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, Patrick Willems Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent , Belgium Center for Plant Systems Biology, VIB , 9052 Ghent , Belgium Department of Biomolecular Medicine, Ghent University , 9052 Ghent , Belgium VIB Center for Medical Biotechnology, VIB , 9052 Ghent , Belgium Correspondence: patwille.willems@ugent.be Search for other works by this author on: Oxford Academic Lieven Sterck Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent , Belgium Center for Plant Systems Biology, VIB , 9052 Ghent , Belgium Search for other works by this author on: Oxford Academic Avilien Dard Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent , Belgium Center for Plant Systems Biology, VIB , 9052 Ghent , Belgium Search for other works by this author on: Oxford Academic Jingjing Huang Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent , Belgium Center for Plant Systems Biology, VIB , 9052 Ghent , Belgium Search for other works by this author on: Oxford Academic Ive De Smet Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent , Belgium Center for Plant Systems Biology, VIB , 9052 Ghent , Belgium Search for other works by this author on: Oxford Academic Kris Gevaert Department of Biomolecular Medicine, Ghent University , 9052 Ghent , Belgium VIB Center for Medical Biotechnology, VIB , 9052 Ghent , Belgium Search for other works by this author on: Oxford Academic Frank Van Breusegem Department of Plant Biotechnology and Bioinformatics, Ghent University , 9052 Ghent , Belgium Center for Plant Systems Biology, VIB , 9052 Ghent , Belgium Correspondence: frank.vanbreusegem@ugent.be Search for other works by this author on: Oxford Academic
https://orcid.org/0000-0003-4607-8893 Journal of Experimental Botany, erae270, https://doi.org/10.1093/jxb/erae270
Published:
14 June 2024
Article history
Received:
23 March 2024
Editorial decision:
06 June 2024
Accepted:
13 June 2024
Published:
14 June 2024
Corrected and typeset:
06 July 2024
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Patrick Willems, Lieven Sterck, Avilien Dard, Jingjing Huang, Ive De Smet, Kris Gevaert, Frank Van Breusegem, The Plant PTM Viewer 2.0: in-depth exploration of plant protein modification landscapes, Journal of Experimental Botany, 2024;, erae270, https://doi.org/10.1093/jxb/erae270
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Abstract
Post-translational modifications (PTMs) greatly increase protein diversity and functionality. To help the plant research community interpret the ever-increasing number of reported PTMs, the Plant PTM Viewer (https://www.psb.ugent.be/PlantPTMViewer) provides an intuitive overview of plant protein PTMs and the tools to assess it. This update includes 62 novel PTM profiling studies, adding a total of 112000 modified peptides reporting plant PTMs, including 14 additional PTM types and three species (moss, tomato, and soybean). Furthermore, an open modification re-analysis of a large-scale Arabidopsis thaliana mass spectrometrytissue atlas identified previously uncharted landscapes of lysine acylations predominant in seed and flower tissues and 3-phosphoglycerylation on glycolytic enzymes in plants. An extra ‘Protein list analysis’ tool was developed for retrieval and assessing the enrichment of PTMs in a protein list of interest. We conducted a protein list analysis on nuclear proteins, revealing a substantial number of redox modifications in the nucleus, confirming previous assumptions regarding the redox regulation of transcription. We encourage the plant research community to use PTM Viewer 2.0 for hypothesis testing and new target discovery, and also to submit new data to expand the coverage of conditions, plant species, and PTM types, thereby enriching our understanding of plant biology.
Crotonylation, 2-hydroxyisobutyrylation, open searches, 3-phosphoglycerylation, Plant PTM Viewer 2.0, post-translational protein modifications, proteomics, PTM database, redox
© The Author(s) 2024. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.
This article is published and distributed under the terms of the Oxford University Press, Standard Journals Publication Model (https://academic.oup.com/pages/standard-publication-reuse-rights)
Editor: Christine Foyer Christine Foyer Editor University of Birmingham , UK Search for other works by this author on: Oxford Academic
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