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Zhang Z, Ye F, Xiong T, Chen J, Cao J, Chen Y, Liu S. Origin, evolution and diversification of plant mechanosensitive channel of small conductance-like (MSL) proteins. BMC PLANT BIOLOGY 2023; 23:462. [PMID: 37794319 PMCID: PMC10552396 DOI: 10.1186/s12870-023-04479-2] [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: 06/03/2023] [Accepted: 09/20/2023] [Indexed: 10/06/2023]
Abstract
Mechanosensitive (MS) ion channels provide efficient molecular mechanism for transducing mechanical forces into intracellular ion fluxes in all kingdoms of life. The mechanosensitive channel of small conductance (MscS) was one of the best-studied MS channels and its homologs (MSL, MscS-like) were widely distributed in cell-walled organisms. However, the origin, evolution and expansion of MSL proteins in plants are still not clear. Here, we identified more than 2100 MSL proteins from 176 plants and conducted a broad-scale phylogenetic analysis. The phylogenetic tree showed that plant MSL proteins were divided into three groups (I, II and III) prior to the emergence of chlorophytae algae, consistent with their specific subcellular localization. MSL proteins were distributed unevenly into each of plant species, and four parallel expansion was identified in angiosperms. In Brassicaceae, most MSL duplicates were derived by whole-genome duplication (WGD)/segmental duplications. Finally, a hypothetical evolutionary model of MSL proteins in plants was proposed based on phylogeny. Our studies illustrate the evolutionary history of the MSL proteins and provide a guide for future functional diversity analyses of these proteins in plants.
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Affiliation(s)
- Zaibao Zhang
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China.
| | - Fan Ye
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Tao Xiong
- College of Life Science, Xinyang Normal University, Xinyang, Henan, China
| | - Jiahui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Jiajia Cao
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Yurui Chen
- College of International Education, Xinyang Normal University, Xinyang, Henan, China
| | - Sushuang Liu
- School of Life and Health Science, Huzhou College, Huzhou, Zhejiang, China
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Oelmüller R, Tseng YH, Gandhi A. Signals and Their Perception for Remodelling, Adjustment and Repair of the Plant Cell Wall. Int J Mol Sci 2023; 24:ijms24087417. [PMID: 37108585 PMCID: PMC10139151 DOI: 10.3390/ijms24087417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 04/04/2023] [Accepted: 04/08/2023] [Indexed: 04/29/2023] Open
Abstract
The integrity of the cell wall is important for plant cells. Mechanical or chemical distortions, tension, pH changes in the apoplast, disturbance of the ion homeostasis, leakage of cell compounds into the apoplastic space or breakdown of cell wall polysaccharides activate cellular responses which often occur via plasma membrane-localized receptors. Breakdown products of the cell wall polysaccharides function as damage-associated molecular patterns and derive from cellulose (cello-oligomers), hemicelluloses (mainly xyloglucans and mixed-linkage glucans as well as glucuronoarabinoglucans in Poaceae) and pectins (oligogalacturonides). In addition, several types of channels participate in mechanosensing and convert physical into chemical signals. To establish a proper response, the cell has to integrate information about apoplastic alterations and disturbance of its wall with cell-internal programs which require modifications in the wall architecture due to growth, differentiation or cell division. We summarize recent progress in pattern recognition receptors for plant-derived oligosaccharides, with a focus on malectin domain-containing receptor kinases and their crosstalk with other perception systems and intracellular signaling events.
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Affiliation(s)
- Ralf Oelmüller
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Yu-Heng Tseng
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany
| | - Akanksha Gandhi
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Department of Plant Physiology, Friedrich-Schiller-University, 07743 Jena, Germany
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Brünger T, Pérez-Palma E, Montanucci L, Nothnagel M, Møller RS, Schorge S, Zuberi S, Symonds J, Lemke JR, Brunklaus A, Traynelis SF, May P, Lal D. Conserved patterns across ion channels correlate with variant pathogenicity and clinical phenotypes. Brain 2023; 146:923-934. [PMID: 36036558 PMCID: PMC9976975 DOI: 10.1093/brain/awac305] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 07/29/2022] [Accepted: 08/09/2022] [Indexed: 11/13/2022] Open
Abstract
Clinically identified genetic variants in ion channels can be benign or cause disease by increasing or decreasing the protein function. As a consequence, therapeutic decision-making is challenging without molecular testing of each variant. Our biophysical knowledge of ion-channel structures and function is just emerging, and it is currently not well understood which amino acid residues cause disease when mutated. We sought to systematically identify biological properties associated with variant pathogenicity across all major voltage and ligand-gated ion-channel families. We collected and curated 3049 pathogenic variants from hundreds of neurodevelopmental and other disorders and 12 546 population variants for 30 ion channel or channel subunits for which a high-quality protein structure was available. Using a wide range of bioinformatics approaches, we computed 163 structural features and tested them for pathogenic variant enrichment. We developed a novel 3D spatial distance scoring approach that enables comparisons of pathogenic and population variant distribution across protein structures. We discovered and independently replicated that several pore residue properties and proximity to the pore axis were most significantly enriched for pathogenic variants compared to population variants. Using our 3D scoring approach, we showed that the strongest pathogenic variant enrichment was observed for pore-lining residues and alpha-helix residues within 5Å distance from the pore axis centre and not involved in gating. Within the subset of residues located at the pore, the hydrophobicity of the pore was the feature most strongly associated with variant pathogenicity. We also found an association between the identified properties and both clinical phenotypes and functional in vitro assays for voltage-gated sodium channels (SCN1A, SCN2A, SCN8A) and N-methyl-D-aspartate receptor (GRIN1, GRIN2A, GRIN2B) encoding genes. In an independent expert-curated dataset of 1422 neurodevelopmental disorder pathogenic patient variants and 679 electrophysiological experiments, we show that pore axis distance is associated with seizure age of onset and cognitive performance as well as differential gain versus loss-of-channel function. In summary, we identified biological properties associated with ion-channel malfunction and show that these are correlated with in vitro functional readouts and clinical phenotypes in patients with neurodevelopmental disorders. Our results suggest that clinical decision support algorithms that predict variant pathogenicity and function are feasible in the future.
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Affiliation(s)
- Tobias Brünger
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
| | - Eduardo Pérez-Palma
- Centro de Genética y Genómica, Facultad de Medicina Clínica Alemana, Universidad de Desarrollo, Santiago 7590943, Chile
| | - Ludovica Montanucci
- Lerner Research Institute Cleveland Clinic, Genomic Medicine Institute, Cleveland, OH 44195, USA
| | - Michael Nothnagel
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
- University Hospital Cologne, 50937 Cologne, Germany
| | - Rikke S Møller
- Department of Epilepsy Genetics and Personalized Treatment, the Danish Epilepsy Center, DK 4293 Dianalund, Denmark
| | - Stephanie Schorge
- Department of Neuroscience, Physiology and Pharmacology, UCL, London WC1E 6BT, UK
| | - Sameer Zuberi
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
- Institute of Health and Wellbeing, University of Glasgow, UK
| | - Joseph Symonds
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
- Institute of Health and Wellbeing, University of Glasgow, UK
| | - Johannes R Lemke
- Institute of Human Genetics, University of Leipzig Medical Center, 04103 Leipzig, Germany
- Center for Rare Diseases, University of Leipzig Medical Center, 04103 Leipzig, Germany
| | - Andreas Brunklaus
- The Paediatric Neurosciences Research Group, Royal Hospital for Children, Glasgow, UK
- Institute of Health and Wellbeing, University of Glasgow, UK
| | - Stephen F Traynelis
- Department of Pharmacology, Emory University School of Medicine, Rollins Research Center, Atlanta, GA 30322-3090, USA
| | - Patrick May
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4362 Esch-sur-Alzette, Luxembourg
| | - Dennis Lal
- Cologne Center for Genomics, University of Cologne, 50931 Cologne, Germany
- Lerner Research Institute Cleveland Clinic, Genomic Medicine Institute, Cleveland, OH 44195, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Epilepsy Center, Neurological Institute, Cleveland Clinic, Cleveland, OH 44195, USA
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Narváez-Barragán DA, Tovar-Herrera OE, Guevara-García A, Serrano M, Martinez-Anaya C. Mechanisms of plant cell wall surveillance in response to pathogens, cell wall-derived ligands and the effect of expansins to infection resistance or susceptibility. FRONTIERS IN PLANT SCIENCE 2022; 13:969343. [PMID: 36082287 PMCID: PMC9445675 DOI: 10.3389/fpls.2022.969343] [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: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 05/13/2023]
Abstract
Cell wall integrity is tightly regulated and maintained given that non-physiological modification of cell walls could render plants vulnerable to biotic and/or abiotic stresses. Expansins are plant cell wall-modifying proteins active during many developmental and physiological processes, but they can also be produced by bacteria and fungi during interaction with plant hosts. Cell wall alteration brought about by ectopic expression, overexpression, or exogenous addition of expansins from either eukaryote or prokaryote origin can in some instances provide resistance to pathogens, while in other cases plants become more susceptible to infection. In these circumstances altered cell wall mechanical properties might be directly responsible for pathogen resistance or susceptibility outcomes. Simultaneously, through membrane receptors for enzymatically released cell wall fragments or by sensing modified cell wall barrier properties, plants trigger intracellular signaling cascades inducing defense responses and reinforcement of the cell wall, contributing to various infection phenotypes, in which expansins might also be involved. Here, we review the plant immune response activated by cell wall surveillance mechanisms, cell wall fragments identified as responsible for immune responses, and expansin's roles in resistance and susceptibility of plants to pathogen attack.
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Affiliation(s)
| | | | | | - Mario Serrano
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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