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Ma L, Xing L, Li Z, Jiang D. Epigenetic control of plant abiotic stress responses. J Genet Genomics 2024:S1673-8527(24)00246-7. [PMID: 39322116 DOI: 10.1016/j.jgg.2024.09.008] [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: 08/15/2024] [Revised: 09/14/2024] [Accepted: 09/16/2024] [Indexed: 09/27/2024]
Abstract
On top of genetic information, organisms have evolved complex and sophisticated epigenetic regulation to adjust gene expression in response to developmental and environmental signals. Key epigenetic mechanisms include DNA methylation, histone modifications and variants, chromatin remodeling, and chemical modifications of RNAs. Epigenetic control of environmental responses is particularly important for plants, which are sessile and unable to move away from adverse environments. Besides enabling plants to rapidly respond to environmental stresses, some stress-induced epigenetic changes can be maintained, providing plants with a pre-adapted state to recurring stresses. Understanding these epigenetic mechanisms offers valuable insights for developing crop varieties with enhanced stress tolerance. Here, we focus on abiotic stresses and summarize recent progress in characterizing stress-induced epigenetic changes and their regulatory mechanisms and roles in plant abiotic stress resistance.
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Affiliation(s)
- Lijun Ma
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237 China
| | - Lihe Xing
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zicong Li
- Ministry of Education Key Laboratory of Plant Development and Environmental Adaption Biology, School of Life Sciences, Shandong University, Qingdao, Shandong 266237 China
| | - Danhua Jiang
- Key Laboratory of Seed Innovation, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore.
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2
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Suppiyar V, Bonthala VS, Shrestha A, Krey S, Stich B. Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.). BMC Genomics 2024; 25:442. [PMID: 38702658 PMCID: PMC11069243 DOI: 10.1186/s12864-024-10367-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.
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Affiliation(s)
- Vithusan Suppiyar
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Venkata Suresh Bonthala
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany.
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany.
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Stephanie Krey
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
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3
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Nishio H, Kawakatsu T, Yamaguchi N. Beyond heat waves: Unlocking epigenetic heat stress memory in Arabidopsis. PLANT PHYSIOLOGY 2024; 194:1934-1951. [PMID: 37878744 DOI: 10.1093/plphys/kiad558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/25/2023] [Accepted: 10/05/2023] [Indexed: 10/27/2023]
Abstract
Plants remember their exposure to environmental changes and respond more effectively the next time they encounter a similar change by flexibly altering gene expression. Epigenetic mechanisms play a crucial role in establishing such memory of environmental changes and fine-tuning gene expression. With the recent advancements in biochemistry and sequencing technologies, it has become possible to characterize the dynamics of epigenetic changes on scales ranging from short term (minutes) to long term (generations). Here, our main focus is on describing the current understanding of the temporal regulation of histone modifications and chromatin changes during exposure to short-term recurring high temperatures and reevaluating them in the context of natural environments. Investigations of the dynamics of histone modifications and chromatin structural changes in Arabidopsis after repeated exposure to heat at short intervals have revealed the detailed molecular mechanisms of short-term heat stress memory, which include histone modification enzymes, chromatin remodelers, and key transcription factors. In addition, we summarize the spatial regulation of heat responses. Based on the natural temperature patterns during summer, we discuss how plants cope with recurring heat stress occurring at various time intervals by utilizing 2 distinct types of heat stress memory mechanisms. We also explore future research directions to provide a more precise understanding of the epigenetic regulation of heat stress memory.
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Affiliation(s)
- Haruki Nishio
- Data Science and AI Innovation Research Promotion Center, Shiga University, Shiga 522-8522, Japan
- Center for Ecological Research, Kyoto University, Shiga 520-2113, Japan
| | - Taiji Kawakatsu
- Institute of Agrobiological Sciences, National Agriculture and Food Research Organization, Tsukuba, Ibaraki 305-8602, Japan
| | - Nobutoshi Yamaguchi
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5, Takayama, Ikoma, Nara 630-0192, Japan
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Şimşek Ö, Isak MA, Dönmez D, Dalda Şekerci A, İzgü T, Kaçar YA. Advanced Biotechnological Interventions in Mitigating Drought Stress in Plants. PLANTS (BASEL, SWITZERLAND) 2024; 13:717. [PMID: 38475564 DOI: 10.3390/plants13050717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/13/2024] [Revised: 02/20/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024]
Abstract
This comprehensive article critically analyzes the advanced biotechnological strategies to mitigate plant drought stress. It encompasses an in-depth exploration of the latest developments in plant genomics, proteomics, and metabolomics, shedding light on the complex molecular mechanisms that plants employ to combat drought stress. The study also emphasizes the significant advancements in genetic engineering techniques, particularly CRISPR-Cas9 genome editing, which have revolutionized the creation of drought-resistant crop varieties. Furthermore, the article explores microbial biotechnology's pivotal role, such as plant growth-promoting rhizobacteria (PGPR) and mycorrhizae, in enhancing plant resilience against drought conditions. The integration of these cutting-edge biotechnological interventions with traditional breeding methods is presented as a holistic approach for fortifying crops against drought stress. This integration addresses immediate agricultural needs and contributes significantly to sustainable agriculture, ensuring food security in the face of escalating climate change challenges.
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Affiliation(s)
- Özhan Şimşek
- Horticulture Department, Agriculture Faculty, Erciyes University, Kayseri 38030, Türkiye
| | - Musab A Isak
- Agricultural Sciences and Technology Department, Graduate School of Natural and Applied Sciences, Erciyes University, Kayseri 38030, Türkiye
| | - Dicle Dönmez
- Biotechnology Research and Application Center, Çukurova University, Adana 01330, Türkiye
| | - Akife Dalda Şekerci
- Horticulture Department, Agriculture Faculty, Erciyes University, Kayseri 38030, Türkiye
| | - Tolga İzgü
- National Research Council of Italy (CNR), Institute of BioEconomy, 50019 Florence, Italy
| | - Yıldız Aka Kaçar
- Horticulture Department, Agriculture Faculty, Çukurova University, Adana 01330, Türkiye
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5
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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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Zhang B, Wang Z, Dai X, Gao J, Zhao J, Ma R, Chen Y, Sun Y, Ma H, Li S, Zhou C, Wang JP, Li W. A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in Populus trichocarpa. THE NEW PHYTOLOGIST 2024; 241:1950-1972. [PMID: 38095236 DOI: 10.1111/nph.19481] [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] [Accepted: 11/22/2023] [Indexed: 02/09/2024]
Abstract
Histone H3 lysine-4 trimethylation (H3K4me3) activating drought-responsive genes in plants for drought adaptation has long been established, but the underlying regulatory mechanisms are unknown. Here, using yeast two-hybrid, bimolecular fluorescence complementation, biochemical analyses, transient and CRISPR-mediated transgenesis in Populus trichocarpa, we unveiled in this adaptation a regulatory interplay between chromatin regulation and gene transactivation mediated by an epigenetic determinant, a PtrSDG2-1-PtrCOMPASS (complex proteins associated with Set1)-like H3K4me3 complex, PtrSDG2-1-PtrWDR5a-1-PtrRbBP5-1-PtrAsh2-2 (PtrSWRA). Under drought conditions, a transcription factor PtrAREB1-2 interacts with PtrSWRA, forming a PtrSWRA-PtrAREB1-2 pentamer, to recruit PtrSWRA to specific promoter elements of drought-tolerant genes, such as PtrHox2, PtrHox46, and PtrHox52, for depositing H3K4me3 to promote and maintain activated state of such genes for tolerance. CRISPR-edited defects in the pentamer impaired drought tolerance and elevated expression of PtrHox2, PtrHox46, or PtrHox52 improved the tolerance as well as growth in P. trichocarpa. Our findings revealed the identity of the underlying H3K4 trimethyltransferase and its interactive arrangement with the COMPASS for catalysis specificity and efficiency. Furthermore, our study uncovered how the H3K4 trimethyltransferase-COMPASS complex is recruited to the effector genes for elevating H3K4me3 marks for improved drought tolerance and growth/biomass production in plants.
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Affiliation(s)
- Baofeng Zhang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Zhuwen Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinghui Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jinfeng Zhao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Rong Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yanjie Chen
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Yi Sun
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Hongyan Ma
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
| | - Jack P Wang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, 150040, China
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7
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Kumar V, Singh B, Kumar Singh R, Sharma N, Muthamilarasan M, Sawant SV, Prasad M. Histone deacetylase 9 interacts with SiHAT3.1 and SiHDA19 to repress dehydration responses through H3K9 deacetylation in foxtail millet. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1098-1111. [PMID: 37889853 DOI: 10.1093/jxb/erad425] [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: 09/08/2023] [Accepted: 10/26/2023] [Indexed: 10/29/2023]
Abstract
Climate change inflicts several stresses on plants, of which dehydration stress severely affects growth and productivity. C4 plants possess better adaptability to dehydration stress; however, the role of epigenetic modifications underlying this trait is unclear. In particular, the molecular links between histone modifiers and their regulation remain elusive. In this study, genome-wide H3K9 acetylation (H3K9ac) enrichment using ChIP-sequencing was performed in two foxtail millet cultivars with contrasting dehydration tolerances (IC403579, cv. IC4-tolerant, and IC480117, cv. IC41-sensitive). It revealed that a histone deacetylase, SiHDA9, was significantly up-regulated in the sensitive cultivar. Further characterization indicated that SiHDA9 interacts with SiHAT3.1 and SiHDA19 to form a repressor complex. SiHDA9 might be recruited through the SiHAT3.1 recognition sequence onto the upstream of dehydration-responsive genes to decrease H3K9 acetylation levels. The silencing of SiHDA9 resulted in the up-regulation of crucial genes, namely, SiRAB18, SiRAP2.4, SiP5CS2, SiRD22, SiPIP1;4, and SiLHCB2.3, which imparted dehydration tolerance in the sensitive cultivar (IC41). Overall, the study provides mechanistic insights into SiHDA9-mediated regulation of dehydration stress response in foxtail millet.
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Affiliation(s)
- Verandra Kumar
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Babita Singh
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Roshan Kumar Singh
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | - Namisha Sharma
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
| | | | - Samir V Sawant
- Plant Molecular Biology and Biotechnology Division, CSIR-National Botanical Research Institute, Rana Pratap Marg, Lucknow 226001, Uttar Pradesh, India
| | - Manoj Prasad
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, Delhi, India
- Department of Plant Sciences, School of Life Sciences, University of Hyderabad, Hyderabad 500046, Telangana, India
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8
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Crawford T, Siebler L, Sulkowska A, Nowack B, Jiang L, Pan Y, Lämke J, Kappel C, Bäurle I. The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis. EMBO J 2024; 43:437-461. [PMID: 38228917 PMCID: PMC10897291 DOI: 10.1038/s44318-023-00024-x] [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: 05/26/2023] [Revised: 12/12/2023] [Accepted: 12/14/2023] [Indexed: 01/18/2024] Open
Abstract
Plants are often exposed to recurring adverse environmental conditions in the wild. Acclimation to high temperatures entails transcriptional responses, which prime plants to better withstand subsequent stress events. Heat stress (HS)-induced transcriptional memory results in more efficient re-induction of transcription upon recurrence of heat stress. Here, we identified CDK8 and MED12, two subunits of the kinase module of the transcription co-regulator complex, Mediator, as promoters of heat stress memory and associated histone modifications in Arabidopsis. CDK8 is recruited to heat-stress memory genes by HEAT SHOCK TRANSCRIPTION FACTOR A2 (HSFA2). Like HSFA2, CDK8 is largely dispensable for the initial gene induction upon HS, and its function in transcriptional memory is thus independent of primary gene activation. In addition to the promoter and transcriptional start region of target genes, CDK8 also binds their 3'-region, where it may promote elongation, termination, or rapid re-initiation of RNA polymerase II (Pol II) complexes during transcriptional memory bursts. Our work presents a complex role for the Mediator kinase module during transcriptional memory in multicellular eukaryotes, through interactions with transcription factors, chromatin modifications, and promotion of Pol II efficiency.
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Affiliation(s)
- Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Lara Siebler
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | | | - Bryan Nowack
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Yufeng Pan
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
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Zhang F, Ma J, Liu Y, Fang J, Wei S, Xie R, Han P, Zhao X, Bo S, Lu Z. A Multi-Omics Analysis Revealed the Diversity of the MYB Transcription Factor Family's Evolution and Drought Resistance Pathways. Life (Basel) 2024; 14:141. [PMID: 38255756 PMCID: PMC10820167 DOI: 10.3390/life14010141] [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: 11/27/2023] [Revised: 01/15/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024] Open
Abstract
The MYB transcription factor family can regulate biological processes such as ABA signal transduction to cope with drought stress, but its evolutionary mechanism and the diverse pathways of response to drought stress in different species are rarely reported. In this study, a total of 4791 MYB family members were identified in 908,757 amino acid sequences from 12 model plants or crops using bioinformatics methods. It was observed that the number of MYB family members had a linear relationship with the chromosome ploidy of species. A phylogenetic analysis showed that the MYB family members evolved in subfamily clusters. In response to drought stress, the pathways of MYB transcription factor families exhibited species-specific diversity, with closely related species demonstrating a higher resemblance. This study provides abundant references for drought resistance research and the breeding of wheat, soybean, and other plants.
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Affiliation(s)
- Fan Zhang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Jie Ma
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Ying Liu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Jing Fang
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Shuli Wei
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Rui Xie
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Pingan Han
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
| | - Xiaoqing Zhao
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
| | - Suling Bo
- College of Computer Information, Inner Mongolia Medical University, Hohhot 010110, China
| | - Zhanyuan Lu
- Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, China; (F.Z.); (J.M.); (Y.L.); (J.F.); (S.W.); (R.X.); (P.H.)
- Key Laboratory of Black Soil Protection and Utilization, Ministry of Agriculture and Rural Areas, Hohhot 010031, China
- Inner Mongolia Key Laboratory of Degradation Farmland Ecological Remediation and Pollution Control, Hohhot 010031, China
- Inner Mongolia Conservation Tillage Engineering Technology Research Center, Hohhot 010031, China
- School of Life Science, Inner Mongolia University, Hohhot 010030, China
- Key Laboratory of Herbage & Endemic Crop Biotechnology, Ministry of Education, Hohhot 010030, China
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10
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Tian Z, Li K, Sun Y, Chen B, Pan Z, Wang Z, Pang B, He S, Miao Y, Du X. Physiological and transcriptional analyses reveal formation of memory under recurring drought stresses in seedlings of cotton (Gossypium hirsutum). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 338:111920. [PMID: 37944705 DOI: 10.1016/j.plantsci.2023.111920] [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: 08/14/2023] [Revised: 10/03/2023] [Accepted: 11/06/2023] [Indexed: 11/12/2023]
Abstract
Plants are frequently subjected to a range of environmental stresses, including drought, salinity, cold, pathogens, and herbivore attacks. To survive in such conditions, plants have evolved a novel adaptive mechanism known as 'stress memory'. The formation of stress memories necessitates coordinated responses at the cellular, genetic/genomic, and epigenetic levels, involving altered physiological responses, gene activation, hyper-induction and chromatin modification. Cotton (Gossypium spp.) is an important economic crop with numerous applications and high economic value. In this study, we establish G. hirsutum drought memory following cycles of mild drought and re-watering treatments and analyzed memory gene expression patterns. Our findings reveal the physiological, biochemical, and molecular mechanisms underlying drought stress memory formation in G. hirsutum. Specifically, H3K4me3, a histone modification, plays a crucial role in regulating [+ /+ ] transcriptional memory. Moreover, we investigated the intergenerational inheritance of drought stress memory in G. hirsutum. Collectively, our data provides theoretical guidance for cotton breeding.
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Affiliation(s)
- Zailong Tian
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China
| | - Kun Li
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China
| | - Yaru Sun
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China
| | - Baojun Chen
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhaoe Pan
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhenzhen Wang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Baoyin Pang
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Shoupu He
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
| | - Yuchen Miao
- State Key Laboratory of Cotton Biology, Henan Joint International Laboratory for Crop Multi-Omics Research, School of Life Sciences, Henan University, Jinming Road, Kaifeng 475004, China.
| | - Xiongming Du
- National Key Laboratory of Cotton Bio-breeding and Integrated Utilization, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya, Hainan 572024, China.
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11
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Ivanova T, Dincheva I, Badjakov I, Iantcheva A. Transcriptional and Metabolic Profiling of Arabidopsis thaliana Transgenic Plants Expressing Histone Acetyltransferase HAC1 upon the Application of Abiotic Stress-Salt and Low Temperature. Metabolites 2023; 13:994. [PMID: 37755274 PMCID: PMC10536276 DOI: 10.3390/metabo13090994] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Revised: 09/02/2023] [Accepted: 09/04/2023] [Indexed: 09/28/2023] Open
Abstract
Augmented knowledge of plant responses upon application of stress could help improve our understanding of plant tolerance under abiotic stress conditions. Histone acetylation plays an important role in gene expression regulation during plant growth and development and in the response of plants to abiotic stress. The current study examines the level of transcripts and free metabolite content in transgenic Arabidopsis thaliana plants expressing a gene encoding histone acetyltransferase from Medicago truncatula (MtHAC1) after its heterologous expression. Stable transgenic plants with HAC1 gain and loss of function were constructed, and their T5 generation was used. Transgenic lines with HAC1-modified expression showed a deviation in root growth dynamics and leaf area compared to the wild-type control. Transcriptional profiles were evaluated after the application of salinity stress caused by 150 mM NaCl at four different time points (0, 24, 48, and 72 h) in treated and non-treated transgenic and control plants. The content and quantity of free metabolites-amino acids, mono- and dicarbohydrates, organic acids, and fatty acids-were assessed at time points 0 h and 72 h in treated and non-treated transgenic and control plants. The obtained transcript profiles of HAC1 in transgenic plants with modified expression and control were assessed after application of cold stress (low temperature, 4 °C).
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Affiliation(s)
| | | | | | - Anelia Iantcheva
- AgroBioInstitute, Agricultural Academy, Blvd. Dragan Tzankov 8, 1164 Sofia, Bulgaria; (T.I.); (I.D.); (I.B.)
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12
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Ost C, Cao HX, Nguyen TL, Himmelbach A, Mascher M, Stein N, Humbeck K. Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes. Int J Mol Sci 2023; 24:12065. [PMID: 37569441 PMCID: PMC10418636 DOI: 10.3390/ijms241512065] [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: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.
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Affiliation(s)
- Charlotte Ost
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Thuy Linh Nguyen
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Göttingen, Germany
| | - Klaus Humbeck
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
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13
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Kappel C, Friedrich T, Oberkofler V, Jiang L, Crawford T, Lenhard M, Bäurle I. Genomic and epigenomic determinants of heat stress-induced transcriptional memory in Arabidopsis. Genome Biol 2023; 24:129. [PMID: 37254211 DOI: 10.1186/s13059-023-02970-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 05/11/2023] [Indexed: 06/01/2023] Open
Abstract
BACKGROUND Transcriptional regulation is a key aspect of environmental stress responses. Heat stress induces transcriptional memory, i.e., sustained induction or enhanced re-induction of transcription, that allows plants to respond more efficiently to a recurrent HS. In light of more frequent temperature extremes due to climate change, improving heat tolerance in crop plants is an important breeding goal. However, not all heat stress-inducible genes show transcriptional memory, and it is unclear what distinguishes memory from non-memory genes. To address this issue and understand the genome and epigenome architecture of transcriptional memory after heat stress, we identify the global target genes of two key memory heat shock transcription factors, HSFA2 and HSFA3, using time course ChIP-seq. RESULTS HSFA2 and HSFA3 show near identical binding patterns. In vitro and in vivo binding strength is highly correlated, indicating the importance of DNA sequence elements. In particular, genes with transcriptional memory are strongly enriched for a tripartite heat shock element, and are hallmarked by several features: low expression levels in the absence of heat stress, accessible chromatin environment, and heat stress-induced enrichment of H3K4 trimethylation. These results are confirmed by an orthogonal transcriptomic data set using both de novo clustering and an established definition of memory genes. CONCLUSIONS Our findings provide an integrated view of HSF-dependent transcriptional memory and shed light on its sequence and chromatin determinants, enabling the prediction and engineering of genes with transcriptional memory behavior.
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Affiliation(s)
- Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Thomas Friedrich
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Vicky Oberkofler
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Li Jiang
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Tim Crawford
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Michael Lenhard
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, 14476, Potsdam, Germany.
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Kudo T, To TK, Kim JM. Simple and universal function of acetic acid to overcome the drought crisis. STRESS BIOLOGY 2023; 3:15. [PMID: 37676400 PMCID: PMC10441936 DOI: 10.1007/s44154-023-00094-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 05/16/2023] [Indexed: 09/08/2023]
Abstract
Acetic acid is a simple and universal compound found in various organisms. Recently, acetic acid was found to play an essential role in conferring tolerance to water deficit stress in plants. This novel mechanism of drought stress tolerance mediated by acetic acid via networks involving phytohormones, genes, and chromatin regulation has great potential for solving the global food crisis and preventing desertification caused by global warming. We highlight the functions of acetic acid in conferring tolerance to water deficit stress.
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Affiliation(s)
| | - Taiko Kim To
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan
| | - Jong-Myong Kim
- Ac-Planta Inc, Tokyo, Japan
- Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan
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15
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Kumar S, Seem K, Mohapatra T. Biochemical and Epigenetic Modulations under Drought: Remembering the Stress Tolerance Mechanism in Rice. Life (Basel) 2023; 13:life13051156. [PMID: 37240801 DOI: 10.3390/life13051156] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2023] [Revised: 05/07/2023] [Accepted: 05/09/2023] [Indexed: 05/28/2023] Open
Abstract
A plant, being a sessile organism, needs to modulate biochemical, physiological, and molecular responses to the environment in a quick and efficient manner to be protected. Drought stress is a frequently occurring abiotic stress that severely affects plant growth, development, and productivity. Short- and long-term memories are well-known phenomena in animals; however, the existence of such remembrance in plants is still being discovered. In this investigation, different rice genotypes were imposed with drought stress just before flowering and the plants were re-watered for recovery from the stress. Seeds collected from the stress-treated (stress-primed) plants were used to raise plants for the subsequent two generations under a similar experimental setup. Modulations in physio-biochemical (chlorophyll, total phenolics and proline contents, antioxidant potential, lipid peroxidation) and epigenetic [5-methylcytosine (5-mC)] parameters were analyzed in the leaves of the plants grown under stress as well as after recovery. There was an increase in proline (>25%) and total phenolic (>19%) contents, antioxidant activity (>7%), and genome-wide 5-mC level (>56%), while a decrease (>9%) in chlorophyll content was recorded to be significant under the stress. Interestingly, a part of the increased proline content, total phenolics content, antioxidant activity, and 5-mC level was retained even after the withdrawal of the stress. Moreover, the increased levels of biochemical and epigenetic parameters were observed to be transmitted/inherited to the subsequent generations. These might help in developing stress-tolerant crops and improving crop productivity under the changing global climate for sustainable food production and global food security.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi 110012, India
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16
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Guo Y, Tan Y, Qu M, Hong K, Zeng L, Wang L, Zhuang C, Qian Q, Hu J, Xiong G. OsWR2 recruits HDA704 to regulate the deacetylation of H4K8ac in the promoter of OsABI5 in response to drought stress. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2023. [PMID: 36920174 DOI: 10.1111/jipb.13481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/13/2023] [Indexed: 06/18/2023]
Abstract
Drought stress is a major environmental factor that limits the growth, development, and yield of rice (Oryza sativa L.). Histone deacetylases (HDACs) are involved in the regulation of drought stress responses. HDA704 is an RPD3/HDA1 class HDAC that mediates the deacetylation of H4K8 (lysine 8 of histone H4) for drought tolerance in rice. In this study, we show that plants overexpressing HDA704 (HDA704-OE) are resistant to drought stress and sensitive to abscisic acid (ABA), whereas HDA704 knockout mutant (hda704) plants displayed decreased drought tolerance and ABA sensitivity. Transcriptome analysis revealed that HDA704 regulates the expression of ABA-related genes in response to drought stress. Moreover, HDA704 was recruited by a drought-resistant transcription factor, WAX SYNTHESIS REGULATORY 2 (OsWR2), and co-regulated the expression of the ABA biosynthesis genes NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3), NCED4, and NCED5 under drought stress. HDA704 also repressed the expression of ABA-INSENSITIVE 5 (OsABI5) and DWARF AND SMALL SEED 1 (OsDSS1) by regulating H4K8ac levels in the promoter regions in response to polyethylene glycol 6000 treatment. In agreement, the loss of OsABI5 function increased resistance to dehydration stress in rice. Our results demonstrate that HDA704 is a positive regulator of the drought stress response and offers avenues for improving drought resistance in rice.
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Affiliation(s)
- Yalu Guo
- Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, 518120, China
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Yiqing Tan
- Plant Phenomics Research Center, Academy of Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Minghao Qu
- College of Animal Science and Technology, Southwest University, Chongqing, 402460, China
| | - Kai Hong
- Plant Phenomics Research Center, Academy of Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
| | - Longjun Zeng
- Yichun Academy of Sciences, Yinchun, 336000, China
| | - Lei Wang
- Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang, 050022, China
| | - Chuxiong Zhuang
- Guangdong Laboratory for Lingnan Modern Agriculture, State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, College of Life Sciences, South China Agricultural University, Guangzhou, 510642, China
| | - Qian Qian
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Jiang Hu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, 310000, China
| | - Guosheng Xiong
- Plant Phenomics Research Center, Academy of Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, 210095, China
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Kambona CM, Koua PA, Léon J, Ballvora A. Stress memory and its regulation in plants experiencing recurrent drought conditions. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2023; 136:26. [PMID: 36788199 PMCID: PMC9928933 DOI: 10.1007/s00122-023-04313-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
Developing stress-tolerant plants continues to be the goal of breeders due to their realized yields and stability. Plant responses to drought have been studied in many different plant species, but the occurrence of stress memory as well as the potential mechanisms for memory regulation is not yet well described. It has been observed that plants hold on to past events in a way that adjusts their response to new challenges without altering their genetic constitution. This ability could enable training of plants to face future challenges that increase in frequency and intensity. A better understanding of stress memory-associated mechanisms leading to alteration in gene expression and how they link to physiological, biochemical, metabolomic and morphological changes would initiate diverse opportunities to breed stress-tolerant genotypes through molecular breeding or biotechnological approaches. In this perspective, this review discusses different stress memory types and gives an overall view using general examples. Further, focusing on drought stress, we demonstrate coordinated changes in epigenetic and molecular gene expression control mechanisms, the associated transcription memory responses at the genome level and integrated biochemical and physiological responses at cellular level following recurrent drought stress exposures. Indeed, coordinated epigenetic and molecular alterations of expression of specific gene networks link to biochemical and physiological responses that facilitate acclimation and survival of an individual plant during repeated stress.
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Affiliation(s)
- Carolyn Mukiri Kambona
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
| | - Patrice Ahossi Koua
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
- Deutsche Saatveredelung AG, Thüler Str. 30, 33154, Salzkotten-Thüle, Germany
| | - Jens Léon
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany
- Field Lab Campus Klein-Altendorf, Rheinische Friedrich-Wilhelms-University, Bonn, Germany
| | - Agim Ballvora
- Department of Plant Breeding, Institut Für Nutzpflanzenwissenschaften Und Ressourcenschutz (INRES), RheinischeFriedrich-Wilhelms-University, Bonn, Germany.
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18
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Gong Y, Li Y, Liu D, Jiang L, Liang H, Wu Y, Wang F, Yang J. Analysis of lysine acetylation in tomato spot wilt virus infection in Nicotiana benthamiana. Front Microbiol 2023; 14:1046163. [PMID: 36819054 PMCID: PMC9935083 DOI: 10.3389/fmicb.2023.1046163] [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: 09/16/2022] [Accepted: 01/16/2023] [Indexed: 02/05/2023] Open
Abstract
Introduction Kac is a model for all acylation modification studies. Kac plays a critical role in eukaryotes and prokaryotes. It is mainly involved in six major biological functions: gene expression, signal transduction, cell development, protein conversion, metabolism, and metabolite transport. Method We investigated and compared the acetylation modification of proteins in healthy and tomato spot wilt virus (TSWV)-infected Nicotiana benthamiana leaves. Result We identified 3,418 acetylated lysine sites on 1962 proteins acetylation of proteins in the TSWV-infected and control groups were compared; it was observed that 408 sites on 294 proteins were upregulated and 284 sites on 219 proteins (involved in pentose phosphate, photosynthesis, and carbon fixation in photosynthesis) were downregulated after the infection. Overall, 35 conserved motifs were identified, of which xxxkxxxxx_K_ Rxxxxxxxxx represented 1,334 (31.63%) enrichment motifs and was the most common combination. Bioinformatic analysis revealed that most of the proteins with Kac sites were located in the chloroplast and cytoplasm. They were involved in biological processes, such as cellular and metabolic processes. Discussion In conclusion, our results revealed that Kac may participate in the regulation of TSWV infection in N. benthamiana.
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Affiliation(s)
- Yanwei Gong
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Ying Li
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China
| | - Dongyang Liu
- Liangshan State Company of Sichuan Province Tobacco Company, Mile, China
| | - Lianqiang Jiang
- Liangshan State Company of Sichuan Province Tobacco Company, Mile, China
| | - Hui Liang
- Liangshan State Company of Sichuan Province Tobacco Company, Mile, China
| | - Yuanhua Wu
- College of Plant Protection, Shenyang Agricultural University, Shenyang, China
| | - Fenglong Wang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China,*Correspondence: Fenglong Wang, ✉
| | - Jinguang Yang
- Key Laboratory of Tobacco Pest Monitoring, Controlling and Integrated Management, Tobacco Research Institute of Chinese Academy of Agricultural Sciences, Qingdao, China,Jinguang Yang, ✉
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Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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20
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Zhao B, Shao Z, Wang L, Zhang F, Chakravarty D, Zong W, Dong J, Song L, Qiao H. MYB44-ENAP1/2 restricts HDT4 to regulate drought tolerance in Arabidopsis. PLoS Genet 2022; 18:e1010473. [PMID: 36413574 PMCID: PMC9681084 DOI: 10.1371/journal.pgen.1010473] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 10/11/2022] [Indexed: 11/23/2022] Open
Abstract
Histone acetylation has been shown to involve in stress responses. However, the detailed molecular mechanisms that how histone deacetylases and transcription factors function in drought stress response remain to be understood. In this research, we show that ENAP1 and ENAP2 are positive regulators of drought tolerance in plants, and the enap1enap2 double mutant is more sensitive to drought stress. Both ENAP1 and ENAP2 interact with MYB44, a transcription factor that interacts with histone deacetylase HDT4. Genetics data show that myb44 null mutation enhances the sensitivity of enap1enap2 to drought stress. Whereas, HDT4 negatively regulates plant drought response, the hdt4 mutant represses enap1enap2myb44 drought sensitive phenotype. In the normal condition, ENAP1/2 and MYB44 counteract the HDT4 function for the regulation of H3K27ac. Upon drought stress, the accumulation of MYB44 and reduction of HDT4 leads to the enrichment of H3K27ac and the activation of target gene expression. Overall, this research provides a novel molecular mechanism by which ENAP1, ENAP2 and MYB44 form a complex to restrict the function of HDT4 in the normal condition; under drought condition, accumulated MYB44 and reduced HDT4 lead to the elevation of H3K27ac and the expression of drought responsive genes, as a result, plants are drought tolerant.
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Affiliation(s)
- Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Zhengyao Shao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Likai Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Fan Zhang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Daveraj Chakravarty
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
| | - Juan Dong
- Department of Plant Biology, Rutgers, The State University of New Jersey, New Brunswick, New Jersey, United States of America
| | - Liang Song
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hong Qiao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, Texas, United States of America
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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Nguyen NH, Vu NT, Cheong JJ. Transcriptional Stress Memory and Transgenerational Inheritance of Drought Tolerance in Plants. Int J Mol Sci 2022; 23:12918. [PMID: 36361708 PMCID: PMC9654142 DOI: 10.3390/ijms232112918] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 10/19/2022] [Accepted: 10/25/2022] [Indexed: 12/03/2023] Open
Abstract
Plants respond to drought stress by producing abscisic acid, a chemical messenger that regulates gene expression and thereby expedites various physiological and cellular processes including the stomatal operation to mitigate stress and promote tolerance. To trigger or suppress gene transcription under drought stress conditions, the surrounding chromatin architecture must be converted between a repressive and active state by epigenetic remodeling, which is achieved by the dynamic interplay among DNA methylation, histone modifications, loop formation, and non-coding RNA generation. Plants can memorize chromatin status under drought conditions to enable them to deal with recurrent stress. Furthermore, drought tolerance acquired during plant growth can be transmitted to the next generation. The epigenetically modified chromatin architectures of memory genes under stressful conditions can be transmitted to newly developed cells by mitotic cell division, and to germline cells of offspring by overcoming the restraints on meiosis. In mammalian cells, the acquired memory state is completely erased and reset during meiosis. The mechanism by which plant cells overcome this resetting during meiosis to transmit memory is unclear. In this article, we review recent findings on the mechanism underlying transcriptional stress memory and the transgenerational inheritance of drought tolerance in plants.
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Affiliation(s)
- Nguyen Hoai Nguyen
- Faculty of Biotechnology, Ho Chi Minh City Open University, Ho Chi Minh City 700000, Vietnam
| | - Nam Tuan Vu
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
| | - Jong-Joo Cheong
- Center for Food and Bioconvergence, Seoul National University, Seoul 08826, Korea
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22
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Rajpal VR, Rathore P, Mehta S, Wadhwa N, Yadav P, Berry E, Goel S, Bhat V, Raina SN. Epigenetic variation: A major player in facilitating plant fitness under changing environmental conditions. Front Cell Dev Biol 2022; 10:1020958. [PMID: 36340045 PMCID: PMC9628676 DOI: 10.3389/fcell.2022.1020958] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 09/21/2022] [Indexed: 11/13/2022] Open
Abstract
Recent research in plant epigenetics has increased our understanding of how epigenetic variability can contribute to adaptive phenotypic plasticity in natural populations. Studies show that environmental changes induce epigenetic switches either independently or in complementation with the genetic variation. Although most of the induced epigenetic variability gets reset between generations and is short-lived, some variation becomes transgenerational and results in heritable phenotypic traits. The short-term epigenetic responses provide the first tier of transient plasticity required for local adaptations while transgenerational epigenetic changes contribute to stress memory and help the plants respond better to recurring or long-term stresses. These transgenerational epigenetic variations translate into an additional tier of diversity which results in stable epialleles. In recent years, studies have been conducted on epigenetic variation in natural populations related to various biological processes, ecological factors, communities, and habitats. With the advent of advanced NGS-based technologies, epigenetic studies targeting plants in diverse environments have increased manifold to enhance our understanding of epigenetic responses to environmental stimuli in facilitating plant fitness. Taking all points together in a frame, the present review is a compilation of present-day knowledge and understanding of the role of epigenetics and its fitness benefits in diverse ecological systems in natural populations.
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Affiliation(s)
- Vijay Rani Rajpal
- Department of Botany, Hansraj College, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | | | - Sahil Mehta
- School of Agricultural Sciences, K.R. Mangalam University, Gurugram, Haryana, India
| | - Nikita Wadhwa
- University School of Biotechnology, Guru Gobind Singh Indraprastha University, New Delhi, India
| | | | - Eapsa Berry
- Maharishi Kanad Bhawan, Delhi School of Climate Change and Sustainability, University of Delhi, Delhi, India
| | - Shailendra Goel
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Vishnu Bhat
- Department of Botany, University of Delhi, Delhi, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
| | - Soom Nath Raina
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh, India
- *Correspondence: Vijay Rani Rajpal, , ; Shailendra Goel, ; Vishnu Bhat, ; Soom Nath Raina,
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23
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Czajka KM, Nkongolo K. Transcriptome analysis of trembling aspen (Populus tremuloides) under nickel stress. PLoS One 2022; 17:e0274740. [PMID: 36227867 PMCID: PMC9560071 DOI: 10.1371/journal.pone.0274740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 09/02/2022] [Indexed: 11/07/2022] Open
Abstract
Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27–45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, this study revealed that a metal transport protein (Potrs038704g29436 –ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.
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Affiliation(s)
- Karolina M. Czajka
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, Canada
| | - Kabwe Nkongolo
- Biomolecular Sciences Program, Laurentian University, Sudbury, Ontario, Canada
- Department of Biology, School of Natural Sciences, Laurentian University, Sudbury, Ontario, Canada
- * E-mail:
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Shen Y, Chi Y, Lu S, Lu H, Shi L. Involvement of JMJ15 in the dynamic change of genome-wide H3K4me3 in response to salt stress. FRONTIERS IN PLANT SCIENCE 2022; 13:1009723. [PMID: 36226276 PMCID: PMC9549339 DOI: 10.3389/fpls.2022.1009723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 08/29/2022] [Indexed: 06/16/2023]
Abstract
Post-translational histone modifications play important roles in regulating chromatin structure and transcriptional regulation. Histone 3 lysine 4 trimethylation (H3K4me3) is a prominent histone modification mainly associated with gene activation. Here we showed that a histone demethylase, JMJ15, belonging to KDM5/JARID group, is involved in salt stress response in Arabidopsis thaliana. Jmj15 loss-of-function mutants displayed increased sensitivity to salt stress. Moreover, knockout of JMJ15 impaired the salt responsive gene expression program and affected H3K4me3 levels of many stress-related genes under salt-stressed condition. Importantly, we demonstrated that JMJ15 regulated the expression level of two WRKY transcription factors, WRKY46 and WRKY70, which were negatively involved in abiotic stress tolerance. Furthermore, JMJ15 directly bound to and demethylated H3K4me3 mark in the promoter and coding regions of WRKY46 and WRKY70, thereby repressing these two WRKY gene expression under salt stress. Overall, our study revealed a novel molecular function of the histone demethylase JMJ15 under salt stress in plants.
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Affiliation(s)
- Yuan Shen
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Yuhao Chi
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Shun Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Huijuan Lu
- School of Pharmacy, Xinxiang Medical University, Xinxiang, China
| | - Lei Shi
- School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
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25
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Molecular and epigenetic basis of heat stress responses and acclimatization in plants. THE NUCLEUS 2022. [DOI: 10.1007/s13237-022-00400-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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26
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Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4696-4715. [PMID: 35429161 DOI: 10.1093/jxb/erac155] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 04/13/2022] [Indexed: 06/14/2023]
Abstract
Flag leaf senescence is an important biological process that drives the remobilization of nutrients to the growing organs of rice. Leaf senescence is controlled by genetic information via gene expression and histone modification, but the precise mechanism is as yet unclear. Here, we analysed genome-wide acetylated lysine residue 9 of histone H3 (H3K9ac) enrichment by chromatin immunoprecipitation-sequencing (ChIP-seq), and examined its association with transcriptomes by RNA-seq during flag leaf aging in rice (Oryza sativa). We found that genome-wide H3K9 acetylation levels increased with age-dependent senescence in rice flag leaf, and there was a positive correlation between the density and breadth of H3K9ac with gene expression and transcript elongation. During flag leaf aging, we observed 1249 up-regulated differentially expressed genes (DEGs) and 996 down-regulated DEGs, showing a strong relationship between temporal changes in gene expression and gain/loss of H3K9ac. We produced a landscape of H3K9 acetylation-modified gene expression targets that include known senescence-associated genes, metabolism-related genes, as well as miRNA biosynthesis-related genes. Our findings reveal a complex regulatory network of metabolism- and senescence-related pathways mediated by H3K9ac, and elucidate patterns of H3K9ac-mediated regulation of gene expression during flag leaf aging in rice.
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Affiliation(s)
- Yu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanyun Li
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuanyuan Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyu Zhang
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Deyu Zhang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiaonan Wang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Binfan Lai
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Dandan Huang
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yakun Xie
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ying Miao
- Fujian Provincial Key Laboratory of Plant Functional Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
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27
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Rogers HJ. Reprogramming rice leaves: another layer of senescence regulation. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:4608-4611. [PMID: 35950460 PMCID: PMC9366317 DOI: 10.1093/jxb/erac178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
This article comments on:Zhang Y, Li Y, Zhang Y, Zhang Z, Zhang D, Wang X, Lai B, Huang D, Gu L, Xie Y, Miao Y. 2022. Genome-wide H3K9 acetylation level increases with age-dependent senescence of flag leaf in rice (Oryza sativa). Journal of Experimental Botany 73,4696–4715.
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Affiliation(s)
- Hilary Joan Rogers
- Cardiff University, School of Biosciences, Sir Martin Evans Building, Museum Avenue, Cardiff CF10 3AX, UK
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28
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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29
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Halder K, Chaudhuri A, Abdin MZ, Majee M, Datta A. Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:1449. [PMID: 35684223 PMCID: PMC9182740 DOI: 10.3390/plants11111449] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Plants' stress response machinery is characterized by an intricate network of signaling cascades that receive and transmit environmental cues and ultimately trigger transcriptional reprogramming. The family of epigenetic regulators that are the key players in the stress-induced signaling cascade comprise of chromatin remodelers, histone modifiers, DNA modifiers and regulatory non-coding RNAs. Changes in the histone modification and DNA methylation lead to major alterations in the expression level and pattern of stress-responsive genes to adjust with abiotic stress conditions namely heat, cold, drought and salinity. The spotlight of this review falls primarily on the chromatin restructuring under severe abiotic stresses, crosstalk between epigenetic regulators along with a brief discussion on stress priming in plants.
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Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
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30
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Sharma M, Kumar P, Verma V, Sharma R, Bhargava B, Irfan M. Understanding plant stress memory response for abiotic stress resilience: Molecular insights and prospects. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2022; 179:10-24. [PMID: 35305363 DOI: 10.1016/j.plaphy.2022.03.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/02/2022] [Accepted: 03/05/2022] [Indexed: 05/25/2023]
Abstract
As sessile species and without the possibility of escape, plants constantly face numerous environmental stresses. To adapt in the external environmental cues, plants adjust themselves against such stresses by regulating their physiological, metabolic and developmental responses to external environmental cues. Certain environmental stresses rarely occur during plant life, while others, such as heat, drought, salinity, and cold are repetitive. Abiotic stresses are among the foremost environmental variables that have hindered agricultural production globally. Through distinct mechanisms, these stresses induce various morphological, biochemical, physiological, and metabolic changes in plants, directly impacting their growth, development, and productivity. Subsequently, plant's physiological, metabolic, and genetic adjustments to the stress occurrence provide necessary competencies to adapt, survive and nurture a condition known as "memory." This review emphasizes the advancements in various epigenetic-related chromatin modifications, DNA methylation, histone modifications, chromatin remodeling, phytohormones, and microRNAs associated with abiotic stress memory. Plants have the ability to respond quickly to stressful situations and can also improve their defense systems by retaining and sustaining stressful memories, allowing for stronger or faster responses to repeated stressful situations. Although there are relatively few examples of such memories, and no clear understanding of their duration, taking into consideration plenty of stresses in nature. Understanding these mechanisms in depth could aid in the development of genetic tools to improve breeding techniques, resulting in higher agricultural yield and quality under changing environmental conditions.
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Affiliation(s)
- Megha Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Pankaj Kumar
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
| | - Vipasha Verma
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Rajnish Sharma
- Department of Biotechnology, Dr. Y.S. Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India
| | - Bhavya Bhargava
- Agrotechnology Division, CSIR-Institute of Himalayan Bioresource Technology, Palampur, 176061, Himachal Pradesh, India
| | - Mohammad Irfan
- Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, USA.
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31
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Xu D, Fang H, Liu J, Chen Y, Gu Y, Sun G, Xia B. ChIP-seq assay revealed histone modification H3K9ac involved in heat shock response of the sea cucumber Apostichopus japonicus. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 820:153168. [PMID: 35051475 DOI: 10.1016/j.scitotenv.2022.153168] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 12/23/2021] [Accepted: 01/12/2022] [Indexed: 06/14/2023]
Abstract
Heat stress poses an increasing threat for the marine invertebrate Apostichopus japonicus. Histone lysine acetylation is a central chromatin modification for epigenetic regulation of gene expression during stress response. In this study, a genome-wide characterization for acetylated lysine 9 on histone H3 (H3K9ac) binding regions in normal temperature (18 °C) and heat-stress conditions (26 °C) via ChIP-seq were carried out. The results that revealed H3K9ac was an extensive epigenetic modulation in A. japonicus. The GO terms "regulation of transcription, DNA-templated" and "transcription coactivator activity" were significantly enriched in both groups. Particularly, various transcriptional factors (TFs) families showed notable modification of H3K9ac. Differentially acetylated regions (DARs) with H3K9ac modification under heat stress were identified with 24 hyperacetylated and 23 hypoacetylated peaks, respectively. We further examined the transcriptional expression for 13 genes with dysregulated H3K9ac level in the promoter regions by qRT-PCR. Combined H3K9ac ChIP-seq characteristics with the transcriptional expression, 5 up-up genes (ZCCHC3, RPA70, MTRR, β-Gal and PHTF2) and 2 down-down genes (PRPF39 and BSL78_10147) were identified. Surprisingly, the increasing mRNA expression of NECAP1 under heat stress was negatively related to the decreasing H3K9ac level in its promoter region. Our research is the first genome-wide characterization for the epigenetic modification H3K9ac in A. japonicus, and will help to advance the understanding of the roles of H3K9ac in transcriptional regulation under heat-stress condition.
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Affiliation(s)
- Dongxue Xu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Huahua Fang
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Ji Liu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yanru Chen
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Yuanxue Gu
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China
| | - Guohua Sun
- School of Agriculture, Ludong University, Yantai, Shandong 264025, China
| | - Bin Xia
- School of Marine Science and Engineering, Qingdao Agricultural University, Qingdao, Shandong 266109, China.
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El-Sappah AH, Rather SA, Wani SH, Elrys AS, Bilal M, Huang Q, Dar ZA, Elashtokhy MMA, Soaud N, Koul M, Mir RR, Yan K, Li J, El-Tarabily KA, Abbas M. Heat Stress-Mediated Constraints in Maize ( Zea mays) Production: Challenges and Solutions. FRONTIERS IN PLANT SCIENCE 2022; 13:879366. [PMID: 35615131 PMCID: PMC9125997 DOI: 10.3389/fpls.2022.879366] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 03/30/2022] [Indexed: 05/05/2023]
Abstract
An increase in temperature and extreme heat stress is responsible for the global reduction in maize yield. Heat stress affects the integrity of the plasma membrane functioning of mitochondria and chloroplast, which further results in the over-accumulation of reactive oxygen species. The activation of a signal cascade subsequently induces the transcription of heat shock proteins. The denaturation and accumulation of misfolded or unfolded proteins generate cell toxicity, leading to death. Therefore, developing maize cultivars with significant heat tolerance is urgently required. Despite the explored molecular mechanism underlying heat stress response in some plant species, the precise genetic engineering of maize is required to develop high heat-tolerant varieties. Several agronomic management practices, such as soil and nutrient management, plantation rate, timing, crop rotation, and irrigation, are beneficial along with the advanced molecular strategies to counter the elevated heat stress experienced by maize. This review summarizes heat stress sensing, induction of signaling cascade, symptoms, heat stress-related genes, the molecular feature of maize response, and approaches used in developing heat-tolerant maize varieties.
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Affiliation(s)
- Ahmed H. El-Sappah
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Department of Genetics, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Shabir A. Rather
- Center for Integrative Conservation, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Menglun, China
| | - Shabir Hussain Wani
- Mountain Research Centre for Field Crops Khudwani Anantnag, SKUAST–Kashmir, Srinagar, India
| | - Ahmed S. Elrys
- Department of Soil Science, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Muhammad Bilal
- School of Life Sciences and Food Engineering, Huaiyin Institute of Technology, Huaian, China
| | - Qiulan Huang
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
- College of Tea Science, Yibin University, Yibin, China
| | - Zahoor Ahmad Dar
- Dryland Agriculture Research Station, SKUAST–Kashmir, Srinagar, India
| | | | - Nourhan Soaud
- Department of Crop Science, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Monika Koul
- Department of Botany, Hansraj College, University of Delhi, New Delhi, India
| | - Reyazul Rouf Mir
- Division of Genetics and Plant Breeding, Faculty of Agriculture (FoA), SKUAST–Kashmir, Sopore, India
| | - Kuan Yan
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Jia Li
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
| | - Khaled A. El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA, Australia
| | - Manzar Abbas
- School of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Key Laboratory of Sichuan Province for Refining Sichuan Tea, Yibin, China
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Guarino F, Cicatelli A, Castiglione S, Agius DR, Orhun GE, Fragkostefanakis S, Leclercq J, Dobránszki J, Kaiserli E, Lieberman-Lazarovich M, Sõmera M, Sarmiento C, Vettori C, Paffetti D, Poma AMG, Moschou PN, Gašparović M, Yousefi S, Vergata C, Berger MMJ, Gallusci P, Miladinović D, Martinelli F. An Epigenetic Alphabet of Crop Adaptation to Climate Change. Front Genet 2022; 13:818727. [PMID: 35251130 PMCID: PMC8888914 DOI: 10.3389/fgene.2022.818727] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 01/28/2022] [Indexed: 01/10/2023] Open
Abstract
Crop adaptation to climate change is in a part attributed to epigenetic mechanisms which are related to response to abiotic and biotic stresses. Although recent studies increased our knowledge on the nature of these mechanisms, epigenetics remains under-investigated and still poorly understood in many, especially non-model, plants, Epigenetic modifications are traditionally divided into two main groups, DNA methylation and histone modifications that lead to chromatin remodeling and the regulation of genome functioning. In this review, we outline the most recent and interesting findings on crop epigenetic responses to the environmental cues that are most relevant to climate change. In addition, we discuss a speculative point of view, in which we try to decipher the “epigenetic alphabet” that underlies crop adaptation mechanisms to climate change. The understanding of these mechanisms will pave the way to new strategies to design and implement the next generation of cultivars with a broad range of tolerance/resistance to stresses as well as balanced agronomic traits, with a limited loss of (epi)genetic variability.
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Affiliation(s)
- Francesco Guarino
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Angela Cicatelli
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Stefano Castiglione
- Dipartimento di Chimica e Biologia “A. Zambelli”, Università Degli Studi di Salerno, Salerno, Italy
| | - Dolores R. Agius
- Centre of Molecular Medicine and Biobanking, University of Malta, Msida, Malta
| | - Gul Ebru Orhun
- Bayramic Vocational College, Canakkale Onsekiz Mart University, Canakkale, Turkey
| | | | - Julie Leclercq
- CIRAD, UMR AGAP, Montpellier, France
- AGAP, Univ Montpellier, CIRAD, INRA, Institut Agro, Montpellier, France
| | - Judit Dobránszki
- Centre for Agricultural Genomics and Biotechnology, FAFSEM, University of Debrecen, Debrecen, Hungary
| | - Eirini Kaiserli
- Institute of Molecular, Cell and Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | | | - Merike Sõmera
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cecilia Sarmiento
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
| | - Cristina Vettori
- Institute of Biosciences and Bioresources (IBBR), National Research Council (CNR), Sesto Fiorentino, Italy
| | - Donatella Paffetti
- Department of Agriculture, Food, Environment and Forestry (DAGRI), University of Florence, Florence, Italy
| | - Anna M. G. Poma
- Department of Clinical Medicine, Public Health, Life and Environmental Sciences, University of L’Aquila, Aquila, Italy
| | - Panagiotis N. Moschou
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology—Hellas, Heraklion, Greece
- Department of Biology, University of Crete, Heraklion, Greece
- Department of Plant Biology, Uppsala BioCenter, Swedish University of Agricultural Sciences and Linnean Center for Plant Biology, Uppsala, Sweden
| | - Mateo Gašparović
- Chair of Photogrammetry and Remote Sensing, Faculty of Geodesy, University of Zagreb, Zagreb, Croatia
| | - Sanaz Yousefi
- Department of Horticultural Science, Bu-Ali Sina University, Hamedan, Iran
| | - Chiara Vergata
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
| | - Margot M. J. Berger
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Philippe Gallusci
- UMR Ecophysiologie et Génomique Fonctionnelle de la Vigne, Université de Bordeaux, INRAE, Bordeaux Science Agro, Bordeaux, France
| | - Dragana Miladinović
- Institute of Field and Vegetable Crops, National Institute of Republic of Serbia, Novi Sad, Serbia
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
| | - Federico Martinelli
- Department of Biology, University of Florence, Sesto Fiorentino, Italy
- *Correspondence: Dragana Miladinović, ; Federico Martinelli,
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Liu X, Quan W, Bartels D. Stress memory responses and seed priming correlate with drought tolerance in plants: an overview. PLANTA 2022; 255:45. [PMID: 35066685 PMCID: PMC8784359 DOI: 10.1007/s00425-022-03828-z] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 01/08/2022] [Indexed: 05/08/2023]
Abstract
Environmental-friendly techniques based on plant stress memory, cross-stress tolerance, and seed priming help sustainable agriculture by mitigating negative effects of dehydration stress. The frequently uneven rainfall distribution caused by global warming will lead to more irregular and multiple abiotic stresses, such as heat stress, dehydration stress, cold stress or the combination of these stresses. Dehydration stress is one of the major environmental factors affecting the survival rate and productivity of plants. Hence, there is an urgent need to develop improved resilient varieties. Presently, technologies based on plant stress memory, cross-stress tolerance and priming of seeds represent fruitful and promising areas of future research and applied agricultural science. In this review, we will provide an overview of plant drought stress memory from physiological, biochemical, molecular and epigenetic perspectives. Drought priming-induced cross-stress tolerance to cold and heat stress will be discussed and the application of seed priming will be illustrated for different species.
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Affiliation(s)
- Xun Liu
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- College of Bioengineering, Sichuan University of Science & Engineering, Zigong, 643000, China
| | - Wenli Quan
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, Hubei, China
| | - Dorothea Bartels
- Institute of Molecular Physiology and Biotechnology of Plants (IMBIO), University of Bonn, Kirschallee 1, 53115, Bonn, Germany.
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35
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Miryeganeh M. Epigenetic Mechanisms of Senescence in Plants. Cells 2022; 11:251. [PMID: 35053367 PMCID: PMC8773728 DOI: 10.3390/cells11020251] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 01/08/2022] [Accepted: 01/10/2022] [Indexed: 12/30/2022] Open
Abstract
Senescence is a major developmental transition in plants that requires a massive reprogramming of gene expression and includes various layers of regulations. Senescence is either an age-dependent or a stress-induced process, and is under the control of complex regulatory networks that interact with each other. It has been shown that besides genetic reprogramming, which is an important aspect of plant senescence, transcription factors and higher-level mechanisms, such as epigenetic and small RNA-mediated regulators, are also key factors of senescence-related genes. Epigenetic mechanisms are an important layer of this multilevel regulatory system that change the activity of transcription factors (TFs) and play an important role in modulating the expression of senescence-related gene. They include chromatin remodeling, DNA methylation, histone modification, and the RNA-mediated control of transcription factors and genes. This review provides an overview of the known epigenetic regulation of plant senescence, which has mostly been studied in the form of leaf senescence, and it also covers what has been reported about whole-plant senescence.
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Affiliation(s)
- Matin Miryeganeh
- Plant Epigenetics Unit, Okinawa Institute of Science and Technology Graduate University, 1919-1 Tancha, Onna-son, Okinawa 904-0412, Japan
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36
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DNA methylation and histone modifications induced by abiotic stressors in plants. Genes Genomics 2021; 44:279-297. [PMID: 34837631 DOI: 10.1007/s13258-021-01191-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 11/14/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND A review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of abiotic stressors on DNA methylation and histone modifications in plants. DISCUSSION Plant DNA methylation and histone modifications in responses to abiotic stressors varied and depended on the type and level of stress, plant tissues, age, and species. A critical analysis of the literature available revealed that 44% of the epigenetic modifications induced by abiotic stressors in plants involved DNA hypomethylation, 40% DNA hypermethylation, and 16% histone modification. The epigenetic changes in plants might be underestimated since most authors used methods such as methylation-sensitive amplification polymorphism (MSAP), High performance liquid chromatography (HPLC), and immunolabeling that are less sensitive compared to bisulfite sequencing and single-base resolution methylome analyses. More over, mechanisms underlying epigenetic changes in plants have not yet been determined since most reports showed only the level or/and distribution of DNA methylation and histone modifications. CONCLUSIONS Various epigenetic mechanisms are involved in response to abiotic stressors, and several of them are still unknown. Integrated analysis of the changes in the genome by omic approaches should help to identify novel components underlying mechanisms involved in DNA methylation and histone modifications associated with plant response to environmental stressors.
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Wang Q, Liu P, Jing H, Zhou XF, Zhao B, Li Y, Jin JB. JMJ27-mediated histone H3K9 demethylation positively regulates drought-stress responses in Arabidopsis. THE NEW PHYTOLOGIST 2021; 232:221-236. [PMID: 34197643 DOI: 10.1111/nph.17593] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Dimethylation of histone H3 at lysine 9 (H3K9me2) is associated with heterochromatinization and transcriptional gene silencing in plants. The activation of sets of genes by drought stress is correlated with reduced H3K9me2 levels, but the role of H3K9 methylation in the regulation of drought-stress responses remains elusive. Here, we show that the Jumonji domain-containing H3K9 demethylase JMJ27 positively regulates drought-stress responses through its histone demethylase activity. RNA-seq analysis identified JMJ27-regulated genes, including positive regulators of drought stress GALACTINOL SYNTHASE 2 (GOLS2) and RESPONSE TO DESICCATION 20 (RD20). Genetic analysis demonstrated that JMJ27 positively regulates drought-stress responses at least partly through GOLS2 and RD20. JMJ27 directly associated with GOLS2 and RD20, and protected these loci from silencing by reducing H3K9me2 levels under normal conditions. REGULATORY PARTICLE NON-ATPASE 1a (RPN1a), a subunit of the 26S proteasome, interacted with JMJ27 and negatively regulated JMJ27 accumulation. Drought stress diminished RPN1a abundance, resulting in increased JMJ27 abundance. The drought stress-promoted occupancy of JMJ27 at GOLS2 and RD20 chromatin may reinforce their transcriptional induction by locally reducing the H3K9me2 levels. These results indicate that the RPN1a-JMJ27 module precisely regulates dynamic H3K9me2 deposition plasticity, ensuring proper adaptation to drought stress in Arabidopsis.
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Affiliation(s)
- Qiongli Wang
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, Fujian, 350002, China
| | - Peng Liu
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Hua Jing
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiao Feng Zhou
- Department of Ornamental Horticulture, China Agricultural University, Beijing, 100193, China
| | - Bo Zhao
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Yuan Li
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jing Bo Jin
- Key Laboratory of Plant Molecular Physiology, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- University of the Chinese Academy of Sciences, Beijing, 100049, China
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38
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Li S, He X, Gao Y, Zhou C, Chiang VL, Li W. Histone Acetylation Changes in Plant Response to Drought Stress. Genes (Basel) 2021; 12:genes12091409. [PMID: 34573391 PMCID: PMC8468061 DOI: 10.3390/genes12091409] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/04/2021] [Accepted: 09/07/2021] [Indexed: 02/07/2023] Open
Abstract
Drought stress causes recurrent damage to a healthy ecosystem because it has major adverse effects on the growth and productivity of plants. However, plants have developed drought avoidance and resilience for survival through many strategies, such as increasing water absorption and conduction, reducing water loss and conversing growth stages. Understanding how plants respond and regulate drought stress would be important for creating and breeding better plants to help maintain a sound ecosystem. Epigenetic marks are a group of regulators affecting drought response and resilience in plants through modification of chromatin structure to control the transcription of pertinent genes. Histone acetylation is an ubiquitous epigenetic mark. The level of histone acetylation, which is regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), determines whether the chromatin is open or closed, thereby controlling access of DNA-binding proteins for transcriptional activation. In this review, we summarize histone acetylation changes in plant response to drought stress, and review the functions of HATs and HDACs in drought response and resistance.
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Affiliation(s)
- Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
- Correspondence: ; Tel.: +86-15114585206
| | - Xu He
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Yuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (X.H.); (Y.G.); (C.Z.); (V.L.C.); (W.L.)
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39
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Plants' Epigenetic Mechanisms and Abiotic Stress. Genes (Basel) 2021; 12:genes12081106. [PMID: 34440280 PMCID: PMC8394019 DOI: 10.3390/genes12081106] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 07/19/2021] [Accepted: 07/20/2021] [Indexed: 12/28/2022] Open
Abstract
Plants are sessile organisms that need to adapt to constantly changing environmental conditions. Unpredictable climate change places plants under a variety of abiotic stresses. Studying the regulation of stress-responsive genes can help to understand plants’ ability to adapt to fluctuating environmental conditions. Changes in epigenetic marks such as histone modifications and DNA methylation are known to regulate gene expression by their dynamic variation in response to stimuli. This can then affect their phenotypic plasticity, which helps with the adaptation of plants to adverse conditions. Epigenetic marks may also provide a mechanistic basis for stress memory, which enables plants to respond more effectively and efficiently to recurring stress and prepare offspring for potential future stresses. Studying epigenetic changes in addition to genetic factors is important to better understand the molecular mechanisms underlying plant stress responses. This review summarizes the epigenetic mechanisms behind plant responses to some main abiotic stresses.
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40
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Singh RK, Prasad M. Delineating the epigenetic regulation of heat and drought response in plants. Crit Rev Biotechnol 2021; 42:548-561. [PMID: 34289772 DOI: 10.1080/07388551.2021.1946004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Being sessile in nature, plants cannot overlook the incursion of unfavorable environmental conditions, including heat and drought. Heat and drought severely affect plant growth, development, reproduction and therefore productivity which poses a severe threat to global food security. Plants respond to these hostile environmental circumstances by rearranging their genomic and molecular architecture. One such modification commonly known as epigenetic changes involves the perishable to inheritable changes in DNA or DNA-binding histone proteins leading to modified chromatin organization. Reversible epigenetic modifications include DNA methylation, exchange of histone variants, histone methylation, histone acetylation, ATP-dependent nucleosome remodeling, and others. These modifications are employed to regulate the spatial and temporal expression of genes in response to external stimuli or specific developmental requirements. Understanding the epigenetic regulation of stress-related gene expression in response to heat and drought would commence manifold avenues for crop improvement through molecular breeding or biotechnological approaches.
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Affiliation(s)
| | - Manoj Prasad
- National Institute of Plant Genome Research, New Delhi, India
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41
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Friedrich T, Oberkofler V, Trindade I, Altmann S, Brzezinka K, Lämke J, Gorka M, Kappel C, Sokolowska E, Skirycz A, Graf A, Bäurle I. Heteromeric HSFA2/HSFA3 complexes drive transcriptional memory after heat stress in Arabidopsis. Nat Commun 2021; 12:3426. [PMID: 34103516 PMCID: PMC8187452 DOI: 10.1038/s41467-021-23786-6] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 05/13/2021] [Indexed: 02/05/2023] Open
Abstract
Adaptive plasticity in stress responses is a key element of plant survival strategies. For instance, moderate heat stress (HS) primes a plant to acquire thermotolerance, which allows subsequent survival of more severe HS conditions. Acquired thermotolerance is actively maintained over several days (HS memory) and involves the sustained induction of memory-related genes. Here we show that FORGETTER3/ HEAT SHOCK TRANSCRIPTION FACTOR A3 (FGT3/HSFA3) is specifically required for physiological HS memory and maintaining high memory-gene expression during the days following a HS exposure. HSFA3 mediates HS memory by direct transcriptional activation of memory-related genes after return to normal growth temperatures. HSFA3 binds HSFA2, and in vivo both proteins form heteromeric complexes with additional HSFs. Our results indicate that only complexes containing both HSFA2 and HSFA3 efficiently promote transcriptional memory by positively influencing histone H3 lysine 4 (H3K4) hyper-methylation. In summary, our work defines the major HSF complex controlling transcriptional memory and elucidates the in vivo dynamics of HSF complexes during somatic stress memory.
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Affiliation(s)
- Thomas Friedrich
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Vicky Oberkofler
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Inês Trindade
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Simone Altmann
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany ,grid.8241.f0000 0004 0397 2876Present Address: School of Life Sciences, University of Dundee, Dundee, UK
| | - Krzysztof Brzezinka
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jörn Lämke
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Michal Gorka
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Christian Kappel
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Ewelina Sokolowska
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Aleksandra Skirycz
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Alexander Graf
- grid.418390.70000 0004 0491 976XMax-Planck-Institute for Molecular Plant Physiology, Potsdam, Germany
| | - Isabel Bäurle
- grid.11348.3f0000 0001 0942 1117Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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Choudhary M, Singh A, Rakshit S. Coping with low moisture stress: Remembering and responding. PHYSIOLOGIA PLANTARUM 2021; 172:1162-1169. [PMID: 33496015 DOI: 10.1111/ppl.13343] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/01/2020] [Accepted: 12/05/2020] [Indexed: 06/12/2023]
Abstract
Low-moisture stress, also referred to as drought, is one of the major factors that negatively impact the agricultural yield. The present scenario of climate change is expected to aggravate it further. Considering the extended time required to develop resistant crops, it is important to prioritize research efforts for coping with low moisture, prevalent in arid and semi-arid regions of the world. While agricultural yield is a tradeoff between many choices, tolerance to biotic and abiotic stresses comes with yield penalties. To balance the tradeoffs and maximize productivity, the use of region-specific cultivars and/or introgression of precise genetic proportions in an elite variety may prove useful. Stress memory is an emerging approach that helps plants to record and respond to repeated stress in an effective manner. In this context, we discuss the role of "stress memory" in imparting drought tolerance in plants. Future research efforts for its effective deployment for "drought hardening" in agricultural settings, along with a discussion on the yield tradeoff involved, is implicated.
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Affiliation(s)
- Mukesh Choudhary
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana, India
| | - Alla Singh
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana, India
| | - Sujay Rakshit
- ICAR-Indian Institute of Maize Research, P.A.U. Campus, Ludhiana, India
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Ectopic Overexpression of Histone H3K4 Methyltransferase CsSDG36 from Tea Plant Decreases Hyperosmotic Stress Tolerance in Arabidopsis thaliana. Int J Mol Sci 2021; 22:ijms22105064. [PMID: 34064673 PMCID: PMC8150943 DOI: 10.3390/ijms22105064] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2021] [Revised: 04/26/2021] [Accepted: 05/01/2021] [Indexed: 02/05/2023] Open
Abstract
Histone methylation plays an important regulatory role in the drought response of many plants, but its regulatory mechanism in the drought response of the tea plant remains poorly understood. Here, drought stress was shown to induce lower relative water content and significantly downregulate the methylations of histone H3K4 in the tea plant. Based on our previous analysis of the SET Domain Group (SDG) gene family, the full-length coding sequence (CDS) of CsSDG36 was cloned from the tea cultivar ‘Fuding Dabaicha’. Bioinformatics analysis showed that the open reading frame (ORF) of the CsSDG36 gene was 3138 bp, encoding 1045 amino acids and containing the conserved structural domains of PWWP, PHD, SET and PostSET. The CsSDG36 protein showed a close relationship to AtATX4 of the TRX subfamily, with a molecular weight of 118,249.89 Da, and a theoretical isoelectric point of 8.87, belonging to a hydrophilic protein without a transmembrane domain, probably located on the nucleus. The expression of CsSDG36 was not detected in the wild type, while it was clearly detected in the over-expression lines of Arabidopsis. Compared with the wild type, the over-expression lines exhibited lower hyperosmotic resistance by accelerating plant water loss, increasing reactive oxygen species (ROS) pressure, and increasing leaf stomatal density. RNA-seq analysis suggested that the CsSDG36 overexpression caused the differential expression of genes related to chromatin assembly, microtubule assembly, and leaf stomatal development pathways. qRT-PCR analysis revealed the significant down-regulation of stomatal development-related genes (BASL, SBT1.2(SDD1), EPF2, TCX3, CHAL, TMM, SPCH, ERL1, and EPFL9) in the overexpression lines. This study provides a novel sight on the function of histone methyltransferase CsSDG36 under drought stress.
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44
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Cui X, Zheng Y, Lu Y, Issakidis-Bourguet E, Zhou DX. Metabolic control of histone demethylase activity involved in plant response to high temperature. PLANT PHYSIOLOGY 2021; 185:1813-1828. [PMID: 33793949 PMCID: PMC8133595 DOI: 10.1093/plphys/kiab020] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 01/07/2021] [Indexed: 05/31/2023]
Abstract
Jumonji C (JmjC) domain proteins are histone lysine demethylases that require ferrous iron and alpha-ketoglutarate (or α-KG) as cofactors in the oxidative demethylation reaction. In plants, α-KG is produced by isocitrate dehydrogenases (ICDHs) in different metabolic pathways. It remains unclear whether fluctuation of α-KG levels affects JmjC demethylase activity and epigenetic regulation of plant gene expression. In this work, we studied the impact of loss of function of the cytosolic ICDH (cICDH) gene on the function of histone demethylases in Arabidopsis thaliana. Loss of cICDH resulted in increases of overall histone H3 lysine 4 trimethylation (H3K4me3) and enhanced mutation defects of the H3K4me3 demethylase gene JMJ14. Genetic analysis suggested that the cICDH mutation may affect the activity of other demethylases, including JMJ15 and JMJ18 that function redundantly with JMJ14 in the plant thermosensory response. Furthermore, we show that mutation of JMJ14 affected both the gene activation and repression programs of the plant thermosensory response and that JMJ14 and JMJ15 repressed a set of genes that are likely to play negative roles in the process. The results provide evidence that histone H3K4 demethylases are involved in the plant response to elevated ambient temperature.
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Affiliation(s)
- Xiaoyun Cui
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Saclay, Orsay 91405, France
| | - Yu Zheng
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Saclay, Orsay 91405, France
- Institute for Interdisciplinary Research, Jianghan University, Wuhan 430056, China
| | - Yue Lu
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding and Key Laboratory of Plant Functional Genomics of the Ministry of Education, College of Agriculture, Yangzhou University, Yangzhou 225009, China
| | | | - Dao-Xiu Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, Université Paris-Saclay, Orsay 91405, France
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
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Li W, Yan J, Wang S, Wang Q, Wang C, Li Z, Zhang D, Ma F, Guan Q, Xu J. Genome-wide analysis of SET-domain group histone methyltransferases in apple reveals their role in development and stress responses. BMC Genomics 2021; 22:283. [PMID: 33874904 PMCID: PMC8054418 DOI: 10.1186/s12864-021-07596-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Accepted: 04/09/2021] [Indexed: 12/13/2022] Open
Abstract
Background Histone lysine methylation plays an important role in plant development and stress responses by activating or repressing gene expression. Histone lysine methylation is catalyzed by a class of SET-domain group proteins (SDGs). Although an increasing number of studies have shown that SDGs play important regulatory roles in development and stress responses, the functions of SDGs in apple remain unclear. Results A total of 67 SDG members were identified in the Malus×domestica genome. Syntenic analysis revealed that most of the MdSDG duplicated gene pairs were associated with a recent genome-wide duplication event of the apple genome. These 67 MdSDG members were grouped into six classes based on sequence similarity and the findings of previous studies. The domain organization of each MdSDG class was characterized by specific patterns, which was consistent with the classification results. The tissue-specific expression patterns of MdSDGs among the 72 apple tissues in the different apple developmental stages were characterized to provide insight into their potential functions in development. The expression profiles of MdSDGs were also investigated in fruit development, the breaking of bud dormancy, and responses to abiotic and biotic stress; the results indicated that MdSDGs might play a regulatory role in development and stress responses. The subcellular localization and putative interaction network of MdSDG proteins were also analyzed. Conclusions This work presents a fundamental comprehensive analysis of SDG histone methyltransferases in apple and provides a basis for future studies of MdSDGs involved in apple development and stress responses. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07596-0.
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Affiliation(s)
- Wenjie Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jinjiao Yan
- College of Forestry, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qianying Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Caixia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhongxing Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Dehui Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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He X, Wang Q, Pan J, Liu B, Ruan Y, Huang Y. Systematic analysis of JmjC gene family and stress--response expression of KDM5 subfamily genes in Brassica napus. PeerJ 2021; 9:e11137. [PMID: 33850662 PMCID: PMC8019318 DOI: 10.7717/peerj.11137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 03/01/2021] [Indexed: 12/21/2022] Open
Abstract
Background Jumonji C (JmjC) proteins exert critical roles in plant development and stress response through the removal of lysine methylation from histones. Brassica napus, which originated from spontaneous hybridization by Brassica rapa and Brassica oleracea, is the most important oilseed crop after soybean. In JmjC proteins of Brassica species, the structure and function and its relationship with the parents and model plant Arabidopsis thaliana remain uncharacterized. Systematic identification and analysis for JmjC family in Brassica crops can facilitate the future functional characterization and oilseed crops improvement. Methods Basing on the conserved JmjC domain, JmjC homologs from the three Brassica species, B. rapa (AA), B. oleracea (CC) and B. napus, were identified from the Brassica database. Some methods, such as phylogenic analysis, chromosomal mapping, HMMER searching, gene structure display and Logos analysis, were used to characterize relationships of the JmjC homologs. Synonymous and nonsynonymous nucleotide substitutions were used to infer the information of gene duplication among homologs. Then, the expression levels of BnKDM5 subfamily genes were checked under abiotic stress by qRT-PCR. Results Sixty-five JmjC genes were identified from B. napus genome, 29 from B. rapa, and 23 from B. oleracea. These genes were grouped into seven clades based on the phylogenetic analysis, and their catalytic activities of demethylation were predicted. The average retention rate of B. napus JmjC genes (B. napus JmjC gene from B. rapa (93.1%) and B. oleracea (82.6%)) exceeded whole genome level. JmjC sequences demonstrated high conservation in domain origination, chromosomal location, intron/exon number and catalytic sites. The gene duplication events were confirmed among the homologs. Many of the BrKDM5 subfamily genes showed higher expression under drought and NaCl treatments, but only a few genes were involved in high temperature stress. Conclusions This study provides the first genome-wide characterization of JmjC genes in Brassica species. The BnJmjC exhibits higher conservation during the formation process of allotetraploid than the average retention rates of the whole B. napus genome. Furthermore, expression profiles of many genes indicated that BnKDM5 subfamily genes are involved in stress response to salt, drought and high temperature.
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Affiliation(s)
- Xinghui He
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Qianwen Wang
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Jiao Pan
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Boyu Liu
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Ying Ruan
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
| | - Yong Huang
- Key Laboratory of Crop Epigenetic Regulation and Development, Hunan Province, Changsha, China.,Key Laboratory of Plant Genetics and Molecular Biology of Education Department, Changsha, Hunan Province, China.,College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan Province, China
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Multifaceted Chromatin Structure and Transcription Changes in Plant Stress Response. Int J Mol Sci 2021; 22:ijms22042013. [PMID: 33670556 PMCID: PMC7922328 DOI: 10.3390/ijms22042013] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 02/15/2021] [Accepted: 02/16/2021] [Indexed: 01/06/2023] Open
Abstract
Sessile plants are exposed throughout their existence to environmental abiotic and biotic stress factors, such as cold, heat, salinity, drought, dehydration, submergence, waterlogging, and pathogen infection. Chromatin organization affects genome stability, and its dynamics are crucial in plant stress responses. Chromatin dynamics are epigenetically regulated and are required for stress-induced transcriptional regulation or reprogramming. Epigenetic regulators facilitate the phenotypic plasticity of development and the survival and reproduction of plants in unfavorable environments, and they are highly diversified, including histone and DNA modifiers, histone variants, chromatin remodelers, and regulatory non-coding RNAs. They contribute to chromatin modifications, remodeling and dynamics, and constitute a multilayered and multifaceted circuitry for sophisticated and robust epigenetic regulation of plant stress responses. However, this complicated epigenetic regulatory circuitry creates challenges for elucidating the common or differential roles of chromatin modifications for transcriptional regulation or reprogramming in different plant stress responses. Particularly, interacting chromatin modifications and heritable stress memories are difficult to identify in the aspect of chromatin-based epigenetic regulation of transcriptional reprogramming and memory. Therefore, this review discusses the recent updates from the three perspectives—stress specificity or dependence of transcriptional reprogramming, the interplay of chromatin modifications, and transcriptional stress memory in plants. This helps solidify our knowledge on chromatin-based transcriptional reprogramming for plant stress response and memory.
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Kumar S, Mohapatra T. Dynamics of DNA Methylation and Its Functions in Plant Growth and Development. FRONTIERS IN PLANT SCIENCE 2021; 12:596236. [PMID: 34093600 PMCID: PMC8175986 DOI: 10.3389/fpls.2021.596236] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 04/19/2021] [Indexed: 05/20/2023]
Abstract
Epigenetic modifications in DNA bases and histone proteins play important roles in the regulation of gene expression and genome stability. Chemical modification of DNA base (e.g., addition of a methyl group at the fifth carbon of cytosine residue) switches on/off the gene expression during developmental process and environmental stresses. The dynamics of DNA base methylation depends mainly on the activities of the writer/eraser guided by non-coding RNA (ncRNA) and regulated by the developmental/environmental cues. De novo DNA methylation and active demethylation activities control the methylation level and regulate the gene expression. Identification of ncRNA involved in de novo DNA methylation, increased DNA methylation proteins guiding DNA demethylase, and methylation monitoring sequence that helps maintaining a balance between DNA methylation and demethylation is the recent developments that may resolve some of the enigmas. Such discoveries provide a better understanding of the dynamics/functions of DNA base methylation and epigenetic regulation of growth, development, and stress tolerance in crop plants. Identification of epigenetic pathways in animals, their existence/orthologs in plants, and functional validation might improve future strategies for epigenome editing toward climate-resilient, sustainable agriculture in this era of global climate change. The present review discusses the dynamics of DNA methylation (cytosine/adenine) in plants, its functions in regulating gene expression under abiotic/biotic stresses, developmental processes, and genome stability.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
- *Correspondence: Suresh Kumar, ; , orcid.org/0000-0002-7127-3079
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Wang H, Liu S, Dai X, Yang Y, Luo Y, Gao Y, Liu X, Wei W, Wang H, Xu X, Reddy ASN, Jaiswal P, Li W, Liu B, Gu L. PSDX: A Comprehensive Multi-Omics Association Database of Populus trichocarpa With a Focus on the Secondary Growth in Response to Stresses. FRONTIERS IN PLANT SCIENCE 2021; 12:655565. [PMID: 34122478 PMCID: PMC8195342 DOI: 10.3389/fpls.2021.655565] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/26/2021] [Indexed: 05/16/2023]
Abstract
Populus trichocarpa (P. trichocarpa) is a model tree for the investigation of wood formation. In recent years, researchers have generated a large number of high-throughput sequencing data in P. trichocarpa. However, no comprehensive database that provides multi-omics associations for the investigation of secondary growth in response to diverse stresses has been reported. Therefore, we developed a public repository that presents comprehensive measurements of gene expression and post-transcriptional regulation by integrating 144 RNA-Seq, 33 ChIP-seq, and six single-molecule real-time (SMRT) isoform sequencing (Iso-seq) libraries prepared from tissues subjected to different stresses. All the samples from different studies were analyzed to obtain gene expression, co-expression network, and differentially expressed genes (DEG) using unified parameters, which allowed comparison of results from different studies and treatments. In addition to gene expression, we also identified and deposited pre-processed data about alternative splicing (AS), alternative polyadenylation (APA) and alternative transcription initiation (ATI). The post-transcriptional regulation, differential expression, and co-expression network datasets were integrated into a new P. trichocarpa Stem Differentiating Xylem (PSDX) database (http://forestry.fafu.edu.cn/db/SDX), which further highlights gene families of RNA-binding proteins and stress-related genes. The PSDX also provides tools for data query, visualization, a genome browser, and the BLAST option for sequence-based query. Much of the data is also available for bulk download. The availability of PSDX contributes to the research related to the secondary growth in response to stresses in P. trichocarpa, which will provide new insights that can be useful for the improvement of stress tolerance in woody plants.
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Affiliation(s)
- Huiyuan Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sheng Liu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiufang Dai
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Yongkang Yang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yunjun Luo
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yubang Gao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuqing Liu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wentao Wei
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Huihui Wang
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xi Xu
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Anireddy S. N. Reddy
- Department of Biology and Program in Cell and Molecular Biology, Colorado State University, Fort Collins, CO, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin, China
| | - Bo Liu
- College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- *Correspondence: Bo Liu,
| | - Lianfeng Gu
- Basic Forestry and Proteomics Research Center, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
- Lianfeng Gu,
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50
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Sahid S, Roy C, Paul S, Datta R. Rice lectin protein r40c1 imparts drought tolerance by modulating S-adenosylmethionine synthase 2, stress-associated protein 8 and chromatin-associated proteins. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:7331-7346. [PMID: 32853345 DOI: 10.1093/jxb/eraa400] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Accepted: 08/25/2020] [Indexed: 06/11/2023]
Abstract
Lectin proteins play an important role in biotic and abiotic stress responses in plants. Although the rice lectin protein Osr40c1 has been reported to be regulated by drought stress, the mechanism of its drought tolerance activity has not been studied so far. In this study, it is shown that expression of the Osr40c1 gene correlates with the drought tolerance potential of various rice cultivars. Transgenic rice plants overexpressing Osr40c1 were significantly more tolerant to drought stress than the wild-type plants. Furthermore, ectopic expression of the Osr40c1 gene in tobacco yielded a similar result. Interestingly, the protein displayed a nucleo-cytoplasmic localization and was found to interact with a number of drought-responsive proteins such as S-adenosylmethionine synthase 2 (OsSAM2), stress-associated protein 8 (OsSAP8), DNA-binding protein MNB1B (OsMNB1B), and histone 4 (OsH4). Silencing of each of these protein partners led to drought sensitivity in otherwise tolerant Osr40c1-expressing transgenic tobacco lines indicating that these partners were crucial for the Osr40c1-mediated drought tolerance in planta. Moreover, the association of Osr40c1 with these partners occurred specifically under drought stress forming a multi-protein complex. Together, our findings delineate a novel role of Osr40c1 in imparting drought tolerance by regulating OsMNB1B, OsSAM2, and OsH4 proteins, which presumably enables OsSAP8 to induce downstream gene expression.
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Affiliation(s)
- Salman Sahid
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
- Department of Botany, Dr A. P. J. Abdul Kalam Government College, New Town, Kolkata, West Bengal, India
| | - Chandan Roy
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
| | - Soumitra Paul
- Department of Botany, University of Calcutta, Kolkata, West Bengal, India
| | - Riddhi Datta
- Department of Botany, Dr A. P. J. Abdul Kalam Government College, New Town, Kolkata, West Bengal, India
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