The Plant PTM Viewer, a central resource for exploring plant protein modifications

Abstract

Summary Post‐translational modifications (PTMs) of proteins are central in any kind of cellular signaling. Modern mass spectrometry technologies enable comprehensive identification and quantification of various PTMs. Given the increased numbers and types of mapped protein modifications, a database is necessary that simultaneously integrates and compares site‐specific information for different PTMs, especially in plants for which the available PTM data are poorly catalogued. Here, we present the Plant PTM Viewer (http://www.psb.ugent.be/PlantPTMViewer), an integrative PTM resource that comprises approximately 370 000 PTM sites for 19 types of protein modifications in plant proteins from five different species. The Plant PTM Viewer provides the user with a protein sequence overview in which the experimentally evidenced PTMs are highlighted together with an estimate of the confidence by which the modified peptides and, if possible, the actual modification sites were identified and with functional protein domains or active site residues. The PTM sequence search tool can query PTM combinations in specific protein sequences, whereas the PTM BLAST tool searches for modified protein sequences to detect conserved PTMs in homologous sequences. Taken together, these tools help to assume the role and potential interplay of PTMs in specific proteins or within a broader systems biology context. The Plant PTM Viewer is an open repository that allows the submission of mass spectrometry‐based PTM data to remain at pace with future PTM plant studies.

TheArabidopsis thalianaPeptideAtlas; harnessing world-wide proteomics data for a comprehensive community proteomics resource

“…The progress of proteomics research of plants has been regularly reviewed, mostly in an attempt to consolidate plant proteome information, including protein detection, various PTMs, abundance measurements, and to provide updates of plant proteomics and mass spectrometry technologies and plant proteome databases (Tan et al, 2017; Misra, 2018). A range of plant proteome databases by individual labs have been developed, mostly for Arabidopsis proteins, typically focused quite narrowly towards a particular aspect of plant proteomics, such as subcellular compartments (San Clemente and Jamet, 2015; Salvi et al, 2018), protein location (SUBA and PPDB) (Sun et al, 2009; Tanz et al, 2013), or PTMs (Schulze et al, 2015; Willems et al, 2019). Most recently, a more comprehensive Arabidopsis proteome database (ATHENA) was released to mine a large scale experimental proteome data set involving multiple tissue types (Mergner et al, 2020).…”

Identification of Sulfenylated Cysteines in Arabidopsis thaliana Proteins Using a Disulfide-Linked Peptide Reporter

“…For instance, the C 598 SEIWDR CL peptides “C#SEIWDR-DLKPSNLLLNANC#DLK” ( Figure 4D ) matched the Cys181 of MITOGEN-ACTIVATED PROTEIN KINASE 4 (MPK4) that had been experimentally verified ( Huang et al, 2019 ). Also, other site-specific reversibly oxidized cysteine studies ( Liu et al, 2014 , 2015 ) and S -nitrosylation studies ( Fares et al, 2011 ; Puyaubert et al, 2014 ; Hu et al, 2015 ) were compared ( Willems et al, 2019 ). In total, 295 S -nitrosylation and 201 reversible previously reported cysteine oxidation sites overlapped with the YAP1C CL sites ( Figure 4C ).…”

“…Thermo RAW files and pLink 2 result tables are available on the PRIDE repository with the identifier PXD016723. The 1,747 sulfenylated cysteine residues identified were submitted to the Plant PTM Viewer (Willems et al, 2019).…”

Genetic mapping of the early responses to salt stress inArabidopsis thaliana

“…The AT1G64300 is an unknown protein kinase with two splice variants, in which the most dominant variant is 717 amino acids in length. Moreover, the predicted location of the serine/threonine kinase domain is towards the C-terminus (274 -508), while the domain of the unknown function (DUF1221) is towards the N-terminus (21 -237) (Willems et al, 2019). In addition, the AT1G64300 is predicted to contain up to 5 transmembrane domains in the positions 31-49, 108-128, 276-294, 329-350 and 435-453 (Hofmann & Stoffel, 1993), and it is predicted to be localised in the endomembrane systems, such as the Golgi apparatus or the endoplasmic reticulum (SUBAcon scores of 0.027 and 0.105), respectively, or in the plasma membrane (SUBAcon score of 0.815).…”