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Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation

Kenny Helsens (UGent) , Petra Van Damme (UGent) , Sven Degroeve (UGent) , Lennart Martens (UGent) , Thomas Arnesen, Joël Vandekerckhove (UGent) and Kris Gevaert (UGent)
(2011) JOURNAL OF PROTEOME RESEARCH. 10(8). p.3578-3589
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
Initiation of protein translation is a well-studied fundamental process, albeit high-throughput and more comprehensive determination of the exact translation initiation sites (TIS) was only recently made possible following the introduction of positional proteomics techniques that target protein N-termini. Precise translation initiation is of crucial importance, as truncated or extended proteins might fold, function, and locate erroneously. Still, as already shown for some proteins, alternative translation initiation can also serve as a regulatory mechanism. By applying N-terminal COFRADIC (combined fractional diagonal chromatography), we here isolated N-terminal peptides of a Saccharomyces cerevisiae proteome and analyzed both annotated and alternative TIS. We analyzed this N-terminome of S. cerevisiae which resulted in the identification of 650 unique N-terminal peptides corresponding to database annotated TIS. Furthermore, 56 unique N(alpha)-acetylated peptides were identified that suggest alternative TIS (MS/MS-based), while MS-based evidence of N(alpha)-acetylation led to an additional 33 such peptides. To improve the overall sensitivity of the analysis, we also included the 5' UTR (untranslated region) in-frame translations together with the yeast protein sequences in UniProtKB/Swiss-Prot. To ensure the quality of the individual peptide identifications, peptide-to-spectrum matches were only accepted at a 99% probability threshold and were subsequently analyzed in detail by the Peptizer tool to automatically ascertain their compliance with several expert criteria. Furthermore, we have also identified 60 MS/MS-based and 117 MS-based N(alpha)-acetylated peptides that point to N(alpha)-acetylation as a post-translational modification since these peptides did not start nor were preceded (in their corresponding protein sequence) by a methionine residue. Next, we evaluated consensus sequence features of nudeic acids and amino acids across each of these groups of peptides and evaluated the results in the context of publicly available data. Taken together, we present a list of 706 annotated and alternative TIS for yeast proteins and found that under normal growth conditions alternative TIS might (co)occur in S. cerevisiae in roughly one tenth of all proteins. Furthermore, we found that the nucleic acid and amino acid features proximate to these alternative TIS favor either guanine or adenine nucleotides following the start codon or acidic amino acids following the initiator methionine. Finally, we also observed an unexpected high number of N(alpha)-acetylated peptides that could not be related to TIS and therefore suggest events of post-translational N(alpha)-acetylation.
Keywords
GENE, CODON, MITOCHONDRIAL, PROTEINS, YEAST, SEQUENCES, START SITES, TRANSFER-RNA, MASS-SPECTROMETRY, N(alpha)-acetylation, KeyWords Plus: EUKARYOTIC RIBOSOMES, N(alpha)-acetylome, proteogenomics, Mass spectrometry, peptide-centric proteomics, COFRADIC, alternative translation initiation, proteomics bioinformatics

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Citation

Please use this url to cite or link to this publication:

Chicago
Helsens, Kenny, Petra Van Damme, Sven Degroeve, Lennart Martens, Thomas Arnesen, Joël Vandekerckhove, and Kris Gevaert. 2011. “Bioinformatics Analysis of a Saccharomyces Cerevisiae N-terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-translational N-terminal Acetylation.” Journal of Proteome Research 10 (8): 3578–3589.
APA
Helsens, K., Van Damme, P., Degroeve, S., Martens, L., Arnesen, T., Vandekerckhove, J., & Gevaert, K. (2011). Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation. JOURNAL OF PROTEOME RESEARCH, 10(8), 3578–3589.
Vancouver
1.
Helsens K, Van Damme P, Degroeve S, Martens L, Arnesen T, Vandekerckhove J, et al. Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation. JOURNAL OF PROTEOME RESEARCH. 2011;10(8):3578–89.
MLA
Helsens, Kenny, Petra Van Damme, Sven Degroeve, et al. “Bioinformatics Analysis of a Saccharomyces Cerevisiae N-terminal Proteome Provides Evidence of Alternative Translation Initiation and Post-translational N-terminal Acetylation.” JOURNAL OF PROTEOME RESEARCH 10.8 (2011): 3578–3589. Print.
@article{1898833,
  abstract     = {Initiation of protein translation is a well-studied fundamental process, albeit high-throughput and more comprehensive determination of the exact translation initiation sites (TIS) was only recently made possible following the introduction of positional proteomics techniques that target protein N-termini. Precise translation initiation is of crucial importance, as truncated or extended proteins might fold, function, and locate erroneously. Still, as already shown for some proteins, alternative translation initiation can also serve as a regulatory mechanism. By applying N-terminal COFRADIC (combined fractional diagonal chromatography), we here isolated N-terminal peptides of a Saccharomyces cerevisiae proteome and analyzed both annotated and alternative TIS. We analyzed this N-terminome of S. cerevisiae which resulted in the identification of 650 unique N-terminal peptides corresponding to database annotated TIS. Furthermore, 56 unique N(alpha)-acetylated peptides were identified that suggest alternative TIS (MS/MS-based), while MS-based evidence of N(alpha)-acetylation led to an additional 33 such peptides. To improve the overall sensitivity of the analysis, we also included the 5' UTR (untranslated region) in-frame translations together with the yeast protein sequences in UniProtKB/Swiss-Prot. To ensure the quality of the individual peptide identifications, peptide-to-spectrum matches were only accepted at a 99\% probability threshold and were subsequently analyzed in detail by the Peptizer tool to automatically ascertain their compliance with several expert criteria. Furthermore, we have also identified 60 MS/MS-based and 117 MS-based N(alpha)-acetylated peptides that point to N(alpha)-acetylation as a post-translational modification since these peptides did not start nor were preceded (in their corresponding protein sequence) by a methionine residue. Next, we evaluated consensus sequence features of nudeic acids and amino acids across each of these groups of peptides and evaluated the results in the context of publicly available data. Taken together, we present a list of 706 annotated and alternative TIS for yeast proteins and found that under normal growth conditions alternative TIS might (co)occur in S. cerevisiae in roughly one tenth of all proteins. Furthermore, we found that the nucleic acid and amino acid features proximate to these alternative TIS favor either guanine or adenine nucleotides following the start codon or acidic amino acids following the initiator methionine. Finally, we also observed an unexpected high number of N(alpha)-acetylated peptides that could not be related to TIS and therefore suggest events of post-translational N(alpha)-acetylation.},
  author       = {Helsens, Kenny and Van Damme, Petra and Degroeve, Sven and Martens, Lennart and Arnesen, Thomas and Vandekerckhove, Jo{\"e}l and Gevaert, Kris},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {GENE,CODON,MITOCHONDRIAL,PROTEINS,YEAST,SEQUENCES,START SITES,TRANSFER-RNA,MASS-SPECTROMETRY,N(alpha)-acetylation,KeyWords Plus: EUKARYOTIC RIBOSOMES,N(alpha)-acetylome,proteogenomics,Mass spectrometry,peptide-centric proteomics,COFRADIC,alternative translation initiation,proteomics bioinformatics},
  language     = {eng},
  number       = {8},
  pages        = {3578--3589},
  title        = {Bioinformatics analysis of a Saccharomyces cerevisiae N-terminal proteome provides evidence of alternative translation initiation and post-translational N-terminal acetylation},
  url          = {http://dx.doi.org/10.1021/pr2007325},
  volume       = {10},
  year         = {2011},
}

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