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Protein arginine methylation is a PTM involved in various cellular processes in eukaryotes. Recent discoveries led to a vast expansion of known sites in higher organisms, indicating that this modification is more widely spread across the proteome than previously assumed. An increased knowledge of sites in lower eukaryotes may facilitate the elucidation of its functions. In this study, we present the discovery of arginine mono-methylation sites in Saccharomyces cerevisiae by a combination of immunoaffinity enrichment and MS/MS. As detection of methylation is prone to yield false positives, we demonstrate the need for stringent measures to avoid elevated false discovery rates. To this end, we employed MethylSILAC in combination with a multistep data analysis strategy. We report 41 unambiguous methylation sites on 13 proteins. Our results indicate that, while substantially less abundant, arginine methylation follows similar patterns as in higher eukaryotes in terms of sequence context and functions of methylated proteins. The majority of sites occur on RNA-binding proteins participating in processes from transcription and splicing to translation and RNA degradation. Additionally, our data suggest a bias for localization of arginine methylation in unstructured regions of proteins, which frequently involves Arg-Gly-Gly motifs or Asn-rich contexts.

Original publication

DOI

10.1002/pmic.201500032

Type

Journal article

Journal

Proteomics

Publication Date

09/2015

Volume

15

Pages

3232 - 3243

Keywords

MethylSILAC, Protein arginine methylation, Systems biology, Tandem mass spectrometry, Yeast, Amino Acid Sequence, Arginine, Isotope Labeling, Methylation, Molecular Sequence Data, Proteome, Saccharomyces cerevisiae Proteins, Systems Biology, Tandem Mass Spectrometry