Willems Patrick, Sterck Lieven, Dard Avilien, Huang Jingjing, De Smet Ive, Gevaert Kris, Van Breusegem Frank
Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium.
Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium.
J Exp Bot. 2024 Aug 12;75(15):4611-4624. doi: 10.1093/jxb/erae270.
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 112 000 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 spectrometry tissue 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.
翻译后修饰（PTMs）极大地增加了蛋白质的多样性和功能。为帮助植物研究界解读报告中数量不断增加的PTMs，植物PTM查看器（https://www.psb.ugent.be/PlantPTMViewer）提供了植物蛋白质PTMs的直观概述以及评估工具。此次更新包括62项新的PTM分析研究，共增加了112000条报告植物PTMs的修饰肽段，其中包括14种额外的PTM类型以及三种植物（苔藓、番茄和大豆）。此外，对拟南芥大规模质谱组织图谱进行的开放修饰重新分析，发现了种子和花组织中主要的赖氨酸酰化以及植物糖酵解酶上的3-磷酸甘油酰化等此前未知的情况。开发了一个额外的“蛋白质列表分析”工具，用于检索和评估感兴趣的蛋白质列表中PTMs的富集情况。我们对核蛋白进行了蛋白质列表分析，发现细胞核中有大量的氧化还原修饰，证实了之前关于转录的氧化还原调控的假设。我们鼓励植物研究界使用PTM查看器2.0进行假设检验和发现新的靶点，同时提交新数据以扩大条件、植物物种和PTM类型的覆盖范围，从而增进我们对植物生物学的理解。
