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Gaude AA, Siqueira RH, Botelho SB, Jalmi SK. Epigenetic arsenal for stress mitigation in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130620. [PMID: 38636616 DOI: 10.1016/j.bbagen.2024.130620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/23/2024] [Accepted: 04/15/2024] [Indexed: 04/20/2024]
Abstract
Plant's ability to perceive, respond to, and ultimately adapt to various stressors is a testament to their remarkable resilience. In response to stresses, plants activate a complex array of molecular and physiological mechanisms. These include the rapid activation of stress-responsive genes, the manufacturing of protective compounds, modulation of cellular processes and alterations in their growth and development patterns to enhance their chances of survival. Epigenetic mechanisms play a pivotal role in shaping the responses of plants to environmental stressors. This review explores the intricate interplay between epigenetic regulation and plant stress mitigation. We delve into the dynamic landscape of epigenetic modifications, highlighting their influence on gene expression and ultimately stress tolerance. This review assembles current research, shedding light on the promising strategies within plants' epigenetic arsenal to thrive amidst adverse conditions.
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Affiliation(s)
- Aishwarya Ashok Gaude
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Roxiette Heromina Siqueira
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Savia Bernadette Botelho
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
| | - Siddhi Kashinath Jalmi
- Discipline of Botany, School of Biological Sciences and Biotechnology, Goa University, Goa 403206, India.
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2
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Jung WJ, Jeong JH, Yoon JS, Seo YW. Genome-wide identification of the plant homeodomain-finger family in rye and ScPHD5 functions in cold tolerance and flowering time. PLANT CELL REPORTS 2024; 43:142. [PMID: 38744747 DOI: 10.1007/s00299-024-03226-7] [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: 02/04/2024] [Accepted: 05/02/2024] [Indexed: 05/16/2024]
Abstract
KEY MESSAGE 111 PHD genes were newly identified in rye genome and ScPHD5's role in regulating cold tolerance and flowering time was suggested. Plant homeodomain (PHD)-finger proteins regulate the physical properties of chromatin and control plant development and stress tolerance. Although rye (Secale cereale L.) is a major winter crop, PHD-finger proteins in rye have not been studied. Here, we identified 111 PHD genes in the rye genome that exhibited diverse gene and protein sequence structures. Phylogenetic tree analysis revealed that PHDs were genetically close in monocots and diverged from those in dicots. Duplication and synteny analyses demonstrated that ScPHDs have undergone several duplications during evolution and that high synteny is conserved among the Triticeae species. Tissue-specific and abiotic stress-responsive gene expression analyses indicated that ScPHDs were highly expressed in spikelets and developing seeds and were responsive to cold and drought stress. One of these genes, ScPHD5, was selected for further functional characterization. ScPHD5 was highly expressed in the spike tissues and was localized in the nuclei of rye protoplasts and tobacco leaves. ScPHD5-overexpressing Brachypodium was more tolerant to freezing stress than wild-type (WT), with increased CBF and COR gene expression. Additionally, these transgenic plants displayed an extremely early flowering phenotype that flowered more than two weeks earlier than the WT, and vernalization genes, rather than photoperiod genes, were increased in the WT. RNA-seq analysis revealed that diverse stress response genes, including HSPs, HSFs, LEAs, and MADS-box genes, were also upregulated in transgenic plants. Our study will help elucidate the roles of PHD genes in plant development and abiotic stress tolerance in rye.
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Affiliation(s)
- Woo Joo Jung
- Institute of Animal Molecular Biotechnology, Korea University, Seoul, 02841, Korea
| | - Ji Hyeon Jeong
- Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea
| | - Jin Seok Yoon
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Korea
| | - Yong Weon Seo
- Department of Plant Biotechnology, Korea University, Seoul, 02841, Korea.
- Ojeong Plant Breeding Research Center, Korea University, Seoul, 02841, Korea.
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3
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Larran AS, Pajoro A, Qüesta JI. Is winter coming? Impact of the changing climate on plant responses to cold temperature. PLANT, CELL & ENVIRONMENT 2023; 46:3175-3193. [PMID: 37438895 DOI: 10.1111/pce.14669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/23/2023] [Accepted: 07/03/2023] [Indexed: 07/14/2023]
Abstract
Climate change is causing alterations in annual temperature regimes worldwide. Important aspects of this include the reduction of winter chilling temperatures as well as the occurrence of unpredicted frosts, both significantly affecting plant growth and yields. Recent studies advanced the knowledge of the mechanisms underlying cold responses and tolerance in the model plant Arabidopsis thaliana. However, how these cold-responsive pathways will readjust to ongoing seasonal temperature variation caused by global warming remains an open question. In this review, we highlight the plant developmental programmes that depend on cold temperature. We focus on the molecular mechanisms that plants have evolved to adjust their development and stress responses upon exposure to cold. Covering both genetic and epigenetic aspects, we present the latest insights into how alternative splicing, noncoding RNAs and the formation of biomolecular condensates play key roles in the regulation of cold responses. We conclude by commenting on attractive targets to accelerate the breeding of increased cold tolerance, bringing up biotechnological tools that might assist in overcoming current limitations. Our aim is to guide the reflection on the current agricultural challenges imposed by a changing climate and to provide useful information for improving plant resilience to unpredictable cold regimes.
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Affiliation(s)
- Alvaro Santiago Larran
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
| | - Alice Pajoro
- National Research Council, Institute of Molecular Biology and Pathology, Rome, Italy
| | - Julia I Qüesta
- Centre for Research in Agricultural Genomics (CRAG) IRTA-CSIC-UAB-UB, Campus UAB, Barcelona, Spain
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4
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Klajn N, Kapczyńska K, Pasikowski P, Glazińska P, Kugiel H, Kęsy J, Wojciechowski W. Regulatory Effects of ABA and GA on the Expression of Conglutin Genes and LAFL Network Genes in Yellow Lupine ( Lupinus luteus L.) Seeds. Int J Mol Sci 2023; 24:12380. [PMID: 37569754 PMCID: PMC10418516 DOI: 10.3390/ijms241512380] [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: 07/28/2023] [Accepted: 07/29/2023] [Indexed: 08/13/2023] Open
Abstract
The maturation of seeds is a process of particular importance both for the plant itself by assuring the survival of the species and for the human population for nutritional and economic reasons. Controlling this process requires a strict coordination of many factors at different levels of the functioning of genetic and hormonal changes as well as cellular organization. One of the most important examples is the transcriptional activity of the LAFL gene regulatory network, which includes LEAFY COTYLEDON1 (LEC1) and LEC1-LIKE (L1L) and ABSCISIC ACID INSENSITIVE3 (ABI3), FUSCA3 (FUS3), and LEC2 (LEAFY COTYLEDON2), as well as hormonal homeostasis-of abscisic acid (ABA) and gibberellins (GA) in particular. From the nutritional point of view, the key to seed development is the ability of seeds to accumulate large amounts of proteins with different structures and properties. The world's food deficit is mainly related to shortages of protein, and taking into consideration the environmental changes occurring on Earth, it is becoming necessary to search for a way to obtain large amounts of plant-derived protein while maintaining the diversity of its origin. Yellow lupin, whose storage proteins are conglutins, is one of the plant species native to Europe that accumulates large amounts of this nutrient in its seeds. In this article we have shown the key changes occurring in the developing seeds of the yellow-lupin cultivar Taper by means of modern molecular biology techniques, including RNA-seq, chromatographic techniques and quantitative PCR analysis. We identified regulatory genes fundamental to the seed-filling process, as well as genes encoding conglutins. We also investigated how exogenous application of ABA and GA3 affects the expression of LlLEC2, LlABI3, LlFUS3, and genes encoding β- and δ-conglutins and whether it results in the amount of accumulated seed storage proteins. The research shows that for each species, even related plants, very specific changes can be identified. Thus the analysis and possibility of using such an approach to improve and stabilize yields requires even more detailed and extended research.
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Affiliation(s)
- Natalia Klajn
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Katarzyna Kapczyńska
- Department of Immunology of Infectious Diseases, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Weigla 12, 53-114 Wroclaw, Poland;
| | - Paweł Pasikowski
- Life Sciences and Biotechnology Center, Łukasiewicz Research Network–PORT Polish Center for Technology Development, Stabłowicka 147, 54-066 Wroclaw, Poland;
- Captor Therapeutics S.A., Duńska 11, 54-427 Wroclaw, Poland
| | - Paulina Glazińska
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Hubert Kugiel
- LABcenter Life Agro Biotechnology Ltd., Gliniana 14, 97-300 Piotrków Trybunalski, Poland; (H.K.); (W.W.)
| | - Jacek Kęsy
- Department of Plant Physiology and Biotechnology, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus University, Lwowska 1, 87-100 Torun, Poland; (P.G.); (J.K.)
| | - Waldemar Wojciechowski
- LABcenter Life Agro Biotechnology Ltd., Gliniana 14, 97-300 Piotrków Trybunalski, Poland; (H.K.); (W.W.)
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Roychowdhury R, Das SP, Gupta A, Parihar P, Chandrasekhar K, Sarker U, Kumar A, Ramrao DP, Sudhakar C. Multi-Omics Pipeline and Omics-Integration Approach to Decipher Plant's Abiotic Stress Tolerance Responses. Genes (Basel) 2023; 14:1281. [PMID: 37372461 DOI: 10.3390/genes14061281] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Revised: 06/03/2023] [Accepted: 06/14/2023] [Indexed: 06/29/2023] Open
Abstract
The present day's ongoing global warming and climate change adversely affect plants through imposing environmental (abiotic) stresses and disease pressure. The major abiotic factors such as drought, heat, cold, salinity, etc., hamper a plant's innate growth and development, resulting in reduced yield and quality, with the possibility of undesired traits. In the 21st century, the advent of high-throughput sequencing tools, state-of-the-art biotechnological techniques and bioinformatic analyzing pipelines led to the easy characterization of plant traits for abiotic stress response and tolerance mechanisms by applying the 'omics' toolbox. Panomics pipeline including genomics, transcriptomics, proteomics, metabolomics, epigenomics, proteogenomics, interactomics, ionomics, phenomics, etc., have become very handy nowadays. This is important to produce climate-smart future crops with a proper understanding of the molecular mechanisms of abiotic stress responses by the plant's genes, transcripts, proteins, epigenome, cellular metabolic circuits and resultant phenotype. Instead of mono-omics, two or more (hence 'multi-omics') integrated-omics approaches can decipher the plant's abiotic stress tolerance response very well. Multi-omics-characterized plants can be used as potent genetic resources to incorporate into the future breeding program. For the practical utility of crop improvement, multi-omics approaches for particular abiotic stress tolerance can be combined with genome-assisted breeding (GAB) by being pyramided with improved crop yield, food quality and associated agronomic traits and can open a new era of omics-assisted breeding. Thus, multi-omics pipelines together are able to decipher molecular processes, biomarkers, targets for genetic engineering, regulatory networks and precision agriculture solutions for a crop's variable abiotic stress tolerance to ensure food security under changing environmental circumstances.
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Affiliation(s)
- Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO)-The Volcani Institute, Rishon Lezion 7505101, Israel
| | - Soumya Prakash Das
- School of Bioscience, Seacom Skills University, Bolpur 731236, West Bengal, India
| | - Amber Gupta
- Dr. Vikram Sarabhai Institute of Cell and Molecular Biology, Faculty of Science, Maharaja Sayajirao University of Baroda, Vadodara 390002, Gujarat, India
| | - Parul Parihar
- Department of Biotechnology and Bioscience, Banasthali Vidyapith, Banasthali 304022, Rajasthan, India
| | - Kottakota Chandrasekhar
- Department of Plant Biochemistry and Biotechnology, Sri Krishnadevaraya College of Agricultural Sciences (SKCAS), Affiliated to Acharya N.G. Ranga Agricultural University (ANGRAU), Guntur 522034, Andhra Pradesh, India
| | - Umakanta Sarker
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Bangabandhu Sheikh Mujibur Rahman Agricultural University, Gazipur 1706, Bangladesh
| | - Ajay Kumar
- Department of Botany, Maharshi Vishwamitra (M.V.) College, Buxar 802102, Bihar, India
| | - Devade Pandurang Ramrao
- Department of Biotechnology, Mizoram University, Pachhunga University College Campus, Aizawl 796001, Mizoram, India
| | - Chinta Sudhakar
- Plant Molecular Biology Laboratory, Department of Botany, Sri Krishnadevaraya University, Anantapur 515003, Andhra Pradesh, India
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Jing Y, Yang Z, Yang R, Zhang Y, Qiao W, Zhou Y, Sun J. PKL is stabilized by MMS21 to negatively regulate Arabidopsis drought tolerance through directly repressing AFL1 transcription. THE NEW PHYTOLOGIST 2023. [PMID: 37209253 DOI: 10.1111/nph.18972] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 04/20/2023] [Indexed: 05/22/2023]
Abstract
Drought stress causes substantial losses in crop production per year worldwide, threatening global food security. Identification of the genetic components underlying drought tolerance in plants is of great importance. In this study, we report that loss-of-function of the chromatin-remodeling factor PICKLE (PKL), which is involved in repression of transcription, enhances drought tolerance of Arabidopsis. At first, we find that PKL interacts with ABI5 to regulate seed germination, but PKL regulates drought tolerance independently of ABI5. Then, we find that PKL is necessary for repressing the drought-tolerant gene AFL1, which is responsible for the drought-tolerant phenotype of pkl mutant. Genetic complementation tests demonstrate that the Chromo domain and ATPase domain but not the PHD domain are required for the function of PKL in regulating drought tolerance. Interestingly, we find that the DNA-binding domain (DBD) is essential for the protein stability of PKL. Furthermore, we demonstrate that the SUMO E3 ligase MMS21 interacts with and enhances the protein stability of PKL. Genetic interaction analysis shows that MMS21 and PKL additively regulate plant drought tolerance. Collectively, our findings uncover a MMS21-PKL-AFL1 module in regulating plant drought tolerance and offer insights into a novel strategy to improve crop drought tolerance.
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Affiliation(s)
- Yexing Jing
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ziyi Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Ruizhen Yang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yunwei Zhang
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Weihua Qiao
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Yun Zhou
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475001, China
| | - Jiaqiang Sun
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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7
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Wang J, Sun Z, Liu H, Yue L, Wang F, Liu S, Su B, Liu B, Kong F, Fang C. Genome-Wide Identification and Characterization of the Soybean Snf2 Gene Family and Expression Response to Rhizobia. Int J Mol Sci 2023; 24:ijms24087250. [PMID: 37108411 PMCID: PMC10138738 DOI: 10.3390/ijms24087250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 04/07/2023] [Accepted: 04/11/2023] [Indexed: 04/29/2023] Open
Abstract
Sucrose nonfermenting 2 (Snf2) family proteins are the core component of chromatin remodeling complexes that can alter chromatin structure and nucleosome position by utilizing the energy of ATP, playing a vital role in transcription regulation, DNA replication, and DNA damage repair. Snf2 family proteins have been characterized in various species including plants, and they have been found to regulate development and stress responses in Arabidopsis. Soybean (Glycine max) is an important food and economic crop worldwide, unlike other non-leguminous crops, soybeans can form a symbiotic relationship with rhizobia for biological nitrogen fixation. However, little is known about Snf2 family proteins in soybean. In this study, we identified 66 Snf2 family genes in soybean that could be classified into six groups like Arabidopsis, unevenly distributed on 20 soybean chromosomes. Phylogenetic analysis with Arabidopsis revealed that these 66 Snf2 family genes could be divided into 18 subfamilies. Collinear analysis showed that segmental duplication was the main mechanism for expansion of Snf2 genes rather than tandem repeats. Further evolutionary analysis indicated that the duplicated gene pairs had undergone purifying selection. All Snf2 proteins contained seven domains, and each Snf2 protein had at least one SNF2_N domain and one Helicase_C domain. Promoter analysis revealed that most Snf2 genes had cis-elements associated with jasmonic acid, abscisic acid, and nodule specificity in their promoter regions. Microarray data and real-time quantitative PCR (qPCR) analysis revealed that the expression profiles of most Snf2 family genes were detected in both root and nodule tissues, and some of them were found to be significantly downregulated after rhizobial infection. In this study, we conducted a comprehensive analysis of the soybean Snf2 family genes and demonstrated their responsiveness to Rhizobia infection. This provides insight into the potential roles of Snf2 family genes in soybean symbiotic nodulation.
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Affiliation(s)
- Jianhao Wang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Zhihui Sun
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Huan Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Lin Yue
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fan Wang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Shuangrong Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Bohong Su
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Baohui Liu
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Fanjiang Kong
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Chao Fang
- Guangzhou Key Laboratory of Crop Gene Editing, Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
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Chen G, Mishina K, Zhu H, Kikuchi S, Sassa H, Oono Y, Komatsuda T. Genome-Wide Analysis of Snf2 Gene Family Reveals Potential Role in Regulation of Spike Development in Barley. Int J Mol Sci 2022; 24:ijms24010457. [PMID: 36613901 PMCID: PMC9820626 DOI: 10.3390/ijms24010457] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 12/16/2022] [Accepted: 12/20/2022] [Indexed: 12/29/2022] Open
Abstract
Sucrose nonfermenting 2 (Snf2) family proteins, as the catalytic core of ATP-dependent chromatin remodeling complexes, play important roles in nuclear processes as diverse as DNA replication, transcriptional regulation, and DNA repair and recombination. The Snf2 gene family has been characterized in several plant species; some of its members regulate flower development in Arabidopsis. However, little is known about the members of the family in barley (Hordeum vulgare). Here, 38 Snf2 genes unevenly distributed among seven chromosomes were identified from the barley (cv. Morex) genome. Phylogenetic analysis categorized them into 18 subfamilies. They contained combinations of 21 domains and consisted of 3 to 34 exons. Evolution analysis revealed that segmental duplication contributed predominantly to the expansion of the family in barley, and the duplicated gene pairs have undergone purifying selection. About eight hundred Snf2 family genes were identified from 20 barley accessions, ranging from 38 to 41 genes in each. Most of these genes were subjected to purification selection during barley domestication. Most were expressed abundantly during spike development. This study provides a comprehensive characterization of barley Snf2 family members, which should help to improve our understanding of their potential regulatory roles in barley spike development.
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Affiliation(s)
- Gang Chen
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Kohei Mishina
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
| | - Hongjing Zhu
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Shinji Kikuchi
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Hidenori Sassa
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
| | - Youko Oono
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
- Correspondence: (Y.O.); (T.K.); Tel.: +81-29-838-7443 (Y.O.); +86-531-6665-8143 (T.K.)
| | - Takao Komatsuda
- Institute of Crop Science, National Agriculture and Food Research Organization (NARO), 2-1-2 Kannondai, Tsukuba 305-8602, Japan
- Graduate School of Horticulture, Chiba University, 648 Matsudo, Matsudo 271-8510, Japan
- Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/Shandong Technology Innovation Center of Wheat, Jinan 252100, China
- Correspondence: (Y.O.); (T.K.); Tel.: +81-29-838-7443 (Y.O.); +86-531-6665-8143 (T.K.)
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9
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Liang Z, Yuan L, Xiong X, Hao Y, Song X, Zhu T, Yu Y, Fu W, Lei Y, Xu J, Liu J, Li JF, Li C. The transcriptional repressors VAL1 and VAL2 mediate genome-wide recruitment of the CHD3 chromatin remodeler PICKLE in Arabidopsis. THE PLANT CELL 2022; 34:3915-3935. [PMID: 35866997 PMCID: PMC9516181 DOI: 10.1093/plcell/koac217] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Accepted: 07/19/2022] [Indexed: 05/30/2023]
Abstract
PICKLE (PKL) is a chromodomain helicase DNA-binding domain 3 (CHD3) chromatin remodeler that plays essential roles in controlling the gene expression patterns that determine developmental identity in plants, but the molecular mechanisms through which PKL is recruited to its target genes remain elusive. Here, we define a cis-motif and trans-acting factors mechanism that governs the genomic occupancy profile of PKL in Arabidopsis thaliana. We show that two homologous trans-factors VIVIPAROUS1/ABI3-LIKE1 (VAL1) and VAL2 physically interact with PKL in vivo, localize extensively to PKL-occupied regions in the genome, and promote efficient PKL recruitment at thousands of target genes, including those involved in seed maturation. Transcriptome analysis and genetic interaction studies reveal a close cooperation of VAL1/VAL2 and PKL in regulating gene expression and developmental fate. We demonstrate that this recruitment operates at two master regulatory genes, ABSCISIC ACID INSENSITIVE3 and AGAMOUS-LIKE 15, to repress the seed maturation program and ensure the seed-to-seedling transition. Together, our work unveils a general rule through which the CHD3 chromatin remodeler PKL binds to its target chromatin in plants.
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Affiliation(s)
- Zhenwei Liang
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Liangbing Yuan
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
- College of Life Sciences, Anhui Normal University, Wuhu 241000, China
| | - Xiangyu Xiong
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yuanhao Hao
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Xin Song
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Tao Zhu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yaoguang Yu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Wei Fu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Yawen Lei
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jianqu Xu
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
| | - Jun Liu
- Guangdong Provincial Key Laboratory for Crop Germplasm Resources Preservation and Utilization, Agro-biological Gene Research Center, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
| | - Jian-Feng Li
- School of Life Sciences, State Key Laboratory of Biocontrol, Guangdong Provincial Key Laboratory of Plant Resource, Sun Yat-Sen University, Guangzhou 510275, China
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10
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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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11
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Coronatine Enhances Chilling Tolerance of Tomato Plants by Inducing Chilling-Related Epigenetic Adaptations and Transcriptional Reprogramming. Int J Mol Sci 2022; 23:ijms231710049. [PMID: 36077443 PMCID: PMC9456409 DOI: 10.3390/ijms231710049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 08/26/2022] [Accepted: 08/30/2022] [Indexed: 11/17/2022] Open
Abstract
Low temperature is an important environmental factor limiting the widespread planting of tropical and subtropical crops. The application of plant regulator coronatine, which is an analog of Jasmonic acid (JA), is an effective approach to enhancing crop’s resistance to chilling stress and other abiotic stresses. However, the function and mechanism of coronatine in promoting chilling resistance of tomato is unknown. In this study, coronatine treatment was demonstrated to significantly increase tomato chilling tolerance. Coronatine increases H3K4me3 modifications to make greater chromatin accessibility in multiple chilling-activated genes. Corresponding to that, the expression of CBFs, other chilling-responsive transcription factor (TF) genes, and JA-responsive genes is significantly induced by coronatine to trigger an extensive transcriptional reprogramming, thus resulting in a comprehensive chilling adaptation. These results indicate that coronatine enhances the chilling tolerance of tomato plants by inducing epigenetic adaptations and transcriptional reprogramming.
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12
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Satyakam, Zinta G, Singh RK, Kumar R. Cold adaptation strategies in plants—An emerging role of epigenetics and antifreeze proteins to engineer cold resilient plants. Front Genet 2022; 13:909007. [PMID: 36092945 PMCID: PMC9459425 DOI: 10.3389/fgene.2022.909007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Cold stress adversely affects plant growth, development, and yield. Also, the spatial and geographical distribution of plant species is influenced by low temperatures. Cold stress includes chilling and/or freezing temperatures, which trigger entirely different plant responses. Freezing tolerance is acquired via the cold acclimation process, which involves prior exposure to non-lethal low temperatures followed by profound alterations in cell membrane rigidity, transcriptome, compatible solutes, pigments and cold-responsive proteins such as antifreeze proteins. Moreover, epigenetic mechanisms such as DNA methylation, histone modifications, chromatin dynamics and small non-coding RNAs play a crucial role in cold stress adaptation. Here, we provide a recent update on cold-induced signaling and regulatory mechanisms. Emphasis is given to the role of epigenetic mechanisms and antifreeze proteins in imparting cold stress tolerance in plants. Lastly, we discuss genetic manipulation strategies to improve cold tolerance and develop cold-resistant plants.
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13
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Xiao W, Sun Y, Xu J, Zhang N, Dong L. uORF-Mediated Translational Regulation of ATF4 Serves as an Evolutionarily Conserved Mechanism Contributing to Non-Small-Cell Lung Cancer (NSCLC) and Stress Response. J Mol Evol 2022; 90:375-388. [PMID: 35962830 PMCID: PMC9375200 DOI: 10.1007/s00239-022-10068-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Accepted: 07/20/2022] [Indexed: 11/30/2022]
Abstract
Diseases and environmental stresses are two distinct challenges for virtually all living organisms. In light of evolution, cellular responses to diseases and stresses might share similar molecular mechanisms, but the detailed regulation pathway is not reported yet. We obtained the transcriptomes and translatomes from several NSCLC (non-small-cell lung cancer) patients as well as from different species under normal or stress conditions. We found that the translation level of gene ATF4 is remarkably enhanced in NSCLC due to the reduced number of ribosomes binding to its upstream open reading frames (uORFs). We also showed the evolutionary conservation of this uORF-ATF4 regulation in the stress response of other species. Molecular experiments showed that knockdown of ATF4 reduced the cell growth rate while overexpression of ATF4 enhanced cell growth, especially for the ATF4 allele with mutated uORFs. Population genetics analyses in multiple species verified that the mutations that abolish uATGs (start codon of uORFs) are highly deleterious, suggesting the functional importance of uORFs. Our study proposes an evolutionarily conserved pattern that enhances the ATF4 translation by uORFs upon stress or disease. We generalized the concept of cellular response to diseases and stresses. These two biological processes may share similar molecular mechanisms.
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Affiliation(s)
- Wenjing Xiao
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China.
| | - Yang Sun
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Jinpeng Xu
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Na Zhang
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
| | - Lina Dong
- Department of Radiotherapy, The Affiliated Hospital of Qingdao University, Qingdao, Shandong, China
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14
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Yang T, Wang D, Tian G, Sun L, Yang M, Yin X, Xiao J, Sheng Y, Zhu D, He H, Zhou Y. Chromatin remodeling complexes regulate genome architecture in Arabidopsis. THE PLANT CELL 2022; 34:2638-2651. [PMID: 35445713 PMCID: PMC9252501 DOI: 10.1093/plcell/koac117] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Accepted: 04/13/2022] [Indexed: 05/29/2023]
Abstract
In eukaryotes, three-dimensional (3D) chromatin architecture maintains genome stability and is important in regulating gene transcription. However, little is known about the mechanisms by which diverse ATP-dependent chromatin remodeling complexes regulate the 3D chromatin structure in plants. We examined the 3D chromatin structure within the ATPase subunit of the SWI/SNF, ISWI, INO80, and CHD remodeling complexes in wild-type (WT) and mutant Arabidopsis thaliana plants by combining high-throughput sequencing with in situ Hi-C, the enrichment of histone marks, nucleosome density, and gene expression. We found that compartment regions switched and compartmental strength was significantly weakened in all four enzyme mutants. Chromatin remodeling complexes differentially regulated the nucleosome distribution pattern and density within the switching compartments. Alterations of nucleosome distribution pattern and density were associated with a reduction in H3K27me3 levels in the chromatin remodeling enzyme mutants and led to compartment switching. Our data show that chromatin remodeling complexes regulate the linear nucleosome distribution pattern and density to promote H3K27me3 deposition, which in turn regulates 3D chromatin structure.
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Affiliation(s)
- Tingting Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Dingyue Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Guangmei Tian
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
- Academy for Advanced Interdisciplinary Studies, Peking University, Beijing 100871, China
| | - Linhua Sun
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
- School of Life Science, Peking University, 100871 Beijing, China
| | - Minqi Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Xiaochang Yin
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Jun Xiao
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, 100101 Beijing, China
- CAS-JIC Centre of Excellence for Plant and Microbial Science, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101 Beijing, China
| | - Yu Sheng
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
| | - Danmeng Zhu
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
- School of Life Science, Peking University, 100871 Beijing, China
| | - Hang He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, 100871 Beijing, China
- School of Life Science, Peking University, 100871 Beijing, China
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15
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Guo M, Zhao H, He Z, Zhang W, She Z, Mohammadi MA, Shi C, Yan M, Tian D, Qin Y. Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice. FRONTIERS IN PLANT SCIENCE 2022; 13:910663. [PMID: 35712583 PMCID: PMC9194907 DOI: 10.3389/fpls.2022.910663] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 05/04/2022] [Indexed: 06/15/2023]
Abstract
Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.
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Affiliation(s)
- Mingliang Guo
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, College of Plant Protection, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Heming Zhao
- Center for Crop Biotechnology, College of Agriculture, Anhui Science and Technology University, Fengyang, China
| | - Zhimei He
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wenchao Zhang
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zeyuan She
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Mohammad Aqa Mohammadi
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Chao Shi
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Maokai Yan
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
| | - Dagang Tian
- Fujian Provincial Key Laboratory of Genetic Engineering for Agriculture, Biotechnology Research Institute, Fujian Academy of Agricultural Sciences, Fuzhou, China
| | - Yuan Qin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab of Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, China
- Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
- Pingtan Science and Technology Research Institute, Fujian Agriculture and Forestry University, Fuzhou, China
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16
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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: 47] [Impact Index Per Article: 23.5] [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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17
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Leal AR, Barros PM, Parizot B, Sapeta H, Vangheluwe N, Andersen TG, Beeckman T, Oliveira MM. Translational profile of developing phellem cells in Arabidopsis thaliana roots. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:899-915. [PMID: 35106861 DOI: 10.1111/tpj.15691] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 12/20/2021] [Accepted: 01/26/2022] [Indexed: 06/14/2023]
Abstract
The phellem is a specialized boundary tissue providing the first line of defense against abiotic and biotic stresses in organs undergoing secondary growth. Phellem cells undergo several differentiation steps, which include cell wall suberization, cell expansion, and programmed cell death. Yet, the molecular players acting particularly in phellem cell differentiation remain poorly described, particularly in the widely used model plant Arabidopsis thaliana. Using specific marker lines we followed the onset and progression of phellem differentiation in A. thaliana roots and further targeted the translatome of newly developed phellem cells using translating ribosome affinity purification followed by mRNA sequencing (TRAP-SEQ). We showed that phellem suberization is initiated early after phellogen (cork cambium) division. The specific translational landscape was organized in three main domains related to energy production, synthesis and transport of cell wall components, and response to stimulus. Novel players in phellem differentiation related to suberin monomer transport and assembly as well as novel transcription regulators were identified. This strategy provided an unprecedented resolution of the translatome of developing phellem cells, giving a detailed and specific view on the molecular mechanisms acting on cell differentiation in periderm tissues of the model plant Arabidopsis.
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Affiliation(s)
- Ana Rita Leal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), GPlantS, Av. da República, 2780-157, Oeiras, Portugal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Pedro Miguel Barros
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), GPlantS, Av. da República, 2780-157, Oeiras, Portugal
| | - Boris Parizot
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Helena Sapeta
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), GPlantS, Av. da República, 2780-157, Oeiras, Portugal
| | - Nick Vangheluwe
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - Tonni Grube Andersen
- Department of Plant Molecular Biology, Biophore, University of Lausanne, CH-1015, Lausanne, Switzerland
| | - Tom Beeckman
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium
- VIB Center for Plant Systems Biology, Technologiepark 71, 9052, Ghent, Belgium
| | - M Margarida Oliveira
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), GPlantS, Av. da República, 2780-157, Oeiras, Portugal
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18
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Guk JY, Jang MJ, Kim S. Identification of novel PHD-finger genes in pepper by genomic re-annotation and comparative analyses. BMC PLANT BIOLOGY 2022; 22:206. [PMID: 35443608 PMCID: PMC9020097 DOI: 10.1186/s12870-022-03580-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 04/06/2022] [Indexed: 06/01/2023]
Abstract
BACKGROUND The plant homeodomain (PHD)-finger gene family that belongs to zinc-finger genes, plays an important role in epigenetics by regulating gene expression in eukaryotes. However, inaccurate annotation of PHD-finger genes hinders further downstream comparative, evolutionary, and functional studies. RESULTS We performed genome-wide re-annotation in Arabidopsis thaliana (Arabidopsis), Oryza sativa (rice), Capsicum annuum (pepper), Solanum tuberosum (potato), and Solanum lycopersicum (tomato) to better understand the role of PHD-finger genes in these species. Our investigation identified 875 PHD-finger genes, of which 225 (26% of total) were newly identified, including 57 (54%) novel PHD-finger genes in pepper. The PHD-finger genes of the five plant species have various integrated domains that may be responsible for the diversification of structures and functions of these genes. Evolutionary analyses suggest that PHD-finger genes were expanded recently by lineage-specific duplication, especially in pepper and potato, resulting in diverse repertoires of PHD-finger genes among the species. We validated the expression of six newly identified PHD-finger genes in pepper with qRT-PCR. Transcriptome analyses suggest potential functions of PHD-finger genes in response to various abiotic stresses in pepper. CONCLUSIONS Our data, including the updated annotation of PHD-finger genes, provide useful information for further evolutionary and functional analyses to better understand the roles of the PHD-finger gene family in pepper.
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Affiliation(s)
- Ji-Yoon Guk
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Min-Jeong Jang
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea
| | - Seungill Kim
- Department of Environmental Horticulture, University of Seoul, Seoul, 02504, Republic of Korea.
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19
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Saeed F, Chaudhry UK, Bakhsh A, Raza A, Saeed Y, Bohra A, Varshney RK. Moving Beyond DNA Sequence to Improve Plant Stress Responses. Front Genet 2022; 13:874648. [PMID: 35518351 PMCID: PMC9061961 DOI: 10.3389/fgene.2022.874648] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Accepted: 03/31/2022] [Indexed: 01/25/2023] Open
Abstract
Plants offer a habitat for a range of interactions to occur among different stress factors. Epigenetics has become the most promising functional genomics tool, with huge potential for improving plant adaptation to biotic and abiotic stresses. Advances in plant molecular biology have dramatically changed our understanding of the molecular mechanisms that control these interactions, and plant epigenetics has attracted great interest in this context. Accumulating literature substantiates the crucial role of epigenetics in the diversity of plant responses that can be harnessed to accelerate the progress of crop improvement. However, harnessing epigenetics to its full potential will require a thorough understanding of the epigenetic modifications and assessing the functional relevance of these variants. The modern technologies of profiling and engineering plants at genome-wide scale provide new horizons to elucidate how epigenetic modifications occur in plants in response to stress conditions. This review summarizes recent progress on understanding the epigenetic regulation of plant stress responses, methods to detect genome-wide epigenetic modifications, and disentangling their contributions to plant phenotypes from other sources of variations. Key epigenetic mechanisms underlying stress memory are highlighted. Linking plant response with the patterns of epigenetic variations would help devise breeding strategies for improving crop performance under stressed scenarios.
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Affiliation(s)
- Faisal Saeed
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Usman Khalid Chaudhry
- Department of Agricultural Genetic Engineering, Faculty of Agricultural Sciences and Technologies, Nigde Omer Halisdemir University, Nigde, Turkey
| | - Allah Bakhsh
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore, Pakistan
| | - Ali Raza
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
| | - Yasir Saeed
- Department of Plant Pathology, Faculty of Agriculture, University of Agriculture, Faisalabad, Pakistan
| | - Abhishek Bohra
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
| | - Rajeev K. Varshney
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Oil Crops Research Institute, Center of Legume Crop Genetics and Systems Biology/College of Agriculture, Fujian Agriculture and Forestry University (FAFU), Fuzhou, China
- State Agricultural Biotechnology Centre, Centre for Crop and Food Innovation, Murdoch University, Murdoch, WA, Australia
- Center of Excellence in Genomics & Systems Biology, International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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20
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Transcriptome Analysis of Populus euphratica under Salt Treatment and PeERF1 Gene Enhances Salt Tolerance in Transgenic Populus alba × Populus glandulosa. Int J Mol Sci 2022; 23:ijms23073727. [PMID: 35409087 PMCID: PMC8998595 DOI: 10.3390/ijms23073727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 03/24/2022] [Accepted: 03/24/2022] [Indexed: 12/02/2022] Open
Abstract
Populus euphratica is mainly distributed in desert environments with dry and hot climate in summer and cold in winter. Compared with other poplars, P. euphratica is more resistant to salt stress. It is critical to investigate the transcriptome and molecular basis of salt tolerance in order to uncover stress-related genes. In this study, salt-tolerant treatment of P. euphratica resulted in an increase in osmo-regulatory substances and recovery of antioxidant enzymes. To improve the mining efficiency of candidate genes, the analysis combining both the transcriptome WGCNA and the former GWAS results was selected, and a range of key regulatory factors with salt resistance were found. The PeERF1 gene was highly connected in the turquoise modules with significant differences in salt stress traits, and the expression levels were significantly different in each treatment. For further functional verification of PeERF1, we obtained stable overexpression and dominant suppression transgenic lines by transforming into Populus alba × Populusglandulosa. The growth and physiological characteristics of the PeERF1 overexpressed plants were better than that of the wild type under salt stress. Transcriptome analysis of leaves of transgenic lines and WT revealed that highly enriched GO terms in DEGs were associated with stress responses, including abiotic stimuli responses, chemical responses, and oxidative stress responses. The result is helpful for in-depth analysis of the salt tolerance mechanism of poplar. This work provides important genes for poplar breeding with salt tolerance.
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21
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Acharya BR, Sandhu D, Dueñas C, Ferreira JFS, Grover KK. Deciphering Molecular Mechanisms Involved in Salinity Tolerance in Guar ( Cyamopsis tetragonoloba (L.) Taub.) Using Transcriptome Analyses. PLANTS (BASEL, SWITZERLAND) 2022; 11:plants11030291. [PMID: 35161272 PMCID: PMC8838131 DOI: 10.3390/plants11030291] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/14/2022] [Accepted: 01/18/2022] [Indexed: 05/09/2023]
Abstract
Guar is a commercially important legume crop known for guar gum. Guar is tolerant to various abiotic stresses, but the mechanisms involved in its salinity tolerance are not well established. This study aimed to understand molecular mechanisms of salinity tolerance in guar. RNA sequencing (RNA-Seq) was employed to study the leaf and root transcriptomes of salt-tolerant (Matador) and salt-sensitive (PI 340261) guar genotypes under control and salinity. Our analyses identified a total of 296,114 unigenes assembled from 527 million clean reads. Transcriptome analysis revealed that the gene expression differences were more pronounced between salinity treatments than between genotypes. Differentially expressed genes associated with stress-signaling pathways, transporters, chromatin remodeling, microRNA biogenesis, and translational machinery play critical roles in guar salinity tolerance. Genes associated with several transporter families that were differentially expressed during salinity included ABC, MFS, GPH, and P-ATPase. Furthermore, genes encoding transcription factors/regulators belonging to several families, including SNF2, C2H2, bHLH, C3H, and MYB were differentially expressed in response to salinity. This study revealed the importance of various biological pathways during salinity stress and identified several candidate genes that may be used to develop salt-tolerant guar genotypes that might be suitable for cultivation in marginal soils with moderate to high salinity or using degraded water.
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Affiliation(s)
- Biswa R. Acharya
- U.S. Salinity Lab (USDA-ARS), 450 W Big Springs Road, Riverside, CA 92507, USA; (B.R.A.); (J.F.S.F.)
- College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA;
| | - Devinder Sandhu
- U.S. Salinity Lab (USDA-ARS), 450 W Big Springs Road, Riverside, CA 92507, USA; (B.R.A.); (J.F.S.F.)
- Correspondence: (D.S.); (K.K.G.)
| | - Christian Dueñas
- College of Natural and Agricultural Sciences, University of California Riverside, 900 University Avenue, Riverside, CA 92521, USA;
| | - Jorge F. S. Ferreira
- U.S. Salinity Lab (USDA-ARS), 450 W Big Springs Road, Riverside, CA 92507, USA; (B.R.A.); (J.F.S.F.)
| | - Kulbhushan K. Grover
- Department of Plant and Environmental Sciences, New Mexico State University, Las Cruces, NM 88003, USA
- Correspondence: (D.S.); (K.K.G.)
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22
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Kumar S, Kaur S, Seem K, Kumar S, Mohapatra T. Understanding 3D Genome Organization and Its Effect on Transcriptional Gene Regulation Under Environmental Stress in Plant: A Chromatin Perspective. Front Cell Dev Biol 2021; 9:774719. [PMID: 34957106 PMCID: PMC8692796 DOI: 10.3389/fcell.2021.774719] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 11/23/2021] [Indexed: 01/17/2023] Open
Abstract
The genome of a eukaryotic organism is comprised of a supra-molecular complex of chromatin fibers and intricately folded three-dimensional (3D) structures. Chromosomal interactions and topological changes in response to the developmental and/or environmental stimuli affect gene expression. Chromatin architecture plays important roles in DNA replication, gene expression, and genome integrity. Higher-order chromatin organizations like chromosome territories (CTs), A/B compartments, topologically associating domains (TADs), and chromatin loops vary among cells, tissues, and species depending on the developmental stage and/or environmental conditions (4D genomics). Every chromosome occupies a separate territory in the interphase nucleus and forms the top layer of hierarchical structure (CTs) in most of the eukaryotes. While the A and B compartments are associated with active (euchromatic) and inactive (heterochromatic) chromatin, respectively, having well-defined genomic/epigenomic features, TADs are the structural units of chromatin. Chromatin architecture like TADs as well as the local interactions between promoter and regulatory elements correlates with the chromatin activity, which alters during environmental stresses due to relocalization of the architectural proteins. Moreover, chromatin looping brings the gene and regulatory elements in close proximity for interactions. The intricate relationship between nucleotide sequence and chromatin architecture requires a more comprehensive understanding to unravel the genome organization and genetic plasticity. During the last decade, advances in chromatin conformation capture techniques for unravelling 3D genome organizations have improved our understanding of genome biology. However, the recent advances, such as Hi-C and ChIA-PET, have substantially increased the resolution, throughput as well our interest in analysing genome organizations. The present review provides an overview of the historical and contemporary perspectives of chromosome conformation capture technologies, their applications in functional genomics, and the constraints in predicting 3D genome organization. We also discuss the future perspectives of understanding high-order chromatin organizations in deciphering transcriptional regulation of gene expression under environmental stress (4D genomics). These might help design the climate-smart crop to meet the ever-growing demands of food, feed, and fodder.
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Affiliation(s)
- Suresh Kumar
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Simardeep Kaur
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
| | - Karishma Seem
- Division of Biochemistry, ICAR-Indian Agricultural Research Institute, New Delhi, India
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23
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Liu J, Chang C. Concerto on Chromatin: Interplays of Different Epigenetic Mechanisms in Plant Development and Environmental Adaptation. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10122766. [PMID: 34961235 PMCID: PMC8705648 DOI: 10.3390/plants10122766] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Revised: 11/30/2021] [Accepted: 12/10/2021] [Indexed: 05/26/2023]
Abstract
Epigenetic mechanisms such as DNA methylation, histone post-translational modifications, chromatin remodeling, and noncoding RNAs, play important roles in regulating plant gene expression, which is involved in various biological processes including plant development and stress responses. Increasing evidence reveals that these different epigenetic mechanisms are highly interconnected, thereby contributing to the complexity of transcriptional reprogramming in plant development processes and responses to environmental stresses. Here, we provide an overview of recent advances in understanding the epigenetic regulation of plant gene expression and highlight the crosstalk among different epigenetic mechanisms in making plant developmental and stress-responsive decisions. Structural, physical, transcriptional and metabolic bases for these epigenetic interplays are discussed.
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Landi S, Capasso G, Esposito S. Different G6PDH isoforms show specific roles in acclimation to cold stress at various growth stages of barley (Hordeum vulgare) and Arabidopsis thaliana. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2021; 169:190-202. [PMID: 34801973 DOI: 10.1016/j.plaphy.2021.11.017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/19/2021] [Accepted: 11/11/2021] [Indexed: 06/13/2023]
Abstract
Low temperatures (0-10 °C) represent a major physiological stress for plants, negatively affecting both their growth rates and overall growth. Cold stress may induce a wide range of negative physiological effects, from oxidative stress to photosynthetic damage. We investigated the effects of low temperatures in two different model plants, Arabidopsis thaliana and Hordeum vulgare. We tested whether the oxidative pentose phosphate pathway (OPPP) is involved in the increase of reductants' levels needed to counteract oxidative stress induced by cold. The expression, occurrence, and activity of different glucose-6-phosphate dehydrogenase (G6PDH, EC 1.1.1.49) isoforms during cold stress and plant recovery from low temperatures, were measured at different growth stages from early germinated to mature pot-grown plants. Our results showed plants exhibited changes in different stress markers; ascorbate peroxidase - APX, catalase - CAT, proline, malondialdehyde, H2O2, NADPH/NADP+. We found that a major role in cold acclimation for cytosolic- and peroxisome-located G6PDHs, and different roles for plastidial/chloroplastic isoforms. This suggests that G6PDH isoforms may regulate redox homeostasis in low temperatures, in order to support the increased and continued demand of reductants during both cold stress and recovery stages. Furthermore, we found a significant involvement of (6PGDH), strengthening the idea that the contribution of the whole oxidative pentose phosphate pathway (OPPP) is required to sustain reductant supply under cold stress.
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Affiliation(s)
- Simone Landi
- Department of Biology, University of Naples Federico II, Complesso Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Giorgia Capasso
- Department of Biology, University of Naples Federico II, Complesso Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy
| | - Sergio Esposito
- Department of Biology, University of Naples Federico II, Complesso Monte Sant'Angelo, Via Cinthia, 80126, Napoli, Italy.
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25
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Yung WS, Li MW, Sze CC, Wang Q, Lam HM. Histone modifications and chromatin remodelling in plants in response to salt stress. PHYSIOLOGIA PLANTARUM 2021; 173:1495-1513. [PMID: 34028035 DOI: 10.1111/ppl.13467] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
In the face of global food security crises, it is necessary to boost agricultural production. One factor hampering the attempts to increase food production is elevated soil salinity, which can be due to salt that is naturally present in the soil or a consequence of excessive or prolonged irrigation or application of fertiliser. In response to environmental stresses, plants activate multiple molecular mechanisms, including the timely activation of stress-responsive transcriptional networks. However, in the case of salt stress, the combined effects of the initial osmotic shock and the subsequent ion-specific stress increase the complexity in the selective regulation of gene expressions involved in restoring or maintaining osmotic balance, ion homeostasis and reactive oxygen species scavenging. Histone modifications and chromatin remodelling are important epigenetic processes that regulate gene expressions by modifying the chromatin status and recruiting transcription regulators. In this review, we have specifically summarised the currently available knowledge on histone modifications and chromatin remodelling in relation to plant responses to salt stress. Current findings have revealed the functional importance of chromatin modifiers in regulating salt tolerance and identified the effector genes affected by epigenetic modifications, although counteraction between modifiers within the same family may occur. Emerging evidence has also illustrated the crosstalk between epigenetic modifications and hormone signalling pathways which involves formation of protein complexes. With an improved understanding of these processes, plant breeders will be able to develop alternative strategies using genome editing technologies for crop improvement.
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Affiliation(s)
- Wai-Shing Yung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ching-Ching Sze
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qianwen Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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26
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Epigenetic control of abiotic stress signaling in plants. Genes Genomics 2021; 44:267-278. [PMID: 34515950 DOI: 10.1007/s13258-021-01163-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmental cues; such responses can be achieved by fine-tuning or controlling genetic and epigenetic regulatory systems. Epigenetic mechanisms such as DNA or histone modifications and modulation of chromatin accessibility have been shown to regulate the expression of stress-responsive genes in struggles against abiotic stresses. OBJECTIVE Herein, the current progress in elucidating the epigenetic regulation of abiotic stress signaling in plants has been summarized in order to further understand the systems plants utilize to effectively respond to abiotic stresses. METHODS This review focuses on the action mechanisms of various components that epigenetically regulate plant abiotic stress responses, mainly in terms of DNA methylation, histone methylation/acetylation, and chromatin remodeling. CONCLUSIONS This review can be considered a basis for further research into understanding the epigenetic control system for abiotic stress responses in plants. Moreover, the knowledge of such systems can be effectively applied in developing novel methods to generate abiotic stress resistant crops.
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27
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Coordinated Role of Nitric Oxide, Ethylene, Nitrogen, and Sulfur in Plant Salt Stress Tolerance. STRESSES 2021. [DOI: 10.3390/stresses1030014] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Salt stress significantly contributes to major losses in agricultural productivity worldwide. The sustainable approach for salinity-accrued toxicity has been explored. The use of plant growth regulators/phytohormones, mineral nutrients and other signaling molecules is one of the major approaches for reversing salt-induced toxicity in plants. Application of the signaling molecules such as nitric oxide (NO) and ethylene (ETH) and major mineral nutrient such as nitrogen (N) and sulfur (S) play significant roles in combatting the major consequences of salt stress impacts in plants. However, the literature available on gaseous signaling molecules (NO/ETH) or/and mineral nutrients (N/S) stands alone, and major insights into the role of NO or/and ETH along with N and S in plant-tolerance to salt remained unclear. Thus, this review aimed to (a) briefly overview salt stress and highlight salt-induced toxicity, (b) appraise the literature reporting potential mechanisms underlying the role of gaseous signaling molecules and mineral nutrient in salt stress tolerance, and (c) discuss NO and ETH along with N and S in relation to salt stress tolerance. In addition, significant issues that have still to be investigated in this context have been mentioned.
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28
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Romero-Montepaone S, Sellaro R, Esteban Hernando C, Costigliolo-Rojas C, Bianchimano L, Ploschuk EL, Yanovsky MJ, Casal JJ. Functional convergence of growth responses to shade and warmth in Arabidopsis. THE NEW PHYTOLOGIST 2021; 231:1890-1905. [PMID: 33909310 DOI: 10.1111/nph.17430] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Shade and warmth promote the growth of the stem, but the degree of mechanistic convergence and functional association between these responses is not clear. We analysed the quantitative impact of mutations and natural genetic variation on the hypocotyl growth responses of Arabidopsis thaliana to shade and warmth, the relationship between the abundance of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and growth stimulation by shade or warmth, the effects of both cues on the transcriptome and the consequences of warm temperature on carbon balance. Growth responses to shade and warmth showed strong genetic linkage and similar dependence on PIF4 levels. Temperature increased growth and phototropism even within a range where damage by extreme high temperatures is unlikely to occur in nature. Both cues enhanced the expression of growth-related genes and reduced the expression of photosynthetic genes. However, only warmth enhanced the expression of genes involved in responses to heat. Warm temperatures substantially increased the amount of light required to compensate for the daily carbon dioxide balance. We propose that the main ecological function of hypocotyl growth responses to warmth is to increase the access of shaded photosynthetic organs to light, which implies functional convergence with shade avoidance.
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Affiliation(s)
- Sofía Romero-Montepaone
- Facultad de Agronomía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Universidad de Buenos Aires, Buenos Aires, C1417DSE, Argentina
| | - Romina Sellaro
- Facultad de Agronomía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Universidad de Buenos Aires, Buenos Aires, C1417DSE, Argentina
| | - Carlos Esteban Hernando
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires, C1405 BWE, Argentina
| | - Cecilia Costigliolo-Rojas
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires, C1405 BWE, Argentina
| | - Luciana Bianchimano
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires, C1405 BWE, Argentina
| | - Edmundo L Ploschuk
- Facultad de Agronomía, Cátedra de Cultivos Industriales, Universidad de Buenos Aires, Av. San Martín 4453, Buenos Aires, C1417DSE, Argentina
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires, C1405 BWE, Argentina
| | - Jorge J Casal
- Facultad de Agronomía, Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura (IFEVA), Universidad de Buenos Aires, Buenos Aires, C1417DSE, Argentina
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires, CONICET, Buenos Aires, C1405 BWE, Argentina
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29
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Hereme R, Galleguillos C, Morales-Navarro S, Molina-Montenegro MA. What if the cold days return? Epigenetic mechanisms in plants to cold tolerance. PLANTA 2021; 254:46. [PMID: 34370110 DOI: 10.1007/s00425-021-03694-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The epigenetic could be an important, but seldom assessed, mechanisms in plants inhabiting cold ecosystems. Thus, this review could help to fill a gap in the current literature. Low temperatures are one of the most critical environmental conditions that negatively affect the growth, development, and geographic distribution of plants. Exposure to low temperatures results in a suit of physiological, biochemical and molecular modifications through the reprogramming of the expression of genes and transcription factors. Scientific evidence shows that the average annual temperature has increased in recent years worldwide, with cold ecosystems (polar and high mountain) being among the most sensitive to these changes. However, scientific evidence also indicates that there would be specific events of low temperatures, due it is highly relevant to know the capacity for adaptation, regulation and epigenetic memory in the face of these events, by plants. Epigenetic regulation has been described to play an important role in the face of environmental stimuli, especially in response to abiotic stress. Several studies on epigenetic mechanisms have focused on responses to stress as drought and/or salinity; however, there is a gap in the current literature considering those related to low temperatures. In this review, we focus on systematizing the information published to date, related to the regulation of epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNA-dependent silencing mechanisms, in the face of plant´s stress due to low temperatures. Finally, we present a schematic model about the potential responses by plants taking in count their epigenetic memory; considering a global warming scenario and with the presence or absence of extreme specific events of low temperatures.
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Affiliation(s)
- Rasme Hereme
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Talca, Chile
| | | | | | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Talca, Chile.
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Universidad Católica del Norte, Coquimbo, Chile.
- Centro de Investigaciones y Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile.
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30
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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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31
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Shen Q, Lin Y, Li Y, Wang G. Dynamics of H3K27me3 Modification on Plant Adaptation to Environmental Cues. PLANTS 2021; 10:plants10061165. [PMID: 34201297 PMCID: PMC8228231 DOI: 10.3390/plants10061165] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 05/30/2021] [Accepted: 06/01/2021] [Indexed: 12/13/2022]
Abstract
Given their sessile nature, plants have evolved sophisticated regulatory networks to confer developmental plasticity for adaptation to fluctuating environments. Epigenetic codes, like tri-methylation of histone H3 on Lys27 (H3K27me3), are evidenced to account for this evolutionary benefit. Polycomb repressive complex 2 (PRC2) and PRC1 implement and maintain the H3K27me3-mediated gene repression in most eukaryotic cells. Plants take advantage of this epigenetic machinery to reprogram gene expression in development and environmental adaption. Recent studies have uncovered a number of new players involved in the establishment, erasure, and regulation of H3K27me3 mark in plants, particularly highlighting new roles in plants’ responses to environmental cues. Here, we review current knowledge on PRC2-H3K27me3 dynamics occurring during plant growth and development, including its writers, erasers, and readers, as well as targeting mechanisms, and summarize the emerging roles of H3K27me3 mark in plant adaptation to environmental stresses.
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32
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In Response to Abiotic Stress, DNA Methylation Confers EpiGenetic Changes in Plants. PLANTS 2021; 10:plants10061096. [PMID: 34070712 PMCID: PMC8227271 DOI: 10.3390/plants10061096] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 05/26/2021] [Accepted: 05/27/2021] [Indexed: 02/07/2023]
Abstract
Epigenetics involves the heritable changes in patterns of gene expression determined by developmental and abiotic stresses, i.e., drought, cold, salinity, trace metals, and heat. Gene expression is driven by changes in DNA bases, histone proteins, the biogenesis of ncRNA, and changes in the nucleotide sequence. To cope with abiotic stresses, plants adopt certain changes driven by a sophisticated biological system. DNA methylation is a primary mechanism for epigenetic variation, which can induce phenotypic alterations in plants under stress. Some of the stress-driven changes in plants are temporary, while some modifications may be stable and inheritable to the next generations to allow them to cope with such extreme stress challenges in the future. In this review, we discuss the pivotal role of epigenetically developed phenotypic characteristics in plants as an evolutionary process participating in adaptation and tolerance responses to abiotic and biotic stresses that alter their growth and development. We emphasize the molecular process underlying changes in DNA methylation, differential variation for different species, the roles of non-coding RNAs in epigenetic modification, techniques for studying DNA methylation, and its role in crop improvement in tolerance to abiotic stress (drought, salinity, and heat). We summarize DNA methylation as a significant future research priority for tailoring crops according to various challenging environmental issues.
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33
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Srivastava AK, Suresh Kumar J, Suprasanna P. Seed 'primeomics': plants memorize their germination under stress. Biol Rev Camb Philos Soc 2021; 96:1723-1743. [PMID: 33961327 DOI: 10.1111/brv.12722] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Revised: 04/06/2021] [Accepted: 04/09/2021] [Indexed: 12/28/2022]
Abstract
Seed priming is a pre-germination treatment administered through various chemical, physical and biological agents, which induce mild stress during the early phases of germination. Priming facilitates synchronized seed germination, better seedling establishment, improved plant growth and enhanced yield, especially in stressful environments. In parallel, the phenomenon of 'stress memory' in which exposure to a sub-lethal stress leads to better responses to future or recurring lethal stresses has gained widespread attention in recent years. The versatility and realistic yield gains associated with seed priming and its connection with stress memory make a critical examination useful for the design of robust approaches for maximizing future yield gains. Herein, a literature review identified selenium, salicylic acid, poly-ethylene glycol, CaCl2 and thiourea as the seed priming agents (SPRs) for which the most studies have been carried out. The average priming duration for SPRs generally ranged from 2 to 48 h, i.e. during phase I/II of germination. The major signalling events for regulating early seed germination, including the DOG1 (delay of germination 1)-abscisic acid (ABA)-heme regulatory module, ABA-gibberellic acid antagonism and nucleus-organelle communication are detailed. We propose that both seed priming and stress memory invoke a 'bet-hedging' strategy in plants, wherein their growth under optimal conditions is compromised in exchange for better growth under stressful conditions. The molecular basis of stress memory is explained at the level of chromatin reorganization, alternative transcript splicing, metabolite accumulation and autophagy. This provides a useful framework to study similar mechanisms operating during seed priming. In addition, we highlight the potential for merging findings on seed priming with those of stress memory, with the dual benefit of advancing fundamental research and boosting crop productivity. Finally, a roadmap for future work, entailing identification of SPR-responsive varieties and the development of dual/multiple-benefit SPRs, is proposed for enhancing SPR-mediated agricultural productivity worldwide.
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Affiliation(s)
- Ashish Kumar Srivastava
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India.,Homi Bhabha National Institute, Mumbai, 400094, India
| | - Jisha Suresh Kumar
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Penna Suprasanna
- Nuclear Agriculture and Biotechnology Division, Bhabha Atomic Research Centre, Mumbai, 400085, India
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34
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Pardal AJ, Piquerez SJM, Dominguez-Ferreras A, Frungillo L, Mastorakis E, Reilly E, Latrasse D, Concia L, Gimenez-Ibanez S, Spoel SH, Benhamed M, Ntoukakis V. Immunity onset alters plant chromatin and utilizes EDA16 to regulate oxidative homeostasis. PLoS Pathog 2021; 17:e1009572. [PMID: 34015058 PMCID: PMC8171942 DOI: 10.1371/journal.ppat.1009572] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 06/02/2021] [Accepted: 04/19/2021] [Indexed: 01/23/2023] Open
Abstract
Perception of microbes by plants leads to dynamic reprogramming of the transcriptome, which is essential for plant health. The appropriate amplitude of this transcriptional response can be regulated at multiple levels, including chromatin. However, the mechanisms underlying the interplay between chromatin remodeling and transcription dynamics upon activation of plant immunity remain poorly understood. Here, we present evidence that activation of plant immunity by bacteria leads to nucleosome repositioning, which correlates with altered transcription. Nucleosome remodeling follows distinct patterns of nucleosome repositioning at different loci. Using a reverse genetic screen, we identify multiple chromatin remodeling ATPases with previously undescribed roles in immunity, including EMBRYO SAC DEVELOPMENT ARREST 16, EDA16. Functional characterization of the immune-inducible chromatin remodeling ATPase EDA16 revealed a mechanism to negatively regulate immunity activation and limit changes in redox homeostasis. Our transcriptomic data combined with MNase-seq data for EDA16 functional knock-out and over-expressor mutants show that EDA16 selectively regulates a defined subset of genes involved in redox signaling through nucleosome repositioning. Thus, collectively, chromatin remodeling ATPases fine-tune immune responses and provide a previously uncharacterized mechanism of immune regulation.
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Affiliation(s)
- Alonso J. Pardal
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Sophie J. M. Piquerez
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | | | - Lucas Frungillo
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Emma Reilly
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Lorenzo Concia
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Selena Gimenez-Ibanez
- Plant Molecular Genetics Department, Centro Nacional de Biotecnología-CSIC (CNB-CSIC), Madrid, Spain
| | - Steven H. Spoel
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRAE, Université de Paris, Orsay, France
| | - Vardis Ntoukakis
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
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35
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Yang L, Lei L, Li P, Wang J, Wang C, Yang F, Chen J, Liu H, Zheng H, Xin W, Zou D. Identification of Candidate Genes Conferring Cold Tolerance to Rice ( Oryza sativa L.) at the Bud-Bursting Stage Using Bulk Segregant Analysis Sequencing and Linkage Mapping. FRONTIERS IN PLANT SCIENCE 2021; 12:647239. [PMID: 33790929 PMCID: PMC8006307 DOI: 10.3389/fpls.2021.647239] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 02/22/2021] [Indexed: 05/29/2023]
Abstract
Low-temperature tolerance during the bud-bursting stage is an important characteristic of direct-seeded rice. The identification of cold-tolerance quantitative trait loci (QTL) in species that can stably tolerate cold environments is crucial for the molecular breeding of rice with such traits. In our study, high-throughput QTL-sequencing analyses were performed in a 460-individual F2 : 3 mapping population to identify the major QTL genomic regions governing cold tolerance at the bud-bursting (CTBB) stage in rice. A novel major QTL, qCTBB9, which controls seed survival rate (SR) under low-temperature conditions of 5°C/9 days, was mapped on the 5.40-Mb interval on chromosome 9. Twenty-six non-synonymous single-nucleotide polymorphism (nSNP) markers were designed for the qCTBB9 region based on re-sequencing data and local QTL mapping conducted using traditional linkage analysis. We mapped qCTBB9 to a 483.87-kb region containing 58 annotated genes, among which six predicted genes contained nine nSNP loci. Quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis revealed that only Os09g0444200 was strongly induced by cold stress. Haplotype analysis further confirmed that the SNP 1,654,225 bp in the Os09g0444200 coding region plays a key role in regulating the cold tolerance of rice. These results suggest that Os09g0444200 is a potential candidate for qCTBB9. Our results are of great significance to explore the genetic mechanism of rice CTBB and to improve the cold tolerance of rice varieties by marker-assisted selection.
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36
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Song ZT, Liu JX, Han JJ. Chromatin remodeling factors regulate environmental stress responses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2021; 63:438-450. [PMID: 33421288 DOI: 10.1111/jipb.13064] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Accepted: 12/23/2020] [Indexed: 05/14/2023]
Abstract
Environmental stress from climate change and agricultural activity threatens global plant biodiversity as well as crop yield and quality. As sessile organisms, plants must maintain the integrity of their genomes and adjust gene expression to adapt to various environmental changes. In eukaryotes, nucleosomes are the basic unit of chromatin around which genomic DNA is packaged by condensation. To enable dynamic access to packaged DNA, eukaryotes have evolved Snf2 (sucrose nonfermenting 2) family proteins as chromatin remodeling factors (CHRs) that modulate the position of nucleosomes on chromatin. During plant stress responses, CHRs are recruited to specific genomic loci, where they regulate the distribution or composition of nucleosomes, which in turn alters the accessibility of these loci to general transcription or DNA damage repair machinery. Moreover, CHRs interplay with other epigenetic mechanisms, including DNA methylation, histone modifications, and deposition of histone variants. CHRs are also involved in RNA processing at the post-transcriptional level. In this review, we discuss major advances in our understanding of the mechanisms by which CHRs function during plants' response to environmental stress.
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Affiliation(s)
- Ze-Ting Song
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jian-Xiang Liu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, 310027, China
| | - Jia-Jia Han
- Yunnan Key Laboratory of Plant Reproductive Adaptation and Evolutionary Ecology, Yunnan University, Kunming, 650500, China
- Laboratory of Ecology and Evolutionary Biology, State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan University, Kunming, 650500, China
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37
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Epigenetic Mechanisms of Plant Adaptation to Biotic and Abiotic Stresses. Int J Mol Sci 2020; 21:ijms21207457. [PMID: 33050358 PMCID: PMC7589735 DOI: 10.3390/ijms21207457] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/27/2020] [Accepted: 10/07/2020] [Indexed: 01/17/2023] Open
Abstract
Unlike animals, plants are immobile and could not actively escape the effects of aggressive environmental factors, such as pathogenic microorganisms, insect pests, parasitic plants, extreme temperatures, drought, and many others. To counteract these unfavorable encounters, plants have evolved very high phenotypic plasticity. In a rapidly changing environment, adaptive phenotypic changes often occur in time frames that are too short for the natural selection of adaptive mutations. Probably, some kind of epigenetic variability underlines environmental adaptation in these cases. Indeed, isogenic plants often have quite variable phenotypes in different habitats. There are examples of successful “invasions” of relatively small and genetically homogenous plant populations into entirely new habitats. The unique capability of quick environmental adaptation appears to be due to a high tendency to transmit epigenetic changes between plant generations. Multiple studies show that epigenetic memory serves as a mechanism of plant adaptation to a rapidly changing environment and, in particular, to aggressive biotic and abiotic stresses. In wild nature, this mechanism underlies, to a very significant extent, plant capability to live in different habitats and endure drastic environmental changes. In agriculture, a deep understanding of this mechanism could serve to elaborate more effective and safe approaches to plant protection.
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38
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Bäurle I, Trindade I. Chromatin regulation of somatic abiotic stress memory. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:5269-5279. [PMID: 32076719 DOI: 10.1093/jxb/eraa098] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/19/2020] [Indexed: 05/20/2023]
Abstract
In nature, plants are often subjected to periods of recurrent environmental stress that can strongly affect their development and productivity. To cope with these conditions, plants can remember a previous stress, which allows them to respond more efficiently to a subsequent stress, a phenomenon known as priming. This ability can be maintained at the somatic level for a few days or weeks after the stress is perceived, suggesting that plants can store information of a past stress during this recovery phase. While the immediate responses to a single stress event have been extensively studied, knowledge on priming effects and how stress memory is stored is still scarce. At the molecular level, memory of a past condition often involves changes in chromatin structure and organization, which may be maintained independently from transcription. In this review, we will summarize the most recent developments in the field and discuss how different levels of chromatin regulation contribute to priming and plant abiotic stress memory.
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Affiliation(s)
- Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Inês Trindade
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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39
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Ruibal C, Castro A, Fleitas AL, Quezada J, Quero G, Vidal S. A Chloroplast COR413 Protein From Physcomitrella patens Is Required for Growth Regulation Under High Light and ABA Responses. FRONTIERS IN PLANT SCIENCE 2020; 11:845. [PMID: 32636864 PMCID: PMC7317016 DOI: 10.3389/fpls.2020.00845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 05/26/2020] [Indexed: 05/17/2023]
Abstract
COR413 genes belong to a poorly characterized group of plant-specific cold-regulated genes initially identified as part of the transcriptional activation machinery of plants during cold acclimation. They encode multispanning transmembrane proteins predicted to target the plasma membrane or the chloroplast inner membrane. Despite being ubiquitous throughout the plant kingdom, little is known about their biological function. In this study, we used reverse genetics to investigate the relevance of a predicted chloroplast localized COR413 protein (PpCOR413im) from the moss Physcomitrella patens in developmental and abiotic stress responses. Expression of PpCOR413im was strongly induced by abscisic acid (ABA) and by various environmental stimuli, including low temperature, hyperosmosis, salinity and high light. In vivo subcellular localization of PpCOR413im-GFP fusion protein revealed that this protein is localized in chloroplasts, confirming the in silico predictions. Loss-of-function mutants of PpCOR413im exhibited growth and developmental alterations such as growth retardation, reduced caulonema formation and hypersensitivity to ABA. Mutants also displayed altered photochemistry under various abiotic stresses, including dehydration and low temperature, and exhibited a dramatic growth inhibition upon exposure to high light. Disruption of PpCOR413im also caused altered chloroplast ultrastructure, increased ROS accumulation, and enhanced starch and sucrose levels under high light or after ABA treatment. In addition, loss of PpCOR413im affected both nuclear and chloroplast gene expression in response to ABA and high light, suggesting a role for this gene downstream of ABA in the regulation of growth and environmental stress responses. Developmental alterations exhibited by PpCOR413im knockout mutants had remarkable similarities to those exhibited by hxk1, a mutant lacking a major chloroplastic hexokinase, an enzyme involved in energy homeostasis. Based on these findings, we propose that PpCOR413im is involved in coordinating energy metabolism with ABA-mediated growth and developmental responses.
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Affiliation(s)
- Cecilia Ruibal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Alexandra Castro
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Andrea L. Fleitas
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Jorge Quezada
- Unidad de Biotecnología Vegetal, Instituto de Biología Molecular y Biotecnología, Carrera de Biología – Facultad de Ciencias Puras y Naturales, Universidad Mayor de San Andrés, La Paz, Bolivia
| | - Gastón Quero
- Departamento de Biología Vegetal, Facultad de Agronomía, Universidad de la República, Montevideo, Uruguay
| | - Sabina Vidal
- Laboratorio de Biología Molecular Vegetal, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
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40
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Chang YN, Zhu C, Jiang J, Zhang H, Zhu JK, Duan CG. Epigenetic regulation in plant abiotic stress responses. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2020; 62:563-580. [PMID: 31872527 DOI: 10.1111/jipb.12901] [Citation(s) in RCA: 214] [Impact Index Per Article: 53.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 02/20/2020] [Indexed: 05/18/2023]
Abstract
In eukaryotic cells, gene expression is greatly influenced by the dynamic chromatin environment. Epigenetic mechanisms, including covalent modifications to DNA and histone tails and the accessibility of chromatin, create various chromatin states for stress-responsive gene expression that is important for adaptation to harsh environmental conditions. Recent studies have revealed that many epigenetic factors participate in abiotic stress responses, and various chromatin modifications are changed when plants are exposed to stressful environments. In this review, we summarize recent progress on the cross-talk between abiotic stress response pathways and epigenetic regulatory pathways in plants. Our review focuses on epigenetic regulation of plant responses to extreme temperatures, drought, salinity, the stress hormone abscisic acid, nutrient limitations and ultraviolet stress, and on epigenetic mechanisms of stress memory.
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Affiliation(s)
- Ya-Nan Chang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chen Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jing Jiang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Huiming Zhang
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Jian-Kang Zhu
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN, 47907, USA
| | - Cheng-Guo Duan
- Shanghai Center for Plant Stress Biology and Center of Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, 201602, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, 475004, China
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41
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Kong L, Liu Y, Wang X, Chang C. Insight into the Role of Epigenetic Processes in Abiotic and Biotic Stress Response in Wheat and Barley. Int J Mol Sci 2020; 21:ijms21041480. [PMID: 32098241 PMCID: PMC7073019 DOI: 10.3390/ijms21041480] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 02/13/2020] [Accepted: 02/19/2020] [Indexed: 02/07/2023] Open
Abstract
Environmental stresses such as salinity, drought, heat, freezing, heavy metal and even pathogen infections seriously threaten the growth and yield of important cereal crops including wheat and barley. There is growing evidence indicating that plants employ sophisticated epigenetic mechanisms to fine-tune their responses to environmental stresses. Here, we provide an overview of recent developments in understanding the epigenetic processes and elements—such as DNA methylation, histone modification, chromatin remodeling, and non-coding RNAs—involved in plant responses to abiotic and biotic stresses in wheat and barley. Potentials of exploiting epigenetic variation for the improvement of wheat and barley are discussed.
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Affiliation(s)
- Lingyao Kong
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Yanna Liu
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiaoyu Wang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
| | - Cheng Chang
- College of Life Sciences, Qingdao University, Qingdao 266071, China; (L.K.); (Y.L.); (X.W.)
- Correspondence: ; Tel.: +86-532-85953227
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42
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Srikant T, Drost HG. How Stress Facilitates Phenotypic Innovation Through Epigenetic Diversity. FRONTIERS IN PLANT SCIENCE 2020; 11:606800. [PMID: 33519857 PMCID: PMC7843580 DOI: 10.3389/fpls.2020.606800] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 12/16/2020] [Indexed: 05/14/2023]
Abstract
Climate adaptation through phenotypic innovation will become the main challenge for plants during global warming. Plants exhibit a plethora of mechanisms to achieve environmental and developmental plasticity by inducing dynamic alterations of gene regulation and by maximizing natural variation through large population sizes. While successful over long evolutionary time scales, most of these mechanisms lack the short-term adaptive responsiveness that global warming will require. Here, we review our current understanding of the epigenetic regulation of plant genomes, with a focus on stress-response mechanisms and transgenerational inheritance. Field and laboratory-scale experiments on plants exposed to stress have revealed a multitude of temporally controlled, mechanistic strategies integrating both genetic and epigenetic changes on the genome level. We analyze inter- and intra-species population diversity to discuss how methylome differences and transposon activation can be harnessed for short-term adaptive efforts to shape co-evolving traits in response to qualitatively new climate conditions and environmental stress.
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43
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Chu D, Wei L. Reduced C-to-U RNA editing rates might play a regulatory role in stress response of Arabidopsis. JOURNAL OF PLANT PHYSIOLOGY 2020; 244:153081. [PMID: 31783167 DOI: 10.1016/j.jplph.2019.153081] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Revised: 11/07/2019] [Accepted: 11/08/2019] [Indexed: 06/10/2023]
Abstract
C-to-U RNA editing is prevalent in the mitochondrial and chloroplast genes in plants. The C-to-U editing rates are constantly very high. During genome evolution, those edited cytidines are likely to be replaced with thymidines at the DNA level. C-to-U editing events are suggested to be designed for reversing the unfavorable T-to-C DNA mutations. Despite the existing theory showing the importance of editing mechanisms, few studies have investigated the genome-wide adaptive signals of the C-to-U editome or the potential function of C-to-U editing events in the stress response. By analyzing the transcriptome and translatome data of normal and heat-shocked Arabidopsis thaliana and the RNA-seq from cold-stressed plants, combined with genome-wide comparison of mitochondrial/chloroplast genes and nuclear genes from multiple aspects, we present the conservational and translational features of each gene and depict the dynamic mitochondrial/chloroplast C-to-U RNA editome. We found that the tAI (tRNA adaptation index) and basic translation levels are lower for mitochondrial/chloroplast genes than for nuclear genes. Interestingly, although we found adaptive signals for the global C-to-U RNA editome in mitochondrial/chloroplast genes, the C-to-U (T) alteration would usually cause a reduction in the codon tAI value. Moreover, the C-to-U editing rates are significantly reduced under heat or cold stress when compared to the normal condition. This reduction is irrelevant to the temperature-sensitive RNA structures. Several cases have illustrated that under heat stress, the reduced C-to-U editing rates alleviate ribosome stalling and consequently facilitate the local translation. Our study reveals that in Arabidopsis thaliana the mitochondrial/chloroplast C-to-U RNA editing rates are reduced under heat or cold stress. This reduction is associated with the alleviation of decreased tAI/translation rate of edited codons. The regulation of C-to-U editing rates could be the tradeoff between quantity and quality. We profile the dynamic change of C-to-U RNA editome under heat stress and propose a potential role of editing sites in the heat response. Our work should be appealing to the plant physiologists as well as the RNA editing community.
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Affiliation(s)
- Duan Chu
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China
| | - Lai Wei
- College of Life Sciences, Beijing Normal University, No. 19 Xinjiekouwai Street, Haidian District, Beijing, China.
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