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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 and Kris Gevaert UGent (2011) JOURNAL OF PROTEOME RESEARCH. 10(8). p.3578-3589
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.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
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
journal title
JOURNAL OF PROTEOME RESEARCH
J. Proteome Res.
volume
10
issue
8
pages
3578 - 3589
Web of Science type
Article
Web of Science id
000293487900025
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
5.113 (2011)
JCR rank
10/72 (2011)
JCR quartile
1 (2011)
ISSN
1535-3893
DOI
10.1021/pr2007325
project
Bioinformatics: from nucleotids to networks (N2N)
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
1898833
handle
http://hdl.handle.net/1854/LU-1898833
date created
2011-09-08 11:53:52
date last changed
2016-12-19 15:41:59
@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},
}

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.