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Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis

Michalis Aivaliotis, Kris Gevaert UGent, Michaela Falb, Andreas Tebbe, Kosta Konstantinidis, Birgit Bisle, Christian Klein, Lennart Martens UGent, An Staes UGent and Evy Timmerman UGent, et al. (2007) JOURNAL OF PROTEOME RESEARCH. 6(6). p.2195-2204
abstract
Characterization of protein N-terminal peptides supports the quality assessment of data derived from genomic sequences ( e.g., the correct assignment of start codons) and hints to in vivo N-terminal modifications such as N-terminal acetylation and removal of the initiator methionine. The current work represents the first large-scale identification of N-terminal peptides from prokaryotes, of the two halophilic euryarchaeota Halobacterium salinarum and Natronomonas pharaonis. Two methods were used that specifically allow the characterization of protein N-terminal peptides: combined fractional diagonal chromatography ( COFRADIC) and strong cation exchange chromatography (SCX), both known to enrich for N-terminally blocked peptides. In addition to these specific methods, N-terminal peptide identifications were extracted from our previous genome-wide proteomic data. Combining all data, 606 N-terminal peptides from Hbt. salinarum and 328 from Nmn. pharaonis were reliably identified. These results constitute the largest available dataset holding identified and characterized protein N-termini for prokaryotes (archaea and bacteria). They allowed the validation/improvement of start codon assignments as automatic gene finders tend to misassign start codons for GC-rich genomes. In addition, the dataset allowed unravelling N-terminal protein maturation in archaea, showing that 60% of the proteins undergo methionine cleavage and that-in contrast to current knowledges-N-alpha-acetylation is common in the archaeal domain of life with 13-18% of the proteins being N alpha-acetylated. The protein sets described in this paper are available by FTP and might be used as reference sets to test the performance of new gene finders.
Please use this url to cite or link to this publication:
author
organization
year
type
journalArticle (original)
publication status
published
subject
keyword
CELLS, Halobacterium salinarum, ACETYLATION, BACTERIA, SEQUENCE, PROTEINS, PATHWAY, SPECIES NRC-1, PROTEOME, GENOME ANNOTATION, MASS-SPECTROMETRY, gene finder, COFRADIC, N-terminal peptide, SCX, ESI Q-TOF, LCMS/MS, halophilic, archaea, Natronomonas pharaonis
journal title
JOURNAL OF PROTEOME RESEARCH
J. Proteome Res.
volume
6
issue
6
pages
2195 - 2204
Web of Science type
Article
Web of Science id
000246893500015
JCR category
BIOCHEMICAL RESEARCH METHODS
JCR impact factor
5.675 (2007)
JCR rank
5/57 (2007)
JCR quartile
1 (2007)
ISSN
1535-3893
DOI
10.1021/pr0700347
language
English
UGent publication?
yes
classification
A1
copyright statement
I have transferred the copyright for this publication to the publisher
id
388877
handle
http://hdl.handle.net/1854/LU-388877
date created
2008-02-26 17:25:00
date last changed
2012-03-02 16:32:50
@article{388877,
  abstract     = {Characterization of protein N-terminal peptides supports the quality assessment of data derived from genomic sequences ( e.g., the correct assignment of start codons) and hints to in vivo N-terminal modifications such as N-terminal acetylation and removal of the initiator methionine. The current work represents the first large-scale identification of N-terminal peptides from prokaryotes, of the two halophilic euryarchaeota Halobacterium salinarum and Natronomonas pharaonis. Two methods were used that specifically allow the characterization of protein N-terminal peptides: combined fractional diagonal chromatography ( COFRADIC) and strong cation exchange chromatography (SCX), both known to enrich for N-terminally blocked peptides. In addition to these specific methods, N-terminal peptide identifications were extracted from our previous genome-wide proteomic data. Combining all data, 606 N-terminal peptides from Hbt. salinarum and 328 from Nmn. pharaonis were reliably identified. These results constitute the largest available dataset holding identified and characterized protein N-termini for prokaryotes (archaea and bacteria). They allowed the validation/improvement of start codon assignments as automatic gene finders tend to misassign start codons for GC-rich genomes. In addition, the dataset allowed unravelling N-terminal protein maturation in archaea, showing that 60\% of the proteins undergo methionine cleavage and that-in contrast to current knowledges-N-alpha-acetylation is common in the archaeal domain of life with 13-18\% of the proteins being N alpha-acetylated. The protein sets described in this paper are available by FTP and might be used as reference sets to test the performance of new gene finders.},
  author       = {Aivaliotis, Michalis and Gevaert, Kris and Falb, Michaela and Tebbe, Andreas and Konstantinidis, Kosta and Bisle, Birgit and Klein, Christian and Martens, Lennart and Staes, An and Timmerman, Evy and Van Damme, Jozef and Siedler, Frank and Pfeiffer, Friedhelm and Vandekerckhove, Jo{\"e}l and Oesterhelt, Dieter},
  issn         = {1535-3893},
  journal      = {JOURNAL OF PROTEOME RESEARCH},
  keyword      = {CELLS,Halobacterium salinarum,ACETYLATION,BACTERIA,SEQUENCE,PROTEINS,PATHWAY,SPECIES NRC-1,PROTEOME,GENOME ANNOTATION,MASS-SPECTROMETRY,gene finder,COFRADIC,N-terminal peptide,SCX,ESI Q-TOF,LCMS/MS,halophilic,archaea,Natronomonas pharaonis},
  language     = {eng},
  number       = {6},
  pages        = {2195--2204},
  title        = {Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis},
  url          = {http://dx.doi.org/10.1021/pr0700347},
  volume       = {6},
  year         = {2007},
}

Chicago
Aivaliotis, Michalis, Kris Gevaert, Michaela Falb, Andreas Tebbe, Kosta Konstantinidis, Birgit Bisle, Christian Klein, et al. 2007. “Large-scale Identification of N-terminal Peptides in the Halophilic Archaea Halobacterium Salinarum and Natronomonas Pharaonis.” Journal of Proteome Research 6 (6): 2195–2204.
APA
Aivaliotis, M., Gevaert, K., Falb, M., Tebbe, A., Konstantinidis, K., Bisle, B., Klein, C., et al. (2007). Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. JOURNAL OF PROTEOME RESEARCH, 6(6), 2195–2204.
Vancouver
1.
Aivaliotis M, Gevaert K, Falb M, Tebbe A, Konstantinidis K, Bisle B, et al. Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis. JOURNAL OF PROTEOME RESEARCH. 2007;6(6):2195–204.
MLA
Aivaliotis, Michalis, Kris Gevaert, Michaela Falb, et al. “Large-scale Identification of N-terminal Peptides in the Halophilic Archaea Halobacterium Salinarum and Natronomonas Pharaonis.” JOURNAL OF PROTEOME RESEARCH 6.6 (2007): 2195–2204. Print.