited reports on the involvement of dynamic changes in histone modification in cold stress response in upland cotton. In this study, the genome of an elite accession, YM11, with considerable cold stress tolerance was de novo assembled, which yielded a genome of 2343.06 Mb with a contig N50 of 88.96 Mb, and a total of 73,821 protein-coding gene models were annotated. Comparisons among YM11 and five Gossypium allopolyploid cotton assemblies highlighted a large amount of structural variations and presence/absence variations. We analyzed transcriptome and metabolome changes in YM11 seedlings subjected to cold stress. Using the CUT&Tag method, genome-wide H3K4me3 and H3K9ac modification patterns and effect of histone changes on gene expression were profiled during cold stress. Significant and consistently changing histone modifications and the gene expressions were screened, of which transcription factors (TFs) were highlighted. Our results suggest a positive correlation between the changes in H3K4me3, H3K9ac modifications and cold stress-responsive gene activation. This genome assembly and comprehensive analysis of genome-wide histone modifications and gene expression provide insights into the genomic variation and epigenetic responses to cold stress in upland cotton.
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Affiliation(s)
- Junduo Wang
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Yajun Liang
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Zhaolong Gong
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Juyun Zheng
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China
| | - Zhiqiang Li
- Adsen Biotechnology Co., Ltd., Urumqi, 830022, Xinjiang, China
| | - Guohui Zhou
- Adsen Biotechnology Co., Ltd., Urumqi, 830022, Xinjiang, China
| | - Yuhui Xu
- Adsen Biotechnology Co., Ltd., Urumqi, 830022, Xinjiang, China.
| | - Xueyuan Li
- Xinjiang Academy of Agricultural Science, Urumqi, 830091, Xinjiang, China.
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Yue C, Cao H, Zhang S, Shen G, Wu Z, Yuan L, Luo L, Zeng L. Multilayer omics landscape analyses reveal the regulatory responses of tea plants to drought stress. Int J Biol Macromol 2023; 253:126582. [PMID: 37652332 DOI: 10.1016/j.ijbiomac.2023.126582] [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: 06/21/2023] [Revised: 08/12/2023] [Accepted: 08/27/2023] [Indexed: 09/02/2023]
Abstract
Adverse environments, especially drought conditions, deeply influence plant development and growth in all aspects, and the yield and quality of tea plants are largely dependent on favorable growth conditions. Although tea plant responses to drought stress (DS) have been studied, a comprehensive multilayer epigenetic, transcriptomic, and proteomic investigation of how tea responds to DS is lacking. In this study, we generated DNA methylome, transcriptome, proteome, and phosphoproteome data to explore multiple regulatory landscapes in the tea plant response to DS. An integrated multiomics analysis revealed the response of tea plants to DS at multiple regulatory levels. Furthermore, a set of DS-responsive genes involved in photosynthesis, transmembrane transportation, phytohormone metabolism and signaling, secondary metabolite pathways, transcription factors, protein kinases, posttranslational and epigenetic modification, and other key stress-responsive genes were identified for further functional investigation. These results reveal the multilayer regulatory landscape of the tea plant response to DS and provide insight into the mechanisms of these DS responses.
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Affiliation(s)
- Chuan Yue
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China.
| | - Hongli Cao
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Shaorong Zhang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Gaojian Shen
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Zhijun Wu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Lianyu Yuan
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Liyong Luo
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China
| | - Liang Zeng
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City/College of Food Science, Southwest University, Chongqing, China.
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Kovalchuk I. Heritable responses to stress in plants. QUANTITATIVE PLANT BIOLOGY 2023; 4:e15. [PMID: 38156078 PMCID: PMC10753343 DOI: 10.1017/qpb.2023.14] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 10/18/2023] [Accepted: 10/19/2023] [Indexed: 12/30/2023]
Abstract
Most plants are adapted to their environments through generations of exposure to all elements. The adaptation process involves the best possible response to fluctuations in the environment based on the genetic and epigenetic make-up of the organism. Many plant species have the capacity to acclimate or adapt to certain stresses, allowing them to respond more efficiently, with fewer resources diverted from growth and development. However, plants can also acquire protection against stress across generations. Such a response is known as an intergenerational response to stress; typically, plants lose most of the tolerance in the subsequent generation when propagated without stress. Occasionally, the protection lasts for more than one generation after stress exposure and such a response is called transgenerational. In this review, we will summarize what is known about inter- and transgenerational responses to stress, focus on phenotypic and epigenetic events, their mechanisms and ecological and evolutionary meaning.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB, Canada
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48
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Julian R, Patrick RM, Li Y. Organ-specific characteristics govern the relationship between histone code dynamics and transcriptional reprogramming during nitrogen response in tomato. Commun Biol 2023; 6:1225. [PMID: 38044380 PMCID: PMC10694154 DOI: 10.1038/s42003-023-05601-8] [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: 06/16/2022] [Accepted: 11/17/2023] [Indexed: 12/05/2023] Open
Abstract
Environmental stimuli trigger rapid transcriptional reprogramming of gene networks. These responses occur in the context of the local chromatin landscape, but the contribution of organ-specific dynamic chromatin modifications in responses to external signals remains largely unexplored. We treated tomato seedlings with a supply of nitrate and measured the genome-wide changes of four histone marks, the permissive marks H3K27ac, H3K4me3, and H3K36me3 and repressive mark H3K27me3, in shoots and roots separately, as well as H3K9me2 in shoots. Dynamic and organ-specific histone acetylation and methylation were observed at functionally relevant gene loci. Integration of transcriptomic and epigenomic datasets generated from the same organ revealed largely syngenetic relations between changes in transcript levels and histone modifications, with the exception of H3K27me3 in shoots, where an increased level of this repressive mark is observed at genes activated by nitrate. Application of a machine learning approach revealed organ-specific rules regarding the importance of individual histone marks, as H3K36me3 is the most successful mark in predicting gene regulation events in shoots, while H3K4me3 is the strongest individual predictor in roots. Our integrated study substantiates a view that during plant environmental responses, the relationships between histone code dynamics and gene regulation are highly dependent on organ-specific contexts.
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Affiliation(s)
- Russell Julian
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ryan M Patrick
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA
| | - Ying Li
- Department of Horticulture & Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA.
- Center for Plant Biology, Purdue University, West Lafayette, IN, 47907, USA.
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Yung WS, Huang C, Li MW, Lam HM. Changes in epigenetic features in legumes under abiotic stresses. THE PLANT GENOME 2023; 16:e20237. [PMID: 35730915 DOI: 10.1002/tpg2.20237] [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: 03/28/2022] [Accepted: 05/16/2022] [Indexed: 06/15/2023]
Abstract
Legume crops are rich in nutritional value for human and livestock consumption. With global climate change, developing stress-resilient crops is crucial for ensuring global food security. Because of their nitrogen-fixing ability, legumes are also important for sustainable agriculture. Various abiotic stresses, such as salt, drought, and elevated temperatures, are known to adversely affect legume production. The responses of plants to abiotic stresses involve complicated cellular processes including stress hormone signaling, metabolic adjustments, and transcriptional regulations. Epigenetic mechanisms play a key role in regulating gene expressions at both transcriptional and posttranscriptional levels. Increasing evidence suggests the importance of epigenetic regulations of abiotic stress responses in legumes, and recent investigations have extended the scope to the epigenomic level using next-generation sequencing technologies. In this review, the current knowledge on the involvement of epigenetic features, including DNA methylation, histone modification, and noncoding RNAs, in abiotic stress responses in legumes is summarized and discussed. Since most of the available information focuses on a single aspect of these epigenetic features, integrative analyses involving omics data in multiple layers are needed for a better understanding of the dynamic chromatin statuses and their roles in transcriptional regulation. The inheritability of epigenetic modifications should also be assessed in future studies for their applications in improving stress tolerance in legumes through the stable epigenetic optimization of gene expressions.
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Affiliation(s)
- Wai-Shing Yung
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Cheng Huang
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
- College of Agronomy, Hunan Agricultural Univ., Changsha, 410128, P.R. China
| | - Man-Wah Li
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
| | - Hon-Ming Lam
- School of Life Sciences and Center for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese Univ. of Hong Kong, Shatin, Hong Kong SAR, P.R. China
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Zhao S, Li Y, Chen G, Wang X, Chen N, Wu X. Genome-wide chromatin interaction profiling reveals a vital role of super-enhancers and rearrangements in host enhancer contacts during BmNPV infection. Genome Res 2023; 33:1958-1974. [PMID: 37871969 PMCID: PMC10760458 DOI: 10.1101/gr.277931.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 10/14/2023] [Indexed: 10/25/2023]
Abstract
As influential regulatory elements in the genome, enhancers control gene expression under specific cellular conditions, and such connections are dynamic under different conditions. However, because of the lack of a genome-wide enhancer-gene connection map, the roles and regulatory pattern of enhancers were poorly investigated in insects, and the dynamic changes of enhancer contacts and functions under different conditions remain elusive. Here, combining Hi-C, ATAC-seq, and H3K27ac ChIP-seq data, we generate the genome-wide enhancer-gene map of silkworm and identify super-enhancers with a role in regulating the expression of vital genes related to cell state maintenance through a sophisticated interaction network. Additionally, a radical attenuation of chromatin interactions is found after infection of Bombyx mori nucleopolyhedrovirus (BmNPV), the main pathogen of silkworm, which directly rearranges the enhancer contacts. Such a rearrangement disturbs the intrinsic enhancer-gene connections in several antiviral genes, resulting in reduced expression of these genes, which accelerates viral infection. Overall, our results reveal the regulatory role of super-enhancers and shed new light on the mechanisms and dynamic changes of the genome-wide enhancer regulatory network.
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Affiliation(s)
- Shudi Zhao
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Yuedong Li
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Guanping Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Xingyang Wang
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Nan Chen
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
| | - Xiaofeng Wu
- College of Animal Sciences, Zhejiang University, Hangzhou 310058, China;
- Key Laboratory of Silkworm and Bee Resource Utilization and Innovation of Zhejiang Province, Hangzhou 310058, China
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