1
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Kara MF, Guo W, Zhang R, Denby K. LsRTDv1, a reference transcript dataset for accurate transcript-specific expression analysis in lettuce. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 120:370-386. [PMID: 39145419 DOI: 10.1111/tpj.16978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 06/20/2024] [Accepted: 07/31/2024] [Indexed: 08/16/2024]
Abstract
Accurate quantification of gene and transcript-specific expression, with the underlying knowledge of precise transcript isoforms, is crucial to understanding many biological processes. Analysis of RNA sequencing data has benefited from the development of alignment-free algorithms which enhance the precision and speed of expression analysis. However, such algorithms require a reference transcriptome. Here we generate a reference transcript dataset (LsRTDv1) for lettuce (cv. Saladin), combining long- and short-read sequencing with publicly available transcriptome annotations, and filtering to keep only transcripts with high-confidence splice junctions and transcriptional start and end sites. LsRTDv1 identifies novel genes (mostly long non-coding RNAs) and increases the number of transcript isoforms per gene in the lettuce genome from 1.4 to 2.7. We show that LsRTDv1 significantly increases the mapping rate of RNA-seq data from a lettuce time-series experiment (mock- and Botrytis cinerea-inoculated) and enables detection of genes that are differentially alternatively spliced in response to infection as well as transcript-specific expression changes. LsRTDv1 is a valuable resource for investigation of transcriptional and alternative splicing regulation in lettuce.
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Affiliation(s)
- Mehmet Fatih Kara
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
| | - Wenbin Guo
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Runxuan Zhang
- Information and Computational Sciences, James Hutton Institute, Dundee, DD2 5DA, UK
| | - Katherine Denby
- Biology Department, Centre for Novel Agricultural Products (CNAP), University of York, Wentworth Way, York, YO10 5DD, UK
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2
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Pratx L, Crawford T, Bäurle I. Mechanisms of heat stress-induced transcriptional memory. CURRENT OPINION IN PLANT BIOLOGY 2024; 81:102590. [PMID: 38968911 DOI: 10.1016/j.pbi.2024.102590] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Revised: 05/29/2024] [Accepted: 06/07/2024] [Indexed: 07/07/2024]
Abstract
Transcriptional memory allows organisms to store information about transcriptional reprogramming in response to a stimulus. In plants, this often involves the response to an abiotic stress, which in nature may be cyclical or recurring. Such transcriptional memory confers sustained induction or enhanced re-activation in response to a recurrent stimulus, which may increase chances of survival and fitness. Heat stress (HS) has emerged as an excellent model system to study transcriptional memory in plants, and much progress has been made in elucidating the molecular mechanisms underlying this phenomenon. Here, we review how histone turnover and transcriptional co-regulator complexes contribute to reprogramming of transcriptional responses.
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Affiliation(s)
- Loris Pratx
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Tim Crawford
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany
| | - Isabel Bäurle
- University of Potsdam, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, D-14476 Potsdam, Germany.
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3
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Zheng S, Zhao W, Liu Z, Geng Z, Li Q, Liu B, Li B, Bai J. Establishment and Maintenance of Heat-Stress Memory in Plants. Int J Mol Sci 2024; 25:8976. [PMID: 39201662 PMCID: PMC11354667 DOI: 10.3390/ijms25168976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2024] [Revised: 08/15/2024] [Accepted: 08/15/2024] [Indexed: 09/02/2024] Open
Abstract
Among the rich repertoire of strategies that allow plants to adapt to high-temperature stress is heat-stress memory. The mechanisms underlying the establishment and maintenance of heat-stress memory are poorly understood, although the chromatin opening state appears to be an important structural basis for maintaining heat-stress memory. The chromatin opening state is influenced by epigenetic modifications, making DNA and histone modifications important entry points for understanding heat-shock memory. Current research suggests that traditional heat-stress signaling pathway components might be involved in chromatin opening, thereby promoting the establishment of heat-stress memory in plants. In this review, we discuss the relationship between chromatin structure-based maintenance and the establishment of heat-stress memory. We also discuss the association between traditional heat-stress signals and epigenetic modifications. Finally, we discuss potential research ideas for exploring plant adaptation to high-temperature stress in the future.
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Affiliation(s)
- Shuzhi Zheng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Weishuang Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zimeng Liu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Ziyue Geng
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Qiang Li
- Dryland Farming Institute of Hebei Academy of Agricultural and Forestry Science, Key Laboratory of Crop Drought Tolerance Research of Hebei Province, Hengshui 053000, China
| | - Binhui Liu
- Dryland Farming Institute of Hebei Academy of Agricultural and Forestry Science, Key Laboratory of Crop Drought Tolerance Research of Hebei Province, Hengshui 053000, China
| | - Bing Li
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Jiaoteng Bai
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Basic Research Center of Cell Biology, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
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4
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Kwak JS, Song JT, Seo HS. E3 SUMO ligase SIZ1 splicing variants localize and function according to external conditions. PLANT PHYSIOLOGY 2024; 195:1601-1623. [PMID: 38497423 PMCID: PMC11142376 DOI: 10.1093/plphys/kiae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 01/08/2024] [Indexed: 03/19/2024]
Abstract
SIZ1 (SAP and MIZ1) is a member of the Siz/PIAS-type RING family of E3 SUMO (small ubiquitin-related modifier) ligases that play key roles in growth, development, and stress responses in plant and animal systems. Nevertheless, splicing variants of SIZ1 have not yet been characterized. Here, we identified four splicing variants of Arabidopsis (Arabidopsis thaliana) SIZ1, which encode three different protein isoforms. The SIZ1 gene encodes an 873-amino acid (aa) protein. Among the four SIZ1 splicing variants (SSVs), SSV1 and SSV4 encode identical 885 aa proteins; SSV2 encodes an 832 aa protein; and SSV3 encodes an 884 aa protein. SSV2 mainly localized to the plasma membrane, whereas SIZ1, SSV1/SSV4, and SSV3 localized to the nucleus. Interestingly, SIZ1 and all SSVs exhibited similar E3 SUMO ligase activities and preferred SUMO1 and SUMO2 for their E3 ligase activity. Transcript levels of SSV2 were substantially increased by heat treatment, while those of SSV1, SSV3, and SSV4 transcripts were unaffected by various abiotic stresses. SSV2 directly interacted with and sumoylated cyclic nucleotide-gated ion channel 6 (CNGC6), a positive thermotolerance regulator, enhancing the stability of CNGC6. Notably, transgenic siz1-2 mutants expressing SSV2 exhibited greater heat stress tolerance than wild-type plants, whereas those expressing SIZ1 were sensitive to heat stress. Furthermore, transgenic cngc6 plants overaccumulating a mutated mCNGC6 protein (K347R, a mutation at the sumoylation site) were sensitive to heat stress, similar to the cngc6 mutants, while transgenic cngc6 plants overaccumulating CNGC6 exhibited restored heat tolerance. Together, we propose that alternative splicing is an important mechanism that regulates the function of SSVs during development or under adverse conditions, including heat stress.
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Affiliation(s)
- Jun Soo Kwak
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
| | - Jong Tae Song
- Department of Applied Biosciences, Kyungpook National University, Daegu 41566, Korea
| | - Hak Soo Seo
- Department of Agriculture, Forestry and Bioresources, Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, Korea
- Bio-MAX Institute, Seoul National University, Seoul 08826, Korea
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5
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Ganie SA, McMulkin N, Devoto A. The role of priming and memory in rice environmental stress adaptation: Current knowledge and perspectives. PLANT, CELL & ENVIRONMENT 2024; 47:1895-1915. [PMID: 38358119 DOI: 10.1111/pce.14855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 12/21/2023] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Plant responses to abiotic stresses are dynamic, following the unpredictable changes of physical environmental parameters such as temperature, water and nutrients. Physiological and phenotypical responses to stress are intercalated by periods of recovery. An earlier stress can be remembered as 'stress memory' to mount a response within a generation or transgenerationally. The 'stress priming' phenomenon allows plants to respond quickly and more robustly to stressors to increase survival, and therefore has significant implications for agriculture. Although evidence for stress memory in various plant species is accumulating, understanding of the mechanisms implicated, especially for crops of agricultural interest, is in its infancy. Rice is a major food crop which is susceptible to abiotic stresses causing constraints on its cultivation and yield globally. Advancing the understanding of the stress response network will thus have a significant impact on rice sustainable production and global food security in the face of climate change. Therefore, this review highlights the effects of priming on rice abiotic stress tolerance and focuses on specific aspects of stress memory, its perpetuation and its regulation at epigenetic, transcriptional, metabolic as well as physiological levels. The open questions and future directions in this exciting research field are also laid out.
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Affiliation(s)
- Showkat Ahmad Ganie
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
| | - Nancy McMulkin
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
| | - Alessandra Devoto
- Department of Biological Sciences, Plant Molecular Science and Centre of Systems and Synthetic Biology, Royal Holloway University of London, Egham, Surrey, UK
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6
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Chen S, Zhang Y, Liu L, Mo Y, Li J, Chen B, Zhou Y, Lin J, Jiang X, Wei L, Ling Y. Transcription and splicing variations of SR genes accompany with genome-wide accumulation of long-introns in pine. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2024; 342:112056. [PMID: 38438082 DOI: 10.1016/j.plantsci.2024.112056] [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: 11/08/2023] [Revised: 02/04/2024] [Accepted: 03/01/2024] [Indexed: 03/06/2024]
Abstract
Most of mRNAs in Eukaryote were matured after the removal of introns in their pre-mRNA transcripts. Serine/arginine-rich (SR) proteins are a group of splicing regulators regulating the splicing processes globally. Expressions of SR proteins themselves were extensively regulated, at both transcription and splicing levels, under different environmental conditions, specially heat stress conditions. The pine genome is characterized by super-long and easily methylated introns in a large number of genes that derived from the extensive accumulation of transposons (TEs). Here, we identified and analyzed the phylogenetic characteristics of 24 SR proteins and their encoding genes from the pine genome. Then we explored transcription and pre-mRNA splicing expression patterns of SR genes in P. massoniana seedlings under normal and heat stress temperature conditions. Our results showed that the transcription patterns of SR genes in pine exhibited significant changes compared to other plant species, and these changes were not strictly correlated with the intron length and DNA methylation intensity of the SR genes. Interestingly, none of the long introns of SR genes underwent alternative splicing (AS) in our experiment. Furthermore, the intensity of AS regulation may be related to the potential DNA methylation intensity of SR genes. Taken together, this study explores for the first time the characteristics of significant variations in the transcription and splicing patterns of SR proteins in a plant species with an over-accumulation of super-long introns.
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Affiliation(s)
- Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Li Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Junyi Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Beibei Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yi Zhou
- Guangdong Academy of Forestry/Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Coastal Shelter-belt Forest Ecosystem National Observation and Research Station Guangzhou, Guangdong 510520, China
| | - Jinxing Lin
- State Key Laboratory of Tree Genetics and Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China
| | - Xingyu Jiang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Long Wei
- Guangdong Academy of Forestry/Guangdong Provincial Key Laboratory of Silviculture, Protection and Utilization/Guangdong Coastal Shelter-belt Forest Ecosystem National Observation and Research Station Guangzhou, Guangdong 510520, China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China; South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China.
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7
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Xu WB, Cao F, Liu P, Yan K, Guo QH. The multifaceted role of RNA-based regulation in plant stress memory. FRONTIERS IN PLANT SCIENCE 2024; 15:1387575. [PMID: 38736453 PMCID: PMC11082352 DOI: 10.3389/fpls.2024.1387575] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/18/2024] [Accepted: 04/15/2024] [Indexed: 05/14/2024]
Abstract
Plants have evolved interconnected regulatory pathways which enable them to respond and adapt to their environments. In plants, stress memory enhances stress tolerance through the molecular retention of prior stressful experiences, fostering rapid and robust responses to subsequent challenges. Mounting evidence suggests a close link between the formation of stress memories and effective future stress responses. However, the mechanism by which environmental stressors trigger stress memory formation is poorly understood. Here, we review the current state of knowledge regarding the RNA-based regulation on stress memory formation in plants and discuss research challenges and future directions. Specifically, we focus on the involvement of microRNAs (miRNAs), small interfering RNAs (siRNAs), long non-coding RNAs (lncRNAs), and alternative splicing (AS) in stress memory formation. miRNAs regulate target genes via post-transcriptional silencing, while siRNAs trigger stress memory formation through RNA-directed DNA methylation (RdDM). lncRNAs guide protein complexes for epigenetic regulation, and AS of pre-mRNAs is crucial to plant stress memory. Unraveling the mechanisms underpinning RNA-mediated stress memory formation not only advances our knowledge of plant biology but also aids in the development of improved stress tolerance in crops, enhancing crop performance and global food security.
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Affiliation(s)
- Wei-Bo Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Fan Cao
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Peng Liu
- Donald Danforth Plant Science Center, St. Louis, MO, United States
| | - Kang Yan
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
| | - Qian-Huan Guo
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, Shandong, China
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8
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Wang Q, Wu Y, Wu W, Lyu L, Li W. A review of changes at the phenotypic, physiological, biochemical, and molecular levels of plants due to high temperatures. PLANTA 2024; 259:57. [PMID: 38307982 DOI: 10.1007/s00425-023-04320-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/23/2023] [Indexed: 02/04/2024]
Abstract
MAIN CONCLUSION This review summarizes the physiological, biochemical, and molecular regulatory network changes in plants in response to high temperature. With the continuous rise in temperature, high temperature has become an important issue limiting global plant growth and development, affecting the phenotype and physiological and biochemical processes of plants and seriously restricting crop yield and tree growth speed. As sessile organisms, plants inevitably encounter high temperatures and improve their heat tolerance by activating molecular networks related to heat stress, such as signal transduction, synthesis of metabolites, and gene expression. Heat tolerance is a polygenic trait regulated by a variety of genes, transcription factors, proteins, and metabolites. Therefore, this review summarizes the changes in physiological, biochemical and molecular regulatory networks in plants under high-temperature conditions to lay a foundation for an in-depth understanding of the mechanisms involved in plant heat tolerance responses.
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Affiliation(s)
- Que Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China
| | - Yaqiong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China.
| | - Wenlong Wu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China
| | - Lianfei Lyu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences (Nanjing Botanical Garden Mem. Sun Yat-Sen), Jiangsu Key Laboratory for the Research and Utilization of Plant Resources, Qian Hu Hou Cun No. 1, Nanjing, 210014, China
| | - Weilin Li
- Co-Innovation Center for Sustainable Forestry in Southern China, College of Forestry, Nanjing Forestry University, 159 Longpan Road, Nanjing, 210037, China.
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9
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Seth P, Sebastian J. Plants and global warming: challenges and strategies for a warming world. PLANT CELL REPORTS 2024; 43:27. [PMID: 38163826 DOI: 10.1007/s00299-023-03083-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/15/2023] [Indexed: 01/03/2024]
Abstract
KEY MESSAGE In this review, we made an attempt to create a holistic picture of plant response to a rising temperature environment and its impact by covering all aspects from temperature perception to thermotolerance. This comprehensive account describing the molecular mechanisms orchestrating these responses and potential mitigation strategies will be helpful for understanding the impact of global warming on plant life. Organisms need to constantly recalibrate development and physiology in response to changes in their environment. Climate change-associated global warming is amplifying the intensity and periodicity of these changes. Being sessile, plants are particularly vulnerable to variations happening around them. These changes can cause structural, metabolomic, and physiological perturbations, leading to alterations in the growth program and in extreme cases, plant death. In general, plants have a remarkable ability to respond to these challenges, supported by an elaborate mechanism to sense and respond to external changes. Once perceived, plants integrate these signals into the growth program so that their development and physiology can be modulated befittingly. This multifaceted signaling network, which helps plants to establish acclimation and survival responses enabled their extensive geographical distribution. Temperature is one of the key environmental variables that affect all aspects of plant life. Over the years, our knowledge of how plants perceive temperature and how they respond to heat stress has improved significantly. However, a comprehensive mechanistic understanding of the process still largely elusive. This review explores how an increase in the global surface temperature detrimentally affects plant survival and productivity and discusses current understanding of plant responses to high temperature (HT) and underlying mechanisms. We also highlighted potential resilience attributes that can be utilized to mitigate the impact of global warming.
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Affiliation(s)
- Pratyay Seth
- Indian Institute of Science Education and Research, Berhampur (IISER Berhampur), Engineering School Road, Berhampur, 760010, Odisha, India
| | - Jose Sebastian
- Indian Institute of Science Education and Research, Berhampur (IISER Berhampur), Engineering School Road, Berhampur, 760010, Odisha, India.
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10
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Punzo P, Suede Cigliano R, Aversano R, Grillo S, Batelli G. Determination of Differential Alternative Splicing Under Stress Conditions. Methods Mol Biol 2024; 2832:67-79. [PMID: 38869788 DOI: 10.1007/978-1-0716-3973-3_5] [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] [Indexed: 06/14/2024]
Abstract
Alternative splicing (AS) is an important mechanism contributing to stress-induced regulation of gene expression and proteome diversity. Massive sequencing technologies allow the identification of transcripts generated via stress-responsive AS, potentially important for adaptation to stress conditions. Several bioinformatics tools have been developed to identify differentially expressed alternative splicing events/transcripts from RNA-sequencing results. This chapter describes a detailed protocol for differential alternative splicing analysis using the rMATS tool. In addition, we provide guidelines for validation of the detected splice variants by qRT-PCR based on the obtained output files.
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Affiliation(s)
- Paola Punzo
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | | | - Riccardo Aversano
- Department of Agricultural Sciences, University of Naples "Federico II", Portici, Italy
| | - Stefania Grillo
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy
| | - Giorgia Batelli
- CNR Institute of Biosciences and Bioresources, Research Division Portici, Portici, Italy.
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11
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Ling Y, Mo Y, Chen S, Mahfouz MM. A Method to Quantitatively Examine Heat Stress-Induced Alternative Splicing in Plants by RNA-Seq and RT-PCR. Methods Mol Biol 2024; 2832:81-98. [PMID: 38869789 DOI: 10.1007/978-1-0716-3973-3_6] [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] [Indexed: 06/14/2024]
Abstract
Alternative splicing (AS) of pre-mRNAs is a type of post-transcriptional regulation in eukaryotes that expands the number of mRNA isoforms. Intron retention is the primary form of AS in plants and occurs more frequently when plants are exposed to environmental stresses. Several wet-lab and bioinformatics techniques are used to detect AS events, but these techniques are technically challenging or unsuitable for studying AS in plants. Here, we report a method that combines RNA-sequencing and reverse transcription PCR for visualizing and validating heat stress-induced AS events in plants, using Arabidopsis thaliana and HEAT SHOCK PROTEIN21 (HSP21) as examples.
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Affiliation(s)
- Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, People's Republic of China
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.
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12
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Zhu Z, Dai Y, Yu G, Zhang X, Chen Q, Kou X, Mehareb EM, Raza G, Zhang B, Wang B, Wang K, Han J. Dynamic physiological and transcriptomic changes reveal memory effects of salt stress in maize. BMC Genomics 2023; 24:726. [PMID: 38041011 PMCID: PMC10690987 DOI: 10.1186/s12864-023-09845-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/26/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Pre-exposing plants to abiotic stresses can induce stress memory, which is crucial for adapting to subsequent stress exposure. Although numerous genes involved in salt stress response have been identified, the understanding of memory responses to salt stress remains limited. RESULTS In this study, we conducted physiological and transcriptional assays on maize plants subjected to recurrent salt stress to characterize salt stress memory. During the second exposure to salt stress, the plants exhibited enhanced salt resistance, as evidenced by increased proline content and higher POD and SOD activity, along with decreased MDA content, indicative of physiological memory behavior. Transcriptional analysis revealed fewer differentially expressed genes and variations in response processes during the second exposure compared to the first, indicative of transcriptional memory behavior. A total of 2,213 salt stress memory genes (SMGs) were identified and categorized into four response patterns. The most prominent group of SMGs consisted of genes with elevated expression during the first exposure to salt stress but reduced expression after recurrent exposure to salt stress, or vice versa ([+ / -] or [- / +]), indicating that a revised response is a crucial process in plant stress memory. Furthermore, nine transcription factors (TFs) (WRKY40, WRKY46, WRKY53, WRKY18, WRKY33, WRKY70, MYB15, KNAT7, and WRKY54) were identified as crucial factors related to salt stress memory. These TFs regulate over 53% of SMGs, underscoring their potential significance in salt stress memory. CONCLUSIONS Our study demonstrates that maize can develop salt stress memory, and the genes identified here will aid in the genetic improvement of maize and other crops.
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Affiliation(s)
- Zhiying Zhu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Yan Dai
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Guangrun Yu
- School of Life Sciences, Nantong University, Nantong, 226019, China
- College of Agriculture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin Zhang
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Qi Chen
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Xiaobing Kou
- School of Life Sciences, Nantong University, Nantong, 226019, China
| | - Eid M Mehareb
- Sugar Crops Research Institute, Agricultural Research Center, Giza, 12619, Egypt
| | - Ghulam Raza
- National Institute for Biotechnology and Genetic Engineering, College Pakistan Institute of Engineering and Applied Sciences (NIBGE-C, PIEAS), Faisalabad, 38000, Pakistan
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Baohua Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China.
| | - Kai Wang
- School of Life Sciences, Nantong University, Nantong, 226019, China.
| | - Jinlei Han
- School of Life Sciences, Nantong University, Nantong, 226019, China.
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13
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Gao R, Lu Y, Wu N, Liu H, Jin X. Comprehensive study of serine/arginine-rich (SR) gene family in rice: characterization, evolution and expression analysis. PeerJ 2023; 11:e16193. [PMID: 37849832 PMCID: PMC10578304 DOI: 10.7717/peerj.16193] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 09/06/2023] [Indexed: 10/19/2023] Open
Abstract
As important regulators of alternative splicing (AS) events, serine/arginine (SR)-rich proteins play indispensable roles in the growth and development of organisms. Until now, the study of SR genes has been lacking in plants. In the current study, we performed genome-wide analysis on the SR gene family in rice. A total of 24 OsSR genes were phylogenetically classified into seven groups, corresponding to seven subfamilies. The OsSR genes' structures, distribution of conserved domains, and protein tertiary structure of OsSR were conserved within each subfamily. The synteny analysis revealed that segmental duplication events were critical for the expansion of OsSR gene family. Moreover, interspecific synteny revealed the distribution of orthologous SR gene pairs between rice and Arabidopsis, sorghum, wheat, and maize. Among all OsSR genes, 14 genes exhibited NAGNAG acceptors, and only four OsSR genes had AS events on the NAGNAG acceptors. Furthermore, the distinct tissue-specific expression patterns of OsSR genes showed that these genes may function in different developmental stages in rice. The AS patterns on the same OsSR gene were variable among the root, stem, leaf, and grains at different filling stages, and some isoforms could only be detected in one or a few of tested tissues. Meanwhile, our results showed that the expression of some OsSR genes changed dramatically under ABA, GA, salt, drought, cold or heat treatment, which were related to the wide distribution of corresponding cis-elements in their promoter regions, suggesting their specific roles in stress and hormone response. This research facilitates our understanding of SR gene family in rice and provides clues for further exploration of the function of OsSR genes.
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Affiliation(s)
- Rui Gao
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Yingying Lu
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Nan Wu
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Hui Liu
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
| | - Xiaoli Jin
- Department of Agronomy, The Key Laboratory of Crop Germplasm Resource of Zhejiang Province, Zhejiang University, Hangzhou, China
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14
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Babbar R, Tiwari LD, Mishra RC, Shimphrui R, Singh AA, Goyal I, Rana S, Kumar R, Sharma V, Tripathi G, Khungar L, Sharma J, Agrawal C, Singh G, Biswas T, Biswal AK, Sahi C, Sarkar NK, Grover A. Arabidopsis plants overexpressing additional copies of heat shock protein Hsp101 showed high heat tolerance and endo-gene silencing. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111639. [PMID: 36796649 DOI: 10.1016/j.plantsci.2023.111639] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 02/08/2023] [Accepted: 02/11/2023] [Indexed: 06/18/2023]
Abstract
Hsp101 chaperone is vital for survival of plants under heat stress. We generated transgenic Arabidopsis thaliana (Arabidopsis) lines with extra copies of Hsp101 gene using diverse approaches. Arabidopsis plants transformed with rice Hsp101 cDNA driven by Arabidopsis Hsp101 promoter (IN lines) showed high heat tolerance while the plants transformed with rice Hsp101 cDNA driven by CaMV35S promoter (C lines) were like wild type plants in heat stress response. Transformation of Col-0 plants with 4633 bp Hsp101 genomic fragment (GF lines) from A. thaliana containing both its coding and the regulatory sequence resulted in mostly over-expressor (OX) lines and a few under-expressor (UX) lines of Hsp101. OX lines showed enhanced heat tolerance while the UX lines were overly heat sensitive. In UX lines, silencing of not only Hsp101 endo-gene was noted but also transcript of choline kinase (CK2) was silenced. Previous work established that in Arabidopsis, CK2 and Hsp101 are convergent gene pairs sharing a bidirectional promoter. The elevated AtHsp101 protein amount in most GF and IN lines was accompanied by lowered CK2 transcript levels under HS. We observed increased methylation of the promoter and gene sequence region in UX lines; however, methylation was lacking in OX lines.
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Affiliation(s)
- Richa Babbar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Lalit Dev Tiwari
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Ratnesh Chandra Mishra
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Rinchuila Shimphrui
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Aditya Abha Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India; Department of Botany, University of Lucknow, Lucknow-226007, India
| | - Isha Goyal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Surbhi Rana
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Ritesh Kumar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Vijyesh Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Gayatri Tripathi
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Lisha Khungar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Jaydeep Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Chhavi Agrawal
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Garima Singh
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Tanya Biswas
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Anup Kumar Biswal
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, MP, India
| | - Chandan Sahi
- Department of Biological Sciences, Indian Institute of Science Education and Research, Bhopal, MP, India
| | - Neelam K Sarkar
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Anil Grover
- Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India.
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15
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Global Analysis of Dark- and Heat-Regulated Alternative Splicing in Arabidopsis. Int J Mol Sci 2023; 24:ijms24065299. [PMID: 36982373 PMCID: PMC10049525 DOI: 10.3390/ijms24065299] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/02/2023] [Accepted: 03/07/2023] [Indexed: 03/12/2023] Open
Abstract
Alternative splicing (AS) is one of the major post-transcriptional regulation mechanisms that contributes to plant responses to various environmental perturbations. Darkness and heat are two common abiotic factors affecting plant growth, yet the involvement and regulation of AS in the plant responses to these signals remain insufficiently examined. In this study, we subjected Arabidopsis seedlings to 6 h of darkness or heat stress and analyzed their transcriptome through short-read RNA sequencing. We revealed that both treatments altered the transcription and AS of a subset of genes yet with different mechanisms. Dark-regulated AS events were found enriched in photosynthesis and light signaling pathways, while heat-regulated AS events were enriched in responses to abiotic stresses but not in heat-responsive genes, which responded primarily through transcriptional regulation. The AS of splicing-related genes (SRGs) was susceptible to both treatments; while dark treatment mostly regulated the AS of these genes, heat had a strong effect on both their transcription and AS. PCR analysis showed that the AS of the Serine/Arginine-rich family gene SR30 was reversely regulated by dark and heat, and heat induced the upregulation of multiple minor SR30 isoforms with intron retention. Our results suggest that AS participates in plant responses to these two abiotic signals and reveal the regulation of splicing regulators during these processes.
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16
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Louis N, Dhankher OP, Puthur JT. Seed priming can enhance and retain stress tolerance in ensuing generations by inducing epigenetic changes and trans-generational memory. PHYSIOLOGIA PLANTARUM 2023; 175:e13881. [PMID: 36840678 DOI: 10.1111/ppl.13881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2022] [Revised: 02/07/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
The significance of priming in enhancing abiotic stress tolerance is well-established in several important crops. Priming positively impacts plant growth and improves stress tolerance at multiple developmental stages, and seed priming is one of the most used methods. Seed priming influences the pre-germinative metabolism that ensures proper germination, early seedling establishment, enhanced stress tolerance and yield, even under unfavourable environmental conditions. Seed priming involves pre-exposure of seeds to mild stress, and this pre-treatment induces specific changes at the physiological and molecular levels. Interestingly, priming can improve the efficiency of the DNA repair mechanism, along with activation of specific signalling proteins and transcription factors for rapid and efficient stress tolerance. Notably, such acquired stress tolerance may be retained for longer duration, namely, later developmental stages or even subsequent generations. Epigenetic and chromatin-based mechanisms such as DNA methylation, histone modifications, and nucleosome positioning are some of the key molecular changes involved in priming/stress memory. Further, the retention of induced epigenetic changes may influence the priming-induced trans-generational stress memory. This review discusses known and plausible seed priming-induced molecular mechanisms that govern germination and stress memory within and across generations, highlighting their role in regulating the plant response to abiotic stresses. Understanding the molecular mechanism for activation of stress-responsive genes and the epigenetic changes resulting from seed priming will help to improve the resiliency of the crops for enhanced productivity under extreme environments.
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Affiliation(s)
- Noble Louis
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, Malapuram, Kerala, India
| | - Om Parkash Dhankher
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts, USA
| | - Jos T Puthur
- Plant Physiology and Biochemistry Division, Department of Botany, University of Calicut, Malapuram, Kerala, India
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17
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Mo Y, Li G, Liu L, Zhang Y, Li J, Yang M, Chen S, Lin Q, Fu G, Zheng D, Ling Y. OsGRF4AA compromises heat tolerance of developing pollen grains in rice. FRONTIERS IN PLANT SCIENCE 2023; 14:1121852. [PMID: 36909437 PMCID: PMC9992635 DOI: 10.3389/fpls.2023.1121852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/11/2023] [Indexed: 06/18/2023]
Abstract
Extreme high temperature at the meiosis stage causes a severe decrease in spikelet fertility and grain yield in rice. The rice variety grain size on chromosome 2 (GS2) contains sequence variations of OsGRF4 (Oryza sativa growth-regulating factor 4; OsGRF4AA ), escaping the microRNA miR396-mediated degradation of this gene at the mRNA level. Accumulation of OsGRF4 enhances nitrogen usage and metabolism, and increases grain size and grain yield. In this study, we found that pollen viability and seed-setting rate under heat stress (HS) decreased more seriously in GS2 than in its comparator, Zhonghua 11 (ZH11). Transcriptomic analysis revealed that, following HS, genes related to carbohydrate metabolic processes were expressed and regulated differentially in the anthers of GS2 and ZH11. Moreover, the expression of genes involved in chloroplast development and photosynthesis, lipid metabolism, and key transcription factors, including eight male sterile genes, were inhibited by HS to a greater extent in GS2 than in ZH11. Interestingly, pre-mRNAs of OsGRF4, and a group of essential genes involved in development and fertilization, were differentially spliced in the anthers of GS2 and ZH11. Taken together, our results suggest that variation in OsGRF4 affects proper transcriptional and splicing regulation of genes under HS, and that this can be mediated by, and also feed back to, carbohydrate and nitrogen metabolism, resulting in a reduction in the heat tolerance of rice anthers.
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Affiliation(s)
- Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, China
| | - Guangyan Li
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Li Liu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Junyi Li
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Meizhen Yang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Qiaoling Lin
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
| | - Guanfu Fu
- State Key Laboratory of Rice Biology, China National Rice Research Institute, Hangzhou, China
| | - Dianfeng Zheng
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, China
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18
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Alternative Splicing in the Regulatory Circuit of Plant Temperature Response. Int J Mol Sci 2023; 24:ijms24043878. [PMID: 36835290 PMCID: PMC9962249 DOI: 10.3390/ijms24043878] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 02/08/2023] [Accepted: 02/10/2023] [Indexed: 02/17/2023] Open
Abstract
As sessile organisms, plants have evolved complex mechanisms to rapidly respond to ever-changing ambient temperatures. Temperature response in plants is modulated by a multilayer regulatory network, including transcriptional and post-transcriptional regulations. Alternative splicing (AS) is an essential post-transcriptional regulatory mechanism. Extensive studies have confirmed its key role in plant temperature response, from adjustment to diurnal and seasonal temperature changes to response to extreme temperatures, which has been well documented by previous reviews. As a key node in the temperature response regulatory network, AS can be modulated by various upstream regulations, such as chromatin modification, transcription rate, RNA binding proteins, RNA structure and RNA modifications. Meanwhile, a number of downstream mechanisms are affected by AS, such as nonsense-mediated mRNA decay (NMD) pathway, translation efficiency and production of different protein variants. In this review, we focus on the links between splicing regulation and other mechanisms in plant temperature response. Recent advances regarding how AS is regulated and the following consequences in gene functional modulation in plant temperature response will be discussed. Substantial evidence suggests that a multilayer regulatory network integrating AS in plant temperature response has been unveiled.
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19
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Boulanger HG, Guo W, Monteiro LDFR, Calixto CPG. Co-expression network of heat-response transcripts: A glimpse into how splicing factors impact rice basal thermotolerance. Front Mol Biosci 2023; 10:1122201. [PMID: 36818043 PMCID: PMC9932781 DOI: 10.3389/fmolb.2023.1122201] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 01/23/2023] [Indexed: 02/05/2023] Open
Abstract
To identify novel solutions to improve rice yield under rising temperatures, molecular components of thermotolerance must be better understood. Alternative splicing (AS) is a major post-transcriptional mechanism impacting plant tolerance against stresses, including heat stress (HS). AS is largely regulated by splicing factors (SFs) and recent studies have shown their involvement in temperature response. However, little is known about the splicing networks between SFs and AS transcripts in the HS response. To expand this knowledge, we constructed a co-expression network based on a publicly available RNA-seq dataset that explored rice basal thermotolerance over a time-course. Our analyses suggest that the HS-dependent control of the abundance of specific transcripts coding for SFs might explain the widespread, coordinated, complex, and delicate AS regulation of critical genes during a plant's inherent response to extreme temperatures. AS changes in these critical genes might affect many aspects of plant biology, from organellar functions to cell death, providing relevant regulatory candidates for future functional studies of basal thermotolerance.
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Affiliation(s)
- Hadrien Georges Boulanger
- Université Paris-Saclay, Gif-sur-Yvette, France,École Nationale Supérieure d'Informatique pour l'Industrie et l’Entreprise, Evry-Courcouronnes, France,Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil
| | - Wenbin Guo
- Information and Computational Sciences, The James Hutton Institute, Dundee, United Kingdom
| | | | - Cristiane Paula Gomes Calixto
- Department of Botany, Institute of Biosciences, University of São Paulo, São Paulo, Brazil,*Correspondence: Cristiane Paula Gomes Calixto,
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20
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He L, Wu Q, Jin Y, Fan Y, Shi H, Wang Y, Yang W. NTR1 is involved in heat stress tolerance through mediating expression regulation and alternative splicing of heat stress genes in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2023; 13:1082511. [PMID: 36704159 PMCID: PMC9871932 DOI: 10.3389/fpls.2022.1082511] [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: 10/28/2022] [Accepted: 12/14/2022] [Indexed: 06/18/2023]
Abstract
As a common adverse environmental factor, heat stress (HS) not only drastically changes the plant transcriptome at the transcription level but also increases alternative splicing (AS), especially intron retention (IR) events. However, the exact mechanisms are not yet well understood. Here, we reported that NTC-related protein 1 (NTR1), which acts as an accessory component for spliceosome disassembly, is necessary for this process. The mutants of NTR1, both the T-DNA insertion and the point mutation identified through ethyl methanesulfonate (EMS) mutagenesis screening, are vulnerable to HS, indicating that NTR1 is essential for plant HS tolerance. At the molecular level, genes of response to heat and response to temperature stimulus are highly enriched among those of heat-induced but less-expressed ntr1 mutants. Moreover, a large portion of HS response (HSR) genes such as heat shock transcription factors (HSFs) and heat shock proteins (HSPs) are less induced by heat treatment, and more AS events, especially IR events, were found in heat-treated ntr1 mutants. Furthermore, HS suppressed the expression of NTR1 and NTR1-associated complex components. Thus, it is very likely that upon HS, the plant reduces the expression of the NTR1-associated complex to fulfill the fast demands for transcription of HSR genes such as HSFs and HSPs, which in turn results in the accumulation of improperly spliced especially IR products and eventually causes harm to plants.
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Affiliation(s)
- Lei He
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Qi Wu
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Ye Jin
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Ye Fan
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Huazhong Shi
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, United States
| | - Yizhong Wang
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
| | - Wannian Yang
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, China
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21
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Ma Z, Li M, Zhang H, Zhao B, Liu Z, Duan S, Meng X, Li G, Guo X. Alternative Splicing of TaHsfA2-7 Is Involved in the Improvement of Thermotolerance in Wheat. Int J Mol Sci 2023; 24:ijms24021014. [PMID: 36674529 PMCID: PMC9861123 DOI: 10.3390/ijms24021014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/29/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
High temperature has severely affected plant growth and development, resulting in reduced production of crops worldwide, especially wheat. Alternative splicing (AS), a crucial post-transcriptional regulatory mechanism, is involved in the growth and development of eukaryotes and the adaptation to environmental changes. Previous transcriptome data suggested that heat shock transcription factor (Hsf) TaHsfA2-7 may form different transcripts by AS. However, it remains unclear whether this post-transcriptional regulatory mechanism of TaHsfA2-7 is related to thermotolerance in wheat (Triticum aestivum). Here, we identified a novel splice variant, TaHsfA2-7-AS, which was induced by high temperature and played a positive role in thermotolerance regulation in wheat. Moreover, TaHsfA2-7-AS is predicted to encode a small truncated TaHsfA2-7 isoform, retaining only part of the DNA-binding domain (DBD). TaHsfA2-7-AS is constitutively expressed in various tissues of wheat. Notably, the expression level of TaHsfA2-7-AS is significantly up-regulated by heat shock (HS) during flowering and grain-filling stages in wheat. Further studies showed that TaHsfA2-7-AS was localized in the nucleus but lacked transcriptional activation activity. Ectopic expression of TaHsfA2-7-AS in yeast exhibited improved thermotolerance. Compared to non-transgenic plants, overexpression of TaHsfA2-7-AS in Arabidopsis results in enhanced tolerance to heat stress. Simultaneously, we also found that TaHsfA1 is directly involved in the transcriptional regulation of TaHsfA2-7 and TaHsfA2-7-AS. In summary, our findings demonstrate the function of TaHsfA2-7-AS splicing variant in response to heat stress and establish a link between regulatory mechanisms of AS and the improvement of thermotolerance in wheat.
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Affiliation(s)
- Zhenyu Ma
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Mingyue Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Huaning Zhang
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Baihui Zhao
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- College of Life Sciences, Hebei Normal University, Shijiazhuang 050024, China
| | - Zihui Liu
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Shuonan Duan
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
| | - Xiangzhao Meng
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- Correspondence: (X.M.); (G.L.)
| | - Guoliang Li
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
- Correspondence: (X.M.); (G.L.)
| | - Xiulin Guo
- Institute of Biotechnology and Food Science, Hebei Academy of Agriculture and Forestry Sciences/Plant Genetic Engineering Center of Hebei Province, Shijiazhuang 050051, China
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22
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Hussain SS, Abbas M, Abbas S, Wei M, El-Sappah AH, Sun Y, Li Y, Ragauskas AJ, Li Q. Alternative splicing: transcriptional regulatory network in agroforestry. FRONTIERS IN PLANT SCIENCE 2023; 14:1158965. [PMID: 37123829 PMCID: PMC10132464 DOI: 10.3389/fpls.2023.1158965] [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: 02/04/2023] [Accepted: 03/13/2023] [Indexed: 05/03/2023]
Abstract
Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNAir) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.
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Affiliation(s)
- Syed Sarfaraz Hussain
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Manzar Abbas
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
| | - Sammar Abbas
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing, China
| | - Mingke Wei
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, Sichuan, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Yuhan Sun
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Yun Li
- State Key Laboratory of Tree Genetics and Breeding, Engineering Technology Research Center of Black Locust of National Forestry and Grassland Administration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Arthur J. Ragauskas
- Department of Forestry, Wildlife, and Fisheries, Center for Renewable Carbon, University of Tennessee Institute of Agriculture, Knoxville, TN, United States
- Joint Institute for Biological Science, Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, United States
- Department of Chemical and Biomolecular Engineering, The University of Tennessee-Knoxville, Knoxville, TN, United States
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
| | - Quanzi Li
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China
- *Correspondence: Yun Li, ; Arthur J. Ragauskas, ; Quanzi Li,
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23
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Lasorella C, Fortunato S, Dipierro N, Jeran N, Tadini L, Vita F, Pesaresi P, de Pinto MC. Chloroplast-localized GUN1 contributes to the acquisition of basal thermotolerance in Arabidopsis thaliana. FRONTIERS IN PLANT SCIENCE 2022; 13:1058831. [PMID: 36618674 PMCID: PMC9813751 DOI: 10.3389/fpls.2022.1058831] [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: 09/30/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Heat stress (HS) severely affects different cellular compartments operating in metabolic processes and represents a critical threat to plant growth and yield. Chloroplasts are crucial for heat stress response (HSR), signaling to the nucleus the environmental challenge and adjusting metabolic and biosynthetic functions accordingly. GENOMES UNCOUPLED 1 (GUN1), a chloroplast-localized protein, has been recognized as one of the main players of chloroplast retrograde signaling. Here, we investigate HSR in Arabidopsis wild-type and gun1 plantlets subjected to 2 hours of HS at 45°C. In wild-type plants, Reactive Oxygen Species (ROS) accumulate promptly after HS, contributing to transiently oxidize the cellular environment and acting as signaling molecules. After 3 hours of physiological recovery at growth temperature (22°C), the induction of enzymatic and non-enzymatic antioxidants prevents oxidative damage. On the other hand, gun1 mutants fail to induce the oxidative burst immediately after HS and accumulate ROS and oxidative damage after 3 hours of recovery at 22°C, thus resulting in enhanced sensitivity to HS. These data suggest that GUN1 is required to oxidize the cellular environment, participating in the acquisition of basal thermotolerance through the redox-dependent plastid-to-nucleus communication.
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Affiliation(s)
- Cecilia Lasorella
- Department of Bioscience, Biotechnology and Environment University of Bari Aldo Moro, Bari, Italy
| | - Stefania Fortunato
- Department of Bioscience, Biotechnology and Environment University of Bari Aldo Moro, Bari, Italy
| | - Nunzio Dipierro
- Department of Bioscience, Biotechnology and Environment University of Bari Aldo Moro, Bari, Italy
| | - Nicolaj Jeran
- Department of Biosciences, University of Milano, Milano, Italy
| | - Luca Tadini
- Department of Biosciences, University of Milano, Milano, Italy
| | - Federico Vita
- Department of Bioscience, Biotechnology and Environment University of Bari Aldo Moro, Bari, Italy
| | - Paolo Pesaresi
- Department of Biosciences, University of Milano, Milano, Italy
| | - Maria Concetta de Pinto
- Department of Bioscience, Biotechnology and Environment University of Bari Aldo Moro, Bari, Italy
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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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Jian G, Mo Y, Hu Y, Huang Y, Ren L, Zhang Y, Hu H, Zhou S, Liu G, Guo J, Ling Y. Variety-Specific Transcriptional and Alternative Splicing Regulations Modulate Salt Tolerance in Rice from Early Stage of Stress. RICE (NEW YORK, N.Y.) 2022; 15:56. [PMID: 36326968 PMCID: PMC9633917 DOI: 10.1186/s12284-022-00599-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 10/11/2022] [Indexed: 06/16/2023]
Abstract
Salt stress poses physiological drought, ionic toxicity and oxidative stress to plants, which causes premature senescence and death of the leaves if the stress sustained. Salt tolerance varied between different rice varieties, but how different rice varieties respond at the early stage of salt stress has been seldom studied comprehensively. By employing third generation sequencing technology, we compared gene expressional changes in leaves of three rice varieties that varied in their level of tolerance after salt stress treatment for 6 h. Commonly up-regulated genes in all rice varieties were related to water shortage response and carbon and amino acids metabolism at the early stage of salt stress, while reactive oxygen species cleavage genes were induced more in salt-tolerant rice. Unexpectedly, genes involved in chloroplast development and photosynthesis were more significantly down-regulated in the two salt tolerant rice varieties 'C34' and 'Nona Bokra'. At the same time, genes coding ribosomal protein were suppressed to a more severe extent in the salt-sensitive rice variety 'IR29'. Interestingly, not only variety-specific gene transcriptional regulation, but also variety-specific mRNA alternative splicing, on both coding and long-noncoding genes, were found at the early stage of salt stress. In summary, differential regulation in gene expression at both transcriptional and post-transcriptional levels, determine and fine-tune the observed response in level of damage in leaves of specific rice genotypes at early stage of salt stress.
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Affiliation(s)
- Guihua Jian
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yan Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yongxiang Huang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Lei Ren
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Yueqin Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Hanqiao Hu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China
| | - Shuangxi Zhou
- Department of Biological Sciences, Macquarie University, North Ryde, NSW, 2019, Australia
| | - Gang Liu
- Hubei Key Laboratory of Food Crop Germplasm and Genetic Improvement, Food Crops Institute, Hubei Academy of Agricultural Sciences, Wuhan, 430064, People's Republic of China
| | - Jianfu Guo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, People's Republic of China.
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26
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Gao Z, Zhou Y, He Y. Molecular epigenetic mechanisms for the memory of temperature stresses in plants. J Genet Genomics 2022; 49:991-1001. [PMID: 35870761 DOI: 10.1016/j.jgg.2022.07.004] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 07/13/2022] [Accepted: 07/13/2022] [Indexed: 12/29/2022]
Abstract
The sessile plants encounter various stresses; some are prolonged, whereas some others are recurrent. Temperature is crucial for plant growth and development, and plants often encounter adverse high temperature fluctuations (heat stresses) as well as prolonged cold exposure such as seasonal temperature drops in winter when grown in temperate regions. Many plants can remember past temperature stresses to get adapted to adverse local temperature changes to ensure survival and/or reproductive success. Here, we summarize chromatin-based mechanisms underlying acquired thermotolerance or thermomemory in plants and review recent progresses on molecular epigenetic understanding of 'remembering of prolonged cold in winter' or vernalization, a process critical for various over-wintering plants to acquire competence to flower in the coming spring. In addition, perspectives on future study in temperature stress memories of economically-important crops are discussed.
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Affiliation(s)
- Zhaoxu Gao
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yue Zhou
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China
| | - Yuehui He
- State Key Laboratory of Protein and Plant Gene Research, School of Advanced Agricultural Sciences, Peking-Tsinghua Center for Life Sciences, Peking University, Beijing 100871, China; Peking University Institute of Advanced Agricultural Sciences, Weifang, Shandong 261325, China.
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27
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Roces V, Lamelas L, Valledor L, Carbó M, Cañal MJ, Meijón M. Integrative analysis in Pinus revealed long-term heat stress splicing memory. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:998-1013. [PMID: 36151923 PMCID: PMC9828640 DOI: 10.1111/tpj.15990] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 08/31/2022] [Accepted: 09/15/2022] [Indexed: 05/09/2023]
Abstract
Due to the current climate change, many studies have described main drivers in abiotic stress. Recent findings suggest that alternative splicing (AS) has a critical role in controlling plant responses to high temperature. AS is a mechanism that allows organisms to create an assortment of RNA transcripts and proteins using a single gene. However, the most important roles of AS in stress could not be rigorously addressed because research has been focused on model species, covering only a narrow phylogenetic and lifecycle spectrum. Thus, AS degree of diversification among more dissimilar taxa in heat response is still largely unknown. To fill this gap, the present study employs a systems biology approach to examine how the AS landscape responds to and 'remembers' heat stress in conifers, a group which has received little attention even though their position can solve key evolutionary questions. Contrary to angiosperms, we found that potential intron retention may not be the most prevalent type of AS. Furthermore, our integrative analysis with metabolome and proteome data places splicing as the main source of variation during the response. Finally, we evaluated possible acquired long-term splicing memory in a diverse subset of events, and although this mechanism seems to be conserved in seed plants, AS dynamics are divergent. These discoveries reveal the particular way of remembering past temperature changes in long-lived plants and open the door to include species with unique features to determine the extent of conservation in gene expression regulation.
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Affiliation(s)
- Víctor Roces
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of AsturiasUniversity of OviedoOviedoAsturiasSpain
| | - Laura Lamelas
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of AsturiasUniversity of OviedoOviedoAsturiasSpain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of AsturiasUniversity of OviedoOviedoAsturiasSpain
| | - María Carbó
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of AsturiasUniversity of OviedoOviedoAsturiasSpain
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of AsturiasUniversity of OviedoOviedoAsturiasSpain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, Faculty of Biology and Biotechnology Institute of AsturiasUniversity of OviedoOviedoAsturiasSpain
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28
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Rodriguez Gallo MC, Li Q, Mehta D, Uhrig RG. Genome-scale analysis of Arabidopsis splicing-related protein kinase families reveals roles in abiotic stress adaptation. BMC PLANT BIOLOGY 2022; 22:496. [PMID: 36273172 PMCID: PMC9587599 DOI: 10.1186/s12870-022-03870-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/04/2022] [Indexed: 05/24/2023]
Abstract
Nearly 60 - 80 % of intron-containing plant genes undergo alternative splicing in response to either stress or plant developmental cues. RNA splicing is performed by a large ribonucleoprotein complex called the spliceosome in conjunction with associated subunits such as serine arginine (SR) proteins, all of which undergo extensive phosphorylation. In plants, there are three main protein kinase families suggested to phosphorylate core spliceosome subunits and related splicing factors based on orthology to human splicing-related kinases: the SERINE/ARGININE PROTEIN KINASES (SRPK), ARABIDOPSIS FUS3 COMPLEMENT (AFC), and Pre-mRNA PROCESSING FACTOR 4 (PRP4K) protein kinases. To better define the conservation and role(s) of these kinases in plants, we performed a genome-scale analysis of the three families across photosynthetic eukaryotes, followed by extensive transcriptomic and bioinformatic analysis of all Arabidopsis thaliana SRPK, AFC, and PRP4K protein kinases to elucidate their biological functions. Unexpectedly, this revealed the existence of SRPK and AFC phylogenetic groups with distinct promoter elements and patterns of transcriptional response to abiotic stress, while PRP4Ks possess no phylogenetic sub-divisions, suggestive of functional redundancy. We also reveal splicing-related kinase families are both diel and photoperiod regulated, implicating different orthologs as discrete time-of-day RNA splicing regulators. This foundational work establishes a number of new hypotheses regarding how reversible spliceosome phosphorylation contributes to both diel plant cell regulation and abiotic stress adaptation in plants.
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Affiliation(s)
- M C Rodriguez Gallo
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - Q Li
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - D Mehta
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada
| | - R G Uhrig
- Department of Biological Sciences, University of Alberta, Edmonton, AB, T6G 2E9, Canada.
- Department of Biochemistry, University of Alberta, Edmonton, AB, Canada.
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29
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Comparative Analysis of Environment-Responsive Alternative Splicing in the Inflorescences of Cultivated and Wild Tomato Species. Int J Mol Sci 2022; 23:ijms231911585. [PMID: 36232886 PMCID: PMC9569760 DOI: 10.3390/ijms231911585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 09/22/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Cultivated tomato (Solanum lycopersicum) is bred for fruit production in optimized environments, in contrast to harsh environments where their ancestral relatives thrive. The process of domestication and breeding has profound impacts on the phenotypic plasticity of plant development and the stress response. Notably, the alternative splicing (AS) of precursor message RNA (pre-mRNA), which is one of the major factors contributing to transcriptome complexity, is responsive to developmental cues and environmental change. To determine a possible association between AS events and phenotypic plasticity, we investigated environment-responsive AS events in the inflorescences of cultivated tomato and its ancestral relatives S. pimpinellifolium. Despite that similar AS frequencies were detected in the cultivated tomato variety Moneymaker and two S. pimpinellifolium accessions under the same growth conditions, 528 genes including splicing factors showed differential splicing in the inflorescences of plants grown in open fields and plastic greenhouses in the Moneymaker variety. In contrast, the two S. pimpinellifolium accessions, LA1589 and LA1781, had 298 and 268 genes showing differential splicing, respectively. Moreover, seven heat responsive genes showed opposite expression patterns in response to changing growth conditions between Moneymaker and its ancestral relatives. Accordingly, there were eight differentially expressed splice variants from genes involved in heat response in Moneymaker. Our results reveal distinctive features of AS events in the inflorescences between cultivated tomato and its ancestral relatives, and show that AS regulation in response to environmental changes is genotype dependent.
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30
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Chen S, Mo Y, Zhang Y, Zhu H, Ling Y. Insights into sweet potato SR proteins: from evolution to species-specific expression and alternative splicing. PLANTA 2022; 256:72. [PMID: 36083517 DOI: 10.1007/s00425-022-03965-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/19/2022] [Indexed: 06/15/2023]
Abstract
SR proteins from sweet potato have conserved functional domains and similar gene structures as that of Arabidopsis and rice in general. However, expression patterns and alternative splicing regulations of SR genes from different species have changed under stresses. Novel alternative splicing regulations were found in sweet potato SR genes. Serine/arginine-rich (SR) proteins play important roles in plant development and stress response by regulating the pre-mRNA splicing process. However, SR proteins have not been identified so far from an important crop sweet potato. Through bioinformatics analysis, our study identified 24 SR proteins from sweet potato, with comprehensively analyzing of protein characteristics, gene structure, chromosome localization, and cis-acting elements in promotors. Salt, heat, and mimic drought stresses triggered extensive but different expressional regulations on sweet potato SR genes. Interestingly, heat stress caused the most active disturbances in both gene transcription and pre-mRNA alternative splicing (AS). Tissue and species-specific transcriptional and pre-mRNA AS regulations in response to stresses were found in sweet potato, in comparison with Arabidopsis and rice. Moreover, novel patterns of pre-mRNA alternative splicing were found in SR proteins from sweet potato. Our study provided an insight into similarities and differences of SR proteins in different plant species from gene sequences to gene structures and stress responses, indicating SR proteins may regulate their downstream genes differently between different species and tissues by varied transcriptional and pre-mRNA AS regulations.
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Affiliation(s)
- Shanlan Chen
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yujian Mo
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yingjie Zhang
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Hongbao Zhu
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China
| | - Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, People's Republic of China.
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31
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Liu Y, Cai Y, Li Y, Zhang X, Shi N, Zhao J, Yang H. Dynamic changes in the transcriptome landscape of Arabidopsis thaliana in response to cold stress. FRONTIERS IN PLANT SCIENCE 2022; 13:983460. [PMID: 36110360 PMCID: PMC9468617 DOI: 10.3389/fpls.2022.983460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 08/04/2022] [Indexed: 06/15/2023]
Abstract
Plants must reprogram gene expression to adapt constantly changing environmental temperatures. With the increased occurrence of extremely low temperatures, the negative effects on plants, especially on growth and development, from cold stress are becoming more and more serious. In this research, strand-specific RNA sequencing (ssRNA-seq) was used to explore the dynamic changes in the transcriptome landscape of Arabidopsis thaliana exposed to cold temperatures (4°C) at different times. In total, 7,623 differentially expressed genes (DEGs) exhibited dynamic temporal changes during the cold treatments. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis showed that the DEGs were enriched in cold response, secondary metabolic processes, photosynthesis, glucosinolate biosynthesis, and plant hormone signal transduction pathways. Meanwhile, long non-coding RNAs (lncRNAs) were identified after the assembly of the transcripts, from which 247 differentially expressed lncRNAs (DElncRNAs) and their potential target genes were predicted. 3,621 differentially alternatively spliced (DAS) genes related to RNA splicing and spliceosome were identified, indicating enhanced transcriptome complexity due to the alternative splicing (AS) in the cold. In addition, 739 cold-regulated transcription factors (TFs) belonging to 52 gene families were identified as well. This research analyzed the dynamic changes of the transcriptome landscape in response to cold stress, which reveals more complete transcriptional patterns during short- and long-term cold treatment and provides new insights into functional studies of that how plants are affected by cold stress.
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Affiliation(s)
- Yue Liu
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yajun Cai
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Yanzhuo Li
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Xiaoling Zhang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Nan Shi
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Jingze Zhao
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
| | - Hongchun Yang
- State Key Laboratory of Hybrid Rice, College of Life Sciences, Wuhan University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- RNA Institute, Wuhan University, Wuhan, China
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32
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The intersection between circadian and heat-responsive regulatory networks controls plant responses to increasing temperatures. Biochem Soc Trans 2022; 50:1151-1165. [PMID: 35758233 PMCID: PMC9246330 DOI: 10.1042/bst20190572] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 06/02/2022] [Accepted: 06/06/2022] [Indexed: 11/17/2022]
Abstract
Increasing temperatures impact plant biochemistry, but the effects can be highly variable. Both external and internal factors modulate how plants respond to rising temperatures. One such factor is the time of day or season the temperature increase occurs. This timing significantly affects plant responses to higher temperatures altering the signaling networks and affecting tolerance levels. Increasing overlaps between circadian signaling and high temperature responses have been identified that could explain this sensitivity to the timing of heat stress. ELF3, a circadian clock component, functions as a thermosensor. ELF3 regulates thermoresponsive hypocotyl elongation in part through its cellular localization. The temperature sensitivity of ELF3 depends on the length of a polyglutamine region, explaining how plant temperature responses vary between species. However, the intersection between the circadian system and increased temperature stress responses is pervasive and extends beyond this overlap in thermosensing. Here, we review the network responses to increased temperatures, heat stress, and the impacts on the mechanisms of gene expression from transcription to translation, highlighting the intersections between the elevated temperature and heat stress response pathways and circadian signaling, focusing on the role of ELF3 as a thermosensor.
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Rosenkranz RRE, Ullrich S, Löchli K, Simm S, Fragkostefanakis S. Relevance and Regulation of Alternative Splicing in Plant Heat Stress Response: Current Understanding and Future Directions. FRONTIERS IN PLANT SCIENCE 2022; 13:911277. [PMID: 35812973 PMCID: PMC9260394 DOI: 10.3389/fpls.2022.911277] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 05/26/2022] [Indexed: 05/26/2023]
Abstract
Alternative splicing (AS) is a major mechanism for gene expression in eukaryotes, increasing proteome diversity but also regulating transcriptome abundance. High temperatures have a strong impact on the splicing profile of many genes and therefore AS is considered as an integral part of heat stress response. While many studies have established a detailed description of the diversity of the RNAome under heat stress in different plant species and stress regimes, little is known on the underlying mechanisms that control this temperature-sensitive process. AS is mainly regulated by the activity of splicing regulators. Changes in the abundance of these proteins through transcription and AS, post-translational modifications and interactions with exonic and intronic cis-elements and core elements of the spliceosomes modulate the outcome of pre-mRNA splicing. As a major part of pre-mRNAs are spliced co-transcriptionally, the chromatin environment along with the RNA polymerase II elongation play a major role in the regulation of pre-mRNA splicing under heat stress conditions. Despite its importance, our understanding on the regulation of heat stress sensitive AS in plants is scarce. In this review, we summarize the current status of knowledge on the regulation of AS in plants under heat stress conditions. We discuss possible implications of different pathways based on results from non-plant systems to provide a perspective for researchers who aim to elucidate the molecular basis of AS under high temperatures.
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Affiliation(s)
| | - Sarah Ullrich
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Karin Löchli
- Molecular Cell Biology of Plants, Goethe University Frankfurt, Frankfurt, Germany
| | - Stefan Simm
- Institute of Bioinformatics, University Medicine Greifswald, Greifswald, Germany
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Nair AU, Bhukya DPN, Sunkar R, Chavali S, Allu AD. Molecular basis of priming-induced acquired tolerance to multiple abiotic stresses in plants. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3355-3371. [PMID: 35274680 DOI: 10.1093/jxb/erac089] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/04/2022] [Indexed: 05/04/2023]
Abstract
The growth, survival, and productivity of plants are constantly challenged by diverse abiotic stresses. When plants are exposed to stress for the first time, they can capture molecular information and store it as a form of memory, which enables them to competently and rapidly respond to subsequent stress(es). This process is referred to as a priming-induced or acquired stress response. In this review, we discuss how (i) the storage and retrieval of the information from stress memory modulates plant physiological, cellular, and molecular processes in response to subsequent stress(es), (ii) the intensity, recurrence, and duration of priming stimuli influences the outcomes of the stress response, and (iii) the varying responses at different plant developmental stages. We highlight current understanding of the distinct and common molecular processes manifested at the epigenetic, (post-)transcriptional, and post-translational levels mediated by stress-associated molecules and metabolites, including phytohormones. We conclude by emphasizing how unravelling the molecular circuitry underlying diverse priming-stimuli-induced stress responses could propel the use of priming as a management practice for crop plants. This practice, in combination with precision agriculture, could aid in increasing yield quantity and quality to meet the rapidly rising demand for food.
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Affiliation(s)
- Akshay U Nair
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Durga Prasad Naik Bhukya
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Ramanjulu Sunkar
- Department of Biochemistry and Molecular Biology, Oklahoma State University, Stillwater, OK 74078, USA
| | - Sreenivas Chavali
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
| | - Annapurna Devi Allu
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati 517507, Andhra Pradesh, India
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35
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Plant DNA Methylation Responds to Nutrient Stress. Genes (Basel) 2022; 13:genes13060992. [PMID: 35741754 PMCID: PMC9222553 DOI: 10.3390/genes13060992] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/23/2022] [Accepted: 05/30/2022] [Indexed: 12/16/2022] Open
Abstract
Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.
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36
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Jo SH, Park HJ, Lee A, Jung H, Park JM, Kwon SY, Kim HS, Lee HJ, Kim YS, Jung C, Cho HS. The Arabidopsis cyclophilin CYP18-1 facilitates PRP18 dephosphorylation and the splicing of introns retained under heat stress. THE PLANT CELL 2022; 34:2383-2403. [PMID: 35262729 PMCID: PMC9134067 DOI: 10.1093/plcell/koac084] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 03/05/2022] [Indexed: 05/13/2023]
Abstract
In plants, heat stress induces changes in alternative splicing, including intron retention; these events can rapidly alter proteins or downregulate protein activity, producing nonfunctional isoforms or inducing nonsense-mediated decay of messenger RNA (mRNA). Nuclear cyclophilins (CYPs) are accessory proteins in the spliceosome complexes of multicellular eukaryotes. However, whether plant CYPs are involved in pre-mRNA splicing remain unknown. Here, we found that Arabidopsis thaliana CYP18-1 is necessary for the efficient removal of introns that are retained in response to heat stress during germination. CYP18-1 interacts with Step II splicing factors (PRP18a, PRP22, and SWELLMAP1) and associates with the U2 and U5 small nuclear RNAs in response to heat stress. CYP18-1 binds to phospho-PRP18a, and increasing concentrations of CYP18-1 are associated with increasing dephosphorylation of PRP18a. Furthermore, interaction and protoplast transfection assays revealed that CYP18-1 and the PP2A-type phosphatase PP2A B'η co-regulate PRP18a dephosphorylation. RNA-seq and RT-qPCR analysis confirmed that CYP18-1 is essential for splicing introns that are retained under heat stress. Overall, we reveal the mechanism of action by which CYP18-1 activates the dephosphorylation of PRP18 and show that CYP18-1 is crucial for the efficient splicing of retained introns and rapid responses to heat stress in plants.
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Affiliation(s)
- Seung Hee Jo
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Hyun Ji Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Areum Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Haemyeong Jung
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Biosystems and Bioengineering, KRIBB School of Biotechnology,
Korea University of Science and Technology, Daejeon 34113, Korea
| | - Jeong Mee Park
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Suk-Yoon Kwon
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyun-Soon Kim
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
| | - Hyo-Jun Lee
- Plant Systems Engineering Research Center, Korea Research Institute of
Bioscience and Biotechnology (KRIBB), Daejeon 34141, Korea
- Department of Functional Genomics, KRIBB School of Bioscience, University
of Science and Technology, Daejeon 34113, Korea
| | - Youn-Sung Kim
- Department of Biotechnology, NongWoo
Bio, Anseong 17558, Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology
Institute/Green Bio Science and Technology, Seoul National University,
Pyeongchang 25354, Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major
in Global Smart Farm, College of Agriculture and Life Sciences, Seoul National
University, Seoul 08826, Korea
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Ding Y, Yang S. Surviving and thriving: How plants perceive and respond to temperature stress. Dev Cell 2022; 57:947-958. [PMID: 35417676 DOI: 10.1016/j.devcel.2022.03.010] [Citation(s) in RCA: 86] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 02/21/2022] [Accepted: 03/17/2022] [Indexed: 12/11/2022]
Abstract
The dramatic temperature fluctuations spurred by climate change inhibit plant growth and threaten crop productivity. Unraveling how plants defend themselves against temperature-stress-induced cellular impairment is not only a crucial fundamental issue but is also of critical importance for agricultural sustainability and food security. Here, we review recent developments in elucidating the molecular mechanisms used by plants to sense and respond to cold and heat stress at multiple levels. We also describe the trade-off between plant growth and responses to high and low temperatures. Finally, we discuss possible strategies that could be used to engineer temperature-stress-tolerant, high-yielding crops.
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Affiliation(s)
- Yanglin Ding
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Shuhua Yang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
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38
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Dastogeer KMG, Zahan MI, Rhaman MS, Sarker MSA, Chakraborty A. Microbe-Mediated Thermotolerance in Plants and Pertinent Mechanisms- A Meta-Analysis and Review. Front Microbiol 2022; 13:833566. [PMID: 35330772 PMCID: PMC8940538 DOI: 10.3389/fmicb.2022.833566] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2021] [Accepted: 02/04/2022] [Indexed: 01/10/2023] Open
Abstract
Microbial symbionts can mediate plant stress responses by enhancing thermal tolerance, but less attention has been paid to measuring these effects across plant-microbe studies. We performed a meta-analysis of published studies as well as discussed with relevant literature to determine how the symbionts influence plant responses under non-stressed versus thermal-stressed conditions. As compared to non-inoculated plants, inoculated plants had significantly higher biomass and photosynthesis under heat stress conditions. A significantly decreased accumulation of malondialdehyde (MDA) and hydrogen peroxide (H2O2) indicated a lower oxidation level in the colonized plants, which was also correlated with the higher activity of catalase, peroxidase, glutathione reductase enzymes due to microbial colonization under heat stress. However, the activity of superoxide dismutase, ascorbate oxidase, ascorbate peroxidase, and proline were variable. Our meta-analysis revealed that microbial colonization influenced plant growth and physiology, but their effects were more noticeable when their host plants were exposed to high-temperature stress than when they grew under ambient temperature conditions. We discussed the mechanisms of microbial conferred plant thermotolerance, including at the molecular level based on the available literature. Further, we highlighted and proposed future directions toward exploring the effects of symbionts on the heat tolerances of plants for their implications in sustainable agricultural production.
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Affiliation(s)
| | - Mst. I. Zahan
- Scientific Officer (Breeding Division), Bangladesh Sugarcrop Research Institute, Pabna, Bangladesh
| | - Mohammad S. Rhaman
- Department of Seed Science and Technology, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Mohammad S. A. Sarker
- Basic and Applied Research on Jute Project, Bangladesh Jute Research Institute (BJRI), Dhaka, Bangladesh
| | - Anindita Chakraborty
- Department of Genetic Engineering and Biotechnology, Shahjalal University of Science and Technology, Sylhet, Bangladesh
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Sun J, Liu Z, Quan J, Li L, Zhao G, Lu J. RNA-seq Analysis Reveals Alternative Splicing Under Heat Stress in Rainbow Trout (Oncorhynchus mykiss). MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:5-17. [PMID: 34787764 DOI: 10.1007/s10126-021-10082-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 11/03/2021] [Indexed: 06/13/2023]
Abstract
Rainbow trout (Oncorhynchus mykiss) is one of the most economically important cold-water farmed species in the world, and transcriptomic studies in response to heat stress have been conducted and will be studied in depth. Alternative splicing (AS), a post-transcriptional regulatory process that regulates gene expression and increases proteomic diversity, is still poorly understood in rainbow trout under heat stress. In the present study, 18,623 alternative splicing events were identified from 9936 genes using RNA transcriptome sequencing technology (RNA-Seq) and genomic information. A total of 2731 differential alternative splicing (DAS) events were found among 2179 differentially expressed genes (DEGs). Gene ontology analysis revealed that the DEGs were mainly enriched in cellular metabolic process, cell part, and organic cyclic compound binding under heat stress. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis displayed that the DEGs were enriched for 39 pathways, and some key pathways, such as lysine degradation, are involved in the regulation of heat stress in liver tissues of rainbow trout. The results were validated by qRT-PCR, confirming reliability of our bioinformatics analysis.
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Affiliation(s)
- Jun Sun
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Zhe Liu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China.
| | - Jinqiang Quan
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Lanlan Li
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Guiyan Zhao
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
| | - Junhao Lu
- College of Animal Science & Technology, Gansu Province, Gansu Agricultural University, No. 1 Yingmen Village, Anning District, Lanzhou, 730070, People's Republic of China
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40
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Post-translational modification: a strategic response to high temperature in plants. ABIOTECH 2022; 3:49-64. [PMID: 36304199 PMCID: PMC9590526 DOI: 10.1007/s42994-021-00067-w] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/22/2021] [Indexed: 11/21/2022]
Abstract
With the increasing global warming, high-temperature stress is affecting plant growth and development with greater frequency. Therefore, an increasing number of studies examining the mechanism of temperature response contribute to a more optimal understanding of plant growth under environmental pressure. Post-translational modification (PTM) provides the rapid reconnection of transcriptional programs including transcription factors and signaling proteins. It is vital that plants quickly respond to changes in the environment in order to survive under stressful situations. Herein, we discuss several types of PTMs that occur in response to warm-temperature and high-temperature stress, including ubiquitination, SUMOylation, phosphorylation, histone methylation, and acetylation. This review provides a valuable resolution to this issue to enable increased crop productivity at high temperatures.
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41
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Qureshi MK, Gawroński P, Munir S, Jindal S, Kerchev P. Hydrogen peroxide-induced stress acclimation in plants. Cell Mol Life Sci 2022; 79:129. [PMID: 35141765 PMCID: PMC11073338 DOI: 10.1007/s00018-022-04156-x] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 02/06/2023]
Abstract
Among all reactive oxygen species (ROS), hydrogen peroxide (H2O2) takes a central role in regulating plant development and responses to the environment. The diverse role of H2O2 is achieved through its compartmentalized synthesis, temporal control exerted by the antioxidant machinery, and ability to oxidize specific residues of target proteins. Here, we examine the role of H2O2 in stress acclimation beyond the well-studied transcriptional reprogramming, modulation of plant hormonal networks and long-distance signalling waves by highlighting its global impact on the transcriptional regulation and translational machinery.
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Affiliation(s)
- Muhammad Kamran Qureshi
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Bosan road, Multan, 60800, Pakistan
| | - Piotr Gawroński
- Department of Plant Genetics, Breeding and Biotechnology, Institute of Biology, Warsaw, University of Life Sciences, Nowoursynowska 159, 02-776, Warsaw, Poland
| | - Sana Munir
- Department of Plant Breeding and Genetics, Faculty of Agricultural Sciences and Technology, Bahauddin Zakariya University, Bosan road, Multan, 60800, Pakistan
| | - Sunita Jindal
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic
| | - Pavel Kerchev
- Department of Molecular Biology and Radiobiology, Faculty of AgriSciences, Mendel University in Brno, Zemědělská 3, 613 00, Brno, Czech Republic.
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42
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Lamelas L, Valledor L, López-Hidalgo C, Cañal MJ, Meijón M. Nucleus and chloroplast: A necessary understanding to overcome heat stress in Pinus radiata. PLANT, CELL & ENVIRONMENT 2022; 45:446-458. [PMID: 34855991 DOI: 10.1111/pce.14238] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 11/23/2021] [Accepted: 11/23/2021] [Indexed: 06/13/2023]
Abstract
The recovery and maintenance of plant homeostasis under stressful environments are complex processes involving organelle crosstalk for a coordinated cellular response. Here, we revealed through nuclear and chloroplast subcellular proteomics, biochemical cell profiles and targeted transcriptomics how chloroplasts and nuclei developed their responses under increased temperatures in a long-lived species (Pinus radiata). Parallel to photosynthetic impairment and reactive oxygen species production in the chloroplast, a DNA damage response was triggered in the nucleus followed by an altered chromatin conformation. In addition, in the nuclei, we found several proteins, such as HEMERA or WHIRLY, which change their locations from the chloroplasts to the nuclei carrying the stress message. Additionally, our data showed a deep rearrangement of RNA metabolism in both organelles, revealing microRNAs and AGO1 as potential regulators of the acclimation mechanisms. Altogether, our study highlights the synchronisation among the different stages required for thermotolerance acquisition in P. radiata, pointing out the role of chromatin conformation and posttranscriptional gene regulation in overcoming heat stress and assuring plant survival for the following years.
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Affiliation(s)
- Laura Lamelas
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Luis Valledor
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Cristina López-Hidalgo
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - María Jesús Cañal
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
| | - Mónica Meijón
- Plant Physiology, Department of Organisms and Systems Biology, University of Oviedo, Biotechnology Institute of Asturias, Oviedo, Asturias, Spain
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43
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Balazadeh S. A 'hot' cocktail: The multiple layers of thermomemory in plants. CURRENT OPINION IN PLANT BIOLOGY 2022; 65:102147. [PMID: 34861588 DOI: 10.1016/j.pbi.2021.102147] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 10/21/2021] [Accepted: 10/23/2021] [Indexed: 06/13/2023]
Abstract
Heat stress (HS) caused by above-optimal temperatures adversely affects plants' growth and development and diminishes crop yields. In natural and agricultural environments, these stresses are often transient but recurrent and may progressively increase in severity over time. In addition to the inherent ability to cope with a single HS event, plants have evolved mechanisms that enhance their capacity to survive and reproduce under such conditions. This involves the establishment of a molecular 'thermomemory' after moderate HS that allows them to withstand a later - and possibly more extreme - HS event. Here, I summarize the current understanding of the molecular and biochemical mechanisms underlying thermomemory across multiple cellular levels and discuss aspects that require further attention.
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Affiliation(s)
- Salma Balazadeh
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476 Potsdam-Golm, Germany; Leiden University, PO Box 9500, 2300 RA, Leiden, the Netherlands.
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44
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Mancini E, Garcia-Molina A. Analysis of Alternative Splicing During the Combinatorial Response to Simultaneous Copper and Iron Deficiency in Arabidopsis Reveals Differential Events in Genes Involved in Amino Acid Metabolism. FRONTIERS IN PLANT SCIENCE 2022; 13:827828. [PMID: 35173758 PMCID: PMC8841432 DOI: 10.3389/fpls.2022.827828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Copper (Cu) and iron (Fe) constitute fundamental nutrients for plant biology but are often limited due to low bioavailability. Unlike responses to single Cu or Fe deprivation, the consequences of simultaneous Cu and Fe deficiency have not yet been fully deciphered. Previously, it was demonstrated that Cu and Fe deficiency applied in combination imposes transcriptome, proteome, and metabolome changes different from those triggered under each deficiency individually. Here, we evaluated the effect of alternative splicing (AS) on the transcriptome of rosette leaves under single and simultaneous Cu and Fe deficiency. Differentially spliced genes (DSGs) and differentially expressed genes (DEGs) coincided in number (2,600 approx.) although the overlapping fraction was minimal (15%). Functional annotation of changes exclusively detected under simultaneous Cu and Fe deficiency revealed that DEGs participated in general stress responses and translation, while DSGs were involved in metabolic reactions, especially amino acid biosynthesis. Interestingly, transcripts encoding central features for tryptophan (Trp) and asparagine (Asn) synthesis - two significantly altered metabolites under simultaneous Cu and Fe deficiency - underwent exclusive intron retention events under the double deficiency. However, transcript and protein amounts for these enzymes did not correlate with Trp and Asn concentration. In consequence, we propose that AS might act as a regulatory mechanism to modify the stability and/or functionality of the enzymes and therefore fine-tune amino acid production during the combinatorial response to simultaneous Cu and Fe deficiency.
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Affiliation(s)
| | - Antoni Garcia-Molina
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
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Kourani M, Mohareb F, Rezwan FI, Anastasiadi M, Hammond JP. Genetic and Physiological Responses to Heat Stress in Brassica napus. FRONTIERS IN PLANT SCIENCE 2022; 13:832147. [PMID: 35449889 PMCID: PMC9016328 DOI: 10.3389/fpls.2022.832147] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 03/04/2022] [Indexed: 05/07/2023]
Abstract
Given the current rise in global temperatures, heat stress has become a major abiotic challenge affecting the growth and development of various crops and reducing their productivity. Brassica napus, the second largest source of vegetable oil worldwide, experiences a drastic reduction in seed yield and quality in response to heat. This review outlines the latest research that explores the genetic and physiological impact of heat stress on different developmental stages of B. napus with a special attention to the reproductive stages of floral progression, organogenesis, and post flowering. Several studies have shown that extreme temperature fluctuations during these crucial periods have detrimental effects on the plant and often leading to impaired growth and reduced seed production. The underlying mechanisms of heat stress adaptations and associated key regulatory genes are discussed. Furthermore, an overview and the implications of the polyploidy nature of B. napus and the regulatory role of alternative splicing in forming a priming-induced heat-stress memory are presented. New insights into the dynamics of epigenetic modifications during heat stress are discussed. Interestingly, while such studies are scarce in B. napus, opposite trends in expression of key genetic and epigenetic components have been identified in different species and in cultivars within the same species under various abiotic stresses, suggesting a complex role of these genes and their regulation in heat stress tolerance mechanisms. Additionally, omics-based studies are discussed with emphasis on the transcriptome, proteome and metabolome of B. napus, to gain a systems level understanding of how heat stress alters its yield and quality traits. The combination of omics approaches has revealed crucial interactions and regulatory networks taking part in the complex machinery of heat stress tolerance. We identify key knowledge gaps regarding the impact of heat stress on B. napus during its yield determining reproductive stages, where in-depth analysis of this subject is still needed. A deeper knowledge of heat stress response components and mechanisms in tissue specific models would serve as a stepping-stone to gaining insights into the regulation of thermotolerance that takes place in this important crop species and support future breeding of heat tolerant crops.
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Affiliation(s)
- Mariam Kourani
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Fady Mohareb
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
- *Correspondence: Fady Mohareb,
| | - Faisal I. Rezwan
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - Maria Anastasiadi
- Bioinformatics Group, Cranfield University, Cranfield, United Kingdom
| | - John P. Hammond
- School of Agriculture, Policy and Development, University of Reading, Reading, United Kingdom
- John P. Hammond,
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Becskei A, Rahaman S. The life and death of RNA across temperatures. Comput Struct Biotechnol J 2022; 20:4325-4336. [PMID: 36051884 PMCID: PMC9411577 DOI: 10.1016/j.csbj.2022.08.008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 08/04/2022] [Accepted: 08/04/2022] [Indexed: 11/05/2022] Open
Abstract
Temperature is an environmental condition that has a pervasive effect on cells along with all the molecules and reactions in them. The mechanisms by which prototypical RNA molecules sense and withstand heat have been identified mostly in bacteria and archaea. The relevance of these phenomena is, however, broader, and similar mechanisms have been recently found throughout the tree of life, from sex determination in reptiles to adaptation of viral RNA polymerases, to genetic disorders in humans. We illustrate the temperature dependence of RNA metabolism with examples from the synthesis to the degradation of mRNAs, and review recently emerged questions. Are cells exposed to greater temperature variations and gradients than previously surmised? How do cells reconcile the conflicting thermal stability requirements of primary and tertiary structures of RNAs? To what extent do enzymes contribute to the temperature compensation of the reaction rates in mRNA turnover by lowering the energy barrier of the catalyzed reactions? We conclude with the ecological, forensic applications of the temperature-dependence of RNA degradation and the biotechnological aspects of mRNA vaccine production.
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47
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Genomics Associated Interventions for Heat Stress Tolerance in Cool Season Adapted Grain Legumes. Int J Mol Sci 2021; 23:ijms23010399. [PMID: 35008831 PMCID: PMC8745526 DOI: 10.3390/ijms23010399] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 12/22/2021] [Accepted: 12/27/2021] [Indexed: 11/16/2022] Open
Abstract
Cool season grain legumes occupy an important place among the agricultural crops and essentially provide multiple benefits including food supply, nutrition security, soil fertility improvement and revenue for farmers all over the world. However, owing to climate change, the average temperature is steadily rising, which negatively affects crop performance and limits their yield. Terminal heat stress that mainly occurred during grain development phases severely harms grain quality and weight in legumes adapted to the cool season, such as lentils, faba beans, chickpeas, field peas, etc. Although, traditional breeding approaches with advanced screening procedures have been employed to identify heat tolerant legume cultivars. Unfortunately, traditional breeding pipelines alone are no longer enough to meet global demands. Genomics-assisted interventions including new-generation sequencing technologies and genotyping platforms have facilitated the development of high-resolution molecular maps, QTL/gene discovery and marker-assisted introgression, thereby improving the efficiency in legumes breeding to develop stress-resilient varieties. Based on the current scenario, we attempted to review the intervention of genomics to decipher different components of tolerance to heat stress and future possibilities of using newly developed genomics-based interventions in cool season adapted grain legumes.
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Ling Y, Mahfouz MM, Zhou S. Pre-mRNA alternative splicing as a modulator for heat stress response in plants. TRENDS IN PLANT SCIENCE 2021; 26:1153-1170. [PMID: 34334317 DOI: 10.1016/j.tplants.2021.07.008] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Revised: 07/01/2021] [Accepted: 07/07/2021] [Indexed: 05/11/2023]
Abstract
The molecular responses of plants to the important abiotic stress, heat stress (HS), have been extensively studied at the transcriptional level. Alternative splicing (AS) is a post-transcriptional regulatory process in which an intron-containing gene can generate more than one mRNA variant. The impact of HS on the pre-mRNA splicing process has been reported in various eukaryotes but seldom discussed in-depth, especially in plants. Here, we review AS regulation in response to HS in different plant species. We discuss potential molecular mechanisms controlling heat-inducible AS regulation in plants and hypothesize that AS regulation participates in heat-priming establishment and HS memory maintenance. We propose that the pre-mRNA splicing variation is an important regulator of plant HS responses (HSRs).
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Affiliation(s)
- Yu Ling
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, 524088, PR China; Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia; South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang, 524088, PR China.
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia.
| | - Shuangxi Zhou
- New Zealand Institute for Plant and Food Research Limited, Hawke's Bay 4130, New Zealand
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49
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Pereira C, Castander-Olarieta A, Sales E, Montalbán IA, Canhoto J, Moncaleán P. Heat Stress in Pinus halepensis Somatic Embryogenesis Induction: Effect in DNA Methylation and Differential Expression of Stress-Related Genes. PLANTS (BASEL, SWITZERLAND) 2021; 10:plants10112333. [PMID: 34834696 PMCID: PMC8622292 DOI: 10.3390/plants10112333] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 10/25/2021] [Accepted: 10/26/2021] [Indexed: 05/13/2023]
Abstract
In the current context of climate change, plants need to develop different mechanisms of stress tolerance and adaptation to cope with changing environmental conditions. Temperature is one of the most important abiotic stresses that forest trees have to overcome. Recent research developed in our laboratory demonstrated that high temperatures during different stages of conifer somatic embryogenesis (SE) modify subsequent phases of the process and the behavior of the resulting ex vitro somatic plants. For this reason, Aleppo pine SE was induced under different heat stress treatments (40 °C for 4 h, 50 °C for 30 min, and 60 °C for 5 min) in order to analyze its effect on the global DNA methylation rates and the differential expression of four stress-related genes at different stages of the SE process. Results showed that a slight decrease of DNA methylation at proliferating embryonal masses (EMs) can correlate with the final efficiency of the process. Additionally, different expression patterns for stress-related genes were found in EMs and needles from the in vitro somatic plants obtained; the DEHYDRATION INDUCED PROTEIN 19 gene was up-regulated in response to heat at proliferating EMs, whereas HSP20 FAMILY PROTEIN and SUPEROXIDE DISMUTASE [Cu-Zn] were down-regulated in needles.
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Affiliation(s)
- Cátia Pereira
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- Department of Forestry Science, NEIKER-BRTA, 01080 Arkaute, Spain; (A.C.-O.); (I.A.M.)
| | | | - Ester Sales
- Departament of Ciencias Agrarias y del Medio Natural, Instituto Universitario de Ciencias Ambientales, Universidad de Zaragoza, Escuela Politécnica Superior, 22071 Huesca, Spain;
| | - Itziar A. Montalbán
- Department of Forestry Science, NEIKER-BRTA, 01080 Arkaute, Spain; (A.C.-O.); (I.A.M.)
| | - Jorge Canhoto
- Center for Functional Ecology, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal;
- Correspondence: (J.C.); (P.M.)
| | - Paloma Moncaleán
- Department of Forestry Science, NEIKER-BRTA, 01080 Arkaute, Spain; (A.C.-O.); (I.A.M.)
- Correspondence: (J.C.); (P.M.)
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50
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John S, Olas JJ, Mueller-Roeber B. Regulation of alternative splicing in response to temperature variation in plants. JOURNAL OF EXPERIMENTAL BOTANY 2021; 72:6150-6163. [PMID: 34028544 PMCID: PMC8483784 DOI: 10.1093/jxb/erab232] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 05/21/2021] [Indexed: 05/08/2023]
Abstract
Plants have evolved numerous molecular strategies to cope with perturbations in environmental temperature, and to adjust growth and physiology to limit the negative effects of extreme temperature. One of the strategies involves alternative splicing of primary transcripts to encode alternative protein products or transcript variants destined for degradation by nonsense-mediated decay. Here, we review how changes in environmental temperature-cold, heat, and moderate alterations in temperature-affect alternative splicing in plants, including crops. We present examples of the mode of action of various temperature-induced splice variants and discuss how these alternative splicing events enable favourable plant responses to altered temperatures. Finally, we point out unanswered questions that should be addressed to fully utilize the endogenous mechanisms in plants to adjust their growth to environmental temperature. We also indicate how this knowledge might be used to enhance crop productivity in the future.
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Affiliation(s)
- Sheeba John
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
| | - Justyna Jadwiga Olas
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Correspondence: or
| | - Bernd Mueller-Roeber
- University of Potsdam, Institute of Biochemistry and Biology, Karl-Liebknecht-Straße, Haus, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Am Muehlenberg, Potsdam, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
- Correspondence: or
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