Abundant Lysine Methylation and N-Terminal Acetylation in Sulfolobus islandicus Revealed by Bottom-Up and Top-Down Proteomics.

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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.", "claims": [{"id": "claim-target-result", "statement": "The study mapped protein methylation across the S. islandicus proteome and found evidence of increasing methylation during cell growth for two chromatin proteins; no statistical method is stated in the abstract. The source data are available through ProteomeXchange under PXD003074 and PXD004179.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:27555370", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "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."}, {"asset": "source:pmid:27555370", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "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."}, {"asset": "source:pmid:27555370", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "These results shed new light on the ubiquitous lysine methylation throughout the S. islandicus proteome."}, {"asset": "source:pmid:27555370", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The data have been deposited to the ProteomeXchange with identifiers PXD003074 and PXD004179."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "The study mapped protein methylation across the S. islandicus proteome and found evidence of increasing methylation during cell growth for two chromatin proteins; no statistical method is stated in the abstract. 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