Sulfolobus islandicus PTM and quantitative study using bottom-up proteomics

Protein posttranslational methylation and acetylation have been reported to occur in archaea, including the genus Sulfolobus, but have never been characterized on a proteome-wide scale. Among important Sulfolobus proteins carrying such modifications are the chromatin proteins that have been described to be methylated and acetylated on lysine side chains, resembling eukaryotic histones in that aspect. To get more insight into the extent of these modifications and their dynamics during the different growth steps of the thermoacidophylic archaeon S. islandicus , we performed a global and deep proteomics analysis using a combination of high-throughput bottom-up and top-down proteomics 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 of 424-526 proteins monitored throughout three cell culture growth stages: Early, Mid and Late. The previously described aKMT4 methyltransferase was found to be potentially responsible for this massive modification.