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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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Kim YJ, Kim WY, Somers DE. HOS15-mediated turnover of PRR7 enhances freezing tolerance. THE NEW PHYTOLOGIST 2024. [PMID: 39155726 DOI: 10.1111/nph.20062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2024] [Accepted: 07/29/2024] [Indexed: 08/20/2024]
Abstract
Arabidopsis PSEUDORESPONSE REGULATOR7 (PRR7) is a core component of the circadian oscillator which also plays a crucial role in freezing tolerance. PRR7 undergoes proteasome-dependent degradation to discretely phase maximal expression in early evening. While its repressive activity on downstream genes is integral to cold regulation, the mechanism of the conditional regulation of the PRR7 abundance is unknown. We used mutant analysis, protein interaction and ubiquitylation assays to establish that the ubiquitin ligase adaptor, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), controls the protein accumulation pattern of PRR7 through direct protein-protein interactions at low temperatures. Freezing tolerance and electrolyte leakage assays show that PRR7 enhances cold temperature sensitivity, supported by ChIP-qPCR at C-REPEAT BINDING FACTOR1 (CBF1) and COLD-REGULATED 15A (COR15A) promoters where PRR7 levels were higher in hos15 mutants. HOS15 mediates PRR7 turnover through enhanced ubiquitylation at low temperature in the dark. Under the same conditions, increased PRR7 association with the promoters of CBFs and COR15A in hos15 correlates with decreased CBF1 and COR15A transcription and enhanced freezing sensitivity. We propose a novel mechanism whereby HOS15-mediated degradation of PRR7 provides an intersection between the circadian system and other cold acclimation pathways that lead to increased freezing tolerance.
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Affiliation(s)
- Yeon Jeong Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center (PBRRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju, 52828, Korea
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH, 43210, USA
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Feng K, Walker JF, Marx HE, Yang Y, Brockington SF, Moore MJ, Rabeler RK, Smith SA. The link between ancient whole-genome duplications and cold adaptations in the Caryophyllaceae. AMERICAN JOURNAL OF BOTANY 2024; 111:e16350. [PMID: 38825760 DOI: 10.1002/ajb2.16350] [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: 01/26/2024] [Revised: 04/26/2024] [Accepted: 04/26/2024] [Indexed: 06/04/2024]
Abstract
PREMISE The Caryophyllaceae (the carnation family) have undergone multiple transitions into colder climates and convergence on cushion plant adaptation, indicating that they may provide a natural system for cold adaptation research. Previous research has suggested that putative ancient whole-genome duplications (WGDs) are correlated with niche shifts into colder climates across the Caryophyllales. Here, we explored the genomic changes potentially involved in one of these discovered shifts in the Caryophyllaceae. METHODS We constructed a data set combining 26 newly generated transcriptomes with 45 published transcriptomes, including 11 cushion plant species across seven genera. With this data set, we inferred a dated phylogeny for the Caryophyllaceae and mapped ancient WGDs and gene duplications onto the phylogeny. We also examined functional groups enriched for gene duplications related to the climatic shift. RESULTS The ASTRAL topology was mostly congruent with the current consensus of relationships within the family. We inferred 15 putative ancient WGDs in the family, including eight that have not been previously published. The oldest ancient WGD (ca. 64.4-56.7 million years ago), WGD1, was found to be associated with a shift into colder climates by previous research. Gene regions associated with ubiquitination were overrepresented in gene duplications retained after WGD1 and those convergently retained by cushion plants in Colobanthus and Eremogone, along with other functional annotations. CONCLUSIONS Gene family expansions induced by ancient WGDs may have contributed to the shifts to cold climatic niches in the Caryophyllaceae. Transcriptomic data are crucial resources that help unravel heterogeneity in deep-time evolutionary patterns in plants.
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Affiliation(s)
- Keyi Feng
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Joseph F Walker
- Department of Biological Sciences, University of Illinois Chicago, Chicago, 60607, IL, USA
| | - Hannah E Marx
- Department of Biology, University of New Mexico, Albuquerque, 87131, NM, USA
| | - Ya Yang
- Department of Plant and Microbial Biology, University of Minnesota-Twin Cities, St. Paul, 55108, MN, USA
| | | | - Michael J Moore
- Department of Biology, Oberlin College, Oberlin, 44074, OH, USA
| | - Richard K Rabeler
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
| | - Stephen A Smith
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, 48109, MI, USA
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Chu W, Chang S, Lin J, Zhang C, Li J, Liu X, Liu Z, Liu D, Yang Q, Zhao D, Liu X, Guo W, Xin M, Yao Y, Peng H, Xie C, Ni Z, Sun Q, Hu Z. Methyltransferase TaSAMT1 mediates wheat freezing tolerance by integrating brassinosteroid and salicylic acid signaling. THE PLANT CELL 2024; 36:2607-2628. [PMID: 38537937 PMCID: PMC11218785 DOI: 10.1093/plcell/koae100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/23/2024] [Indexed: 07/04/2024]
Abstract
Cold injury is a major environmental stress affecting the growth and yield of crops. Brassinosteroids (BRs) and salicylic acid (SA) play important roles in plant cold tolerance. However, whether or how BR signaling interacts with the SA signaling pathway in response to cold stress is still unknown. Here, we identified an SA methyltransferase, TaSAMT1 that converts SA to methyl SA (MeSA) and confers freezing tolerance in wheat (Triticum aestivum). TaSAMT1 overexpression greatly enhanced wheat freezing tolerance, with plants accumulating more MeSA and less SA, whereas Tasamt1 knockout lines were sensitive to freezing stress and accumulated less MeSA and more SA. Spraying plants with MeSA conferred freezing tolerance to Tasamt1 mutants, but SA did not. We revealed that BRASSINAZOLE-RESISTANT 1 (TaBZR1) directly binds to the TaSAMT1 promoter and induces its transcription. Moreover, TaBZR1 interacts with the histone acetyltransferase TaHAG1, which potentiates TaSAMT1 expression via increased histone acetylation and modulates the SA pathway during freezing stress. Additionally, overexpression of TaBZR1 or TaHAG1 altered TaSAMT1 expression and improved freezing tolerance. Our results demonstrate a key regulatory node that connects the BR and SA pathways in the plant cold stress response. The regulatory factors or genes identified could be effective targets for the genetic improvement of freezing tolerance in crops.
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Affiliation(s)
- Wei Chu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Shumin Chang
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Jingchen Lin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Chenji Zhang
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Jinpeng Li
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Xingbei Liu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Zehui Liu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Debiao Liu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Qun Yang
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Danyang Zhao
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Xiaoyu Liu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Weilong Guo
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Mingming Xin
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Yingyin Yao
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Huiru Peng
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Chaojie Xie
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Zhongfu Ni
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Qixin Sun
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
| | - Zhaorong Hu
- Frontiers Science Center for Molecular Design Breeding/Key Laboratory of Crop Heterosis and Utilization (MOE)/Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, No. 2 Yuanmingyuan Xi Road, Haidian District, Beijing 100193, PR China
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Kim YJ, Kim WY, Somers DE. HOS15-mediated turnover of PRR7 enhances freezing tolerance. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.20.599783. [PMID: 38979283 PMCID: PMC11230174 DOI: 10.1101/2024.06.20.599783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Arabidopsis PSEUDO RESPONSE REGULATOR7 (PRR7) is a core component of the circadian oscillator which also plays a crucial role in freezing tolerance. PRR7 undergoes proteasome-dependent degradation to discretely phase maximal expression in early evening. While its transcriptional repressive activity on downstream genes is integral to cold regulation, the mechanism of the conditional regulation of the PRR7 protein activity is unknown. We used double mutant analysis, protein interaction and ubiquitylation assays to establish that the ubiquitin ligase adaptor, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), controls the protein accumulation pattern of PRR7 through direct protein-protein interactions. Freezing tolerance and electrolyte leakage assays show that PRR7 enhances cold temperature sensitivity, supported by ChIP-qPCR at C-REPEAT BINDING FACTOR (CBF) and COLD REGULATED 15A (COR15A) promoters where PRR7 levels were higher in hos15 mutants. We establish that HOS15 mediates PRR7 protein turnover through enhanced ubiquitylation at low temperature in the dark. Under the same conditions, increased PRR7 association with the promoter regions of CBFs and COR15A in hos15 correlates with decreased CBF1 and COR15A transcription and enhanced freezing sensitivity. We propose a novel mechanism whereby HOS15-mediated regulation of PRR7 provides an intersection between the circadian system and other cold acclimation pathways leading to freezing tolerance through upregulation of CBF1 and COR15A.
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Affiliation(s)
- Yeon Jeong Kim
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Woe Yeon Kim
- Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center (PBRRC), Plant Molecular Biology and Biotechnology Research Center (PMBBRC), Gyeongsang National University, Jinju 52828, Republic of Korea
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
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Leydon AR, Downing B, Sanchez JS, Loll-Krippleber R, Belliveau NM, Rodriguez-Mias RA, Bauer A, Watson IJ, Bae L, Villén J, Brown GW, Nemhauser JL. A conserved function of corepressors is to nucleate assembly of the transcriptional preinitiation complex. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.01.587599. [PMID: 38617365 PMCID: PMC11014602 DOI: 10.1101/2024.04.01.587599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
The plant corepressor TPL is recruited to diverse chromatin contexts, yet its mechanism of repression remains unclear. Previously, we have leveraged the fact that TPL retains its function in a synthetic transcriptional circuit in the yeast model Saccharomyces cerevisiae to localize repressive function to two distinct domains. Here, we employed two unbiased whole genome approaches to map the physical and genetic interactions of TPL at a repressed locus. We identified SPT4, SPT5 and SPT6 as necessary for repression with the SPT4 subunit acting as a bridge connecting TPL to SPT5 and SPT6. We also discovered the association of multiple additional constituents of the transcriptional preinitiation complex at TPL-repressed promoters, specifically those involved in early transcription initiation events. These findings were validated in yeast and plants through multiple assays, including a novel method to analyze conditional loss of function of essential genes in plants. Our findings support a model where TPL nucleates preassembly of the transcription activation machinery to facilitate rapid onset of transcription once repression is relieved.
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Affiliation(s)
| | - Benjamin Downing
- Department of Biology, University of Washington, Seattle, 98195, USA
| | | | | | | | | | - Andrew Bauer
- Department of Biology, University of Washington, Seattle, 98195, USA
| | | | - Lena Bae
- Department of Biology, University of Washington, Seattle, 98195, USA
| | - Judit Villén
- Department of Genome Sciences, University of Washington, Seattle, 98195, USA
| | - Grant W. Brown
- Department of Biochemistry and Donnelly Centre, University of Toronto, Toronto, Ontario, CA
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Siddique AB, Parveen S, Rahman MZ, Rahman J. Revisiting plant stress memory: mechanisms and contribution to stress adaptation. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2024; 30:349-367. [PMID: 38623161 PMCID: PMC11016036 DOI: 10.1007/s12298-024-01422-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 02/04/2024] [Accepted: 02/22/2024] [Indexed: 04/17/2024]
Abstract
Highly repetitive adverse environmental conditions are encountered by plants multiple times during their lifecycle. These repetitive encounters with stresses provide plants an opportunity to remember and recall the experiences of past stress-associated responses, resulting in better adaptation towards those stresses. In general, this phenomenon is known as plant stress memory. According to our current understanding, epigenetic mechanisms play a major role in plants stress memory through DNA methylation, histone, and chromatin remodeling, and modulating non-coding RNAs. In addition, transcriptional, hormonal, and metabolic-based regulations of stress memory establishment also exist for various biotic and abiotic stresses. Plant memory can also be generated by priming the plants using various stressors that improve plants' tolerance towards unfavorable conditions. Additionally, the application of priming agents has been demonstrated to successfully establish stress memory. However, the interconnection of all aspects of the underlying mechanisms of plant stress memory is not yet fully understood, which limits their proper utilization to improve the stress adaptations in plants. This review summarizes the recent understanding of plant stress memory and its potential applications in improving plant tolerance towards biotic and abiotic stresses.
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Affiliation(s)
- Abu Bakar Siddique
- Tasmanian Institute of Agriculture, University of Tasmania, Prospect, TAS 7250 Australia
| | - Sumaya Parveen
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, 1207 Bangladesh
| | - Md Zahidur Rahman
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, 1207 Bangladesh
| | - Jamilur Rahman
- Department of Genetics and Plant Breeding, Faculty of Agriculture, Sher-e-Bangla Agricultural University, Sher-e-Bangla Nagar, Dhaka, 1207 Bangladesh
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Kovalchuk I. Role of Epigenetic Factors in Response to Stress and Establishment of Somatic Memory of Stress Exposure in Plants. PLANTS (BASEL, SWITZERLAND) 2023; 12:3667. [PMID: 37960024 PMCID: PMC10648063 DOI: 10.3390/plants12213667] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/18/2023] [Accepted: 10/21/2023] [Indexed: 11/15/2023]
Abstract
All species are well adapted to their environment. Stress causes a magnitude of biochemical and molecular responses in plants, leading to physiological or pathological changes. The response to various stresses is genetically predetermined, but is also controlled on the epigenetic level. Most plants are adapted to their environments through generations of exposure to all elements. Many plant species have the capacity to acclimate or adapt to certain stresses using the mechanism of priming. In most cases, priming is a somatic response allowing plants to deal with the same or similar stress more efficiently, with fewer resources diverted from growth and development. Priming likely relies on multiple mechanisms, but the differential expression of non-coding RNAs, changes in DNA methylation, histone modifications, and nucleosome repositioning play a crucial role. Specifically, we emphasize the role of BRM/CHR17, BRU1, FGT1, HFSA2, and H2A.Z proteins as positive regulators, and CAF-1, MOM1, DDM1, and SGS3 as potential negative regulators of somatic stress memory. In this review, we will discuss the role of epigenetic factors in response to stress, priming, and the somatic memory of stress exposures.
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Affiliation(s)
- Igor Kovalchuk
- Department of Biological Sciences, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
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Rehman S, Ahmad Z, Ramakrishnan M, Kalendar R, Zhuge Q. Regulation of plant epigenetic memory in response to cold and heat stress: towards climate resilient agriculture. Funct Integr Genomics 2023; 23:298. [PMID: 37700098 DOI: 10.1007/s10142-023-01219-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/18/2023] [Accepted: 08/23/2023] [Indexed: 09/14/2023]
Abstract
Plants have evolved to adapt and grow in hot and cold climatic conditions. Some also adapt to daily and seasonal temperature changes. Epigenetic modifications play an important role in regulating plant tolerance under such conditions. DNA methylation and post-translational modifications of histone proteins influence gene expression during plant developmental stages and under stress conditions, including cold and heat stress. While short-term modifications are common, some modifications may persist and result in stress memory that can be inherited by subsequent generations. Understanding the mechanisms of epigenomes responding to stress and the factors that trigger stress memory is crucial for developing climate-resilient agriculture, but such an integrated view is currently limited. This review focuses on the plant epigenetic stress memory during cold and heat stress. It also discusses the potential of machine learning to modify stress memory through epigenetics to develop climate-resilient crops.
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Affiliation(s)
- Shamsur Rehman
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, 210037, China
- Bamboo Research Institute, Nanjing Forestry University, Nanjing, 210037, China
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, Viikinkaari 1, FI-00014 University of Helsinki, Helsinki, Finland.
- Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan.
| | - Qiang Zhuge
- Co-Innovation Center for Sustainable Forestry in Southern China, Key Laboratory of Forest Genetics and Biotechnology, College of Biology and the Environment, Nanjing Forestry University, Ministry of Education, Nanjing, China.
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Wang C, Tang Y, Li Y, Hu C, Li J, Lyu A. Genome-wide identification and bioinformatics analysis of the WD40 transcription factor family and candidate gene screening for anthocyanin biosynthesis in Rhododendron simsii. BMC Genomics 2023; 24:488. [PMID: 37633914 PMCID: PMC10463391 DOI: 10.1186/s12864-023-09604-x] [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: 04/26/2023] [Accepted: 08/19/2023] [Indexed: 08/28/2023] Open
Abstract
WD40 transcription factors (TFs) constitute a large gene family in eukaryotes, playing diverse roles in cellular processes. However, their functions in the major ornamental plant, Rhododendron simsii, remain poorly understood. In this study, we identified 258 WD40 proteins in the R. simsii genome, which exhibited an uneven distribution across chromosomes. Based on domain compositions and phylogenetic analysis, we classified these 258 RsWD40 proteins into 42 subfamilies and 47 clusters. Comparative genomic analysis suggested that the expansion of the WD40 gene family predates the divergence of green algae and higher plants, indicating an ancient origin. Furthermore, by analyzing the duplication patterns of RsWD40 genes, we found that transposed duplication played a major role in their expansion. Notably, the majority of RsWD40 gene duplication pairs underwent purifying selection during evolution. Synteny analysis identified significant orthologous gene pairs between R. simsii and Arabidopsis thaliana, Oryza sativa, Vitis vinifera, and Malus domestica. We also investigated potential candidate genes involved in anthocyanin biosynthesis during different flower development stages in R. simsii using RNA-seq data. Specifically, we identified 10 candidate genes during the bud stage and 7 candidate genes during the full bloom stage. GO enrichment analysis of these candidate genes revealed the potential involvement of the ubiquitination process in anthocyanin biosynthesis. Overall, our findings provide a valuable foundation for further investigation and functional analysis of WD40 genes, as well as research on the molecular mechanisms underlying anthocyanin biosynthesis in Rhododendron species.
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Affiliation(s)
- Cheng Wang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yafang Tang
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Yan Li
- Department of Biology and Chemical Engineering, Weihai Vocational College, Weihai, 264200, China
| | - Chao Hu
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Jingyi Li
- Key Laboratory for Quality Control of Characteristic Fruits and Vegetables of Hubei Province, College of Life Science and Technology, Hubei Engineering University, Xiaogan, 432000, China
| | - Ang Lyu
- Institute of Quality Standard and Testing Technology for Agro-Products, Hubei Academy of Agricultural Science, Wuhan, 430064, China.
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Yu T, Zhang J, Cao J, Ma X, Li W, Yang G. Hub Gene Mining and Co-Expression Network Construction of Low-Temperature Response in Maize of Seedling by WGCNA. Genes (Basel) 2023; 14:1598. [PMID: 37628649 PMCID: PMC10454290 DOI: 10.3390/genes14081598] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2023] [Revised: 08/02/2023] [Accepted: 08/04/2023] [Indexed: 08/27/2023] Open
Abstract
Weighted gene co-expression network analysis (WGCNA) is a research method in systematic biology. It is widely used to identify gene modules related to target traits in multi-sample transcriptome data. In order to further explore the molecular mechanism of maize response to low-temperature stress at the seedling stage, B144 (cold stress tolerant) and Q319 (cold stress sensitive) provided by the Maize Research Institute of Heilongjiang Academy of Agricultural Sciences were used as experimental materials, and both inbred lines were treated with 5 °C for 0 h, 12 h, and 24 h, with the untreated material as a control. Eighteen leaf samples were used for transcriptome sequencing, with three biological replicates. Based on the above transcriptome data, co-expression networks of weighted genes associated with low-temperature-tolerance traits were constructed by WGCNA. Twelve gene modules significantly related to low-temperature tolerance at the seedling stage were obtained, and a number of hub genes involved in low-temperature stress regulation pathways were discovered from the four modules with the highest correlation with target traits. These results provide clues for further study on the molecular genetic mechanisms of low-temperature tolerance in maize at the seedling stage.
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Affiliation(s)
- Tao Yu
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.Z.); (J.C.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jianguo Zhang
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.Z.); (J.C.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Jingsheng Cao
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.Z.); (J.C.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
- Key Laboratory of Germplasm Resources Creation and Utilization of Maize, Harbin 150086, China
| | - Xuena Ma
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.Z.); (J.C.)
| | - Wenyue Li
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.Z.); (J.C.)
| | - Gengbin Yang
- Maize Research Institute of Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China; (J.Z.); (J.C.)
- Key Laboratory of Biology and Genetics Improvement of Maize in Northern Northeast Region, Ministry of Agriculture and Rural Affairs, Harbin 150086, China
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12
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Zuo DD, Ahammed GJ, Guo DL. Plant transcriptional memory and associated mechanism of abiotic stress tolerance. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 201:107917. [PMID: 37523825 DOI: 10.1016/j.plaphy.2023.107917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 07/02/2023] [Accepted: 07/26/2023] [Indexed: 08/02/2023]
Abstract
Plants face various adverse environmental conditions, particularly with the ongoing changes in global climate, which drastically affect the growth, development and productivity of crops. To cope with these stresses, plants have evolved complex mechanisms, and one of the crucial ways is to develop transcriptional memories from stress exposure. This induced learning enables plants to better and more strongly restart the response and adaptation mechanism to stress when similar or dissimilar stresses reoccur. Understanding the molecular mechanism behind plant transcriptional memory of stress can provide a theoretical basis for breeding stress-tolerant crops with resilience to future climates. Here we review the recent research progress on the transcriptional memory of plants under various stresses and the applications of underlying mechanisms for sustainable agricultural production. We propose that a thorough understanding of plant transcriptional memory is crucial for both agronomic management and resistant breeding, and thus may help to improve agricultural yield and quality under changing climatic conditions.
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Affiliation(s)
- Ding-Ding Zuo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Golam Jalal Ahammed
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China
| | - Da-Long Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, 471023, China; Henan Engineering Technology Research Center of Quality Regulation of Horticultural Plants, Luoyang, 471023, China.
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Li L, Li Q, Chen B, Wang J, Ding F, Wang P, Zhang X, Hou J, Luo R, Li X, Zheng J, Yang S, Yang L, Zhu L, Sun S, Ma C, Li Q, Li Y, Hu J. Identification of candidate genes that regulate the trade-off between seedling cold tolerance and fruit quality in melon ( Cucumis melo L.). HORTICULTURE RESEARCH 2023; 10:uhad093. [PMID: 37416729 PMCID: PMC10321389 DOI: 10.1093/hr/uhad093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2022] [Accepted: 05/01/2023] [Indexed: 07/08/2023]
Abstract
Trade-offs between survival and growth are widely observed in plants. Melon is an annual, trailing herb that produces economically valuable fruits that are traditionally cultivated in early spring in China. Melon seedlings are sensitive to low temperatures, and thus usually suffer from cold stress during the early growth period. However, little is known about the mechanism behind the trade-offs between seedling cold tolerance and fruit quality in melon. In this study, a total of 31 primary metabolites were detected from the mature fruits of eight melon lines that differ with respect to seedling cold tolerance; these included 12 amino acids, 10 organic acids, and 9 soluble sugars. Our results showed that concentrations of most of the primary metabolites in the cold-resistant melons were generally lower than in the cold-sensitive melons; the greatest difference in metabolite levels was observed between the cold-resistant line H581 and the moderately cold-resistant line HH09. The metabolite and transcriptome data for these two lines were then subjected to weighted correlation network analysis, resulting in the identification of five key candidate genes underlying the balancing between seedling cold tolerance and fruit quality. Among these genes, CmEAF7 might play multiple roles in regulating chloroplast development, photosynthesis, and the ABA pathway. Furthermore, multi-method functional analysis showed that CmEAF7 can certainly improve both seedling cold tolerance and fruit quality in melon. Our study identified an agriculturally important gene, CmEAF7, and provides a new insight into breeding methods to develop melon cultivars with seedling cold tolerance and high fruit quality.
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Affiliation(s)
- Lili Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Qiong Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Bin Chen
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jiyu Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Fei Ding
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Panqiao Wang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiuyue Zhang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Juan Hou
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Renren Luo
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Xiang Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jingwen Zheng
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Sen Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Luming Yang
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Lei Zhu
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Shouru Sun
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Changsheng Ma
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Qin Li
- The Seed Management Station of Zhengzhou City, Zhengzhou 450001, China
| | - Ying Li
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
| | - Jianbin Hu
- College of Horticulture, Henan Agricultural University, Zhengzhou 450002, China
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14
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Ahn G, Park HJ, Jeong SY, Shin GI, Ji MG, Cha JY, Kim J, Kim MG, Yun DJ, Kim WY. HOS15 represses flowering by promoting GIGANTEA degradation in response to low temperature in Arabidopsis. PLANT COMMUNICATIONS 2023:100570. [PMID: 36864727 PMCID: PMC10363504 DOI: 10.1016/j.xplc.2023.100570] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/13/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Flowering is the primary stage of the plant developmental transition and is tightly regulated by environmental factors such as light and temperature. However, the mechanisms by which temperature signals are integrated into the photoperiodic flowering pathway are still poorly understood. Here, we demonstrate that HOS15, which is known as a GI transcriptional repressor in the photoperiodic flowering pathway, controls flowering time in response to low ambient temperature. At 16°C, the hos15 mutant exhibits an early flowering phenotype, and HOS15 acts upstream of photoperiodic flowering genes (GI, CO, and FT). GI protein abundance is increased in the hos15 mutant and is insensitive to the proteasome inhibitor MG132. Furthermore, the hos15 mutant has a defect in low ambient temperature-mediated GI degradation, and HOS15 interacts with COP1, an E3 ubiquitin ligase for GI degradation. Phenotypic analyses of the hos15 cop1 double mutant revealed that repression of flowering by HOS15 is dependent on COP1 at 16°C. However, the HOS15-COP1 interaction was attenuated at 16°C, and GI protein abundance was additively increased in the hos15 cop1 double mutant, indicating that HOS15 acts independently of COP1 in GI turnover at low ambient temperature. This study proposes that HOS15 controls GI abundance through multiple modes as an E3 ubiquitin ligase and transcriptional repressor to coordinate appropriate flowering time in response to ambient environmental conditions such as temperature and day length.
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Affiliation(s)
- Gyeongik Ahn
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Hee Jin Park
- Department of Biological Sciences, College of Natural Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Song Yi Jeong
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Gyeong-Im Shin
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Myung Geun Ji
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Joon-Yung Cha
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Jeongsik Kim
- Faculty of Science Education and Interdisciplinary Graduate Program in Advanced Convergence Technology and Science, Jeju National University, Jeju 63243, Republic of Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, PMBBRC, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Dae-Jin Yun
- Institute of Glocal Disease Control, Konkuk University, Seoul 05029, Republic of Korea; Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Woe-Yeon Kim
- Research Institute of Life Science, Institute of Agricultural and Life Science, Gyeongsang National University, Jinju 52828, Republic of Korea; Division of Applied Life Science (BK21 Four), Plant Biological Rhythm Research Center, Plant Molecular Biology and Biotechnology Research Center, Graduate School of Gyeongsang National University, Jinju 52828, Republic of Korea.
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Vera Hernández PF, Mendoza Onofre LE, Rosas Cárdenas FDF. Responses of sorghum to cold stress: A review focused on molecular breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1124335. [PMID: 36909409 PMCID: PMC9996117 DOI: 10.3389/fpls.2023.1124335] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 01/30/2023] [Indexed: 06/18/2023]
Abstract
Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.
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Affiliation(s)
- Pedro Fernando Vera Hernández
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
| | | | - Flor de Fátima Rosas Cárdenas
- Instituto Politécnico Nacional, Centro de Investigación en Biotecnología Aplicada, Ex-Hacienda San Juan Molino Carretera Estatal Tecuexcomac-Tepetitla, Tlaxcala, Mexico
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Huang LJ, Wang Y, Lin Z, Jiang D, Luo Y, Li N. The role of corepressor HOS15-mediated epigenetic regulation of flowering. FRONTIERS IN PLANT SCIENCE 2023; 13:1101912. [PMID: 36704168 PMCID: PMC9871556 DOI: 10.3389/fpls.2022.1101912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 12/21/2022] [Indexed: 06/18/2023]
Abstract
Regulation of gene expression underpins gene function and is essential for regulation of physiological roles. Epigenetic modifications regulate gene transcription by physically facilitating relaxation or condensation of target loci in chromatin. Transcriptional corepressors are involved in chromatin remodeling and regulate gene expression by establishing repressive complexes. Genetic and biochemical studies reveal that a member of the Groucho/Thymidine uptake 1 (Gro/Tup1) corepressor family, HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15), is recruited via the evening complex (EC) to the GIGANTEA (GI) promoter to repress gene expression, and modulating flowering time. Therefore, HOS15 connects photoperiodic pathway and epigenetic mechanism to control flowering time in plants. In addition, growing body of evidence support a diverse roles of the epigenetic regulator HOS15 in fine-tuning plant development and growth by integrating intrinsic genetic components and various environmental signals.
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Affiliation(s)
- Li-Jun Huang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yukun Wang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Zeng Lin
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Dong Jiang
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yong Luo
- School of Chemistry and Environmental Science, Xiangnan University, Chenzhou, China
| | - Ning Li
- State Key Laboratory of Cultivation and Protection for Non-Wood Forest Trees, College of Forestry, Central South University of Forestry and Technology, Changsha, China
- Key Laboratory of Forest Bio-resources and Integrated Pest Management for Higher Education in Hunan Province, Central South University of Forestry and Technology, Changsha, China
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Lim CJ, Park KS, Ali A, Park J, Ryou SM, Shen M, Khan HA, Bader ZE, Zareen S, Bae MJ, Choi JH, Xu ZY, Pardo JM, Yun DJ. Negative regulation of floral transition in Arabidopsis by HOS15-PWR-HDA9 complex. FRONTIERS IN PLANT SCIENCE 2023; 13:1105988. [PMID: 36684790 PMCID: PMC9853073 DOI: 10.3389/fpls.2022.1105988] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/16/2022] [Indexed: 06/17/2023]
Abstract
Arabidopsis HOS15/PWR/HDA9 repressor complex, which is similar to the TBL1/NcoR1/HDAC complex in animals, plays a well-known role in epigenetic regulation. PWR and HDA9 have been reported to interact with each other and modulate the flowering time by repressing AGL19 expression, whereas HOS15 and HDA9, together with the photoperiodic evening complex, regulate flowering time through repression of GI transcription. However, the role of the HOS15/PWR/HDA9 core repressor complex as a functional unit in the regulation of flowering time is yet to be explored. In this study, we reported that the loss-of-function hos15-2/pwr/hda9 triple mutant accumulates higher transcript levels of AGL19 and exhibits an early flowering phenotype similar to those of hos15, pwr, and hda9 single mutants. Interestingly, the accumulation of HOS15 in the nucleus was drastically reduced in pwr and hda9 mutants. As a result, HOS15 could not perform its role in histone deacetylation or interaction with H3 in the nucleus. Furthermore, HOS15 is also associated with the same region of the AGL19 promoter known for PWR-HDA9 binding. The acetylation level of the AGL19 promoter was increased in the hos15-2 mutant, similar to the pwr and hda9 mutants. Therefore, our findings reveal that the HOS15/PWR/HDA9 repressor complex deacetylates the promoter region of AGL19, thereby negatively regulating AGL19 transcription, which leads to early flowering in Arabidopsis.
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Affiliation(s)
- Chae Jin Lim
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Global Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Seung Min Ryou
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Department of Agronomy, Agricultural College, Yanbian University, Yanji, China
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zein Eddin Bader
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Shah Zareen
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Min Jae Bae
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Jong Hyoo Choi
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Jose M. Pardo
- Institute of Plant Biochemistry and Photosynthesis, Consejo Superior de Investigaciones 17 Cientificas and Universidad de Sevilla, Seville, Spain
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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Tian Y, Hou Y, Song Y. LncRNAs elevate plant adaptation under low temperature by maintaining local chromatin landscape. PLANT SIGNALING & BEHAVIOR 2022; 17:2014677. [PMID: 35352623 PMCID: PMC8973372 DOI: 10.1080/15592324.2021.2014677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 12/01/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
Epigenetic regulation is one of the most precise and subtle ways of gene regulation, including DNA modification, histone modification, RNA modification, histone variants, chromatin remodeling, and long non-coding RNAs (lncRNAs). Chromatin modification is the most basic type of epigenetic regulation, which plays a key role in a myriad of developmental and physiological processes that have been thoroughly studied. These modifications are usually completed by a series of conserved chromatin modification complexes in eukaryotes. In recent years, a series of lncRNAs in organisms also have been described as having irreplaceable functions in biological environment adaptation, especially in biotic and abiotic stresses. Moreover, these molecules form a sophisticated regulatory network through mutual cross-regulation to achieve quantitative expression of key environmental response genes to external signals. For instance, the function of lncRNAs will directly or indirectly depend on the function of the chromatin modification complex. In this review, we mainly focus on chromatin modification, lncRNA, and their coordination mechanism to achieve the high adaptability of plants in low-temperature environments. We highlight recent findings and insights into lncRNA-mediated local chromatin environment changes during plant growth under low temperature via chromatin modification complexes, including target gene specificity for different lncRNA.
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Affiliation(s)
- Yongke Tian
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yukang Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yuan Song
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
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Comprehensive Analyses of the Histone Deacetylases Tuin (HDT) Gene Family in Brassicaceae Reveals Their Roles in Stress Response. Int J Mol Sci 2022; 24:ijms24010525. [PMID: 36613968 PMCID: PMC9820156 DOI: 10.3390/ijms24010525] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/18/2022] [Accepted: 12/19/2022] [Indexed: 12/30/2022] Open
Abstract
Histone deacetylases tuin (HDT) is a plant-specific protein subfamily of histone deacetylation enzymes (HDAC) which has a variety of functions in plant development, hormone signaling and stress response. Although the HDT family's genes have been studied in many plant species, they have not been characterized in Brassicaceae. In this study, 14, 8 and 10 HDT genes were identified in Brassica napus, Brassica rapa and Brassica oleracea, respectively. According to phylogenetic analysis, the HDTs were divided into four groups: HDT1(HD2A), HDT2(HD2B), HDT3(HD2C) and HDT4(HD2D). There was an expansion of HDT2 orthologous genes in Brassicaceae. Most of the HDT genes were intron-rich and conserved in gene structure, and they coded for proteins with a nucleoplasmin-like (NPL) domain. Expression analysis showed that B. napus, B. rapa, and B. oleracea HDT genes were expressed in different organs at different developmental stages, while different HDT subgroups were specifically expressed in specific organs and tissues. Interestingly, most of the Bna/Br/BoHDT2 members were expressed in flowers, buds and siliques, suggesting they have an important role in the development of reproductive organs in Brassicaceae. Expression of BnaHDT was induced by various hormones, such as ABA and ethylene treatment, and some subgroups of genes were responsive to heat treatment. The expression of most HDT members was strongly induced by cold stress and freezing stress after non-cold acclimation, while it was slightly induced after cold acclimation. In this study, the HDT gene family of Brassicaceae was analyzed for the first time, which helps in understanding the function of BnaHDT in regulating plant responses to abiotic stresses, especially freezing stresses.
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Ramakrishnan M, Zhang Z, Mullasseri S, Kalendar R, Ahmad Z, Sharma A, Liu G, Zhou M, Wei Q. Epigenetic stress memory: A new approach to study cold and heat stress responses in plants. FRONTIERS IN PLANT SCIENCE 2022; 13:1075279. [PMID: 36570899 PMCID: PMC9772030 DOI: 10.3389/fpls.2022.1075279] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 05/28/2023]
Abstract
Understanding plant stress memory under extreme temperatures such as cold and heat could contribute to plant development. Plants employ different types of stress memories, such as somatic, intergenerational and transgenerational, regulated by epigenetic changes such as DNA and histone modifications and microRNAs (miRNA), playing a key role in gene regulation from early development to maturity. In most cases, cold and heat stresses result in short-term epigenetic modifications that can return to baseline modification levels after stress cessation. Nevertheless, some of the modifications may be stable and passed on as stress memory, potentially allowing them to be inherited across generations, whereas some of the modifications are reactivated during sexual reproduction or embryogenesis. Several stress-related genes are involved in stress memory inheritance by turning on and off transcription profiles and epigenetic changes. Vernalization is the best example of somatic stress memory. Changes in the chromatin structure of the Flowering Locus C (FLC) gene, a MADS-box transcription factor (TF), maintain cold stress memory during mitosis. FLC expression suppresses flowering at high levels during winter; and during vernalization, B3 TFs, cold memory cis-acting element and polycomb repressive complex 1 and 2 (PRC1 and 2) silence FLC activation. In contrast, the repression of SQUAMOSA promoter-binding protein-like (SPL) TF and the activation of Heat Shock TF (HSFA2) are required for heat stress memory. However, it is still unclear how stress memory is inherited by offspring, and the integrated view of the regulatory mechanisms of stress memory and mitotic and meiotic heritable changes in plants is still scarce. Thus, in this review, we focus on the epigenetic regulation of stress memory and discuss the application of new technologies in developing epigenetic modifications to improve stress memory.
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Affiliation(s)
- Muthusamy Ramakrishnan
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Zhijun Zhang
- Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Sileesh Mullasseri
- Department of Zoology, St. Albert’s College (Autonomous), Kochi, Kerala, India
| | - Ruslan Kalendar
- Helsinki Institute of Life Science HiLIFE, Biocenter 3, University of Helsinki, Helsinki, Finland
- National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
| | - Zishan Ahmad
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Anket Sharma
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Guohua Liu
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
| | - Mingbing Zhou
- State Key Laboratory of Subtropical Silviculture, Bamboo Industry Institute, Zhejiang A&F University, Hangzhou, Zhejiang, China
- Zhejiang Provincial Collaborative Innovation Center for Bamboo Resources and High-Efficiency Utilization, Zhejiang A&F University, Hangzhou, Zhejiang, China
| | - Qiang Wei
- Co-Innovation Center for Sustainable Forestry in Southern China, Bamboo Research Institute, Key Laboratory of National Forestry and Grassland Administration on Subtropical Forest Biodiversity Conservation, College of Biology and the Environment, Nanjing Forestry University, Nanjing, Jiangsu, China
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21
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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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22
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Tahir MS, Karagiannis J, Tian L. HD2A and HD2C co-regulate drought stress response by modulating stomatal closure and root growth in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:1062722. [PMID: 36507458 PMCID: PMC9727301 DOI: 10.3389/fpls.2022.1062722] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Histone deacetylase 2 (HD2) is a unique family of histone deacetylases (HDACs) in plants. Despite evidence that certain HD2 family HDACs play an important role in plant growth and stress response, the coordination of HD2s in these processes remains largely unknown. We found that HD2-type, HD2A and HD2C coordinate to play a role in drought stress response in Arabidopsis. We showed that the hd2a.hd2c double mutant (Mac16) exhibit decreased drought survival and increased water loss as compared to the single mutants, hd2a and hd2c. Gene expression analysis showed that the ABI1 and ABI2 genes were upregulated and SLAC1 was downregulated which led to the modified stomatal functioning in the Mac16 as compared to the single mutants. Overexpression of HD2A and HD2C showed enhanced drought survival and decreased water loss. We also showed that the GA2ox1 and GA2ox2 genes, which are involved in the catabolism of bioactive gibberellic acids, were upregulated in the Mac16 as compared to the single mutants, which led to a decreased root growth in the Mac16. Furthermore, we showed that HD2A and HD2C can physically interact and increased genome-wide H3K9 acetylation was observed in the Mac16, compared to the single mutants. Overall, our investigation revealed that HD2A and HD2C coordinate to play a cumulative role in drought stress response and root growth in Arabidopsis.
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Affiliation(s)
- Muhammad Sufyan Tahir
- Department of Biology, University of Western Ontario, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Jim Karagiannis
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Lining Tian
- Department of Biology, University of Western Ontario, London, ON, Canada
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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23
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A single helix repression domain is functional across diverse eukaryotes. Proc Natl Acad Sci U S A 2022; 119:e2206986119. [PMID: 36191192 PMCID: PMC9564828 DOI: 10.1073/pnas.2206986119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The corepressor TOPLESS (TPL) and its paralogs coordinately regulate a large number of genes critical to plant development and immunity. As in many members of the larger pan-eukaryotic Tup1/TLE/Groucho corepressor family, TPL contains a Lis1 Homology domain (LisH), whose function is not well understood. We have previously found that the LisH in TPL-and specifically the N-terminal 18 amino acid alpha-helical region (TPL-H1)-can act as an autonomous repression domain. We hypothesized that homologous domains across diverse LisH-containing proteins could share the same function. To test that hypothesis, we built a library of H1s that broadly sampled the sequence and evolutionary space of LisH domains, and tested their activity in a synthetic transcriptional repression assay in Saccharomyces cerevisiae. Using this approach, we found that repression activity was highly conserved and likely the ancestral function of this motif. We also identified key residues that contribute to repressive function. We leveraged this new knowledge for two applications. First, we tested the role of mutations found in somatic cancers on repression function in two human LisH-containing proteins. Second, we validated function of many of our repression domains in plants, confirming that these sequences should be of use to synthetic biology applications across many eukaryotes.
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24
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Chen S, Li D, Chen S, He J, Wang Z, Yang G, Lu Z. Identifying and expression analysis of WD40 transcription factors in walnut. THE PLANT GENOME 2022; 15:e20229. [PMID: 35904050 DOI: 10.1002/tpg2.20229] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
Walnut (Juglans regia L.) is an important woody oil plant and will be affected by abiotic and biological stress during its growth and development. The WD-repeat (WD40) protein is widely involved in plant growth, development, metabolism, and abiotic stress response. To explore the stress response mechanism of walnut, based on the complete sequencing results of the walnut genome, this study identified and analyzed the physiological, biochemical, genetic structure, and conservative protein motifs of 42 JrWD40 genes, whose expression to abnormal temperature were tested to predict the potential biological function. The results showed that the open reading frame (ORF) of theseWD40 genes were 807-2,460 bp, encoding peptides were 29,610.55-90,387.98 Da covering 268-819 amino acids, as well as 12-112 phosphorylation sites. JrWD40 proteins were highly conserved with four to five WD40 domains and shared certain similarity to WD40 proteins from Arabidopsis thaliana (L.) Heynh. JrWD40 genes can be induced to varying degrees by low and high temperature treatments. JrWD40-32, JrWD40-27, JrWD40-35, and JrWD40-21 are affected by high temperature more seriously and their expression levels are higher; while JrWD40-37, JrWD40-26, JrWD40-20, JrWD40-24, and other genes are inhibited under low temperature stress. JrWD40-40, JrWD40-28, and JrWD40-18 were first suppressed with low expression, while as the treatment time prolonging, the expression level was increased under cold condition. JrWD40-14, JrWD40-18, JrWD40-34, and JrWD40-3 displayed strong transcriptions response to both heat and cold stress. These results indicated that JrWD40 genes can participate in walnut adaptation to adversity and can be used as important candidates for walnut resistance molecular breeding.
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Affiliation(s)
- Shuwen Chen
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
- Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
| | - Dapei Li
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
- Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
| | - Sisi Chen
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
- Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
| | - Jianing He
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
- Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
| | - Zengbin Wang
- College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
| | - Guiyan Yang
- Laboratory of Walnut Research Center, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
- Key Laboratory of Economic Plant Resources Development and Utilization in Shaanxi Province, College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
| | - Zhoumin Lu
- College of Forestry, Northwest A & F Univ., Yangling, Shaanxi, 712100, China
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Satyakam, Zinta G, Singh RK, Kumar R. Cold adaptation strategies in plants—An emerging role of epigenetics and antifreeze proteins to engineer cold resilient plants. Front Genet 2022; 13:909007. [PMID: 36092945 PMCID: PMC9459425 DOI: 10.3389/fgene.2022.909007] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 07/21/2022] [Indexed: 11/13/2022] Open
Abstract
Cold stress adversely affects plant growth, development, and yield. Also, the spatial and geographical distribution of plant species is influenced by low temperatures. Cold stress includes chilling and/or freezing temperatures, which trigger entirely different plant responses. Freezing tolerance is acquired via the cold acclimation process, which involves prior exposure to non-lethal low temperatures followed by profound alterations in cell membrane rigidity, transcriptome, compatible solutes, pigments and cold-responsive proteins such as antifreeze proteins. Moreover, epigenetic mechanisms such as DNA methylation, histone modifications, chromatin dynamics and small non-coding RNAs play a crucial role in cold stress adaptation. Here, we provide a recent update on cold-induced signaling and regulatory mechanisms. Emphasis is given to the role of epigenetic mechanisms and antifreeze proteins in imparting cold stress tolerance in plants. Lastly, we discuss genetic manipulation strategies to improve cold tolerance and develop cold-resistant plants.
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26
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Role of Epigenetics in Modulating Phenotypic Plasticity against Abiotic Stresses in Plants. Int J Genomics 2022; 2022:1092894. [PMID: 35747076 PMCID: PMC9213152 DOI: 10.1155/2022/1092894] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 05/25/2022] [Indexed: 12/13/2022] Open
Abstract
Plants being sessile are always exposed to various environmental stresses, and to overcome these stresses, modifications at the epigenetic level can prove vital for their long-term survival. Epigenomics refers to the large-scale study of epigenetic marks on the genome, which include covalent modifications of histone tails (acetylation, methylation, phosphorylation, ubiquitination, and the small RNA machinery). Studies based on epigenetics have evolved over the years especially in understanding the mechanisms at transcriptional and posttranscriptional levels in plants against various environmental stimuli. Epigenomic changes in plants through induced methylation of specific genes that lead to changes in their expression can help to overcome various stress conditions. Recent studies suggested that epigenomics has a significant potential for crop improvement in plants. By the induction and modulation of various cellular processes like DNA methylation, histone modification, and biogenesis of noncoding RNAs, the plant genome can be activated which can help in achieving a quicker response against various plant stresses. Epigenetic modifications in plants allow them to adjust under varied environmental stresses by modulating their phenotypic plasticity and at the same time ensure the quality and yield of crops. The plasticity of the epigenome helps to adapt the plants during pre- and postdevelopmental processes. The variation in DNA methylation in different organisms exhibits variable phenotypic responses. The epigenetic changes also occur sequentially in the genome. Various studies indicated that environmentally stimulated epimutations produce variable responses especially in differentially methylated regions (DMR) that play a major role in the management of stress conditions in plants. Besides, it has been observed that environmental stresses cause specific changes in the epigenome that are closely associated with phenotypic modifications. However, the relationship between epigenetic modifications and phenotypic plasticity is still debatable. In this review, we will be discussing the role of various factors that allow epigenetic changes to modulate phenotypic plasticity against various abiotic stress in plants.
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27
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Meng J, Wen Z, Li M, Cheng T, Zhang Q, Sun L. HDACs Gene Family Analysis of Eight Rosaceae Genomes Reveals the Genomic Marker of Cold Stress in Prunus mume. Int J Mol Sci 2022; 23:5957. [PMID: 35682633 PMCID: PMC9180812 DOI: 10.3390/ijms23115957] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 05/19/2022] [Accepted: 05/20/2022] [Indexed: 02/01/2023] Open
Abstract
Histone deacetylases (HDACs) play important roles in plant growth, development, and stress response. However, the pattern of how they are expressed in response to cold stress in the ornamental woody plant Prunus mume is poorly understood. Here, we identify 121 RoHDACs from eight Rosaceae plants of which 13 PmHDACs genes are from P. mume. A phylogenetic analysis suggests that the RoHDACs family is classified into three subfamilies, HDA1/RPD3, HD2, and SIR2. We identify 11 segmental duplication gene pairs of RoHDACs and find, via a sequence alignment, that the HDACs gene family, especially the plant-specific HD2 family, has experienced gene expansion and contraction at a recent genome evolution history. Each of the three HDACs subfamilies has its own conserved domains. The expression of PmHDACs in mei is found to be tissue-specific or tissue-wide. RNA-seq data and qRT-PCR experiments in cold treatments suggest that almost all PmHDACs genes-especially PmHDA1/6/14, PmHDT1, and PmSRT1/2-significantly respond to cold stress. Our analysis provides a fundamental insight into the phylogenetic relationship of the HDACs family in Rosaceae plants. Expression profiles of PmHDACs in response to cold stress could provide an important clue to improve the cold hardiness of mei.
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Affiliation(s)
| | | | | | | | | | - Lidan Sun
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, School of Landscape Architecture, Beijing Forestry University, Beijing 100083, China; (J.M.); (Z.W.); (M.L.); (T.C.); (Q.Z.)
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28
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Liu X, Luo M, Li M, Wei J. Transcriptomic Analysis Reveals LncRNAs Associated with Flowering of Angelica sinensis during Vernalization. Curr Issues Mol Biol 2022; 44:1867-1888. [PMID: 35678657 PMCID: PMC9164074 DOI: 10.3390/cimb44050128] [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: 03/24/2022] [Revised: 04/19/2022] [Accepted: 04/23/2022] [Indexed: 11/16/2022] Open
Abstract
Angelica sinensis is a “low-temperature and long-day” perennial plant that produces bioactive compounds such as phthalides, organic acids, and polysaccharides for various types of clinical agents, including those with cardio-cerebrovascular, hepatoprotective, and immunomodulatory effects. To date, the regulatory mechanism of flowering under the photoperiod has been revealed, while the regulatory network of flowering genes during vernalization, especially in the role of lncRNAs, has yet to be identified. Here, lncRNAs associated with flowering were identified based on the full-length transcriptomic analysis of A. sinensis at vernalization and freezing temperatures, and the coexpressed mRNAs of lncRNAs were validated by qRT-PCR. We obtained a total of 2327 lncRNAs after assessing the protein-coding potential of coexpressed mRNAs, with 607 lncRNAs aligned against the TAIR database of model plant Arabidopsis, 345 lncRNAs identified, and 272 lncRNAs characterized on the SwissProt database. Based on the biological functions of coexpressed mRNAs, the 272 lncRNAs were divided into six categories: (1) chromatin, DNA/RNA and protein modification; (2) flowering; (3) stress response; (4) metabolism; (5) bio-signaling; and (6) energy and transport. The differential expression levels of representatively coexpressed mRNAs were almost consistent with the flowering of A. sinensis. It can be concluded that the flowering of A. sinensis is positively or negatively regulated by lncRNAs, which provides new insights into the regulation mechanism of the flowering of A. sinensis.
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Affiliation(s)
- Xiaoxia Liu
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
| | - Mimi Luo
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
| | - Mengfei Li
- State Key Laboratory of Aridland Crop Science, College of Life Science and Technology, Gansu Agricultural University, Lanzhou 730070, China; (X.L.); (M.L.)
- Correspondence: (M.L.); (J.W.)
| | - Jianhe Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China
- Correspondence: (M.L.); (J.W.)
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29
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Ashraf MA, Rahman A. Cellular Protein Trafficking: A New Player in Low-Temperature Response Pathway. PLANTS (BASEL, SWITZERLAND) 2022; 11:933. [PMID: 35406913 PMCID: PMC9003145 DOI: 10.3390/plants11070933] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/28/2022] [Indexed: 06/14/2023]
Abstract
Unlike animals, plants are unable to escape unfavorable conditions, such as extremities of temperature. Among abiotic variables, the temperature is notableas it affects plants from the molecular to the organismal level. Because of global warming, understanding temperature effects on plants is salient today and should be focused not only on rising temperature but also greater variability in temperature that is now besetting the world's natural and agricultural ecosystems. Among the temperature stresses, low-temperature stress is one of the major stresses that limits crop productivity worldwide. Over the years, although substantial progress has been made in understanding low-temperature response mechanisms in plants, the research is more focused on aerial parts of the plants rather than on the root or whole plant, and more efforts have been made in identifying and testing the major regulators of this pathway preferably in the model organism rather than in crop plants. For the low-temperature stress response mechanism, ICE-CBF regulatory pathway turned out to be the solely established pathway, and historically most of the low-temperature research is focused on this single pathway instead of exploring other alternative regulators. In this review, we tried to take an in-depth look at our current understanding of low temperature-mediated plant growth response mechanism and present the recent advancement in cell biological studies that have opened a new horizon for finding promising and potential alternative regulators of the cold stress response pathway.
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Affiliation(s)
- M Arif Ashraf
- Biology Department, University of Massachusetts, Amherst, MA 01003, USA
| | - Abidur Rahman
- The United Graduate School of Agricultural Sciences, Iwate University, Morioka 020-8550, Japan
- Department of Plant Biosciences, Faculty of Agriculture, Iwate University, Morioka 020-8550, Japan
- Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, Saskatoon, SK S7N 5A8, Canada
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30
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Nouraei S, Mia MS, Liu H, Turner NC, Yan G. Transcriptome Analyses of Near Isogenic Lines Reveal Putative Drought Tolerance Controlling Genes in Wheat. FRONTIERS IN PLANT SCIENCE 2022; 13:857829. [PMID: 35422827 PMCID: PMC9005202 DOI: 10.3389/fpls.2022.857829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 02/24/2022] [Indexed: 05/08/2023]
Abstract
Drought stress, especially at the grain-filling stage, is a major constraint for wheat production. Drought tolerance is a complex trait controlled by a large array of genes and pathways. This study conducted gene expression profiling on two pairs of near-isogenic lines (NILs) for an important qDSI.4B.1 QTL conferring drought tolerance on the short arm of chromosome 4B in wheat. Analysis showed 1,614 genome-wide differentially expressed genes (DEGs) between the tolerant and susceptible isolines in both NIL pairs. Six common DEGs were found between NIL1 and NIL2 at both 7 and 14 days after stress induction, with two of them having single nucleotide polymorphism (SNP) variants. These six genes that were confirmed by quantitative real-time PCR (qRT-PCR) expression analysis are considered candidate genes for drought tolerance mediated by qDSI.4B.1 QTL with their main contributions to gene regulation, cell elongation, protein quality control, secondary metabolism, and hormone signaling. These six candidate genes and the highest number of DEGs and variants (SNPs/indels) were located between 49 and 137 Mbp of 4BS, making this interval the most probable location for the qDSI.4B.1 locus. Additionally, 765 and 84 DEGs were detected as responsive genes to drought stress in tolerant and susceptible isolines, respectively. According to gene ontology (GO), protein phosphorylation, oxidation reduction, and regulation of transcription were top biological processes involved in the drought response and tolerance. These results provide insights into stress responses regulated by the 4BS locus and have identified candidate genes and genetic markers that can be used for fine mapping of the qDSI.4B.1 locus and, ultimately, in wheat breeding programs for drought tolerance.
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Affiliation(s)
- Sina Nouraei
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Md Sultan Mia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
- Department of Primary Industries and Regional Development, Northam, WA, Australia
| | - Hui Liu
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Neil C. Turner
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
| | - Guijun Yan
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- The UWA Institute of Agriculture, The University of Western Australia, Perth, WA, Australia
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31
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Zareen S, Ali A, Lim CJ, Khan HA, Park J, Xu ZY, Yun DJ. The Transcriptional Corepressor HOS15 Mediates Dark-Induced Leaf Senescence in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:828264. [PMID: 35283908 PMCID: PMC8914473 DOI: 10.3389/fpls.2022.828264] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 01/14/2022] [Indexed: 05/23/2023]
Abstract
Multiple endogenous and environmental signals regulate the intricate and highly complex processes driving leaf senescence in plants. A number of genes have been identified in a variety of plant species, including Arabidopsis, which influence leaf senescence. Previously, we have shown that HOS15 is a multifunctional protein that regulates several physiological processes, including plant growth and development under adverse environmental conditions. HOS15 has also been reported to form a chromatin remodeling complex with PWR and HDA9 and to regulate the chromatin structure of numerous genes. However, unlike PWR and HDA9, the involvement of HOS15 in leaf senescence is yet to be identified. Here, we report that HOS15, together with PWR and HDA9, promotes leaf senescence via transcriptional regulation of SAG12/29, senescence marker genes, and CAB1/RCBS1A, photosynthesis-related genes. The expression of ORE1, SAG12, and SAG29 was downregulated in hos15-2 plants, whereas the expression of photosynthesis-related genes, CAB1 and RCBS1A, was upregulated. HOS15 also promoted senescence through dark stress, as its mutation led to a much greener phenotype than that of the WT. Phenotypes of double and triple mutants of HOS15 with PWR and HDA9 produced phenotypes similar to those of a single hos15-2. In line with this observation, the expression levels of NPX1, APG9, and WRKY57 were significantly elevated in hos15-2 and hos15/pwr, hos15/hda9, and hos15/pwr/hda9 mutants compared to those in the WT. Surprisingly, the total H3 acetylation level decreased in age-dependent manner and under dark stress in WT; however, it remained the same in hos15-2 plants regardless of dark stress, suggesting that dark-induced deacetylation requires functional HOS15. More interestingly, the promoters of APG9, NPX1, and WRKY57 were hyperacetylated in hos15-2 plants compared to those in WT plants. Our data reveal that HOS15 acts as a positive regulator and works in the same repressor complex with PWR and HDA9 to promote leaf senescence through aging and dark stress by repressing NPX1, APG9, and WRKY57 acetylation.
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Affiliation(s)
- Shah Zareen
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Akhtar Ali
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Center of Plant Systems Biology and Biotechnology, Plovdiv, Bulgaria
| | - Chae Jin Lim
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Haris Ali Khan
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Junghoon Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
| | - Zheng-Yi Xu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
| | - Dae-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, South Korea
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun, China
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32
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Genome Wide Identification and Characterization of Apple WD40 Proteins and Expression Analysis in Response to ABA, Drought, and Low Temperature. HORTICULTURAE 2022. [DOI: 10.3390/horticulturae8020141] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Basic WD40 proteins, which are characterized by a conserved WD40 domain, comprise a superfamily of regulatory proteins in plants and play important roles in plant growth and development. However, WD40 genes have been rarely studied in apple (Malus × domestica Borkh.). In this study, 346 WD40 genes classified in 12 subfamilies, were identified in the apple genome. Evolutionary analysis of WD40 proteins in apple and Arabidopsis revealed that the genes were classifiable into 14 groups, and the exon/intron structure of each group showed a similar structure. Analysis of collinearity showed that the large-scale amplification of WD40 genes in apple was largely attributable to recent whole-genome replication events. Nineteen candidate stress-related genes, selected by GO annotation and comparison with Arabidopsis homologs, showed different expression profiles in six organs at different developmental stages in response to exogenous abscisic acid (ABA), drought, and low temperature. Eight genes (MdWD40-17, 24, 70, 74, 219, 256, 283, and 307) showed a distinct response to one or more treatments (ABA, drought, and low temperature) as indicated by quantitative real-time PCR analysis. Taken together, these data provide rich resources for further study of MdWD40 genes and their potential roles in stress responses in apple.
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33
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Feng L, Lin H, Kang M, Ren Y, Yu X, Xu Z, Wang S, Li T, Yang W, Hu Q. A chromosome-level genome assembly of an alpine plant Crucihimalaya lasiocarpa provides insights into high-altitude adaptation. DNA Res 2022; 29:dsac004. [PMID: 35094078 PMCID: PMC8801980 DOI: 10.1093/dnares/dsac004] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Indexed: 11/23/2022] Open
Abstract
It remains largely unknown how plants adapt to high-altitude habitats. Crucihimalaya (Brassicaceae) is an alpine genus occurring in the Qinghai-Tibet Plateau characterized by cold temperatures and strong ultraviolet radiation. Here, we generated a chromosome-level genome for C. lasiocarpa with a total size of 255.8 Mb and a scaffold N50 size of 31.9 Mb. We first examined the karyotype origin of this species and found that the karyotype of five chromosomes resembled the ancestral karyotype of the Brassicaceae family, while the other three showed strong chromosomal structural variations. In combination with the rough genome sequence of another congener (C. himalaica), we found that the significantly expanded gene families and positively selected genes involved in alpine adaptation have occurred since the origin of this genus. Our new findings provide valuable information for the chromosomal karyotype evolution of Brassicaceae and investigations of high-altitude environment adaptation of the genus.
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Affiliation(s)
- Landi Feng
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Hao Lin
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Minghui Kang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Yumeng Ren
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Xi Yu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Zhanpeng Xu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Shuo Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Ting Li
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Wenjie Yang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
| | - Quanjun Hu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu 610065, China
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Yung WS, Li MW, Sze CC, Wang Q, Lam HM. Histone modifications and chromatin remodelling in plants in response to salt stress. PHYSIOLOGIA PLANTARUM 2021; 173:1495-1513. [PMID: 34028035 DOI: 10.1111/ppl.13467] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Revised: 05/04/2021] [Accepted: 05/18/2021] [Indexed: 06/12/2023]
Abstract
In the face of global food security crises, it is necessary to boost agricultural production. One factor hampering the attempts to increase food production is elevated soil salinity, which can be due to salt that is naturally present in the soil or a consequence of excessive or prolonged irrigation or application of fertiliser. In response to environmental stresses, plants activate multiple molecular mechanisms, including the timely activation of stress-responsive transcriptional networks. However, in the case of salt stress, the combined effects of the initial osmotic shock and the subsequent ion-specific stress increase the complexity in the selective regulation of gene expressions involved in restoring or maintaining osmotic balance, ion homeostasis and reactive oxygen species scavenging. Histone modifications and chromatin remodelling are important epigenetic processes that regulate gene expressions by modifying the chromatin status and recruiting transcription regulators. In this review, we have specifically summarised the currently available knowledge on histone modifications and chromatin remodelling in relation to plant responses to salt stress. Current findings have revealed the functional importance of chromatin modifiers in regulating salt tolerance and identified the effector genes affected by epigenetic modifications, although counteraction between modifiers within the same family may occur. Emerging evidence has also illustrated the crosstalk between epigenetic modifications and hormone signalling pathways which involves formation of protein complexes. With an improved understanding of these processes, plant breeders will be able to develop alternative strategies using genome editing technologies for crop improvement.
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Affiliation(s)
- Wai-Shing Yung
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Man-Wah Li
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Ching-Ching Sze
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Qianwen Wang
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Hon-Ming Lam
- School of Life Sciences and Centre for Soybean Research of the State Key Laboratory of Agrobiotechnology, The Chinese University of Hong Kong, Shatin, Hong Kong, China
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Syngelaki E, Paetzold C, Hörandl E. Gene Expression Profiles Suggest a Better Cold Acclimation of Polyploids in the Alpine Species Ranunculus kuepferi (Ranunculaceae). Genes (Basel) 2021; 12:1818. [PMID: 34828424 PMCID: PMC8625111 DOI: 10.3390/genes12111818] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 11/16/2021] [Accepted: 11/17/2021] [Indexed: 12/17/2022] Open
Abstract
Alpine habitats are shaped by harsh abiotic conditions and cold climates. Temperature stress can affect phenotypic plasticity, reproduction, and epigenetic profiles, which may affect acclimation and adaptation. Distribution patterns suggest that polyploidy seems to be advantageous under cold conditions. Nevertheless, whether temperature stress can induce gene expression changes in different cytotypes, and how the response is initialized through gene set pathways and epigenetic control remain vague for non-model plants. The perennial alpine plant Ranunculus kuepferi was used to investigate the effect of cold stress on gene expression profiles. Diploid and autotetraploid individuals were exposed to cold and warm conditions in climate growth chambers and analyzed via transcriptome sequencing and qRT-PCR. Overall, cold stress changed gene expression profiles of both cytotypes and induced cold acclimation. Diploids changed more gene set pathways than tetraploids, and suppressed pathways involved in ion/cation homeostasis. Tetraploids mostly activated gene set pathways related to cell wall and plasma membrane. An epigenetic background for gene regulation in response to temperature conditions is indicated. Results suggest that perennial alpine plants can respond to temperature extremes via altered gene expression. Tetraploids are better acclimated to cold conditions, enabling them to colonize colder climatic areas in the Alps.
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Affiliation(s)
- Eleni Syngelaki
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
| | - Claudia Paetzold
- Department of Botany and Molecular Evolution, Senckenberg Research Institute, 60325 Frankfurt am Main, Germany;
| | - Elvira Hörandl
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium), Georg-August-Universität Göttingen, 37073 Göttingen, Germany;
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Sepulveda-Garcia E, Fulton EC, Parlan EV, O’Connor LE, Fleming AA, Replogle AJ, Rocha-Sosa M, Gendron JM, Thines B. Unique N-Terminal Interactions Connect F-BOX STRESS INDUCED (FBS) Proteins to a WD40 Repeat-like Protein Pathway in Arabidopsis. PLANTS (BASEL, SWITZERLAND) 2021; 10:2228. [PMID: 34686037 PMCID: PMC8537223 DOI: 10.3390/plants10102228] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 10/08/2021] [Accepted: 10/11/2021] [Indexed: 11/17/2022]
Abstract
SCF-type E3 ubiquitin ligases provide specificity to numerous selective protein degradation events in plants, including those that enable survival under environmental stress. SCF complexes use F-box (FBX) proteins as interchangeable substrate adaptors to recruit protein targets for ubiquitylation. FBX proteins almost universally have structure with two domains: A conserved N-terminal F-box domain interacts with a SKP protein and connects the FBX protein to the core SCF complex, while a C-terminal domain interacts with the protein target and facilitates recruitment. The F-BOX STRESS INDUCED (FBS) subfamily of plant FBX proteins has an atypical structure, however, with a centrally located F-box domain and additional conserved regions at both the N- and C-termini. FBS proteins have been linked to environmental stress networks, but no ubiquitylation target(s) or biological function has been established for this subfamily. We have identified two WD40 repeat-like proteins in Arabidopsis that are highly conserved in plants and interact with FBS proteins, which we have named FBS INTERACTING PROTEINs (FBIPs). FBIPs interact exclusively with the N-terminus of FBS proteins, and this interaction occurs in the nucleus. FBS1 destabilizes FBIP1, consistent with FBIPs being ubiquitylation targets SCFFBS1 complexes. This work indicates that FBS proteins may function in stress-responsive nuclear events, and it identifies two WD40 repeat-like proteins as new tools with which to probe how an atypical SCF complex, SCFFBS, functions via FBX protein N-terminal interaction events.
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Affiliation(s)
- Edgar Sepulveda-Garcia
- Instituto de Biotecnología, Universidad del Papaloapan, Tuxtepec 68301, Mexico;
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico;
| | - Elena C. Fulton
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Emily V. Parlan
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Lily E. O’Connor
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Anneke A. Fleming
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Amy J. Replogle
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
| | - Mario Rocha-Sosa
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62250, Mexico;
| | - Joshua M. Gendron
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06511, USA;
| | - Bryan Thines
- Biology Department, University of Puget Sound, Tacoma, WA 98416, USA; (E.C.F.); (E.V.P.); (L.E.O.); (A.A.F.); (A.J.R.)
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Xie W, Tang Q, Yan F, Tao Z. Transcriptional memory and response to adverse temperatures in plants. J Zhejiang Univ Sci B 2021; 22:791-804. [PMID: 34636184 DOI: 10.1631/jzus.b2100287] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Temperature is one of the major environmental signals controlling plant development, geographical distribution, and seasonal behavior. Plants perceive adverse temperatures, such as high, low, and freezing temperatures, as stressful signals that can cause physiological defects and even death. As sessile organisms, plants have evolved sophisticated mechanisms to adapt to recurring stressful environments through changing gene expression or transcriptional reprogramming. Transcriptional memory refers to the ability of primed plants to remember previously experienced stress and acquire enhanced tolerance to similar or different stresses. Epigenetic modifications mediate transcriptional memory and play a key role in adapting to adverse temperatures. Understanding the mechanisms of the formation, maintenance, and resetting of stress-induced transcriptional memory will not only enable us to understand why there is a trade-off between plant defense and growth, but also provide a theoretical basis for generating stress-tolerant crops optimized for future climate change. In this review, we summarize recent advances in dissecting the mechanisms of plant transcriptional memory in response to adverse temperatures, based mainly on studies of the model plant Arabidopsis thaliana. We also discuss remaining questions that are important for further understanding the mechanisms of transcriptional memory during the adverse temperature response.
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Affiliation(s)
- Wei Xie
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Qianqian Tang
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Fei Yan
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China.,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Zeng Tao
- State Key Laboratory of Rice Biology, Zhejiang University, Hangzhou 310058, China. .,Ministry of Agriculture Key Laboratory of Molecular Biology of Crop Pathogens and Insects, Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China.
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38
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Epigenetic control of abiotic stress signaling in plants. Genes Genomics 2021; 44:267-278. [PMID: 34515950 DOI: 10.1007/s13258-021-01163-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/02/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUND Although plants may be regularly exposed to various abiotic stresses, including drought, salt, cold, heat, heavy metals, and UV-B throughout their lives, it is not possible to actively escape from such stresses due to the immobile nature of plants. To overcome adverse environmental stresses, plants have developed adaptive systems that allow appropriate responses to diverse environmental cues; such responses can be achieved by fine-tuning or controlling genetic and epigenetic regulatory systems. Epigenetic mechanisms such as DNA or histone modifications and modulation of chromatin accessibility have been shown to regulate the expression of stress-responsive genes in struggles against abiotic stresses. OBJECTIVE Herein, the current progress in elucidating the epigenetic regulation of abiotic stress signaling in plants has been summarized in order to further understand the systems plants utilize to effectively respond to abiotic stresses. METHODS This review focuses on the action mechanisms of various components that epigenetically regulate plant abiotic stress responses, mainly in terms of DNA methylation, histone methylation/acetylation, and chromatin remodeling. CONCLUSIONS This review can be considered a basis for further research into understanding the epigenetic control system for abiotic stress responses in plants. Moreover, the knowledge of such systems can be effectively applied in developing novel methods to generate abiotic stress resistant crops.
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Tahir MS, Tian L. HD2-type histone deacetylases: unique regulators of plant development and stress responses. PLANT CELL REPORTS 2021; 40:1603-1615. [PMID: 34041586 DOI: 10.1007/s00299-021-02688-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/23/2021] [Indexed: 06/12/2023]
Abstract
Plants have developed sophisticated and complex epigenetic regulation-based mechanisms to maintain stable growth and development under diverse environmental conditions. Histone deacetylases (HDACs) are important epigenetic regulators in eukaryotes that are involved in the deacetylation of lysine residues of histone H3 and H4 proteins. Plants have developed a unique HDAC family, HD2, in addition to the RPD3 and Sir2 families, which are also present in other eukaryotes. HD2s are well conserved plant-specific HDACs, which were first identified as nucleolar phosphoproteins in maize. The HD2 family plays important roles not only in fundamental developmental processes, including seed germination, root and leaf development, floral transition, and seed development but also in regulating plant responses to biotic and abiotic stresses. Some of the HD2 members coordinate with each other to function. The HD2 family proteins also show functional association with RPD3-type HDACs and other transcription factors as a part of repression complexes in gene regulatory networks involved in environmental stress responses. This review aims to analyse and summarise recent research progress in the HD2 family, and to describe their role in plant growth and development and in response to different environmental stresses.
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Affiliation(s)
- Muhammad Sufyan Tahir
- Department of Biology, University of Western Ontario, London, ON, Canada.
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada.
| | - Lining Tian
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
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40
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Hereme R, Galleguillos C, Morales-Navarro S, Molina-Montenegro MA. What if the cold days return? Epigenetic mechanisms in plants to cold tolerance. PLANTA 2021; 254:46. [PMID: 34370110 DOI: 10.1007/s00425-021-03694-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 08/02/2021] [Indexed: 06/13/2023]
Abstract
The epigenetic could be an important, but seldom assessed, mechanisms in plants inhabiting cold ecosystems. Thus, this review could help to fill a gap in the current literature. Low temperatures are one of the most critical environmental conditions that negatively affect the growth, development, and geographic distribution of plants. Exposure to low temperatures results in a suit of physiological, biochemical and molecular modifications through the reprogramming of the expression of genes and transcription factors. Scientific evidence shows that the average annual temperature has increased in recent years worldwide, with cold ecosystems (polar and high mountain) being among the most sensitive to these changes. However, scientific evidence also indicates that there would be specific events of low temperatures, due it is highly relevant to know the capacity for adaptation, regulation and epigenetic memory in the face of these events, by plants. Epigenetic regulation has been described to play an important role in the face of environmental stimuli, especially in response to abiotic stress. Several studies on epigenetic mechanisms have focused on responses to stress as drought and/or salinity; however, there is a gap in the current literature considering those related to low temperatures. In this review, we focus on systematizing the information published to date, related to the regulation of epigenetic mechanisms such as DNA methylation, histone modification, and non-coding RNA-dependent silencing mechanisms, in the face of plant´s stress due to low temperatures. Finally, we present a schematic model about the potential responses by plants taking in count their epigenetic memory; considering a global warming scenario and with the presence or absence of extreme specific events of low temperatures.
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Affiliation(s)
- Rasme Hereme
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Talca, Chile
| | | | | | - Marco A Molina-Montenegro
- Instituto de Ciencias Biológicas, Universidad de Talca, Campus Talca, Talca, Chile.
- Centro de Estudios Avanzados en Zonas Áridas (CEAZA), Universidad Católica del Norte, Coquimbo, Chile.
- Centro de Investigaciones y Estudios Avanzados del Maule (CIEAM), Universidad Católica del Maule, Talca, Chile.
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41
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Leydon AR, Wang W, Gala HP, Gilmour S, Juarez-Solis S, Zahler ML, Zemke JE, Zheng N, Nemhauser JL. Repression by the Arabidopsis TOPLESS corepressor requires association with the core mediator complex. eLife 2021; 10:66739. [PMID: 34075876 PMCID: PMC8203292 DOI: 10.7554/elife.66739] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/31/2021] [Indexed: 02/06/2023] Open
Abstract
The plant corepressor TOPLESS (TPL) is recruited to a large number of loci that are selectively induced in response to developmental or environmental cues, yet the mechanisms by which it inhibits expression in the absence of these stimuli are poorly understood. Previously, we had used the N-terminus of Arabidopsis thaliana TPL to enable repression of a synthetic auxin response circuit in Saccharomyces cerevisiae (yeast). Here, we leveraged the yeast system to interrogate the relationship between TPL structure and function, specifically scanning for repression domains. We identified a potent repression domain in Helix 8 located within the CRA domain, which directly interacted with the Mediator middle module subunits Med21 and Med10. Interactions between TPL and Mediator were required to fully repress transcription in both yeast and plants. In contrast, we found that multimer formation, a conserved feature of many corepressors, had minimal influence on the repression strength of TPL.
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Affiliation(s)
| | - Wei Wang
- Department of Pharmacology, Seattle, United States
| | - Hardik P Gala
- Department of Biology, University of Washington, Seattle, United States
| | - Sabrina Gilmour
- Department of Biology, University of Washington, Seattle, United States
| | | | - Mollye L Zahler
- Department of Biology, University of Washington, Seattle, United States
| | - Joseph E Zemke
- Department of Biology, University of Washington, Seattle, United States
| | - Ning Zheng
- Department of Pharmacology, Seattle, United States.,Howard Hughes Medical Institute, University of Washington, Seattle, United States
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Kamal KY, Khodaeiaminjan M, Yahya G, El-Tantawy AA, Abdel El-Moneim D, El-Esawi MA, Abd-Elaziz MAA, Nassrallah AA. Modulation of cell cycle progression and chromatin dynamic as tolerance mechanisms to salinity and drought stress in maize. PHYSIOLOGIA PLANTARUM 2021; 172:684-695. [PMID: 33159351 DOI: 10.1111/ppl.13260] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Revised: 10/12/2020] [Accepted: 10/28/2020] [Indexed: 05/14/2023]
Abstract
Salinity and drought are the major abiotic stresses that disturb several aspects of maize plants growth at the cellular level, one of these aspects is cell cycle machinery. In our study, we dissected the molecular alterations and downstream effectors of salinity and drought stress on cell cycle regulation and chromatin remodeling. Effects of salinity and drought stress were determined on maize seedlings using 200 mM NaCl (induced salinity stress), and 250 mM mannitol (induced drought stress) treatments, then cell cycle progression and chromatin remodeling dynamics were investigated. Seedlings displayed severe growth defects, including inhibition of root growth. Interestingly, stress treatments induced cell cycle arrest in S-phase with extensive depletion of cyclins B1 and A1. Further investigation of gene expression profiles of cell cycle regulators showed the downregulation of the CDKA, CDKB, CYCA, and CYCB. These results reveal the direct link between salinity and drought stress and cell cycle deregulation leading to a low cell proliferation rate. Moreover, abiotic stress alters chromatin remodeling dynamic in a way that directs the cell cycle arrest. We observed low DNA methylation patterns accompanied by dynamic histone modifications that favor chromatin decondensation. Also, the high expression of DNA topoisomerase 2, 6 family was detected as consequence of DNA damage. In conclusion, in response to salinity and drought stress, maize seedlings exhibit modulation of cell cycle progression, resulting in the cell cycle arrest through chromatin remodeling.
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Affiliation(s)
- Khaled Y Kamal
- Agronomy Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
- Redox Biology and Cell Signaling Laboratory, Department of Health and Kinesiology, Graduate Faculty of Nutrition, Texas A&M University, Texas, USA
| | - Mortaza Khodaeiaminjan
- Department of Molecular Biology, Centre of the Region Haná for Biotechnological and Agricultural Research, Faculty of Science, Palacký University, Olomouc, The Czech Republic
| | - Galal Yahya
- Microbiology and Immunology Department, Faculty of Pharmacy, Zagazig University, Zagazig, Egypt
- Department of Molecular Genetics, Faculty of Biology, Technical University of Kaiserslautern, Kaiserslautern, Germany
| | - Ahmed A El-Tantawy
- Ornamental Horticulture Department, Faculty of Agriculture, Cairo University, Cairo, Egypt
| | - Diaa Abdel El-Moneim
- Department of Plant production (Genetic branch), Faculty of Environmental and Agricultural Sciences, Arish University, Arish, Egypt
| | | | - Mohamed A A Abd-Elaziz
- Maize Research Department, Field Crops Research Institute, Agriculture Research Center, Giza, Egypt
| | - Amr A Nassrallah
- Biochemistry Department, Faculty of Agriculture, Cairo University, Cairo, Egypt
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Lim CJ, Ali A, Park J, Shen M, Park KS, Baek D, Yun DJ. HOS15-PWR chromatin remodeling complex positively regulates cold stress in Arabidopsis. PLANT SIGNALING & BEHAVIOR 2021; 16:1893978. [PMID: 33641608 PMCID: PMC8078502 DOI: 10.1080/15592324.2021.1893978] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/18/2021] [Accepted: 02/18/2021] [Indexed: 06/12/2023]
Abstract
Cold stress is a major environmental constraint that restrains plant growth and productivity. To cope with cold stress, plants must be able to perceive a cold signal and regulate the expression of cold-regulated (COR) genes. In our recent study, we showed that Arabidopsis HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENE 15 (HOS15) acts as a substrate receptor for CULLIN4-based ubiquitin E3 ligase complex to promote cold-induced histone deacetylase 2 C (HD2C) degradation that allows the activation of COR genes. Additionally, we found that POWERDRESS (PWR), a HOS15-interacting protein, is required for the association of HOS15 with COR gene chromatin and HD2C degradation. The HOS15/PWR complex interacts with and recruits CBF transcription factors to the promoters of COR genes. Collectively, our previous findings suggest that HOS15 and PWR function as positive regulators for the expression of COR genes, and promote cold tolerance. Accordingly, we herein discuss the role of PWR in cold tolerance.
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Affiliation(s)
- Chae Jin Lim
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Akhtar Ali
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Junghoon Park
- Institute of Glocal Disease Control, Konkuk University, Seoul, Republic of Korea
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Mingzhe Shen
- Division of Applied Life Science (Bk21plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki Suk Park
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
| | - Dongwon Baek
- Division of Applied Life Science (Bk21plus), Plant Molecular Biology and Biotechnology Research Center, Research Institute of Life Sciences, Gyeongsang National University, Jinju, Republic of Korea
| | - Dea-Jin Yun
- Department of Biomedical Science and Engineering, Konkuk University, Seoul, Republic of Korea
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Liu H, Liu B, Lou S, Bi H, Tang H, Tong S, Song Y, Chen N, Zhang H, Jiang Y, Liu J. CHYR1 ubiquitinates the phosphorylated WRKY70 for degradation to balance immunity in Arabidopsis thaliana. THE NEW PHYTOLOGIST 2021; 230:1095-1109. [PMID: 33492673 DOI: 10.1111/nph.17231] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 01/15/2021] [Indexed: 05/24/2023]
Abstract
It is critically important for plants to control the trade-off between normal growth and pathogen immunity. However, the underlying molecular mechanism remains largely unknown. Here we report such a mechanism controlled by WRKY70 and its partner CHYR1 in Arabidopsis. We found that both levels of the WRKY70 target gene SARD1 and the phosphorylated forms of WRKY70 were increased in WRKY70OE plants upon Pst DC3000 infection. Mechanistically, phosphorylation of WRKY70 at Thr22 and Ser34 occurs, which then activates SARD1 expression through binding to a WT box. Phosphorylated WRKY70 is degraded by 26S proteasome via CHYR1 when resuming normal growth after infection. In addition, nonphosphorylated WRKY70 represses SARD1 expression by binding to both W (inhibitory activity site) and WT (active activity site) boxes. The binding of WRKY70 to alternative cis-elements of SARD1 through a phosphorylation-mediated switch controlled by CHYR1 contributes to modulating the balance between immunity and growth.
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Affiliation(s)
- Huanhuan Liu
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Bao Liu
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Shangling Lou
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Hao Bi
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Hu Tang
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Shaofei Tong
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yan Song
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Ningning Chen
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Han Zhang
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Yuanzhong Jiang
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
| | - Jianquan Liu
- Key Laboratory for Bio-resources and Eco-environment, College of Life Science & State Key, Laboratory of Hydraulics & Mountain River Engineering, Sichuan University, Chengdu, 610065, China
- State Key Laboratory of Grassland Agro-ecosystem, Institute of Innovation Ecology, Lanzhou University, Lanzhou, 730000, China
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45
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Perspectives for epigenetic editing in crops. Transgenic Res 2021; 30:381-400. [PMID: 33891288 DOI: 10.1007/s11248-021-00252-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 03/29/2021] [Indexed: 01/10/2023]
Abstract
Site-specific nucleases (SSNs) have drawn much attention in plant biotechnology due to their ability to drive precision mutagenesis, gene targeting or allele replacement. However, when devoid of its nuclease activity, the underlying DNA-binding activity of SSNs can be used to bring other protein functional domains close to specific genomic sites, thus expanding further the range of applications of the technology. In particular, the addition of functional domains encoding epigenetic effectors and chromatin modifiers to the CRISPR/Cas ribonucleoprotein complex opens the possibility to introduce targeted epigenomic modifications in plants in an easily programmable manner. Here we examine some of the most important agronomic traits known to be controlled epigenetically and review the best studied epigenetic catalytic effectors in plants, such as DNA methylases/demethylases or histone acetylases/deacetylases and their associated marks. We also review the most efficient strategies developed to date to functionalize Cas proteins with both catalytic and non-catalytic epigenetic effectors, and the ability of these domains to influence the expression of endogenous genes in a regulatable manner. Based on these new technical developments, we discuss the possibilities offered by epigenetic editing tools in plant biotechnology and their implications in crop breeding.
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McCoy RM, Julian R, Kumar SRV, Ranjan R, Varala K, Li Y. A Systems Biology Approach to Identify Essential Epigenetic Regulators for Specific Biological Processes in Plants. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10020364. [PMID: 33668664 PMCID: PMC7918732 DOI: 10.3390/plants10020364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 02/02/2021] [Accepted: 02/07/2021] [Indexed: 05/05/2023]
Abstract
Upon sensing developmental or environmental cues, epigenetic regulators transform the chromatin landscape of a network of genes to modulate their expression and dictate adequate cellular and organismal responses. Knowledge of the specific biological processes and genomic loci controlled by each epigenetic regulator will greatly advance our understanding of epigenetic regulation in plants. To facilitate hypothesis generation and testing in this domain, we present EpiNet, an extensive gene regulatory network (GRN) featuring epigenetic regulators. EpiNet was enabled by (i) curated knowledge of epigenetic regulators involved in DNA methylation, histone modification, chromatin remodeling, and siRNA pathways; and (ii) a machine-learning network inference approach powered by a wealth of public transcriptome datasets. We applied GENIE3, a machine-learning network inference approach, to mine public Arabidopsis transcriptomes and construct tissue-specific GRNs with both epigenetic regulators and transcription factors as predictors. The resultant GRNs, named EpiNet, can now be intersected with individual transcriptomic studies on biological processes of interest to identify the most influential epigenetic regulators, as well as predicted gene targets of the epigenetic regulators. We demonstrate the validity of this approach using case studies of shoot and root apical meristem development.
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Affiliation(s)
- Rachel M. McCoy
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Russell Julian
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Shoban R. V. Kumar
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Rajeev Ranjan
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Kranthi Varala
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
| | - Ying Li
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, IN 47907, USA; (R.M.M.); (R.J.); (S.R.V.K.); (R.R.); (K.V.)
- Center for Plant Biology, Purdue University, West Lafayette, IN 47907, USA
- Correspondence: ; Tel.: +1-765-494-0104
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Mayer BF, Charron J. Transcriptional memories mediate the plasticity of cold stress responses to enable morphological acclimation in Brachypodium distachyon. THE NEW PHYTOLOGIST 2021; 229:1615-1634. [PMID: 32966623 PMCID: PMC7820978 DOI: 10.1111/nph.16945] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Accepted: 09/04/2020] [Indexed: 05/03/2023]
Abstract
Plants that successfully acclimate to stress can resume growth under stressful conditions. The grass Brachypodium distachyon can grow a cold-adaptive morphology during cold acclimation. Studies on transcriptional memory (TM) have revealed that plants can be primed for stress by adjusting their transcriptional responses, but the function of TM in stress acclimation is not well understood. We investigated the function of TM during cold acclimation in B. distachyon. Quantitative polymerase chain reaction (qPCR), RNA-seq and chromatin immunoprecipitation qPCR analyses were performed on plants exposed to repeated episodes of cold to characterize the presence and stability of TM during the stress and growth responses of cold acclimation. Transcriptional memory mainly dampened stress responses as growth resumed and as B. distachyon became habituated to cold stress. Although permanent on vernalization gene VRN1, TMs were short-term and reversible on cold-stress genes. Growing under cold conditions also coincided with the acquisition of new and targeted cold-induced transcriptional responses. Overall, TM provided plasticity to cold stress responses during cold acclimation in B. distachyon, leading to stress habituation, acquired stress responses, and resumed growth. Our study shows that chromatin-associated TMs are involved in tuning plant responses to environmental change and, as such, regulate both stress and developmental components that characterize cold-climate adaptation in B. distachyon.
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Affiliation(s)
- Boris F. Mayer
- Department of Plant ScienceMcGill University21, 111 LakeshoreSainte‐Anne‐de‐BellevueCanada
| | - Jean‐Benoit Charron
- Department of Plant ScienceMcGill University21, 111 LakeshoreSainte‐Anne‐de‐BellevueCanada
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Chang CYY, Bräutigam K, Hüner NPA, Ensminger I. Champions of winter survival: cold acclimation and molecular regulation of cold hardiness in evergreen conifers. THE NEW PHYTOLOGIST 2021; 229:675-691. [PMID: 32869329 DOI: 10.1111/nph.16904] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Accepted: 07/31/2020] [Indexed: 06/11/2023]
Abstract
Evergreen conifers are champions of winter survival, based on their remarkable ability to acclimate to cold and develop cold hardiness. Counterintuitively, autumn cold acclimation is triggered not only by exposure to low temperature, but also by a combination of decreasing temperature, decreasing photoperiod and changes in light quality. These environmental cues control a network of signaling pathways that coordinate cold acclimation and cold hardiness in overwintering conifers, leading to cessation of growth, bud dormancy, freezing tolerance and changes in energy metabolism. Advances in genomic, transcriptomic and metabolomic tools for conifers have improved our understanding of how trees sense and respond to changes in temperature and light during cold acclimation and the development of cold hardiness, but there remain considerable gaps deserving further research in conifers. In the first section of this review, we focus on the physiological mechanisms used by evergreen conifers to adjust metabolism seasonally and to protect overwintering tissues against winter stresses. In the second section, we review how perception of low temperature and photoperiod regulate the induction of cold acclimation. Finally, we explore the evolutionary context of cold acclimation in conifers and evaluate challenges imposed on them by changing climate and discuss emerging areas of research in the field.
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Affiliation(s)
- Christine Yao-Yun Chang
- Soil and Crop Sciences Section, School of Integrative Plant Science, Cornell University, Ithaca, NY, 14853, USA
| | - Katharina Bräutigam
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
| | - Norman P A Hüner
- Department of Biology and The Biotron Experimental Climate Change Research Centre, Western University, London, ON, N6A5B7, Canada
| | - Ingo Ensminger
- Department of Biology, University of Toronto, Mississauga, ON, L5L1C6, Canada
- Graduate Department of Cell and Systems Biology, University of Toronto, Toronto, ON, M5S 3G5, Canada
- Graduate Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, M5S 3B2, Canada
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49
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HOS15 is a transcriptional corepressor of NPR1-mediated gene activation of plant immunity. Proc Natl Acad Sci U S A 2020; 117:30805-30815. [PMID: 33199617 PMCID: PMC7720166 DOI: 10.1073/pnas.2016049117] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Immune responses protect organisms against biotic challenges but can also produce deleterious effects, such as inflammation and necrosis. This growth-defense trade-off necessitates fine control of immune responses, including the activation of defense gene expression. The transcriptional coactivator NPR1 is a key regulatory hub of immune activation in plant cells. Surprisingly, full activation of NPR1-activated defense genes requires proteasome-mediated degradation of NPR1 induced by a CUL3-based E3 ubiquitin ligase complex. Our work demonstrates that HOS15 is the specificity determinant of a CUL1-based E3 ubiquitin ligase complex that limits defense gene expression by targeting NPR1 for proteasome-mediated degradation. Thus, distinct ubiquitin-based degradation pathways coordinately modulate the timing and amplitude of transcriptional outputs during plant defense. Transcriptional regulation is a complex and pivotal process in living cells. HOS15 is a transcriptional corepressor. Although transcriptional repressors generally have been associated with inactive genes, increasing evidence indicates that, through poorly understood mechanisms, transcriptional corepressors also associate with actively transcribed genes. Here, we show that HOS15 is the substrate receptor for an SCF/CUL1 E3 ubiquitin ligase complex (SCFHOS15) that negatively regulates plant immunity by destabilizing transcriptional activation complexes containing NPR1 and associated transcriptional activators. In unchallenged conditions, HOS15 continuously eliminates NPR1 to prevent inappropriate defense gene expression. Upon defense activation, HOS15 preferentially associates with phosphorylated NPR1 to stimulate rapid degradation of transcriptionally active NPR1 and thus limit the extent of defense gene expression. Our findings indicate that HOS15-mediated ubiquitination and elimination of NPR1 produce effects contrary to those of CUL3-containing ubiquitin ligase that coactivate defense gene expression. Thus, HOS15 plays a key role in the dynamic regulation of pre- and postactivation host defense.
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50
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de Rooij PGH, Perrella G, Kaiserli E, van Zanten M. The diverse and unanticipated roles of histone deacetylase 9 in coordinating plant development and environmental acclimation. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:6211-6225. [PMID: 32687569 PMCID: PMC7586748 DOI: 10.1093/jxb/eraa335] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 07/15/2020] [Indexed: 05/04/2023]
Abstract
Plants tightly control gene transcription to adapt to environmental conditions and steer growth and development. Different types of epigenetic modifications are instrumental in these processes. In recent years, an important role for the chromatin-modifying RPD3/HDA1 class I HDAC HISTONE DEACETYLASE 9 (HDA9) emerged in the regulation of a multitude of plant traits and responses. HDACs are widely considered transcriptional repressors and are typically part of multiprotein complexes containing co-repressors, DNA, and histone-binding proteins. By catalyzing the removal of acetyl groups from lysine residues of histone protein tails, HDA9 negatively controls gene expression in many cases, in concert with interacting proteins such as POWERDRESS (PWR), HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15), WRKY53, ELONGATED HYPOCOTYL 5 (HY5), ABA INSENSITIVE 4 (ABI4), and EARLY FLOWERING 3 (ELF3). However, HDA9 activity has also been directly linked to transcriptional activation. In addition, following the recent breakthrough discovery of mutual negative feedback regulation between HDA9 and its interacting WRKY-domain transcription factor WRKY53, swift progress in gaining understanding of the biology of HDA9 is expected. In this review, we summarize knowledge on this intriguing versatile-and long under-rated-protein and propose novel leads to further unravel HDA9-governed molecular networks underlying plant development and environmental biology.
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Affiliation(s)
- Peter G H de Rooij
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan, CH Utrecht, The Netherlands
| | - Giorgio Perrella
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
- ENEA - Trisaia Research Centre 75026, Rotondella (Matera), Italy
| | - Eirini Kaiserli
- Institute of Molecular, Cell & Systems Biology, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University, Padualaan, CH Utrecht, The Netherlands
- Correspondence:
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