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Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications

BACKGROUND: The methylation of eukaryotic proteins has been proposed to be widespread, but this has not been conclusively shown to date. In this study, we examined 36,854 previously generated peptide mass spectra from 2,607 Saccharomyces cerevisiae proteins for the presence of arginine and lysine me...

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Autores principales: Pang, Chi Nam Ignatius, Gasteiger, Elisabeth, Wilkins, Marc R
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830191/
https://www.ncbi.nlm.nih.gov/pubmed/20137074
http://dx.doi.org/10.1186/1471-2164-11-92
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author Pang, Chi Nam Ignatius
Gasteiger, Elisabeth
Wilkins, Marc R
author_facet Pang, Chi Nam Ignatius
Gasteiger, Elisabeth
Wilkins, Marc R
author_sort Pang, Chi Nam Ignatius
collection PubMed
description BACKGROUND: The methylation of eukaryotic proteins has been proposed to be widespread, but this has not been conclusively shown to date. In this study, we examined 36,854 previously generated peptide mass spectra from 2,607 Saccharomyces cerevisiae proteins for the presence of arginine and lysine methylation. This was done using the FindMod tool and 5 filters that took advantage of the high number of replicate analysis per protein and the presence of overlapping peptides. RESULTS: A total of 83 high-confidence lysine and arginine methylation sites were found in 66 proteins. Motif analysis revealed many methylated sites were associated with MK, RGG/RXG/RGX or WXXXR motifs. Functionally, methylated proteins were significantly enriched for protein translation, ribosomal biogenesis and assembly and organellar organisation and were predominantly found in the cytoplasm and ribosome. Intriguingly, methylated proteins were seen to have significantly longer half-life than proteins for which no methylation was found. Some 43% of methylated lysine sites were predicted to be amenable to ubiquitination, suggesting methyl-lysine might block the action of ubiquitin ligase. CONCLUSIONS: This study suggests protein methylation to be quite widespread, albeit associated with specific functions. Large-scale tandem mass spectroscopy analyses will help to further confirm the modifications reported here.
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spelling pubmed-28301912010-03-02 Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications Pang, Chi Nam Ignatius Gasteiger, Elisabeth Wilkins, Marc R BMC Genomics Research Article BACKGROUND: The methylation of eukaryotic proteins has been proposed to be widespread, but this has not been conclusively shown to date. In this study, we examined 36,854 previously generated peptide mass spectra from 2,607 Saccharomyces cerevisiae proteins for the presence of arginine and lysine methylation. This was done using the FindMod tool and 5 filters that took advantage of the high number of replicate analysis per protein and the presence of overlapping peptides. RESULTS: A total of 83 high-confidence lysine and arginine methylation sites were found in 66 proteins. Motif analysis revealed many methylated sites were associated with MK, RGG/RXG/RGX or WXXXR motifs. Functionally, methylated proteins were significantly enriched for protein translation, ribosomal biogenesis and assembly and organellar organisation and were predominantly found in the cytoplasm and ribosome. Intriguingly, methylated proteins were seen to have significantly longer half-life than proteins for which no methylation was found. Some 43% of methylated lysine sites were predicted to be amenable to ubiquitination, suggesting methyl-lysine might block the action of ubiquitin ligase. CONCLUSIONS: This study suggests protein methylation to be quite widespread, albeit associated with specific functions. Large-scale tandem mass spectroscopy analyses will help to further confirm the modifications reported here. BioMed Central 2010-02-05 /pmc/articles/PMC2830191/ /pubmed/20137074 http://dx.doi.org/10.1186/1471-2164-11-92 Text en Copyright ©2010 Pang et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Pang, Chi Nam Ignatius
Gasteiger, Elisabeth
Wilkins, Marc R
Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
title Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
title_full Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
title_fullStr Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
title_full_unstemmed Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
title_short Identification of arginine- and lysine-methylation in the proteome of Saccharomyces cerevisiae and its functional implications
title_sort identification of arginine- and lysine-methylation in the proteome of saccharomyces cerevisiae and its functional implications
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2830191/
https://www.ncbi.nlm.nih.gov/pubmed/20137074
http://dx.doi.org/10.1186/1471-2164-11-92
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