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Barré-Villeneuve C, Azevedo-Favory J. R-Methylation in Plants: A Key Regulator of Plant Development and Response to the Environment. Int J Mol Sci 2024; 25:9937. [PMID: 39337424 PMCID: PMC11432338 DOI: 10.3390/ijms25189937] [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: 08/23/2024] [Revised: 09/11/2024] [Accepted: 09/12/2024] [Indexed: 09/30/2024] Open
Abstract
Although arginine methylation (R-methylation) is one of the most important post-translational modifications (PTMs) conserved in eukaryotes, it has not been studied to the same extent as phosphorylation and ubiquitylation. Technical constraints, which are in the process of being resolved, may partly explain this lack of success. Our knowledge of R-methylation has recently evolved considerably, particularly in metazoans, where misregulation of the enzymes that deposit this PTM is implicated in several diseases and cancers. Indeed, the roles of R-methylation have been highlighted through the analyses of the main actors of this pathway: the PRMT writer enzymes, the TUDOR reader proteins, and potential "eraser" enzymes. In contrast, R-methylation has been much less studied in plants. Even so, it has been shown that R-methylation in plants, as in animals, regulates housekeeping processes such as transcription, RNA silencing, splicing, ribosome biogenesis, and DNA damage. R-methylation has recently been highlighted in the regulation of membrane-free organelles in animals, but this role has not yet been demonstrated in plants. The identified R-met targets modulate key biological processes such as flowering, shoot and root development, and responses to abiotic and biotic stresses. Finally, arginine demethylases activity has mostly been identified in vitro, so further studies are needed to unravel the mechanism of arginine demethylation.
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Affiliation(s)
- Clément Barré-Villeneuve
- Crop Biotechnics, Department of Biosystems, KU Leuven, 3000 Leuven, Belgium
- KU Leuven Plant Institute (LPI), KU Leuven, 3000 Leuven, Belgium
| | - Jacinthe Azevedo-Favory
- CNRS, Laboratoire Génome et Développement des Plantes, UMR 5096, 66860 Perpignan, France
- Laboratoire Génome et Développement des Plantes, Université Perpignan Via Domitia, UMR 5096, 66860 Perpignan, France
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2
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Liu R, Yang Z, Yang T, Wang Z, Chen X, Zhu J, Ren A, Shi L, Yu H, Zhao M. PRMT5 regulates the polysaccharide content by controlling the splicing of thaumatin-like protein in Ganoderma lucidum. Microbiol Spectr 2023; 11:e0290623. [PMID: 37882562 PMCID: PMC10715077 DOI: 10.1128/spectrum.02906-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 09/07/2023] [Indexed: 10/27/2023] Open
Abstract
IMPORTANCE PRMT5 contributes to secondary metabolite biosynthesis in Ganoderma lucidum. However, the mechanism through which PRMT5 regulates the biosynthesis of secondary metabolites remains unclear. In the current study, PRMT5 silencing led to a significant decrease in the biosynthesis of polysaccharides from G. lucidum through the action of the alternative splicing of TLP. A shorter TLP2 isoform can directly bind to PGI and regulated polysaccharide biosynthesis. These results suggest that PRMT5 enhances PGI activity by regulating TLP binding to PGI. The results of the current study reveal a novel target gene for PRMT5-mediated alternative splicing and provide a reference for the identification of PRMT5 regulatory target genes.
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Affiliation(s)
- Rui Liu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zhengyan Yang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Tao Yang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Zi Wang
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xin Chen
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Jing Zhu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Ang Ren
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Liang Shi
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Hanshou Yu
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Mingwen Zhao
- Key Laboratory of Agricultural Environmental Microbiology, Ministry of Agriculture; Microbiology Department, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
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3
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Lepri A, Longo C, Messore A, Kazmi H, Madia VN, Di Santo R, Costi R, Vittorioso P. Plants and Small Molecules: An Up-and-Coming Synergy. PLANTS (BASEL, SWITZERLAND) 2023; 12:1729. [PMID: 37111951 PMCID: PMC10145415 DOI: 10.3390/plants12081729] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 04/16/2023] [Accepted: 04/18/2023] [Indexed: 06/19/2023]
Abstract
The emergence of Arabidopsis thaliana as a model system has led to a rapid and wide improvement in molecular genetics techniques for studying gene function and regulation. However, there are still several drawbacks that cannot be easily solved with molecular genetic approaches, such as the study of unfriendly species, which are of increasing agronomic interest but are not easily transformed, thus are not prone to many molecular techniques. Chemical genetics represents a methodology able to fill this gap. Chemical genetics lies between chemistry and biology and relies on small molecules to phenocopy genetic mutations addressing specific targets. Advances in recent decades have greatly improved both target specificity and activity, expanding the application of this approach to any biological process. As for classical genetics, chemical genetics also proceeds with a forward or reverse approach depending on the nature of the study. In this review, we addressed this topic in the study of plant photomorphogenesis, stress responses and epigenetic processes. We have dealt with some cases of repurposing compounds whose activity has been previously proven in human cells and, conversely, studies where plants have been a tool for the characterization of small molecules. In addition, we delved into the chemical synthesis and improvement of some of the compounds described.
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Affiliation(s)
- A. Lepri
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - C. Longo
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - A. Messore
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - H. Kazmi
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
| | - V. N. Madia
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Di Santo
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - R. Costi
- Department of Chemistry and Technology of Drug, Istituto Pasteur Italia—Fondazione Cenci Bolognetti, Sapienza University of Rome, Piazzale Aldo Moro 5, 00185 Rome, Italy; (A.M.); (V.N.M.); (R.D.S.); (R.C.)
| | - P. Vittorioso
- Department of Biology and Biotechnology “Charles Darwin”, Sapienza University of Rome, 00185 Rome, Italy; (A.L.); (C.L.); (H.K.)
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Willems P, Van Ruyskensvelde V, Maruta T, Pottie R, Fernández-Fernández ÁD, Pauwels J, Hannah MA, Gevaert K, Van Breusegem F, Van der Kelen K. Mutation of Arabidopsis SME1 and Sm core assembly improves oxidative stress resilience. Free Radic Biol Med 2023; 200:117-129. [PMID: 36870374 DOI: 10.1016/j.freeradbiomed.2023.02.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 01/18/2023] [Accepted: 02/27/2023] [Indexed: 03/06/2023]
Abstract
Alternative splicing is a key posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, designated the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Smith (Sm) antigen protein SME1 to alleviate photorespiratory H2O2-dependent cell death in catalase deficient plants. Similar attenuation of cell death was observed upon chemical inhibition of the spliceosome, suggesting pre-mRNA splicing inhibition to be responsible for the observed cell death alleviation. Furthermore, the sme1-2 mutants showed increased tolerance to the reactive oxygen species inducing herbicide methyl viologen. Both an mRNA-seq and shotgun proteomic analysis in sme1-2 mutants displayed a constitutive molecular stress response, together with extensive alterations in pre-mRNA splicing of transcripts encoding metabolic enzymes and RNA binding proteins, even under unstressed conditions. Using SME1 as a bait to identify protein interactors, we provide experimental evidence for almost 50 homologs of the mammalian spliceosome-associated protein to reside in the Arabidopsis thaliana spliceosome complexes and propose roles in pre-mRNA splicing for four uncharacterized plant proteins. Furthermore, as for sme1-2, a mutant in the Sm core assembly protein ICLN resulted in a decreased sensitivity to methyl viologen. Taken together, these data show that both a perturbed Sm core composition and assembly results in the activation of a defense response and in enhanced resilience to oxidative stress.
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Affiliation(s)
- Patrick Willems
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Technologiepark 75, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, Technologiepark 75, 9052, Ghent, Belgium.
| | - Valerie Van Ruyskensvelde
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Takanori Maruta
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium; Department of Life Sciences, Faculty of Life and Environmental Sciences, Shimane University, 1060 Nishikawatsu-cho, Matsue, Shimane, 690-8504, Japan.
| | - Robin Pottie
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Álvaro D Fernández-Fernández
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Jarne Pauwels
- Department of Biomolecular Medicine, Ghent University, Technologiepark 75, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, Technologiepark 75, 9052, Ghent, Belgium.
| | - Matthew A Hannah
- BASF Belgium Coordination Center, Innovation Center Gent, Technologiepark 101, 9052, Ghent, Belgium.
| | - Kris Gevaert
- Department of Biomolecular Medicine, Ghent University, Technologiepark 75, 9052, Ghent, Belgium; Center for Medical Biotechnology, VIB, Technologiepark 75, 9052, Ghent, Belgium.
| | - Frank Van Breusegem
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
| | - Katrien Van der Kelen
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 71, 9052, Ghent, Belgium; Center for Plant Systems Biology, VIB, Technologiepark 71, 9052, Ghent, Belgium.
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5
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Mateos JL, Sanchez SE, Legris M, Esteve-Bruna D, Torchio JC, Petrillo E, Goretti D, Blanco-Touriñán N, Seymour DK, Schmid M, Weigel D, Alabadí D, Yanovsky MJ. PICLN modulates alternative splicing and light/temperature responses in plants. PLANT PHYSIOLOGY 2023; 191:1036-1051. [PMID: 36423226 PMCID: PMC9922395 DOI: 10.1093/plphys/kiac527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Plants undergo transcriptome reprograming to adapt to daily and seasonal fluctuations in light and temperature conditions. While most efforts have focused on the role of master transcription factors, the importance of splicing factors modulating these processes is now emerging. Efficient pre-mRNA splicing depends on proper spliceosome assembly, which in plants and animals requires the methylosome complex. Ion Chloride nucleotide-sensitive protein (PICLN) is part of the methylosome complex in both humans and Arabidopsis (Arabidopsis thaliana), and we show here that the human PICLN ortholog rescues phenotypes of Arabidopsis picln mutants. Altered photomorphogenic and photoperiodic responses in Arabidopsis picln mutants are associated with changes in pre-mRNA splicing that partially overlap with those in PROTEIN ARGININE METHYL TRANSFERASE5 (prmt5) mutants. Mammalian PICLN also acts in concert with the Survival Motor Neuron (SMN) complex component GEMIN2 to modulate the late steps of UsnRNP assembly, and many alternative splicing events regulated by PICLN but not PRMT5, the main protein of the methylosome, are controlled by Arabidopsis GEMIN2. As with GEMIN2 and SM PROTEIN E1/PORCUPINE (SME1/PCP), low temperature, which increases PICLN expression, aggravates morphological and molecular defects of picln mutants. Taken together, these results establish a key role for PICLN in the regulation of pre-mRNA splicing and in mediating plant adaptation to daily and seasonal fluctuations in environmental conditions.
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Affiliation(s)
- Julieta L Mateos
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
- RNA Biology and Molecular Physiology, Faculty of Biology, Bielefeld University, Biele-feld 33615, Germany
| | - Sabrina E Sanchez
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
| | - Martina Legris
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - David Esteve-Bruna
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politecnica de Valencia), Valencia 46022, Spain
| | - Jeanette C Torchio
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
| | - Ezequiel Petrillo
- Instituto de Fisiología, Biología Molecular y Neurociencias (IFIBYNE-UBA-CONICET) and Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Buenos Aires C1428EHA, Argentina
| | - Daniela Goretti
- Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea SE-901 87, Sweden
| | - Noel Blanco-Touriñán
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politecnica de Valencia), Valencia 46022, Spain
| | - Danelle K Seymour
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - Markus Schmid
- Department of Plant Physiology, Umea Plant Science Centre, Umea University, Umea SE-901 87, Sweden
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Biology Tübingen, Tübingen 72076, Germany
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas (CSIC-Universidad Politecnica de Valencia), Valencia 46022, Spain
| | - Marcelo J Yanovsky
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires–Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires C1405BWE, Argentina
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6
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Kufel J, Diachenko N, Golisz A. Alternative splicing as a key player in the fine-tuning of the immunity response in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2022; 23:1226-1238. [PMID: 35567423 PMCID: PMC9276941 DOI: 10.1111/mpp.13228] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/13/2022] [Indexed: 06/01/2023]
Abstract
Plants, like animals, are constantly exposed to abiotic and biotic stresses, which often inhibit plant growth and development, and cause tissue damage, disease, and even plant death. Efficient and timely response to stress requires appropriate co- and posttranscriptional reprogramming of gene expression. Alternative pre-mRNA splicing provides an important layer of this regulation by controlling the level of factors involved in stress response and generating additional protein isoforms with specific features. Recent high-throughput studies have revealed that several defence genes undergo alternative splicing that is often affected by pathogen infection. Despite extensive work, the exact mechanisms underlying these relationships are still unclear, but the contribution of alternative protein isoforms to the defence response and the role of regulatory factors, including components of the splicing machinery, have been established. Modulation of gene expression in response to stress includes alternative splicing, chromatin remodelling, histone modifications, and nucleosome occupancy. How these processes affect plant immunity is mostly unknown, but these facets open new regulatory possibilities. Here we provide an overview of the current state of knowledge and recent findings regarding the growing importance of alternative splicing in plant response to biotic stress.
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Affiliation(s)
- Joanna Kufel
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Nataliia Diachenko
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
| | - Anna Golisz
- Institute of Genetics and BiotechnologyFaculty of BiologyUniversity of WarsawWarsawPoland
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7
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Golisz A, Krzyszton M, Stepien M, Dolata J, Piotrowska J, Szweykowska-Kulinska Z, Jarmolowski A, Kufel J. Arabidopsi s Spliceosome Factor SmD3 Modulates Immunity to Pseudomonas syringae Infection. FRONTIERS IN PLANT SCIENCE 2021; 12:765003. [PMID: 34925413 PMCID: PMC8678131 DOI: 10.3389/fpls.2021.765003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 11/11/2021] [Indexed: 06/02/2023]
Abstract
SmD3 is a core component of the small nuclear ribonucleoprotein (snRNP) that is essential for pre-mRNA splicing. The role of Arabidopsis SmD3 in plant immunity was assessed by testing sensitivity of smd3a and smd3b mutants to Pseudomonas syringae pv. tomato (Pst) DC3000 infection and its pathogenesis effectors flagellin (flg22), EF-Tu (elf18) and coronatine (COR). Both smd3 mutants exhibited enhanced susceptibility to Pst accompanied by marked changes in the expression of key pathogenesis markers. mRNA levels of major biotic stress response factors were also altered upon treatment with Pseudomonas effectors. Our genome-wide transcriptome analysis of the smd3b-1 mutant infected with Pst, verified by northern and RT-qPCR, showed that lack of SmD3-b protein deregulates defense against Pst infection at the transcriptional and posttranscriptional levels including defects in splicing and an altered pattern of alternative splicing. Importantly, we show that SmD3-b dysfunction impairs mainly stomatal immunity as a result of defects in stomatal development. We propose that it is the malfunction of the stomata that is the primary cause of an altered mutant response to the pathogen. Other changes in the smd3b-1 mutant involved enhanced elf18- and flg22-induced callose deposition, reduction of flg22-triggered production of early ROS and boost of secondary ROS caused by Pst infection. Together, our data indicate that SmD3 contributes to the plant immune response possibly via regulation of mRNA splicing of key pathogenesis factors.
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Affiliation(s)
- Anna Golisz
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Michal Krzyszton
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Monika Stepien
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Jakub Dolata
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Justyna Piotrowska
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
| | - Zofia Szweykowska-Kulinska
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Artur Jarmolowski
- Department of Gene Expression, Faculty of Biology, Institute of Molecular Biology and Biotechnology, Adam Mickiewicz University, Poznań, Poland
| | - Joanna Kufel
- Faculty of Biology, Institute of Genetics and Biotechnology, University of Warsaw, Warsaw, Poland
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8
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Dikaya V, El Arbi N, Rojas-Murcia N, Nardeli SM, Goretti D, Schmid M. Insights into the role of alternative splicing in plant temperature response. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab234. [PMID: 34105719 DOI: 10.1093/jxb/erab234] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Indexed: 05/21/2023]
Abstract
Alternative splicing occurs in all eukaryotic organisms. Since the first description of multiexon genes and the splicing machinery, the field has expanded rapidly, especially in animals and yeast. However, our knowledge about splicing in plants is still quite fragmented. Though eukaryotes show some similarity in the composition and dynamics of the splicing machinery, observations of unique plant traits are only starting to emerge. For instance, plant alternative splicing is closely linked to their ability to perceive various environmental stimuli. Due to their sessile lifestyle, temperature is a central source of information allowing plants to adjust their development to match current growth conditions. Hence, seasonal temperature fluctuations and day-night cycles can strongly influence plant morphology across developmental stages. Here we discuss the available data about temperature-dependent alternative splicing in plants. Given its fragmented state it is not always possible to fit specific observations into a coherent picture, yet it is sufficient to estimate the complexity of this field and the need of further research. Better understanding of alternative splicing as a part of plant temperature response and adaptation may also prove to be a powerful tool for both, fundamental and applied sciences.
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Affiliation(s)
- Varvara Dikaya
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nabila El Arbi
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Nelson Rojas-Murcia
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Sarah Muniz Nardeli
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Daniela Goretti
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, Umeå, Sweden
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing, People's Republic of China
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9
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Whole-Seedling-Based Chemical Genetic Screens in Arabidopsis. Methods Mol Biol 2020. [PMID: 33270190 DOI: 10.1007/978-1-0716-0954-5_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Forward genetics has been extremely powerful for dissecting biological pathways in various model organisms. However, it is limited by the fact that redundant gene families and essential genes cannot be readily uncovered through such methods. Chemical genetics, on the other hand, provides a valuable complementary approach to probe biological processes and is suitable for not only genetic model organisms but also genetically less tractable species. We describe here a high-throughput chemical genetic screening method simply based on plant growth and developmental phenotypes in Arabidopsis. It was successfully utilized to study plant immunity and can be easily adapted for dissecting other plant signal transduction pathways.
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Kapos P, Devendrakumar KT, Li X. Plant NLRs: From discovery to application. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 279:3-18. [PMID: 30709490 DOI: 10.1016/j.plantsci.2018.03.010] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 03/01/2018] [Accepted: 03/02/2018] [Indexed: 05/09/2023]
Abstract
Plants require a complex immune system to defend themselves against a wide range of pathogens which threaten their growth and development. The nucleotide-binding leucine-rich repeat proteins (NLRs) are immune sensors that recognize effectors delivered by pathogens. The first NLR was cloned more than twenty years ago. Since this initial discovery, NLRs have been described as key components of plant immunity responsible for pathogen recognition and triggering defense responses. They have now been described in most of the well-studied mulitcellular plant species, with most having large NLR repertoires. As research has progressed so has the understanding of how NLRs interact with their recognition substrates and how they in turn activate downstream signalling. It has also become apparent that NLR regulation occurs at the transcriptional, post-transcriptional, translational, and post-translational levels. Even before the first NLR was cloned, breeders were utilising such genes to increase crop performance. Increased understanding of the mechanistic details of the plant immune system enable the generation of plants resistant against devastating pathogens. This review aims to give an updated summary of the NLR field.
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Affiliation(s)
- Paul Kapos
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Karen Thulasi Devendrakumar
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Xin Li
- Michael Smith Laboratories, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada; Department of Botany, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada.
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Saijo Y, Loo EPI, Yasuda S. Pattern recognition receptors and signaling in plant-microbe interactions. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 93:592-613. [PMID: 29266555 DOI: 10.1111/tpj.13808] [Citation(s) in RCA: 232] [Impact Index Per Article: 38.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Revised: 12/09/2017] [Accepted: 12/14/2017] [Indexed: 05/20/2023]
Abstract
Plants solely rely on innate immunity of each individual cell to deal with a diversity of microbes in the environment. Extracellular recognition of microbe- and host damage-associated molecular patterns leads to the first layer of inducible defenses, termed pattern-triggered immunity (PTI). In plants, pattern recognition receptors (PRRs) described to date are all membrane-associated receptor-like kinases or receptor-like proteins, reflecting the prevalence of apoplastic colonization of plant-infecting microbes. An increasing inventory of elicitor-active patterns and PRRs indicates that a large number of them are limited to a certain range of plant groups/species, pointing to dynamic and convergent evolution of pattern recognition specificities. In addition to common molecular principles of PRR signaling, recent studies have revealed substantial diversification between PRRs in their functions and regulatory mechanisms. This serves to confer robustness and plasticity to the whole PTI system in natural infections, wherein different PRRs are simultaneously engaged and faced with microbial assaults. We review the functional significance and molecular basis of PRR-mediated pathogen recognition and disease resistance, and also an emerging role for PRRs in homeostatic association with beneficial or commensal microbes.
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Affiliation(s)
- Yusuke Saijo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Eliza Po-Iian Loo
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
| | - Shigetaka Yasuda
- Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, 630-0192, Japan
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