title: Expanding the yeast protein arginine methylome.
abstract: 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.
authors.affiliation: Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.|Chemistry Research Laboratory, University of Oxford, Oxford, UK.
authors.forename: Michael
authors.initials: M
authors.lastname: Plank
authors.affiliation: Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
authors.forename: Roman
authors.initials: R
authors.lastname: Fischer
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
authors.forename: Vincent
authors.initials: V
authors.lastname: Geoghegan
authors.affiliation: Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
authors.forename: Philip D
authors.initials: PD
authors.lastname: Charles
authors.affiliation: Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
authors.forename: Rebecca
authors.initials: R
authors.lastname: Konietzny
authors.affiliation: Sir William Dunn School of Pathology, University of Oxford, Oxford, UK.
authors.forename: Oreste
authors.initials: O
authors.lastname: Acuto
authors.affiliation: Department of Biochemistry, University of Oxford, Oxford, UK.
authors.forename: Catherine
authors.initials: C
authors.lastname: Pears
authors.affiliation: Chemistry Research Laboratory, University of Oxford, Oxford, UK.
authors.forename: Christopher J
authors.initials: CJ
authors.lastname: Schofield
authors.affiliation: Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
authors.forename: Benedikt M
authors.initials: BM
authors.lastname: Kessler
mesh_terms: D000595:Amino Acid Sequence; D001120:Arginine / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D007553:Isotope Labeling; D008745:Methylation; D008969:Molecular Sequence Data; D020543:Proteome / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000032:analysis* / Q000737:chemistry / Q000378:metabolism; D049490:Systems Biology; D053719:Tandem Mass Spectrometry
chemical_list: D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D001120:Arginine
keywords: MethylSILAC; Protein arginine methylation; Systems biology; Tandem mass spectrometry; Yeast