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Shilpa, Thakur R, Prasad P. Epigenetic regulation of abiotic stress responses in plants. Biochim Biophys Acta Gen Subj 2024; 1868:130661. [PMID: 38885816 DOI: 10.1016/j.bbagen.2024.130661] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 02/15/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024]
Abstract
Plants face a wide array of challenges in their environment, both from living organisms (biotic stresses) and non-living factors (abiotic stresses). Among the major abiotic stressors affecting crop plants, variations in temperature, water availability, salinity, and cold pose significant threats to crop yield and the quality of produce. Plants possess remarkable adaptability and resilience, and they employ a range of genetic and epigenetic mechanisms to respond and cope with abiotic stresses. A few crucial set of epigenetic mechanisms that support plants in their battle against these stresses includes DNA methylation and histone modifications. These mechanisms play a pivotal role in enabling plants to endure and thrive under challenging environmental conditions. The mechanisms of different epigenetic mechanisms in responding to the abiotic stresses vary. Each plant species and type of stress may trigger distinct epigenetic responses, highlighting the complexity of the plant's ability to adapt under stress conditions. This review focuses on the paramount importance of epigenetics in enhancing a plant's ability to survive and excel under various abiotic stresses. It highlights recent advancements in our understanding of the epigenetic mechanisms that contribute to abiotic stress tolerance in plants. This growing knowledge is pivotal for shaping future efforts aimed at mitigating the impact of abiotic stresses on diverse crop plants.
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Affiliation(s)
- Shilpa
- Department of Biotechnology, Dr Yashwant Singh Parmar University of Horticulture and Forestry, Solan, Himachal Pradesh, India.
| | - Rajnikant Thakur
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India
| | - Pramod Prasad
- ICAR-Indian Institute of Wheat and Barley Research, Regional Station, Shimla-2, Himachal Pradesh, India.
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Alakärppä E, Salo HM, Suokas M, Jokipii-Lukkari S, Vuosku J, Häggman H. Targeted bisulfite sequencing of Scots pine adaptation-related genes. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 346:112173. [PMID: 38944158 DOI: 10.1016/j.plantsci.2024.112173] [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: 05/13/2024] [Revised: 06/24/2024] [Accepted: 06/27/2024] [Indexed: 07/01/2024]
Abstract
During environmental changes, epigenetic processes can enable adaptive responses faster than natural selection. In plants, very little is known about the role of DNA methylation during long-term adaptation. Scots pine is a widely distributed coniferous species which must adapt to different environmental conditions throughout its long lifespan. Thus, epigenetic modifications may contribute towards this direction. We provide bisulfite next-generation sequencing data from the putative promoters and exons of eight adaptation-related genes (A3IP2, CCA1, COL1, COL2, FTL2, MFT1, PHYO, and ZTL) in three Scots pine populations located in northern and southern parts of Finland. DNA methylation levels were studied in the two seed tissues: the maternal megagametophyte which contributes to embryo viability, and the biparental embryo which represents the next generation. In most genes, differentially methylated cytosines (DMCs) were in line with our previously demonstrated gene expression differences found in the same Scots pine populations. In addition, we found a strong correlation of total methylation levels between the embryo and megagametophyte tissues of a given individual tree, which indicates that DNA methylation can be inherited from the maternal parent. In conclusion, our results imply that DNA methylation differences may contribute to the adaptation of Scots pine populations in different climatic conditions.
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Affiliation(s)
- Emmi Alakärppä
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu FI-90014, Finland.
| | - Heikki M Salo
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu FI-90014, Finland
| | - Marko Suokas
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu FI-90014, Finland
| | - Soile Jokipii-Lukkari
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu FI-90014, Finland
| | - Jaana Vuosku
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu FI-90014, Finland
| | - Hely Häggman
- Ecology and Genetics Research Unit, University of Oulu, PO Box 3000, Oulu FI-90014, Finland
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Plskova Z, Van Breusegem F, Kerchev P. Redox regulation of chromatin remodelling in plants. PLANT, CELL & ENVIRONMENT 2024; 47:2780-2792. [PMID: 38311877 DOI: 10.1111/pce.14843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 12/23/2023] [Accepted: 01/22/2024] [Indexed: 02/06/2024]
Abstract
Changes in the cellular redox balance that occur during plant responses to unfavourable environmental conditions significantly affect a myriad of redox-sensitive processes, including those that impact on the epigenetic state of the chromatin. Various epigenetic factors, like histone modifying enzymes, chromatin remodelers, and DNA methyltransferases can be targeted by oxidative posttranslational modifications. As their combined action affects the epigenetic regulation of gene expression, they form an integral part of plant responses to (a)biotic stress. Epigenetic changes triggered by unfavourable environmental conditions are intrinsically linked with primary metabolism that supplies intermediates and donors, such acetyl-CoA and S-adenosyl-methionine, that are critical for the epigenetic decoration of histones and DNA. Here, we review the recent advances in our understanding of redox regulation of chromatin remodelling, dynamics of epigenetic marks, and the interplay between epigenetic control of gene expression, redox signalling and primary metabolism within an (a)biotic stress context.
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Affiliation(s)
- Zuzana Plskova
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
- VIB Center of Plant Systems Biology, Ghent, Belgium
| | - Frank Van Breusegem
- VIB Center of Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, UGent, Ghent, Belgium
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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Liu L, Si L, Zhang L, Guo R, Wang R, Dong H, Guo C. Metabolomics and transcriptomics analysis revealed the response mechanism of alfalfa to combined cold and saline-alkali stress. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38943631 DOI: 10.1111/tpj.16896] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 06/03/2024] [Accepted: 06/13/2024] [Indexed: 07/01/2024]
Abstract
Cold and saline-alkali stress are frequently encountered by plants, and they often occur simultaneously in saline-alkali soils at mid to high latitudes, constraining forage crop distribution and production. However, the mechanisms by which forage crops respond to the combination of cold and saline-alkali stress remain unknown. Alfalfa (Medicago sativa L.) is one of the most essential forage grasses in the world. In this study, we analyzed the complex response mechanisms of two alfalfa species (Zhaodong [ZD] and Blue Moon [BM]) to combined cold and saline-alkali stress using multi-omics. The results revealed that ZD had a greater ability to tolerate combined stress than BM. The tricarboxylic acid cycles of the two varieties responded positively to the combined stress, with ZD accumulating more sugars, amino acids, and jasmonic acid. The gene expression and flavonoid content of the flavonoid biosynthesis pathway were significantly different between the two varieties. Weighted gene co-expression network analysis and co-expression network analysis based on RNA-Seq data suggested that the MsMYB12 gene may respond to combined stress by regulating the flavonoid biosynthesis pathway. MsMYB12 can directly bind to the promoter of MsFLS13 and promote its expression. Moreover, MsFLS13 overexpression can enhance flavonol accumulation and antioxidant capacity, which can improve combined stress tolerance. These findings provide new insights into improving alfalfa resistance to combined cold and saline-alkali stress, showing that flavonoids are essential for plant resistance to combined stresses, and provide theoretical guidance for future breeding programs.
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Affiliation(s)
- Lei Liu
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 Shida Road, Limin Development Zone, Harbin, Heilongjiang, 150025, People's Republic of China
| | - Liang Si
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 Shida Road, Limin Development Zone, Harbin, Heilongjiang, 150025, People's Republic of China
| | - Lishuang Zhang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 Shida Road, Limin Development Zone, Harbin, Heilongjiang, 150025, People's Republic of China
| | - Rui Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 Shida Road, Limin Development Zone, Harbin, Heilongjiang, 150025, People's Republic of China
| | - Ruixin Wang
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 Shida Road, Limin Development Zone, Harbin, Heilongjiang, 150025, People's Republic of China
| | - Haimei Dong
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 Shida Road, Limin Development Zone, Harbin, Heilongjiang, 150025, People's Republic of China
| | - Changhong Guo
- Key Laboratory of Molecular Cytogenetics and Genetic Breeding of Heilongjiang Province, College of Life Science and Technology, Harbin Normal University, No. 1 Shida Road, Limin Development Zone, Harbin, Heilongjiang, 150025, People's Republic of China
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Cheng J, Wang J, Bi S, Li M, Wang L, Wang L, Li T, Zhang X, Gao Y, Zhu L, Wang C. GLABRA 2 regulates ETHYLENE OVERPRODUCER 1 accumulation during nutrient deficiency-induced root hair growth. PLANT PHYSIOLOGY 2024; 195:1906-1924. [PMID: 38497551 DOI: 10.1093/plphys/kiae129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 01/10/2024] [Indexed: 03/19/2024]
Abstract
Root hairs (RHs), extensive structures of root epidermal cells, are important for plant nutrient acquisition, soil anchorage, and environmental interactions. Excessive production of the phytohormone ethylene (ET) leads to substantial root hair growth, manifested as tolerance to plant nutrient deficiencies. However, the molecular basis of ET production during root hair growth in response to nutrient starvation remains unknown. Herein, we found that a critical transcription factor, GLABRA 2 (GL2), inhibits ET production during root hair growth in Arabidopsis (Arabidopsis thaliana). GL2 directly binds to the promoter of the gene encoding ET OVERPRODUCER 1 (ETO1), one of the most important ET-production-regulation factors, in vitro and in vivo, and then regulates the accumulation and function of ETO1 in root hair growth. The GL2-regulated-ETO1 module is required for promoting root hair growth under nitrogen, phosphorus, or potassium deficiency. Genome-wide analysis revealed numerous genes, such as ROOT HAIR DEFECTIVE 6-LIKE 4, ETHYLENE-INSENSITIVE 3-LIKE 2, ROOT HAIR SPECIFIC 13, are involved in the GL2-regulated-ETO1 module. Our work reveals a key transcription mechanism in the control of ET production during root hair growth under three major nutrient deficiencies.
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Affiliation(s)
- Jianing Cheng
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Jinshu Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Shuangtian Bi
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Mingyang Li
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lina Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lu Wang
- Institute of Germplasm Resource and Biotechnology; Tianjin Academy of Agricultural Sciences, Tianjin 300384, China
- State Key Laboratory of Vegetable Biobreeding, Tianjin Academy of Agricultural Sciences, Tianjin 300392, China
| | - Tong Li
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Xiaolan Zhang
- College of Horticulture, Shenyang Agricultural University, Shenyang 110866, China
| | - Yue Gao
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
| | - Lei Zhu
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100083, China
| | - Che Wang
- College of Bioscience and Biotechnology, Shenyang Agricultural University, Shenyang 110866, China
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Suppiyar V, Bonthala VS, Shrestha A, Krey S, Stich B. Genome-wide identification and expression analysis of the SET domain-containing gene family in potato (Solanum tuberosum L.). BMC Genomics 2024; 25:442. [PMID: 38702658 PMCID: PMC11069243 DOI: 10.1186/s12864-024-10367-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/30/2024] [Indexed: 05/06/2024] Open
Abstract
Genes containing the SET domain can catalyse histone lysine methylation, which in turn has the potential to cause changes to chromatin structure and regulation of the transcription of genes involved in diverse physiological and developmental processes. However, the functions of SET domain-containing (StSET) genes in potato still need to be studied. The objectives of our study can be summarized as in silico analysis to (i) identify StSET genes in the potato genome, (ii) systematically analyse gene structure, chromosomal distribution, gene duplication events, promoter sequences, and protein domains, (iii) perform phylogenetic analyses, (iv) compare the SET domain-containing genes of potato with other plant species with respect to protein domains and orthologous relationships, (v) analyse tissue-specific expression, and (vi) study the expression of StSET genes in response to drought and heat stresses. In this study, we identified 57 StSET genes in the potato genome, and the genes were physically mapped onto eleven chromosomes. The phylogenetic analysis grouped these StSET genes into six clades. We found that tandem duplication through sub-functionalisation has contributed only marginally to the expansion of the StSET gene family. The protein domain TDBD (PFAM ID: PF16135) was detected in StSET genes of potato while it was absent in all other previously studied species. This study described three pollen-specific StSET genes in the potato genome. Expression analysis of four StSET genes under heat and drought in three potato clones revealed that these genes might have non-overlapping roles under different abiotic stress conditions and durations. The present study provides a comprehensive analysis of StSET genes in potatoes, and it serves as a basis for further functional characterisation of StSET genes towards understanding their underpinning biological mechanisms in conferring stress tolerance.
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Affiliation(s)
- Vithusan Suppiyar
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
| | - Venkata Suresh Bonthala
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany.
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany.
| | - Asis Shrestha
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Stephanie Krey
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
| | - Benjamin Stich
- Institute for Quantitative Genetics and Genomics of Plants, Heinrich Heine University, Düsseldorf, 40225, Germany
- Cluster of Excellence On Plant Sciences, From Complex Traits Towards Synthetic Modules, Heinrich Heine University, Düsseldorf, 40225, Germany
- Present Address: Julius Kühn-Institut (JKI), Institute for Breeding Research On Agricultural Crops, Rudolf-Schick-Platz 3a, OT Groß Lüsewitz, Sanitz, 18190, Germany
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Song Y, He J, Guo J, Xie Y, Ma Z, Liu Z, Niu C, Li X, Chu B, Tahir MM, Xu J, Ma F, Guan Q. The chromatin remodeller MdRAD5B enhances drought tolerance by coupling MdLHP1-mediated H3K27me3 in apple. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:617-634. [PMID: 37874929 PMCID: PMC10893944 DOI: 10.1111/pbi.14210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 09/25/2023] [Accepted: 10/06/2023] [Indexed: 10/26/2023]
Abstract
RAD5B belongs to the Rad5/16-like group of the SNF2 family, which often functions in chromatin remodelling. However, whether RAD5B is involved in chromatin remodelling, histone modification, and drought stress tolerance is largely unclear. We identified a drought-inducible chromatin remodeler, MdRAD5B, which positively regulates apple drought tolerance. Transposase-accessible chromatin with high-throughput sequencing (ATAC-seq) analysis showed that MdRAD5B affects the expression of 466 drought-responsive genes through its chromatin remodelling function in response to drought stress. In addition, MdRAD5B interacts with and degrades MdLHP1, a crucial regulator of histone H3 trimethylation at K27 (H3K27me3), through the ubiquitin-independent 20S proteasome. Chromatin immunoprecipitation-sequencing (ChIP-seq) analysis revealed that MdRAD5B modulates the H3K27me3 deposition of 615 genes in response to drought stress. Genetic interaction analysis showed that MdRAD5B mediates the H3K27me3 deposition of drought-responsive genes through MdLHP1, which causes their expression changes under drought stress. Our results unravelled a dual function of MdRAD5B in gene expression modulation in apple in response to drought, that is, via the regulation of chromatin remodelling and H3K27me3.
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Affiliation(s)
- Yi Song
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Junxing Guo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Yinpeng Xie
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Ziqing Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Zeyuan Liu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Chundong Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Xuewei Li
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Baohua Chu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Muhammad Mobeen Tahir
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of HorticultureNorthwest A&F UniversityYanglingChina
- Shenzhen Research InstituteNorthwest A&F UniversityShenzhenChina
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Xue R, Guo R, Li Q, Lin T, Wu Z, Gao N, Wu F, Tong L, Zeng R, Song Y, Wang J. Rice responds to Spodoptera frugiperda infestation via epigenetic regulation of H3K9ac in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways. PLANT CELL REPORTS 2024; 43:78. [PMID: 38393406 DOI: 10.1007/s00299-024-03160-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/01/2023] [Accepted: 01/16/2024] [Indexed: 02/25/2024]
Abstract
KEY MESSAGE This study provided important insights into the complex epigenetic regulatory of H3K9ac-modified genes involved in the jasmonic acid signaling and phenylpropanoid biosynthesis pathways of rice in response to Spodoptera frugiperda infestation. Physiological and molecular mechanisms underlying plant responses to insect herbivores have been well studied, while epigenetic modifications such as histone acetylation and their potential regulation at the genomic level of hidden genes remain largely unknown. Histone 3 lysine 9 acetylation (H3K9ac) is an epigenetic marker widely distributed in plants that can activate gene transcription. In this study, we provided the genome-wide profiles of H3K9ac in rice (Oryza sativa) infested by fall armyworm (Spodoptera frugiperda, FAW) using CUT&Tag-seq and RNA-seq. There were 3269 and 4609 up-regulated genes identified in plants infested by FAW larvae for 3 h and 12 h, respectively, which were mainly enriched in alpha-linolenic acid and phenylpropanoid pathways according to transcriptomic analysis. In addition, CUT&Tag-seq analysis revealed increased H3K9ac in FAW-infested plants, and there were 422 and 543 up-regulated genes enriched with H3K9ac observed at 3 h and 12 h after FAW feeding, respectively. Genes with increased H3K9ac were mainly enriched in the transcription start site (TSS), suggesting that H3K9ac is related to gene transcription. Integrative analysis of both RNA-seq and CUT&Tag-seq data showed that up-expressed genes with H3K9ac enrichment were mainly involved in the jasmonic acid (JA) and phenylpropanoid pathways. Particularly, two spermidine hydroxycinnamoyl transferase genes SHT1 and SHT2 involved in phenolamide biosynthesis were highly modified by H3K9ac in FAW-infested plants. Furthermore, the Ossht1 and Ossht2 transgenic lines exhibited decreased resistance against FAW larvae. Our findings suggest that rice responds to insect herbivory via H3K9ac epigenetic regulation in the JA signaling and phenolamide biosynthesis pathways.
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Affiliation(s)
- Rongrong Xue
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Ruiqing Guo
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Qing Li
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Tianhuang Lin
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Zicha Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Ning Gao
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Fei Wu
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Lu Tong
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
| | - Rensen Zeng
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yuanyuan Song
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
| | - Jie Wang
- Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, College of Agriculture, Fujian Agriculture and Forestry University, Jinshan, Fuzhou, 350002, China.
- Key Laboratory of Biological Breeding for Fujian and Taiwan Crops, Ministry of Agriculture and Rural Affairs, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, 350002, China.
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Abdulraheem MI, Xiong Y, Moshood AY, Cadenas-Pliego G, Zhang H, Hu J. Mechanisms of Plant Epigenetic Regulation in Response to Plant Stress: Recent Discoveries and Implications. PLANTS (BASEL, SWITZERLAND) 2024; 13:163. [PMID: 38256717 PMCID: PMC10820249 DOI: 10.3390/plants13020163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024]
Abstract
Plant stress is a significant challenge that affects the development, growth, and productivity of plants and causes an adverse environmental condition that disrupts normal physiological processes and hampers plant survival. Epigenetic regulation is a crucial mechanism for plants to respond and adapt to stress. Several studies have investigated the role of DNA methylation (DM), non-coding RNAs, and histone modifications in plant stress responses. However, there are various limitations or challenges in translating the research findings into practical applications. Hence, this review delves into the recent recovery, implications, and applications of epigenetic regulation in response to plant stress. To better understand plant epigenetic regulation under stress, we reviewed recent studies published in the last 5-10 years that made significant contributions, and we analyzed the novel techniques and technologies that have advanced the field, such as next-generation sequencing and genome-wide profiling of epigenetic modifications. We emphasized the breakthrough findings that have uncovered specific genes or pathways and the potential implications of understanding plant epigenetic regulation in response to stress for agriculture, crop improvement, and environmental sustainability. Finally, we concluded that plant epigenetic regulation in response to stress holds immense significance in agriculture, and understanding its mechanisms in stress tolerance can revolutionize crop breeding and genetic engineering strategies, leading to the evolution of stress-tolerant crops and ensuring sustainable food production in the face of climate change and other environmental challenges. Future research in this field will continue to unveil the intricacies of epigenetic regulation and its potential applications in crop improvement.
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Affiliation(s)
- Mukhtar Iderawumi Abdulraheem
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Yani Xiong
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Abiodun Yusuff Moshood
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
| | - Gregorio Cadenas-Pliego
- Centro de Investigación en Química Aplicada, Blvd. Enrique Reyna 140, Saltillo 25294, Mexico;
| | - Hao Zhang
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
| | - Jiandong Hu
- Department of Electrical Engineering, Henan Agricultural University, Zhengzhou 450002, China or (M.I.A.); (Y.X.); (A.Y.M.); (H.Z.)
- Henan International Joint Laboratory of Laser Technology in Agriculture Science, Zhengzhou 450002, China
- State Key Laboratory of Wheat and Maize Crop Science, Zhengzhou 450002, China
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10
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Perrella G, Fasano C, Donald NA, Daddiego L, Fang W, Martignago D, Carr C, Conti L, Herzyk P, Amtmann A. Histone Deacetylase Complex 1 and histone 1 epigenetically moderate stress responsiveness of Arabidopsis thaliana seedlings. THE NEW PHYTOLOGIST 2024; 241:166-179. [PMID: 37565540 PMCID: PMC10953426 DOI: 10.1111/nph.19165] [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: 03/23/2023] [Accepted: 07/05/2023] [Indexed: 08/12/2023]
Abstract
Early responses of plants to environmental stress factors prevent damage but can delay growth and development in fluctuating conditions. Optimising these trade-offs requires tunability of plant responsiveness to environmental signals. We have previously reported that Histone Deacetylase Complex 1 (HDC1), which interacts with multiple proteins in histone deacetylation complexes, regulates the stress responsiveness of Arabidopsis seedlings, but the underlying mechanism remained elusive. Here, we show that HDC1 attenuates transcriptome re-programming in salt-treated seedlings, and we identify two genes (LEA and MAF5) that inhibit seedling establishment under salt stress downstream of HDC1. HDC1 attenuates their transcriptional induction by salt via a dual mechanism involving H3K9/14 deacetylation and H3K27 trimethylation. The latter, but not the former, was also abolished in a triple knockout mutant of the linker histone H1, which partially mimics the hypersensitivity of the hdc1-1 mutant to salt stress. Although stress-induced H3K27me3 accumulation required both H1 and HDC1, it was not fully recovered by complementing hdc1-1 with a truncated, H1-binding competent HDC1 suggesting other players or independent inputs. The combined findings reveal a dual brake function of HDC1 via regulating both active and repressive epigenetic marks on stress-inducible genes. This natural 'anti-panic' device offers a molecular leaver to tune stress responsiveness in plants.
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Affiliation(s)
- Giorgio Perrella
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Carlo Fasano
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Naomi A. Donald
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Loretta Daddiego
- Italian National Agency for New Technologies, Energy and Sustainable Economic DevelopmentTrisaia Research CentreRotondella (Matera)75026Italy
| | - Weiwei Fang
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Damiano Martignago
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Craig Carr
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
| | - Lucio Conti
- Department of BiosciencesUniversità degli Studi di MilanoVia Celoria 26Milan20133Italy
| | - Pawel Herzyk
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
- Glasgow Polyomics, Wolfson Wohl Cancer Research CentreUniversity of GlasgowGlasgowG61 1QHUK
| | - Anna Amtmann
- Plant Science GroupSchool of Molecular Biosciences (SMB), University of GlasgowGlasgowG12 8QQUK
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11
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Ost C, Cao HX, Nguyen TL, Himmelbach A, Mascher M, Stein N, Humbeck K. Drought-Stress-Related Reprogramming of Gene Expression in Barley Involves Differential Histone Modifications at ABA-Related Genes. Int J Mol Sci 2023; 24:12065. [PMID: 37569441 PMCID: PMC10418636 DOI: 10.3390/ijms241512065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/25/2023] [Accepted: 07/26/2023] [Indexed: 08/13/2023] Open
Abstract
Plants respond to drought by the major reprogramming of gene expression, enabling the plant to survive this threatening environmental condition. The phytohormone abscisic acid (ABA) serves as a crucial upstream signal, inducing this multifaceted process. This report investigated the drought response in barley plants (Hordeum vulgare, cv. Morex) at both the epigenome and transcriptome levels. After a ten-day drought period, during which the soil water content was reduced by about 35%, the relative chlorophyll content, as well as the photosystem II efficiency of the barley leaves, decreased by about 10%. Furthermore, drought-related genes such as HvS40 and HvA1 were already induced compared to the well-watered controls. Global ChIP-Seq analysis was performed to identify genes in which histones H3 were modified with euchromatic K4 trimethylation or K9 acetylation during drought. By applying stringent exclusion criteria, 129 genes loaded with H3K4me3 and 2008 genes loaded with H3K9ac in response to drought were identified, indicating that H3K9 acetylation reacts to drought more sensitively than H3K4 trimethylation. A comparison with differentially expressed genes enabled the identification of specific genes loaded with the euchromatic marks and induced in response to drought treatment. The results revealed that a major proportion of these genes are involved in ABA signaling and related pathways. Intriguingly, two members of the protein phosphatase 2C family (PP2Cs), which play a crucial role in the central regulatory machinery of ABA signaling, were also identified through this approach.
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Affiliation(s)
- Charlotte Ost
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Hieu Xuan Cao
- Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, 37077 Göttingen, Germany
| | - Thuy Linh Nguyen
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
| | - Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstraße 3, Gatersleben, 06466 Seeland, Germany
- Center of Integrated Breeding Research (CiBreed), Georg-August University of Göttingen, 37073 Göttingen, Germany
| | - Klaus Humbeck
- Institute of Biology, Martin Luther University Halle-Wittenberg, Weinbergweg 10, 06120 Halle, Germany
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12
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Giannelli G, Potestio S, Visioli G. The Contribution of PGPR in Salt Stress Tolerance in Crops: Unravelling the Molecular Mechanisms of Cross-Talk between Plant and Bacteria. PLANTS (BASEL, SWITZERLAND) 2023; 12:plants12112197. [PMID: 37299176 DOI: 10.3390/plants12112197] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Revised: 05/29/2023] [Accepted: 05/31/2023] [Indexed: 06/12/2023]
Abstract
Soil salinity is a major abiotic stress in global agricultural productivity with an estimated 50% of arable land predicted to become salinized by 2050. Since most domesticated crops are glycophytes, they cannot be cultivated on salt soils. The use of beneficial microorganisms inhabiting the rhizosphere (PGPR) is a promising tool to alleviate salt stress in various crops and represents a strategy to increase agricultural productivity in salt soils. Increasing evidence underlines that PGPR affect plant physiological, biochemical, and molecular responses to salt stress. The mechanisms behind these phenomena include osmotic adjustment, modulation of the plant antioxidant system, ion homeostasis, modulation of the phytohormonal balance, increase in nutrient uptake, and the formation of biofilms. This review focuses on the recent literature regarding the molecular mechanisms that PGPR use to improve plant growth under salinity. In addition, very recent -OMICs approaches were reported, dissecting the role of PGPR in modulating plant genomes and epigenomes, opening up the possibility of combining the high genetic variations of plants with the action of PGPR for the selection of useful plant traits to cope with salt stress conditions.
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Affiliation(s)
- Gianluigi Giannelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Silvia Potestio
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
| | - Giovanna Visioli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, 43124 Parma, Italy
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13
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Han M, Cui R, Wang D, Huang H, Rui C, Malik WA, Wang J, Zhang H, Xu N, Liu X, Lei Y, Jiang T, Sun L, Ni K, Fan Y, Zhang Y, Wang J, Chen X, Lu X, Yin Z, Wang S, Guo L, Zhao L, Chen C, Ye W. Combined transcriptomic and metabolomic analyses elucidate key salt-responsive biomarkers to regulate salt tolerance in cotton. BMC PLANT BIOLOGY 2023; 23:245. [PMID: 37161359 PMCID: PMC10170727 DOI: 10.1186/s12870-023-04258-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 04/28/2023] [Indexed: 05/11/2023]
Abstract
BACKGROUND Cotton is an important industrial crop and a pioneer crop for saline-alkali land restoration. However, the molecular mechanism underlying the cotton response to salt is not completely understood. METHODS Here, we used metabolome data and transcriptome data to analyze the salt tolerance regulatory network of cotton and metabolic biomarkers. RESULTS In this study, cotton was stressed at 400 m M NaCl for 0 h, 3 h, 24 h and 48 h. NaCl interfered with cotton gene expression, altered metabolite contents and affected plant growth. Metabolome analysis showed that NaCl stress increased the contents of amino acids, sugars and ABA, decreased the amount of vitamin and terpenoids. K-means cluster analysis of differentially expressed genes showed that the continuously up-regulated genes were mainly enriched in metabolic pathways such as flavonoid biosynthesis and amino acid biosynthesis. CONCLUSION The four metabolites of cysteine (Cys), ABA(Abscisic acid), turanose, and isopentenyladenine-7-N-glucoside (IP7G) were consistently up-regulated under salt stress, which may indicate that they are potential candidates for cotton under salt stress biomarkers. Combined transcriptome and metabolome analysis revealed accumulation of cysteine, ABA, isopentenyladenine-7-N-glucoside and turanose were important for salt tolerance in cotton mechanism. These results will provide some metabolic insights and key metabolite biomarkers for salt stress tolerance, which may help to understanding of the metabolite response to salt stress in cotton and develop a foundation for cotton to grow better in saline soil.
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Affiliation(s)
- Mingge Han
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Ruifeng Cui
- Anyang Institute of Technology, Anyang, 455000, Henan, China
| | - Delong Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Hui Huang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Cun Rui
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Waqar Afzal Malik
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Jing Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Hong Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Nan Xu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xiaoyu Liu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Yuqian Lei
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Tiantian Jiang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Liangqing Sun
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Kesong Ni
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Yapeng Fan
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Yuexin Zhang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Junjuan Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xiugui Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Xuke Lu
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Zujun Yin
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Shuai Wang
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Lixue Guo
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Lanjie Zhao
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Chao Chen
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China
| | - Wuwei Ye
- Institute of Cotton Research of Chinese Academy of Agricultural Sciences / Zhengzhou Research Base, State Key Laboratory of Cotton Biology, School of Agricultural Sciences, Zhengzhou University, Anyang, 455000, Henan, China.
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14
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Jie L, Sanagi M, Luo Y, Maeda H, Fukao Y, Chiba Y, Yanagisawa S, Yamaguchi J, Takagi J, Sato T. Histone chaperone NUCLEOSOME ASSEMBLY PROTEIN 1 proteins affect plant growth under nitrogen deficient conditions in Arabidopsis thaliana. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2023; 40:93-98. [PMID: 38439935 PMCID: PMC10910346 DOI: 10.5511/plantbiotechnology.22.1219a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 12/19/2022] [Indexed: 03/06/2024]
Abstract
Nitrogen (N) availability is one of the most important factors regulating plant metabolism and growth as it affects global gene expression profiles. Dynamic changes in chromatin structure, including histone modifications and nucleosome assembly/disassembly, have been extensively shown to regulate gene expression under various environmental stresses in plants. However, the involvement of chromatin related changes in plant nutrient responses has been demonstrated only in a few studies to date. In this study, we investigated the function of histone chaperone NUCLEOSOME ASSEMBLY PROTEIN1 (NAP1) proteins under N deficient conditions in Arabidopsis. In the nap1;1 nap1;2 nap1;3 triple mutant (m123-1), the expression of N-responsive marker genes and growth of lateral roots were decreased under N deficient conditions. In addition, the m123-1 plants showed a delay in N deficiency-induced leaf senescence. Taken together, these results suggest that NAP1s affect plant growth under N deficient conditions in Arabidopsis.
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Affiliation(s)
- Linnan Jie
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Miho Sanagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yongming Luo
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Haruna Maeda
- Graduate School of Life Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Yoichiro Fukao
- College of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Yukako Chiba
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Shuichi Yanagisawa
- Plant Functional Biotechnology, Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo 113-8657, Japan
| | - Junji Yamaguchi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Junpei Takagi
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
| | - Takeo Sato
- Faculty of Science, Hokkaido University, Sapporo, Hokkaido 060-0810, Japan
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15
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Ghouili E, Sassi K, Hidri Y, M’Hamed HC, Somenahally A, Xue Q, Jebara M, Nefissi Ouertani R, Riahi J, de Oliveira AC, Abid G, Muhovski Y. Effects of Date Palm Waste Compost Application on Root Proteome Changes of Barley ( Hordeum vulgare L.). PLANTS (BASEL, SWITZERLAND) 2023; 12:526. [PMID: 36771612 PMCID: PMC9921465 DOI: 10.3390/plants12030526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Revised: 01/15/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
Proteomic analysis was performed to investigate the differentially abundant proteins (DAPs) in barley roots during the tillering stage. Bioinformatic tools were used to interpret the biological function, the pathway analysis and the visualisation of the network amongst the identified proteins. A total of 72 DAPs (33 upregulated and 39 downregulated) among a total of 2580 proteins were identified in response to compost treatment, suggesting multiple pathways of primary and secondary metabolism, such as carbohydrates and energy metabolism, phenylpropanoid pathway, glycolysis pathway, protein synthesis and degradation, redox homeostasis, RNA processing, stress response, cytoskeleton organisation, and phytohormone metabolic pathways. The expression of DAPs was further validated by qRT-PCR. The effects on barley plant development, such as the promotion of root growth and biomass increase, were associated with a change in energy metabolism and protein synthesis. The activation of enzymes involved in redox homeostasis and the regulation of stress response proteins suggest a protective effect of compost, consequently improving barley growth and stress acclimation through the reduction of the environmental impact of productive agriculture. Overall, these results may facilitate a better understanding of the molecular mechanism of compost-promoted plant growth and provide valuable information for the identification of critical genes/proteins in barley as potential targets of compost.
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Affiliation(s)
- Emna Ghouili
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Khaled Sassi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Yassine Hidri
- Laboratory of Integrated Olive Production in the Humid, Sub-humid and Semi-arid Region (LR16IO3), Olive Tree Institute, Cité Mahragène, P.O. Box 208, Tunis 1082, Tunisia
| | - Hatem Cheikh M’Hamed
- Agronomy Laboratory, National Institute of Agronomic Research of Tunis (INRAT), Carthage University, Hedi Karray Street, Ariana 2049, Tunisia
| | - Anil Somenahally
- Department of Soil and Crop Sciences, Texas A&M University, 370 Olsen Blvd, College Station, TX 77843-2474, USA
| | - Qingwu Xue
- Texas A&M AgriLife Research and Extension Center, Amarillo, TX 79403-6603, USA
| | - Moez Jebara
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Rim Nefissi Ouertani
- Laboratory of Plant Molecular Physiology, Centre of Biotechnology of Borj Cedria, P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Jouhaina Riahi
- Laboratory of Agronomy, National Agronomy Institute of Tunisia (INAT), University of Carthage, Avenue Charles Nicolle, Tunis-Mahrajène, P.O. Box 43, Tunis 1082, Tunisia
| | - Ana Caroline de Oliveira
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
| | - Ghassen Abid
- Laboratory of Legumes and Sustainable Agrosystems, Centre of Biotechnology of Borj-Cedria, (L2AD, CBBC), P.O. Box 901, Hammam-Lif 2050, Tunisia
| | - Yordan Muhovski
- Biological Engineering Unit, Department of Life Sciences, Walloon Agricultural Research Centre, Chaussée de Charleroi, P.O. Box 234, 5030 Gembloux, Belgium
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16
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Liu Y, Wang J, Liu B, Xu ZY. Dynamic regulation of DNA methylation and histone modifications in response to abiotic stresses in plants. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:2252-2274. [PMID: 36149776 DOI: 10.1111/jipb.13368] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 09/22/2022] [Indexed: 06/16/2023]
Abstract
DNA methylation and histone modification are evolutionarily conserved epigenetic modifications that are crucial for the expression regulation of abiotic stress-responsive genes in plants. Dynamic changes in gene expression levels can result from changes in DNA methylation and histone modifications. In the last two decades, how epigenetic machinery regulates abiotic stress responses in plants has been extensively studied. Here, based on recent publications, we review how DNA methylation and histone modifications impact gene expression regulation in response to abiotic stresses such as drought, abscisic acid, high salt, extreme temperature, nutrient deficiency or toxicity, and ultraviolet B exposure. We also review the roles of epigenetic mechanisms in the formation of transgenerational stress memory. We posit that a better understanding of the epigenetic underpinnings of abiotic stress responses in plants may facilitate the design of more stress-resistant or -resilient crops, which is essential for coping with global warming and extreme environments.
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Affiliation(s)
- Yutong Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Jie Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, 130024, China
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17
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Rajasheker G, Nagaraju M, Varghese RP, Jalaja N, Somanaboina AK, Singam P, Ramakrishna C, Penna S, Sreenivasulu N, Kishor PBK. Identification and analysis of proline-rich proteins and hybrid proline-rich proteins super family genes from Sorghum bicolor and their expression patterns to abiotic stress and zinc stimuli. FRONTIERS IN PLANT SCIENCE 2022; 13:952732. [PMID: 36226297 PMCID: PMC9549341 DOI: 10.3389/fpls.2022.952732] [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: 05/25/2022] [Accepted: 08/16/2022] [Indexed: 06/16/2023]
Abstract
Systematic genome-wide analysis of Sorghum bicolor revealed the identification of a total of 48 homologous genes comprising 21 proline-rich proteins (PRPs) and 27 hybrid proline-rich proteins (HyPRPs). Comprehensive scrutiny of these gene homologs was conducted for gene structure, phylogenetic investigations, chromosome mapping, and subcellular localization of proteins. Promoter analysis uncovered the regions rich with phosphorous- (BIHD), ammonium-, sulfur-responsive (SURE), and iron starvation-responsive (IRO2) along with biotic, abiotic, and development-specific cis-elements. Further, PRPs exhibit more methylation and acetylation sites in comparison with HyPRPs. miRNAs have been predicted which might play a role in cleavage and translation inhibition. Several of the SbPRP genes were stimulated in a tissue-specific manner under drought, salt, heat, and cold stresses. Additionally, exposure of plants to abscisic acid (ABA) and zinc (Zn) also triggered PRP genes in a tissue-dependent way. Among them, SbPRP17 has been found upregulated markedly in all tissues irrespective of the stress imposed. The expressions of SbHyPRPs, especially SbHyPRP2, SbHyPRP6, and SbHyPRP17 were activated under all stresses in all three tissues. On the other hand, SbHyPRP8 (root only) and SbHyPRP12 (all three tissues) were highly responsive to cold stress and ABA while SbHyPRP26 was induced by drought and Zn in the stem. Taken together, this study indicates the critical roles that SbPRPs and SbHyPRPs play during diverse abiotic stress conditions and notably the plausible roles that these genes play upon exposure to zinc, the crucial micronutrient in plants.
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Affiliation(s)
| | - Marka Nagaraju
- Biochemistry Division, ICMR-National Institute of Nutrition, Hyderabad, India
| | - Rinku Polachirakkal Varghese
- Department of Biotechnology, Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Vadlamudi, India
- School of Biosciences and Technology, Vellore Institute of Technology, Vellore, India
| | - Naravula Jalaja
- Department of Biotechnology, Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Vadlamudi, India
| | - Anil Kumar Somanaboina
- Department of Biotechnology, Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Vadlamudi, India
| | - Prashant Singam
- Department of Genetics and Biotechnology, Osmania University, Hyderabad, India
| | | | - Suprasanna Penna
- Nuclear Agriculture and Biotechnology, Bhabha Atomic Research Center, Mumbai, India
| | - Nese Sreenivasulu
- Consumer-driven Grain Quality and Nutrition Research Unit, International Rice Research Institute, Los Baños, Philippines
| | - P. B. Kavi Kishor
- Department of Biotechnology, Vignan’s Foundation for Science, Technology & Research (Deemed to be University), Vadlamudi, India
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18
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Wang S, He J, Deng M, Wang C, Wang R, Yan J, Luo M, Ma F, Guan Q, Xu J. Integrating ATAC-seq and RNA-seq Reveals the Dynamics of Chromatin Accessibility and Gene Expression in Apple Response to Drought. Int J Mol Sci 2022; 23:ijms231911191. [PMID: 36232500 PMCID: PMC9570298 DOI: 10.3390/ijms231911191] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Revised: 09/19/2022] [Accepted: 09/21/2022] [Indexed: 11/16/2022] Open
Abstract
Drought resistance in plants is influenced by multiple signaling pathways that involve various transcription factors, many target genes, and multiple types of epigenetic modifications. Studies on epigenetic modifications of drought focus on DNA methylation and histone modifications, with fewer on chromatin remodeling. Changes in chromatin accessibility can play an important role in abiotic stress in plants by affecting RNA polymerase binding and various regulatory factors. However, the changes in chromatin accessibility during drought in apples are not well understood. In this study, the landscape of chromatin accessibility associated with the gene expression of apple (GL3) under drought conditions was analyzed by Assay for Transposase Accessible Chromatin with high-throughput sequencing (ATAC-seq) and RNA-seq. Differential analysis between drought treatment and control identified 23,466 peaks of upregulated chromatin accessibility and 2447 peaks of downregulated accessibility. The drought-induced chromatin accessibility changed genes were mainly enriched in metabolism, stimulus, and binding pathways. By combining results from differential analysis of RNA-seq and ATAC-seq, we identified 240 genes with higher chromatin accessibility and increased gene expression under drought conditions that may play important functions in the drought response process. Among them, a total of nine transcription factor genes were identified, including ATHB7, HAT5, and WRKY26. These transcription factor genes are differentially expressed with different chromatin accessibility motif binding loci that may participate in apple response to drought by regulating downstream genes. Our study provides a reference for chromatin accessibility under drought stress in apples and the results will facilitate subsequent studies on chromatin remodelers and transcription factors.
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Affiliation(s)
- Shicong Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Jieqiang He
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Mengting Deng
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Caixia Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Ruifeng Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Jinjiao Yan
- College of Forestry, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Minrong Luo
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Fengwang Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Qingmei Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
| | - Jidi Xu
- State Key Laboratory of Crop Stress Biology for Arid Areas/Shaanxi Key Laboratory of Apple, College of Horticulture, Northwest Agricultural and Forestry University, Yangling, Xianyang 712100, China
- Correspondence:
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19
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Siemiatkowska B, Chiara M, Badiger BG, Riboni M, D'Avila F, Braga D, Salem MAA, Martignago D, Colanero S, Galbiati M, Giavalisco P, Tonelli C, Juenger TE, Conti L. GIGANTEA Is a Negative Regulator of Abscisic Acid Transcriptional Responses and Sensitivity in Arabidopsis. PLANT & CELL PHYSIOLOGY 2022; 63:1285-1297. [PMID: 35859344 DOI: 10.1093/pcp/pcac102] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 07/11/2022] [Accepted: 07/20/2022] [Indexed: 06/15/2023]
Abstract
Transcriptional reprogramming plays a key role in drought stress responses, preceding the onset of morphological and physiological acclimation. The best-characterized signal regulating gene expression in response to drought is the phytohormone abscisic acid (ABA). ABA-regulated gene expression, biosynthesis and signaling are highly organized in a diurnal cycle, so that ABA-regulated physiological traits occur at the appropriate time of day. The mechanisms that underpin such diel oscillations in ABA signals are poorly characterized. Here we uncover GIGANTEA (GI) as a key gatekeeper of ABA-regulated transcriptional and physiological responses. Time-resolved gene expression profiling by RNA sequencing under different irrigation scenarios indicates that gi mutants produce an exaggerated ABA response, despite accumulating wild-type levels of ABA. Comparisons with ABA-deficient mutants confirm the role of GI in controlling ABA-regulated genes, and the analysis of leaf temperature, a read-out for transpiration, supports a role for GI in the control of ABA-regulated physiological processes. Promoter regions of GI/ABA-regulated transcripts are directly targeted by different classes of transcription factors (TFs), especially PHYTOCHROME-INTERACTING FACTOR and -BINDING FACTOR, together with GI itself. We propose a model whereby diel changes in GI control oscillations in ABA responses. Peak GI accumulation at midday contributes to establishing a phase of reduced ABA sensitivity and related physiological responses, by gating DNA binding or function of different classes of TFs that cooperate or compete with GI at target regions.
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Affiliation(s)
- Beata Siemiatkowska
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Matteo Chiara
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Bhaskara G Badiger
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Matteo Riboni
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Francesca D'Avila
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via Antonio di Rudinì, 8, Milano 20142, Italy
| | - Daniele Braga
- Dipartimento di Scienze della Salute, Università degli Studi di Milano, Via Antonio di Rudinì, 8, Milano 20142, Italy
| | - Mohamed Abd Allah Salem
- Department of Pharmacognosy, Faculty of Pharmacy, Menoufia University, Gamal Abd El Nasr st., Shibin Elkom, Menoufia 32511, Egypt
| | - Damiano Martignago
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Sara Colanero
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Massimo Galbiati
- Istituto di Biologia e Biotecnologia Agraria-IBBA, CNR, Via Edoardo Bassini, 15, Milano 20133, Italy
| | - Patrick Giavalisco
- Max Planck Institute for Biology of Ageing, Joseph Stelzmann Str. 9b, Cologne 50931, Germany
| | - Chiara Tonelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
| | - Thomas E Juenger
- Department of Integrative Biology, The University of Texas at Austin, 2415 Speedway, Austin, TX 78712, USA
| | - Lucio Conti
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria, 26, Milano 20133, Italy
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20
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Xiao M, Wang J, Xu F. Methylation hallmarks on the histone tail as a linker of osmotic stress and gene transcription. FRONTIERS IN PLANT SCIENCE 2022; 13:967607. [PMID: 36035677 PMCID: PMC9399788 DOI: 10.3389/fpls.2022.967607] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 07/25/2022] [Indexed: 06/12/2023]
Abstract
Plants dynamically manipulate their gene expression in acclimation to the challenging environment. Hereinto, the histone methylation tunes the gene transcription via modulation of the chromatin accessibility to transcription machinery. Osmotic stress, which is caused by water deprivation or high concentration of ions, can trigger remarkable changes in histone methylation landscape and genome-wide reprogramming of transcription. However, the dynamic regulation of genes, especially how stress-inducible genes are timely epi-regulated by histone methylation remains largely unclear. In this review, recent findings on the interaction between histone (de)methylation and osmotic stress were summarized, with emphasis on the effects on histone methylation profiles imposed by stress and how histone methylation works to optimize the performance of plants under stress.
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21
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Genome-Wide Identification and Spatial Expression Analysis of Histone Modification Gene Families in the Rubber Dandelion Taraxacum kok-saghyz. PLANTS 2022; 11:plants11162077. [PMID: 36015381 PMCID: PMC9415798 DOI: 10.3390/plants11162077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 07/29/2022] [Accepted: 08/04/2022] [Indexed: 11/17/2022]
Abstract
Taraxacum kok-saghyz (Tks), also known as the Russian dandelion, is a recognized alternative source of natural rubber quite comparable, for quality and use, to the one obtained from the so-called rubber tree, Hevea brasiliensis. In addition to that, Tks roots produce several other compounds, including inulin, whose use in pharmaceutical and dietary products is quite extensive. Histone-modifying genes (HMGs) catalyze a series of post-translational modifications that affect chromatin organization and conformation, which, in turn, regulate many downstream processes, including gene expression. In this study, we present the first analysis of HMGs in Tks. Altogether, we identified 154 putative Tks homologs: 60 HMTs, 34 HDMs, 42 HATs, and 18 HDACs. Interestingly, whilst most of the classes showed similar numbers in other plant species, including M. truncatula and A. thaliana, HATs and HMT-PRMTs were indeed more abundant in Tks. Composition and structure analysis of Tks HMG proteins showed, for some classes, the presence of novel domains, suggesting a divergence from the canonical HMG model. The analysis of publicly available transcriptome datasets, combined with spatial expression of different developmental tissues, allowed us to identify several HMGs with a putative role in metabolite biosynthesis. Overall, our work describes HMG genomic organization and sets the premises for the functional characterization of epigenetic modifications in rubber-producing plants.
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22
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A review on CRISPR/Cas-based epigenetic regulation in plants. Int J Biol Macromol 2022; 219:1261-1271. [DOI: 10.1016/j.ijbiomac.2022.08.182] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 04/13/2022] [Accepted: 08/29/2022] [Indexed: 01/09/2023]
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23
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Ali S, Khan N, Tang Y. Epigenetic marks for mitigating abiotic stresses in plants. JOURNAL OF PLANT PHYSIOLOGY 2022; 275:153740. [PMID: 35716656 DOI: 10.1016/j.jplph.2022.153740] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2021] [Revised: 03/02/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Abiotic stressors are one of the major factors affecting agricultural output. Plants have evolved adaptive systems to respond appropriately to various environmental cues. These responses can be accomplished by modulating or fine-tuning genetic and epigenetic regulatory mechanisms. Understanding the response of plants' molecular features to abiotic stress is a priority in the current period of continued environmental changes. Epigenetic modifications are necessary that control gene expression by changing chromatin status and recruiting various transcription regulators. The present study summarized the current knowledge on epigenetic modifications concerning plant responses to various environmental stressors. The functional relevance of epigenetic marks in regulating stress tolerance has been revealed, and epigenetic changes impact the effector genes. This study looks at the epigenetic mechanisms that govern plant abiotic stress responses, especially DNA methylation, histone methylation/acetylation, chromatin remodeling, and various metabolites. Plant breeders will benefit from a thorough understanding of these processes to create alternative crop improvement approaches. Genome editing with clustered regularly interspaced short palindromic repeat/CRISPR-associated proteins (CRISPR/Cas) provides genetic tools to make agricultural genetic engineering more sustainable and publicly acceptable.
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Affiliation(s)
- Shahid Ali
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
| | - Naeem Khan
- Department of Agronomy, Institute of Food and Agricultural Sciences, University of Florida, FL, 32611, USA
| | - Yulin Tang
- Guangdong Provincial Key Laboratory for Plant Epigenetics, Shenzhen Key Laboratory of Marine Bioresource & Eco-environmental Science, Longhua Institute of Innovative Biotechnology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen, 518060, Guangdong Province, China; Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, China.
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24
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Bulbul Ahmed M, Humayan Kabir A. Understanding of the various aspects of gene regulatory networks related to crop improvement. Gene 2022; 833:146556. [PMID: 35609798 DOI: 10.1016/j.gene.2022.146556] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 03/14/2022] [Accepted: 05/06/2022] [Indexed: 12/30/2022]
Abstract
The hierarchical relationship between transcription factors, associated proteins, and their target genes is defined by a gene regulatory network (GRN). GRNs allow us to understand how the genotype and environment of a plant are incorporated to control the downstream physiological responses. During plant growth or environmental acclimatization, GRNs are diverse and can be differently regulated across tissue types and organs. An overview of recent advances in the development of GRN that speed up basic and applied plant research is given here. Furthermore, the overview of genome and transcriptome involving GRN research along with the exciting advancement and application are discussed. In addition, different approaches to GRN predictions were elucidated. In this review, we also describe the role of GRN in crop improvement, crop plant manipulation, stress responses, speed breeding and identifying genetic variations/locus. Finally, the challenges and prospects of GRN in plant biology are discussed.
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Affiliation(s)
- Md Bulbul Ahmed
- Plant Science Department, McGill University, 21111 lakeshore Road, Ste. Anne de Bellevue H9X3V9, Quebec, Canada; Institut de Recherche en Biologie Végétale (IRBV), University of Montreal, Montréal, Québec H1X 2B2, Canada.
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25
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Villagómez-Aranda AL, Feregrino-Pérez AA, García-Ortega LF, González-Chavira MM, Torres-Pacheco I, Guevara-González RG. Activating stress memory: eustressors as potential tools for plant breeding. PLANT CELL REPORTS 2022; 41:1481-1498. [PMID: 35305133 PMCID: PMC8933762 DOI: 10.1007/s00299-022-02858-x] [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: 12/08/2021] [Accepted: 02/26/2022] [Indexed: 05/08/2023]
Abstract
Plants are continuously exposed to stress conditions, such that they have developed sophisticated and elegant survival strategies, which are reflected in their phenotypic plasticity, priming capacity, and memory acquisition. Epigenetic mechanisms play a critical role in modulating gene expression and stress responses, allowing malleability, reversibility, stability, and heritability of favourable phenotypes to enhance plant performance. Considering the urgency to improve our agricultural system because of going impacting climate change, potential and sustainable strategies rely on the controlled use of eustressors, enhancing desired characteristics and yield and shaping stress tolerance in crops. However, for plant breeding purposes is necessary to focus on the use of eustressors capable of establishing stable epigenetic marks to generate a transgenerational memory to stimulate a priming state in plants to face the changing environment.
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Affiliation(s)
- A L Villagómez-Aranda
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - A A Feregrino-Pérez
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - L F García-Ortega
- Laboratory of Learning and Research in Biological Computing, Centre for Research and Advanced Studies, National Polytechnic Institute (CINVESTAV), Irapuato, Guanajuato, Mexico
| | - M M González-Chavira
- Molecular Markers Laboratory, Bajío Experimental Field, National Institute for Forestry, Agriculture and Livestock Research (INIFAP), Celaya-San Miguel de Allende, Celaya, Guanajuato, Mexico
| | - I Torres-Pacheco
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico
| | - R G Guevara-González
- Biosystems Engineering Group. Engineering Faculty, Amazcala Campus, Autonomous University of Querétaro, Highway Chichimequillas s/n Km 1, Amazcala, El Marques, Querétaro, Mexico.
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26
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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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27
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Halder K, Chaudhuri A, Abdin MZ, Majee M, Datta A. Chromatin-Based Transcriptional Reprogramming in Plants under Abiotic Stresses. PLANTS (BASEL, SWITZERLAND) 2022; 11:1449. [PMID: 35684223 PMCID: PMC9182740 DOI: 10.3390/plants11111449] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/23/2022] [Indexed: 06/15/2023]
Abstract
Plants' stress response machinery is characterized by an intricate network of signaling cascades that receive and transmit environmental cues and ultimately trigger transcriptional reprogramming. The family of epigenetic regulators that are the key players in the stress-induced signaling cascade comprise of chromatin remodelers, histone modifiers, DNA modifiers and regulatory non-coding RNAs. Changes in the histone modification and DNA methylation lead to major alterations in the expression level and pattern of stress-responsive genes to adjust with abiotic stress conditions namely heat, cold, drought and salinity. The spotlight of this review falls primarily on the chromatin restructuring under severe abiotic stresses, crosstalk between epigenetic regulators along with a brief discussion on stress priming in plants.
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Affiliation(s)
- Koushik Halder
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Abira Chaudhuri
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Malik Z. Abdin
- Centre for Transgenic Plant Development, Department of Biotechnology, School of Chemical and Life Sciences, Jamia Hamdard, New Delhi 110062, India;
| | - Manoj Majee
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
| | - Asis Datta
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi 110067, India; (K.H.); (A.C.); (M.M.)
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28
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Ji SX, Wang XD, Lin ZK, Wan FH, Lü ZC, Liu WX. Characterization of Chromatin Remodeling Genes Involved in Thermal Tolerance of Biologically Invasive Bemisia tabaci. Front Physiol 2022; 13:865172. [PMID: 35669578 PMCID: PMC9163341 DOI: 10.3389/fphys.2022.865172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2022] [Accepted: 04/13/2022] [Indexed: 11/13/2022] Open
Abstract
As an invasive species, Bemisia tabaci Mediterranean (MED) has notable potential to adapt to a wide range of environmental temperatures, which enables it to successfully spread after invasion and occupy habitats over a wide latitude range. It has been postulated that chromatin remodeling mechanisms are related to the rapid acquisition of adaptive traits and thermal resistance in invasive species; however, relevant experimental evidence is scarce. To identify the molecular characteristics and assess the role of chromatin remodelers in thermal stress within invasive MED and native Asia II 1 of the B. tabaci species complex, we identified 13 switching defective/sucrose non-fermenting (SWI/SNF) and 10 imitation switch (ISWI) family members in the B. tabaci genome, analyzed their molecular characteristics and structures, and identified key mutation sites between MED and Asia II 1, then cloned the catalytic subunits, and revealed the difference in thermal tolerance function. The results showed that the expression levels of Bt-BRM-1 and Bt-BRM-2 were significantly higher in MED than in Asia II 1 during heat stress, and Bt-BRM-2 expression was significantly higher during cold stress. In addition, RNA interference results indicated that the two target genes had similar temperature tolerance function in the both two cryptic species. This study is the first to identify and analyze the molecular characteristics of SWI/SNF and ISWI family members and reveal their potential key roles in temperature tolerance in poikilothermic ectotherms. The results will assist in understanding the underlying temperature adaptation mechanism of invasive insects and will enrich stress adaptation research systems from an epigenetic perspective.
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Affiliation(s)
- Shun-Xia Ji
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiao-Di Wang
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ze-Kai Lin
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Fang-Hao Wan
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China
| | - Zhi-Chuang Lü
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
- *Correspondence: Zhi-Chuang Lü,
| | - Wan-Xue Liu
- State Key Laboratory for Biology of Plant Diseases and Insect Pests, Institute of Plant Protection, Chinese Academy of Agricultural Sciences, Beijing, China
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Perrella G, Bäurle I, van Zanten M. Epigenetic regulation of thermomorphogenesis and heat stress tolerance. THE NEW PHYTOLOGIST 2022; 234:1144-1160. [PMID: 35037247 DOI: 10.1111/nph.17970] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 12/13/2021] [Indexed: 06/14/2023]
Abstract
Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.
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Affiliation(s)
- Giorgio Perrella
- Italian National Agency for New Technologies, Energy and Sustainable Economic Development (ENEA), Trisaia Research Centre, S.S. Ionica, km 419.5, 75026, Rotondella (Matera), Italy
| | - Isabel Bäurle
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, D-14476, Potsdam, Germany
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, the Netherlands
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30
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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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Singroha G, Kumar S, Gupta OP, Singh GP, Sharma P. Uncovering the Epigenetic Marks Involved in Mediating Salt Stress Tolerance in Plants. Front Genet 2022; 13:811732. [PMID: 35495170 PMCID: PMC9053670 DOI: 10.3389/fgene.2022.811732] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 03/15/2022] [Indexed: 12/29/2022] Open
Abstract
The toxic effects of salinity on agricultural productivity necessitate development of salt stress tolerance in food crops in order to meet the escalating demands. Plants use sophisticated epigenetic systems to fine-tune their responses to environmental cues. Epigenetics is the study of heritable, covalent modifications of DNA and histone proteins that regulate gene expression without altering the underlying nucleotide sequence and consequently modify the phenotype. Epigenetic processes such as covalent changes in DNA, histone modification, histone variants, and certain non-coding RNAs (ncRNA) influence chromatin architecture to regulate its accessibility to the transcriptional machinery. Under salt stress conditions, there is a high frequency of hypermethylation at promoter located CpG sites. Salt stress results in the accumulation of active histones marks like H3K9K14Ac and H3K4me3 and the downfall of repressive histone marks such as H3K9me2 and H3K27me3 on salt-tolerance genes. Similarly, the H2A.Z variant of H2A histone is reported to be down regulated under salt stress conditions. A thorough understanding of the plasticity provided by epigenetic regulation enables a modern approach to genetic modification of salt-resistant cultivars. In this review, we summarize recent developments in understanding the epigenetic mechanisms, particularly those that may play a governing role in the designing of climate smart crops in response to salt stress.
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Moore BM, Lee YS, Wang P, Azodi C, Grotewold E, Shiu SH. Modeling temporal and hormonal regulation of plant transcriptional response to wounding. THE PLANT CELL 2022; 34:867-888. [PMID: 34865154 PMCID: PMC8824630 DOI: 10.1093/plcell/koab287] [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: 11/24/2020] [Accepted: 11/18/2021] [Indexed: 06/02/2023]
Abstract
Plants respond to wounding stress by changing gene expression patterns and inducing the production of hormones including jasmonic acid. This wounding transcriptional response activates specialized metabolism pathways such as the glucosinolate pathways in Arabidopsis thaliana. While the regulatory factors and sequences controlling a subset of wound-response genes are known, it remains unclear how wound response is regulated globally. Here, we how these responses are regulated by incorporating putative cis-regulatory elements, known transcription factor binding sites, in vitro DNA affinity purification sequencing, and DNase I hypersensitive sites to predict genes with different wound-response patterns using machine learning. We observed that regulatory sites and regions of open chromatin differed between genes upregulated at early and late wounding time-points as well as between genes induced by jasmonic acid and those not induced. Expanding on what we currently know, we identified cis-elements that improved model predictions of expression clusters over known binding sites. Using a combination of genome editing, in vitro DNA-binding assays, and transient expression assays using native and mutated cis-regulatory elements, we experimentally validated four of the predicted elements, three of which were not previously known to function in wound-response regulation. Our study provides a global model predictive of wound response and identifies new regulatory sequences important for wounding without requiring prior knowledge of the transcriptional regulators.
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Affiliation(s)
| | | | - Peipei Wang
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824, USA
| | - Christina Azodi
- St. Vincent’s Institute of Medical Research, Fitzroy 3065, Victoria, Australia
| | - Erich Grotewold
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824, USA
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Grape ASR-Silencing Sways Nuclear Proteome, Histone Marks and Interplay of Intrinsically Disordered Proteins. Int J Mol Sci 2022; 23:ijms23031537. [PMID: 35163458 PMCID: PMC8835812 DOI: 10.3390/ijms23031537] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 01/25/2022] [Accepted: 01/26/2022] [Indexed: 01/27/2023] Open
Abstract
In order to unravel the functions of ASR (Abscisic acid, Stress, Ripening-induced) proteins in the nucleus, we created a new model of genetically transformed grape embryogenic cells by RNAi-knockdown of grape ASR (VvMSA). Nuclear proteomes of wild-type and VvMSA-RNAi grape cell lines were analyzed by quantitative isobaric tagging (iTRAQ 8-plex). The most significantly up- or down-regulated nuclear proteins were involved in epigenetic regulation, DNA replication/repair, transcription, mRNA splicing/stability/editing, rRNA processing/biogenesis, metabolism, cell division/differentiation and stress responses. The spectacular up-regulation in VvMSA-silenced cells was that of the stress response protein VvLEA D-29 (Late Embryogenesis Abundant). Both VvMSA and VvLEA D-29 genes displayed strong and contrasted responsiveness to auxin depletion, repression of VvMSA and induction of VvLEA D-29. In silico analysis of VvMSA and VvLEA D-29 proteins highlighted their intrinsically disordered nature and possible compensatory relationship. Semi-quantitative evaluation by medium-throughput immunoblotting of eighteen post-translational modifications of histones H3 and H4 in VvMSA-knockdown cells showed significant enrichment/depletion of the histone marks H3K4me1, H3K4me3, H3K9me1, H3K9me2, H3K36me2, H3K36me3 and H4K16ac. We demonstrate that grape ASR repression differentially affects members of complex nucleoprotein structures and may not only act as molecular chaperone/transcription factor, but also participates in plant responses to developmental and environmental cues through epigenetic mechanisms.
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Lopez L, Perrella G, Calderini O, Porceddu A, Panara F. Genome-Wide Identification of Histone Modification Gene Families in the Model Legume Medicago truncatula and Their Expression Analysis in Nodules. PLANTS 2022; 11:plants11030322. [PMID: 35161303 PMCID: PMC8838541 DOI: 10.3390/plants11030322] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 01/12/2022] [Accepted: 01/20/2022] [Indexed: 01/22/2023]
Abstract
Histone methylation and acetylation are key processes in the epigenetic regulation of plant growth, development, and responses to environmental stimuli. The genes encoding for the enzymes that are responsible for these chromatin post-translational modifications, referred to as histone modification genes (HMGs), have been poorly investigated in Leguminosae species, despite their importance for establishment and activity of nitrogen-fixing nodules. In silico analysis of Medicago truncatula HMGs identified 81 histone methyltransferases, 46 histone demethylases, 64 histone acetyltransferases, and 15 histone deacetylases. MtHMGs were analyzed for their structure and domain composition, and some combinations that were not yet reported in other plant species were identified. Genes have been retrieved from M. truncatula A17 and R108 genotypes as well as M. sativa CADL and Zhongmu No.1; the gene number and distribution were compared with Arabidopsis thaliana. Furthermore, by analyzing the expression data that were obtained at various developmental stages and in different zones of nitrogen-fixing nodules, we identified MtHMG loci that could be involved in nodule development and function. This work sets a reference for HMG genomic organization in legumes which will be useful for functional investigation that is aimed at elucidating HMGs involvement in nodule development and symbiotic nitrogen fixation.
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Affiliation(s)
- Loredana Lopez
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
| | - Giorgio Perrella
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
| | - Ornella Calderini
- Institute of Biosciences and Bioresources, Consiglio Nazionale delle Ricerche, 06128 Perugia, Italy
- Correspondence: (O.C.); (F.P.); Tel.: +39-075-501-4858 (O.C.); +39-0835-974-523 (F.P.)
| | - Andrea Porceddu
- Department of Agriculture, University of Sassari, Viale Italia, 39a, 07100 Sassari, Italy;
| | - Francesco Panara
- Trisaia Research Center, Italian National Agency for New Technologies Energy and Sustainable Economic Development (ENEA), 75026 Rotondella, Italy; (L.L.); (G.P.)
- Correspondence: (O.C.); (F.P.); Tel.: +39-075-501-4858 (O.C.); +39-0835-974-523 (F.P.)
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35
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Lohani N, Singh MB, Bhalla PL. Biological Parts for Engineering Abiotic Stress Tolerance in Plants. BIODESIGN RESEARCH 2022; 2022:9819314. [PMID: 37850130 PMCID: PMC10521667 DOI: 10.34133/2022/9819314] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2023] Open
Abstract
It is vital to ramp up crop production dramatically by 2050 due to the increasing global population and demand for food. However, with the climate change projections showing that droughts and heatwaves becoming common in much of the globe, there is a severe threat of a sharp decline in crop yields. Thus, developing crop varieties with inbuilt genetic tolerance to environmental stresses is urgently needed. Selective breeding based on genetic diversity is not keeping up with the growing demand for food and feed. However, the emergence of contemporary plant genetic engineering, genome-editing, and synthetic biology offer precise tools for developing crops that can sustain productivity under stress conditions. Here, we summarize the systems biology-level understanding of regulatory pathways involved in perception, signalling, and protective processes activated in response to unfavourable environmental conditions. The potential role of noncoding RNAs in the regulation of abiotic stress responses has also been highlighted. Further, examples of imparting abiotic stress tolerance by genetic engineering are discussed. Additionally, we provide perspectives on the rational design of abiotic stress tolerance through synthetic biology and list various bioparts that can be used to design synthetic gene circuits whose stress-protective functions can be switched on/off in response to environmental cues.
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Affiliation(s)
- Neeta Lohani
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Mohan B. Singh
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Prem L. Bhalla
- Plant Molecular Biology and Biotechnology Laboratory, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC 3010, Australia
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36
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Kuchaříková H, Plšková Z, Zdráhal Z, Fojtová M, Kerchev P, Lochmanová G. Quantitative Analysis of Posttranslational Modifications of Plant Histones. Methods Mol Biol 2022; 2526:241-257. [PMID: 35657525 DOI: 10.1007/978-1-0716-2469-2_18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Reshaping of the chromatin landscape under oxidative stress is of paramount importance for mounting an effective stress response. Unbiased systemic identification and quantification of histone marks is crucial for understanding the epigenetic component of plant responses to adverse environmental conditions. We describe a detailed method for isolation of plant histones and subsequent bottom-up proteomics approach for characterization of acetylation and methylation status. By performing label-free quantitative mass spectrometry analysis, relative abundances of histone marks can be statistically compared between experimental conditions.
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Affiliation(s)
- Hana Kuchaříková
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Zuzana Plšková
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Zbyněk Zdráhal
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Miloslava Fojtová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic
| | - Pavel Kerchev
- Phytophthora Research Centre, Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Gabriela Lochmanová
- Mendel Centre for Plant Genomics and Proteomics, Central European Institute of Technology, Masaryk University, Brno, Czech Republic.
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Transcriptional Association between mRNAs and Their Paired Natural Antisense Transcripts Following Fusarium oxysporum Inoculation in Brassica rapa L. HORTICULTURAE 2021. [DOI: 10.3390/horticulturae8010017] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Long noncoding RNAs (lncRNAs) play important roles in abiotic and biotic stress responses; however, studies on the mechanism of regulation of lncRNA expression are limited in plants. The present study examined the relationship between lncRNA expression level and two active histone modifications (H3K4me3 and H3K36me3) in Brassica rapa. Both histone marks were enriched in the chromatin regions encoding lncRNAs, especially around the transcription start site. The transcription level of long intergenic noncoding RNAs was positively associated with the level of H3K4me3 and H3K36me3, while this association was not observed in natural antisense RNAs (NATs) and intronic noncoding RNAs. As coordinate expression of mRNAs and paired NATs under biotic stress treatment has been identified, the transcriptional relationship between mRNAs and their paired NATs following Fusarium oxysporum f. sp. conglutinans (Foc) inoculation was examined. A positive association of expression levels between mRNAs and their paired NATs following Foc inoculation was observed. This association held for several defense-response-related genes and their NAT pairs. These results suggest that coordinate expression of mRNAs and paired NATs plays a role in the defense response against Foc.
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38
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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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Jain M, Garg R. Enhancers as potential targets for engineering salinity stress tolerance in crop plants. PHYSIOLOGIA PLANTARUM 2021; 173:1382-1391. [PMID: 33837536 DOI: 10.1111/ppl.13421] [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: 02/08/2021] [Revised: 03/19/2021] [Accepted: 04/06/2021] [Indexed: 06/12/2023]
Abstract
Enhancers represent noncoding regulatory regions of the genome located distantly from their target genes. They regulate gene expression programs in a context-specific manner via interacting with promoters of one or more target genes and are generally associated with transcription factor binding sites and epi(genomic)/chromatin features, such as regions of chromatin accessibility and histone modifications. The enhancers are difficult to identify due to the modularity of their associated features. Although enhancers have been studied extensively in human and animals, only a handful of them has been identified in few plant species till date due to nonavailability of plant-specific experimental and computational approaches for their discovery. Being an important regulatory component of the genome, enhancers represent potential targets for engineering agronomic traits, including salinity stress tolerance in plants. Here, we provide a review of the available experimental and computational approaches along with the associated sequence and chromatin/epigenetic features for the discovery of enhancers in plants. In addition, we provide insights into the challenges and future prospects of enhancer research in plant biology with emphasis on potential applications in engineering salinity stress tolerance in crop plants.
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Affiliation(s)
- Mukesh Jain
- School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Rohini Garg
- Department of Life Sciences, School of Natural Sciences, Shiv Nadar University, Gautam Buddha Nagar, Uttar Pradesh, India
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40
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Chele KH, Steenkamp P, Piater LA, Dubery IA, Huyser J, Tugizimana F. A Global Metabolic Map Defines the Effects of a Si-Based Biostimulant on Tomato Plants under Normal and Saline Conditions. Metabolites 2021; 11:metabo11120820. [PMID: 34940578 PMCID: PMC8709197 DOI: 10.3390/metabo11120820] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/10/2021] [Accepted: 11/13/2021] [Indexed: 01/19/2023] Open
Abstract
The ongoing unpredictability of climate changes is exponentially exerting a negative impact on crop production, further aggravating detrimental abiotic stress effects. Several research studies have been focused on the genetic modification of crop plants to achieve more crop resilience against such stress factors; however, there has been a paradigm shift in modern agriculture focusing on more organic, eco-friendly and long-lasting systems to improve crop yield. As such, extensive research into the use of microbial and nonmicrobial biostimulants has been at the core of agricultural studies to improve crop growth and development, as well as to attain tolerance against several biotic and abiotic stresses. However, the molecular mechanisms underlying the biostimulant activity remain enigmatic. Thus, this study is a liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics approach to unravel the hypothetical biochemical framework underlying effects of a nonmicrobial biostimulant (a silicon-based formulation) on tomato plants (Solanum lycopersium) under salinity stress conditions. This metabolomics study postulates that Si-based biostimulants could alleviate salinity stress in tomato plants through modulation of the primary metabolism involving changes in the tricarboxylic acid cycle, fatty acid and numerous amino acid biosynthesis pathways, with further reprogramming of several secondary metabolism pathways such as the phenylpropanoid pathway, flavonoid biosynthesis pathways including flavone and flavanol biosynthesis. Thus, the postulated hypothetical framework, describing biostimulant-induced metabolic events in tomato plants, provides actionable knowledge necessary for industries and farmers to, confidently and innovatively, explore, design, and fully implement Si-based formulations and strategies into agronomic practices for sustainable agriculture and food production.
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Affiliation(s)
- Kekeletso H. Chele
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Paul Steenkamp
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
| | - Johan Huyser
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa;
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (K.H.C.); (P.S.); (L.A.P.); (I.A.D.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa;
- Correspondence: ; Tel.: +27-011-559-7784
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41
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Rashid MM, Vaishnav A, Verma RK, Sharma P, Suprasanna P, Gaur RK. Epigenetic regulation of salinity stress responses in cereals. Mol Biol Rep 2021; 49:761-772. [PMID: 34773178 DOI: 10.1007/s11033-021-06922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 10/30/2021] [Indexed: 10/19/2022]
Abstract
Cereals are important crops and are exposed to various types of environmental stresses that affect the overall growth and yield. Among the various abiotic stresses, salt stress is a major environmental factor that influences the genetic, physiological, and biochemical responses of cereal crops. Epigenetic regulation which includes DNA methylation, histone modification, and chromatin remodelling plays an important role in salt stress tolerance. Recent studies in rice genomics have highlighted that the epigenetic changes are heritable and therefore can be considered as molecular signatures. An epigenetic mechanism under salinity induces phenotypic responses involving modulations in gene expression. Association between histone modification and altered DNA methylation patterns and differential gene expression has been evidenced for salt sensitivity in rice and other cereal crops. In addition, epigenetics also creates stress memory that helps the plant to better combat future stress exposure. In the present review, we have discussed epigenetic influences in stress tolerance, adaptation, and evolution processes. Understanding the epigenetic regulation of salinity could help for designing salt-tolerant varieties leading to improved crop productivity.
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Affiliation(s)
- Md Mahtab Rashid
- Department of Mycology and Plant Pathology, Institute of Agricultural Sciences, Banaras Hindu University, Varanasi, Uttar Pradesh, India.,Department of Plant Pathology, Bihar Agricultural University, Sabour, Bhagalpur, Bihar, India
| | - Anukool Vaishnav
- Department of Biotechnology, GLA University, Mathura, Uttar Pradesh, 281121, India.,Agroecology and Environment, Agroscope (Reckenholz), 8046, Zürich, Switzerland
| | - Rakesh Kumar Verma
- Department of Biosciences, Mody University of Science and Technology, Lakshmangarh, Sikar, Rajasthan, India
| | - Pradeep Sharma
- Department of Biotechnology, ICAR-Indian Institute of Wheat and Barley Research, Karnal, Haryana, India
| | - P Suprasanna
- Nuclear Agriculture & Biotechnology Division, Bhabha Atomic Research Centre, Trombay, Mumbai, 400085, India
| | - R K Gaur
- Department of Biotechnology, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India.
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42
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Lai D, Huang X, Wang C, Ow DW. Arabidopsis OXIDATIVE STRESS 3 enhances stress tolerance in Schizosaccharomyces pombe by promoting histone subunit replacement that upregulates drug-resistant genes. Genetics 2021; 219:6371188. [PMID: 34740252 DOI: 10.1093/genetics/iyab149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/04/2021] [Indexed: 11/14/2022] Open
Abstract
Histone replacement in chromatin-remodeling plays an important role in eukaryotic gene expression. New histone variants replacing their canonical counterparts often lead to a change in transcription, including responses to stresses caused by temperature, drought, salinity, and heavy metals. In this study, we describe a chromatin-remodeling process triggered by eviction of Rad3/Tel1-phosphorylated H2Aα, in which a heterologous plant protein AtOXS3 can subsequently bind fission yeast HA2.Z and Swc2, a component of the SWR1 complex, to facilitate replacement of H2Aα with H2A.Z. The histone replacement increases occupancy of the oxidative stress-responsive transcription factor Pap1 at the promoters of at least three drug-resistant genes, which enhances their transcription and hence primes the cell for higher stress tolerance.
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Affiliation(s)
- Dingwang Lai
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Xiuting Huang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Changhu Wang
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - David W Ow
- Plant Gene Engineering Center, Chinese Academy of Sciences Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
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Soil Salinity, a Serious Environmental Issue and Plant Responses: A Metabolomics Perspective. Metabolites 2021; 11:metabo11110724. [PMID: 34822381 PMCID: PMC8620211 DOI: 10.3390/metabo11110724] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Revised: 10/16/2021] [Accepted: 10/18/2021] [Indexed: 12/12/2022] Open
Abstract
The effects of global warming have increasingly led to devastating environmental stresses, such as heat, salinity, and drought. Soil salinization is a serious environmental issue and results in detrimental abiotic stress, affecting 7% of land area and 33% of irrigated lands worldwide. The proportion of arable land facing salinity is expected to rise due to increasing climate change fuelled by anthropogenic activities, exacerbating the threat to global food security for the exponentially growing populace. As sessile organisms, plants have evolutionarily developed mechanisms that allow ad hoc responses to salinity stress. The orchestrated mechanisms include signalling cascades involving phytohormones, kinases, reactive oxygen species (ROS), and calcium regulatory networks. As a pillar in a systems biology approach, metabolomics allows for comprehensive interrogation of the biochemistry and a deconvolution of molecular mechanisms involved in plant responses to salinity. Thus, this review highlights soil salinization as a serious environmental issue and points to the negative impacts of salinity on plants. Furthermore, the review summarises mechanisms regulating salinity tolerance on molecular, cellular, and biochemical levels with a focus on metabolomics perspectives. This critical synthesis of current literature is an opportunity to revisit the current models regarding plant responses to salinity, with an invitation to further fundamental research for novel and actionable insights.
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Dominguez PG, Conti G, Duffy T, Insani M, Alseekh S, Asurmendi S, Fernie AR, Carrari F. Multiomics analyses reveal the roles of the ASR1 transcription factor in tomato fruits. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6490-6509. [PMID: 34100923 DOI: 10.1093/jxb/erab269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 06/05/2021] [Indexed: 06/12/2023]
Abstract
The transcription factor ASR1 (ABA, STRESS, RIPENING 1) plays multiple roles in plant responses to abiotic stresses as well as being involved in the regulation of central metabolism in several plant species. However, despite the high expression of ASR1 in tomato fruits, large scale analyses to uncover its function in fruits are still lacking. In order to study its function in the context of fruit ripening, we performed a multiomics analysis of ASR1-antisense transgenic tomato fruits at the transcriptome and metabolome levels. Our results indicate that ASR1 is involved in several pathways implicated in the fruit ripening process, including cell wall, amino acid, and carotenoid metabolism, as well as abiotic stress pathways. Moreover, we found that ASR1-antisense fruits are more susceptible to the infection by the necrotrophic fungus Botrytis cinerea. Given that ASR1 could be regulated by fruit ripening regulators such as FRUITFULL1/FRUITFULL2 (FUL1/FUL2), NON-RIPENING (NOR), and COLORLESS NON-RIPENING (CNR), we positioned it in the regulatory cascade of red ripe tomato fruits. These data extend the known range of functions of ASR1 as an important auxiliary regulator of tomato fruit ripening.
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Affiliation(s)
- Pia Guadalupe Dominguez
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Gabriela Conti
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
- Facultad de Agronomía. Cátedra de Genética. Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Tomás Duffy
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Marina Insani
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Saleh Alseekh
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Sebastián Asurmendi
- Instituto de Agrobiotecnología y Biología Molecular (IABIMO), Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Hurlingham, Buenos Aires, Argentina
| | - Alisdair R Fernie
- Max-Planck-Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology, 4000 Plovdiv, Bulgaria
| | - Fernando Carrari
- Facultad de Agronomía. Cátedra de Genética. Universidad de Buenos Aires, Buenos Aires, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET), Ciudad Universitaria, C1428EHA Buenos Aires, Argentina
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Barrero-Gil J, Mouriz A, Piqueras R, Salinas J, Jarillo JA, Piñeiro M. A MRG-operated chromatin switch at SOC1 attenuates abiotic stress responses during the floral transition. PLANT PHYSIOLOGY 2021; 187:462-471. [PMID: 34618146 PMCID: PMC8418395 DOI: 10.1093/plphys/kiab275] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/21/2021] [Indexed: 06/13/2023]
Abstract
Plants react to environmental challenges by integrating external cues with endogenous signals to optimize survival and reproductive success. However, the mechanisms underlying this integration remain obscure. While stress conditions are known to impact plant development, how developmental transitions influence responses to adverse conditions has not been addressed. Here, we reveal a molecular mechanism of stress response attenuation during the onset of flowering in Arabidopsis (Arabidopsis thaliana). We show that Arabidopsis MORF-RELATED GENE (MRG) proteins, components of the NuA4 histone acetyltransferase complex that bind trimethylated-lysine 36 in histone H3 (H3K36me3), function as a chromatin switch on the floral integrator SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) to coordinate flowering initiation with plant responsiveness to hostile environments. MRG proteins are required to activate SOC1 expression during flowering induction by promoting histone H4 acetylation. In turn, SOC1 represses a broad array of genes that mediate abiotic stress responses. We propose that during the transition from vegetative to reproductive growth, the MRG-SOC1 module constitutes a central hub in a mechanism that tunes down stress responses to enhance the reproductive success and plant fitness at the expense of costly efforts for adaptation to challenging environments.
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Affiliation(s)
- Javier Barrero-Gil
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - Alfonso Mouriz
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Raquel Piqueras
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Julio Salinas
- Departamento de Biotecnología Microbiana y de Plantas, Centro Investigaciones Biológicas “Margarita Salas”, CSIC, Madrid, Spain
| | - José A. Jarillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
| | - Manuel Piñeiro
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (UPM)–Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA-CSIC), Campus Montegancedo UPM, 28223 Pozuelo de Alarcón (Madrid), Spain
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Chaudhary S, Jabre I, Syed NH. Epigenetic differences in an identical genetic background modulate alternative splicing in A. thaliana. Genomics 2021; 113:3476-3486. [PMID: 34391867 DOI: 10.1016/j.ygeno.2021.08.006] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Revised: 08/02/2021] [Accepted: 08/10/2021] [Indexed: 11/19/2022]
Abstract
How stable and temperature-dependent variations in DNA methylation and nucleosome occupancy influence alternative splicing (AS) remains poorly understood in plants. To answer this, we generated transcriptome, whole-genome bisulfite, and MNase sequencing data for an epigenetic Recombinant Inbred Line (epiRIL) of A. thaliana at normal and cold temperature. For comparative analysis, the same data sets for the parental ecotype Columbia (Col-0) were also generated, whereas for DNA methylation, previously published high confidence methylation profiles of Col-0 were used. Significant epigenetic differences in an identical genetic background were observed between Col-0 and epiRIL lines under normal and cold temperatures. Our transcriptome data revealed that differential DNA methylation and nucleosome occupancy modulate expression levels of many genes and AS in response to cold. Collectively, DNA methylation and nucleosome levels exhibit characteristic patterns around intron-exon boundaries at normal and cold conditions, and any perturbation in them, in an identical genetic background is sufficient to modulate AS in Arabidopsis.
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Affiliation(s)
- Saurabh Chaudhary
- School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK; Cardiff School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK.
| | - Ibtissam Jabre
- School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK; Department of Microbial Sciences, School of Biosciences and Medicine, Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - Naeem H Syed
- School of Psychology and Life Sciences, Canterbury Christ Church University, Canterbury CT1 1QU, UK.
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Comparative ribosome profiling reveals distinct translational landscapes of salt-sensitive and -tolerant rice. BMC Genomics 2021; 22:612. [PMID: 34384368 PMCID: PMC8359061 DOI: 10.1186/s12864-021-07922-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 08/03/2021] [Indexed: 01/27/2023] Open
Abstract
BACKGROUND Soil salinization represents a serious threat to global rice production. Although significant research has been conducted to understand salt stress at the genomic, transcriptomic and proteomic levels, few studies have focused on the translatomic responses to this stress. Recent studies have suggested that transcriptional and translational responses to salt stress can often operate independently. RESULTS We sequenced RNA and ribosome-protected fragments (RPFs) from the salt-sensitive rice (O. sativa L.) cultivar 'Nipponbare' (NB) and the salt-tolerant cultivar 'Sea Rice 86' (SR86) under normal and salt stress conditions. A large discordance between salt-induced transcriptomic and translatomic alterations was found in both cultivars, with more translationally regulated genes being observed in SR86 in comparison to NB. A biased ribosome occupancy, wherein RPF depth gradually increased from the 5' ends to the 3' ends of coding regions, was revealed in NB and SR86. This pattern was strengthened by salt stress, particularly in SR86. On the contrary, the strength of ribosome stalling was accelerated in salt-stressed NB but decreased in SR86. CONCLUSIONS This study revealed that translational reprogramming represents an important layer of salt stress responses in rice, and the salt-tolerant cultivar SR86 adopts a more flexible translationally adaptive strategy to cope with salt stress compared to the salt susceptible cultivar NB. The differences in translational dynamics between NB and SR86 may derive from their differing levels of ribosome stalling under salt stress.
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48
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Park M, Williams DS, Turpin ZM, Wiggins ZJ, Tsolova VM, Onokpise OU, Bass HW. Differential nuclease sensitivity profiling uncovers a drought responsive change in maize leaf chromatin structure for two large retrotransposon derivatives, Uloh and Vegu. PLANT DIRECT 2021; 5:e337. [PMID: 34430792 PMCID: PMC8365550 DOI: 10.1002/pld3.337] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 05/19/2021] [Accepted: 06/21/2021] [Indexed: 06/13/2023]
Abstract
Plant chromatin dynamics are generally recognized as playing a role in the genomic response to environmental stress. Although stress-induced transcriptional activities of LTR-retrotransposons have been reported, whether the stress response can be detected at the level of chromatin structure for LTR-retrotransposons is largely unknown. Using differential nuclease sensitivity profiling, we identified that two out of 29 maize LTR-retrotransposon families change their chromatin structure in response to drought stress in leaf tissue. The two LTR-retrotransposon families, uloh and vegu, are classified as nonautonomous LTR-retrotransposons. Differently from other families, the chromatin structure of these two families shifted from more open in normal conditions to more closed following drought stress. Although uloh and vegu lack sequence similarity, most of them shared an intriguing feature of having a new and uncharacterized insertion of a DNA sequence near one side of an LTR. In the uloh family, nine members with a strong drought response also exhibited a drought-induced reduction of published H3K4me3 histone modification in the inserted DNA region, implicating this modification in the chromatin structural changes. Our results provide new insight into how LTR-retrotransposons can alter their chromatin structure following stress response in plants.
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Affiliation(s)
- Minkyu Park
- Center for Viticulture and Small Fruit ResearchFlorida A&M UniversityTallahasseeFloridaUSA
| | - Delvin S. Williams
- College of Agriculture and Food SciencesFlorida A&M UniversityTallahasseeFloridaUSA
| | - Zachary M. Turpin
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
| | | | - Violeta M. Tsolova
- Center for Viticulture and Small Fruit ResearchFlorida A&M UniversityTallahasseeFloridaUSA
| | | | - Hank W. Bass
- Department of Biological ScienceFlorida State UniversityTallahasseeFloridaUSA
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Lephatsi MM, Meyer V, Piater LA, Dubery IA, Tugizimana F. Plant Responses to Abiotic Stresses and Rhizobacterial Biostimulants: Metabolomics and Epigenetics Perspectives. Metabolites 2021; 11:457. [PMID: 34357351 PMCID: PMC8305699 DOI: 10.3390/metabo11070457] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 07/12/2021] [Accepted: 07/13/2021] [Indexed: 01/14/2023] Open
Abstract
In response to abiotic stresses, plants mount comprehensive stress-specific responses which mediate signal transduction cascades, transcription of relevant responsive genes and the accumulation of numerous different stress-specific transcripts and metabolites, as well as coordinated stress-specific biochemical and physiological readjustments. These natural mechanisms employed by plants are however not always sufficient to ensure plant survival under abiotic stress conditions. Biostimulants such as plant growth-promoting rhizobacteria (PGPR) formulation are emerging as novel strategies for improving crop quality, yield and resilience against adverse environmental conditions. However, to successfully formulate these microbial-based biostimulants and design efficient application programs, the understanding of molecular and physiological mechanisms that govern biostimulant-plant interactions is imperatively required. Systems biology approaches, such as metabolomics, can unravel insights on the complex network of plant-PGPR interactions allowing for the identification of molecular targets responsible for improved growth and crop quality. Thus, this review highlights the current models on plant defence responses to abiotic stresses, from perception to the activation of cellular and molecular events. It further highlights the current knowledge on the application of microbial biostimulants and the use of epigenetics and metabolomics approaches to elucidate mechanisms of action of microbial biostimulants.
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Affiliation(s)
- Motseoa M. Lephatsi
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Vanessa Meyer
- School of Molecular and Cell Biology, University of the Witwatersrand, Private Bag 3, WITS, Johannesburg 2050, South Africa;
| | - Lizelle A. Piater
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Ian A. Dubery
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
| | - Fidele Tugizimana
- Department of Biochemistry, University of Johannesburg, Auckland Park, Johannesburg 2006, South Africa; (M.M.L.); (L.A.P.); (I.A.D.)
- International Research and Development Division, Omnia Group, Ltd., Johannesburg 2021, South Africa
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50
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Samo N, Ebert A, Kopka J, Mozgová I. Plant chromatin, metabolism and development - an intricate crosstalk. CURRENT OPINION IN PLANT BIOLOGY 2021; 61:102002. [PMID: 33497897 DOI: 10.1016/j.pbi.2021.102002] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/01/2020] [Accepted: 01/04/2021] [Indexed: 06/12/2023]
Abstract
Chromatin structure influences DNA accessibility and underlying gene expression. Disturbances of chromatin structure often result in pleiotropic developmental phenotypes. Interactions between chromatin modifications and development have been the main focus of epigenetic studies. Recent years brought major advance in uncovering and understanding connections between chromatin organisation in the nucleus and metabolic processes that take place in the cytoplasm or other cellular compartments. Products of primary metabolism and cell redox states influence chromatin-modifying complexes, and chromatin modifiers in turn affect expression of metabolic genes. Current evidence indicates that complex interaction loops between these biological system layers exist. Applying interdisciplinary and holistic approaches will decipher causality and molecular mechanisms of the dynamic crosstalk between chromatin structure, metabolism and plant growth and development.
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Affiliation(s)
- Naseem Samo
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic
| | - Alina Ebert
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Joachim Kopka
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Iva Mozgová
- Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice, Czech Republic.
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