Immunoaffinity Enrichment and Mass Spectrometry Analysis of Protein Methylation

Cell Signaling Technology, United States
Molecular &amp Cellular Proteomics (Impact Factor: 6.56). 10/2013; 13(1). DOI: 10.1074/mcp.O113.027870
Source: PubMed


Protein methylation is a common posttranslational modification that mostly occurs on arginine and lysine residues. Arginine methylation has been reported to regulate RNA processing, gene transcription, DNA damage repair, protein translocation, and signal transduction. Lysine methylation is best known to regulate histone function and is involved in epigenetic regulation of gene transcription. To better study protein methylation, we have developed highly specific antibodies against monomethyl arginine, asymmetric dimethyl arginine, and monomethyl, dimethyl, and trimethyl lysine motifs respectively. These antibodies were used to perform immunoaffinity purification (IAP) of methyl peptides followed by LC-MS/MS analysis to identify and quantify arginine and lysine methylation sites in several model studies. Overall, we identified over 1000 arginine methylation sites in human cell lines and mouse tissues, and approximately 160 lysine methylation sites in human cell line HCT116. The methylation sites that were identified in this study exceed those found in the literature to date. Detailed analysis of arginine-methylated proteins observed in mouse brain compared to those found in mouse embryo shows tissue-specific distribution of arginine methylation, and extends the type of proteins that are known to be arginine methylated to many new protein types. Many arginine-methylated proteins that we identified from the brain including receptors, ion channels, transporters, and vesicle proteins, are involved in synaptic transmission, while the most abundant methylated proteins identified from mouse embryo are transcriptional regulators and RNA processing proteins.

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Available from: Jeffrey Silva, Jul 25, 2015
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    • "The approach combining antibody-enrichment of Arg-methylated proteins and MS analysis identified 200 putatively methylated proteins, yet exact methylation sites were unavailable [14]. In recent years, antibody enrichment was widely utilized to the global identification of methylation sites on Lys or Arg residue [8] [9] [10] [11]. It should be noted that the use of pan-antibody significantly advanced the detection of protein methylome, however, the enrichment efficiency remains to be improved. "
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    ABSTRACT: Unlabelled: Protein methylation catalyzed by SAM-dependent methyltransferase represents a major PTM involved in many important biological processes. Because methylation can occur on nitrogen, oxygen and sulfur centers and multiple methylation states exist on the nitrogen centers, methylproteome remains poorly documented. Here we present the methylation by isotope labeled SAM (MILS) strategy for a highly-confident analysis of the methylproteome of the yeast Saccharomyces cerevisiae based on the online multidimensional μHPLC/MS/MS technology. We identified 43 methylated proteins, containing 68 methylation events associated with 64 methylation sites. More than 90% of these methylation events were previously unannotated in Uniprot database. Our results indicated, 1) over 2.6% of identified S. cerevisiae proteins are methylated, 2) the amino acid residue preference of protein methylation follows the order Lys≫Arg>Asp>Asn≈Gln≈His>Glu>Cys, and 3) the methylation state on nitrogen center is largely exclusive. As our dataset covers various types of methylation centers, it provides rich information about yeast methylproteome and should significantly contribute to the field of protein methylation. Biological significance: In this paper, we presented the methylation by isotope labeled SAM (MILS) strategy for a highly-confident analysis of the methylproteome of the yeast S. cerevisiae and collected a comprehensive list of proteins methylated on a set of distinct residues (K, R, N, E, D, Q, H, C). Our study provided useful information about the amino acid residue preference and methylation state distributions on nitrogen centers of protein methylation in S. cerevisiae.
    Journal of Proteomics 08/2014; 114. DOI:10.1016/j.jprot.2014.07.032 · 3.89 Impact Factor
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    • "The methylation of proteins is emerging as one of the most widespread protein post-translational modifications [1]. It predominantly occurs on lysine and arginine residues, but has also been documented on glutamine, asparagine, cysteine, histidine and glutamate residues [2]. "
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    ABSTRACT: Here we describe the discovery of S. cerevisiae protein YJR129Cp as a new eukaryotic seven-beta-strand lysine methyltransferase. An immunoblotting screen of 21 putative methyltransferases showed a loss in the methylation of elongation factor 2 (EF2) on knockout of YJR129C. Mass spectrometric analysis of EF2 tryptic peptides localized this loss of methylation to lysine 509, in peptide LVEGLKR. In vitro methylation, using recombinant methyltransferases and purified EF2, validated YJR129Cp as responsible for methylation of lysine 509 and Efm2p as responsible for methylation at lysine 613. Contextualised on previously described protein structures, both sites of methylation were found at the interaction interface between EF2 and the 40S ribosomal subunit. In line with the recently discovered Efm1 and Efm2 we propose that YJR129C be named elongation factor methyltransferase 3 (Efm3). The human homolog of Efm3 is likely to be the putative methyltransferase FAM86A, according to sequence homology and multiple lines of literature evidence.
    Biochemical and Biophysical Research Communications 07/2014; 451(2). DOI:10.1016/j.bbrc.2014.07.110 · 2.30 Impact Factor
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    • "Low specificity and sensitivity of previously available pan-methyllysine antibodies have limited the use of this approach. Recently, a cocktail of antibodies was developed to enrich methylated peptides (Guo et al, 2014) and has successfully yielded a significant number of novel methylation sites. This novel approach identified 165 sites across a wide variety of sequences in histones, elongation factors and chaperone proteins in HCT116 cells. "
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    ABSTRACT: Large-scale characterization of post-translational modifications (PTMs), such as phosphorylation, acetylation and ubiquitination, has highlighted their importance in the regulation of a myriad of signaling events. While high-throughput technologies have tremendously helped cataloguing the proteins modified by these PTMs, the identification of lysine-methylated proteins, a PTM involving the transfer of one, two or three methyl groups to the ε-amine of a lysine side chain, has lagged behind. While the initial findings were focused on the methylation of histone proteins, several studies have recently identified novel non-histone lysine-methylated proteins. This review provides a compilation of all lysine methylation sites reported to date. We also present key examples showing the impact of lysine methylation and discuss the circuitries wired by this important PTM.
    Molecular Systems Biology 04/2014; 10(4). DOI:10.1002/msb.134974 · 10.87 Impact Factor
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