title: Uncovering the protein lysine and arginine methylation network in Arabidopsis chloroplasts.
abstract: Post-translational modification of proteins by the addition of methyl groups to the side chains of Lys and Arg residues is proposed to play important roles in many cellular processes. In plants, identification of non-histone methylproteins at a cellular or subcellular scale is still missing. To gain insights into the extent of this modification in chloroplasts we used a bioinformatics approach to identify protein methyltransferases targeted to plastids and set up a workflow to specifically identify Lys and Arg methylated proteins from proteomic data used to produce the Arabidopsis chloroplast proteome. With this approach we could identify 31 high-confidence Lys and Arg methylation sites from 23 chloroplastic proteins, of which only two were previously known to be methylated. These methylproteins are split between the stroma, thylakoids and envelope sub-compartments. They belong to essential metabolic processes, including photosynthesis, and to the chloroplast biogenesis and maintenance machinery (translation, protein import, division). Also, the in silico identification of nine protein methyltransferases that are known or predicted to be targeted to plastids provided a foundation to build the enzymes/substrates relationships that govern methylation in chloroplasts. Thereby, using in vitro methylation assays with chloroplast stroma as a source of methyltransferases we confirmed the methylation sites of two targets, plastid ribosomal protein L11 and the β-subunit of ATP synthase. Furthermore, a biochemical screening of recombinant chloroplastic protein Lys methyltransferases allowed us to identify the enzymes involved in the modification of these substrates. The present study provides a useful resource to build the methyltransferases/methylproteins network and to elucidate the role of protein methylation in chloroplast biology.
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Claude
authors.initials: C
authors.lastname: Alban
authors.affiliation: Université Grenoble Alpes, Grenoble, France; CEA, iRTSV, Biologie à Grande Echelle, Grenoble, France; INSERM, U1038, Grenoble, France.
authors.forename: Marianne
authors.initials: M
authors.lastname: Tardif
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Morgane
authors.initials: M
authors.lastname: Mininno
authors.affiliation: Université Grenoble Alpes, Grenoble, France; CEA, iRTSV, Biologie à Grande Echelle, Grenoble, France; INSERM, U1038, Grenoble, France.
authors.forename: Sabine
authors.initials: S
authors.lastname: Brugière
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Annabelle
authors.initials: A
authors.lastname: Gilgen
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Sheng
authors.initials: S
authors.lastname: Ma
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Meryl
authors.initials: M
authors.lastname: Mazzoleni
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Océane
authors.initials: O
authors.lastname: Gigarel
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Martin-Laffon
authors.affiliation: Université Grenoble Alpes, Grenoble, France; CEA, iRTSV, Biologie à Grande Echelle, Grenoble, France; INSERM, U1038, Grenoble, France.
authors.forename: Myriam
authors.initials: M
authors.lastname: Ferro
authors.affiliation: Université Grenoble Alpes, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; CNRS, UMR5168, Grenoble, France; CEA, iRTSV, Laboratoire de Physiologie Cellulaire & Végétale, Grenoble, France; INRA, USC1359, Grenoble, France.
authors.forename: Stéphane
authors.initials: S
authors.lastname: Ravanel
mesh_terms: D020816:Amino Acid Motifs; D017360:Arabidopsis / Q000235:genetics / Q000378:metabolism*; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism*; D001120:Arginine / Q000378:metabolism; D002736:Chloroplasts / Q000378:metabolism*; D030562:Databases, Protein; D042541:Intracellular Space / Q000378:metabolism; D008239:Lysine / Q000378:metabolism; D013058:Mass Spectrometry; D008745:Methylation; D008780:Methyltransferases / Q000378:metabolism; D008958:Models, Molecular; D011487:Protein Conformation; D021381:Protein Transport; D011994:Recombinant Proteins / Q000737:chemistry / Q000235:genetics / Q000302:isolation & purification / Q000378:metabolism
chemical_list: D029681:Arabidopsis Proteins; D011994:Recombinant Proteins; D001120:Arginine; D008780:Methyltransferases; D008239:Lysine
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