title: Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics.
abstract: Protein post-translational methylation has been reported to occur in archaea, including members of the genus Sulfolobus, but has never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modification are the chromatin proteins that have been described to be methylated on lysine side chains, resembling eukaryotic histones in that aspect. To get more insight into the extent of this modification and its dynamics during the different growth steps of the thermoacidophylic archaeon S. islandicus LAL14/1, we performed a global and deep proteomic analysis using a combination of high-throughput bottom-up and top-down approaches on a single high-resolution mass spectrometer. 1,931 methylation sites on 751 proteins were found by the bottom-up analysis, with methylation sites on 526 proteins monitored throughout three cell culture growth stages: early-exponential, mid-exponential, and stationary. The top-down analysis revealed 3,978 proteoforms arising from 681 proteins, including 292 methylated proteoforms, 85 of which were comprehensively characterized. Methylated proteoforms of the five chromatin proteins (Alba1, Alba2, Cren7, Sul7d1, Sul7d2) were fully characterized by a combination of bottom-up and top-down data. The top-down analysis also revealed an increase of methylation during cell growth for two chromatin proteins, which had not been evidenced by bottom-up. These results shed new light on the ubiquitous lysine methylation throughout the S. islandicus proteome. Furthermore, we found that S. islandicus proteins are frequently acetylated at the N terminus, following the removal of the N-terminal methionine. This study highlights the great value of combining bottom-up and top-down proteomics for obtaining an unprecedented level of accuracy in detecting differentially modified intact proteoforms. The data have been deposited to the ProteomeXchange with identifiers PXD003074 and PXD004179.
authors.affiliation: From the ‡Structural Mass Spectrometry and Proteomics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 75015 Paris, France.
authors.forename: Egor A
authors.initials: EA
authors.lastname: Vorontsov
authors.affiliation: §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France.
authors.forename: Elena
authors.initials: E
authors.lastname: Rensen
authors.affiliation: §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France.
authors.forename: David
authors.initials: D
authors.lastname: Prangishvili
authors.affiliation: §Unit of the Molecular Biology of Gene in Extremophiles, Department of Microbiology, Institut Pasteur, 75015 Paris, France; julia.chamot-rooke@pasteur krupovic@pasteur.fr.
authors.forename: Mart
authors.initials: M
authors.lastname: Krupovic
authors.affiliation: From the ‡Structural Mass Spectrometry and Proteomics Unit, Structural Biology and Chemistry Department, Institut Pasteur, 75015 Paris, France; julia.chamot-rooke@pasteur krupovic@pasteur.fr.|¶UMR3528 CNRS, Paris, France.
authors.forename: Julia
authors.initials: J
authors.lastname: Chamot-Rooke
mesh_terms: D000107:Acetylation; D019843:Archaeal Proteins / Q000378:metabolism*; D002843:Chromatin / Q000378:metabolism; D002853:Chromatography, Liquid / Q000379:methods; D008239:Lysine / Q000737:chemistry*; D008745:Methylation; D011499:Protein Processing, Post-Translational; D040901:Proteomics / Q000379:methods*; D016944:Sulfolobus / Q000254:growth & development* / Q000378:metabolism; D053719:Tandem Mass Spectrometry / Q000379:methods
chemical_list: D019843:Archaeal Proteins; D002843:Chromatin; D008239:Lysine