The low molecular weight proteome of Halobacterium salinarum

Christian Klein; Michalis Aivaliotis; Jesper Velgaard Olsen; Michaela Falb; Hüseyin Besir; Beatrix Scheffer; Birgit Bisle; Andreas Tebbe; Kosta Konstantinidis; Frank Siedler; Friedhelm Pfeiffer; Matthias Mann; Dieter Oesterhelt

doi:10.1021/pr060634q

The low molecular weight proteome of Halobacterium salinarum

Christian Klein, Michalis Aivaliotis, Jesper Velgaard Olsen, Michaela Falb, Hüseyin Besir, Beatrix Scheffer, Birgit Bisle, Andreas Tebbe, Kosta Konstantinidis, Frank Siedler, Friedhelm Pfeiffer, Matthias Mann, Dieter Oesterhelt

56 Citations (Scopus)

Abstract

Systematic investigation of low molecular weight proteins (LMW, below 20 kDa) in the archaeon Halobacterium salinarum resulted in a 6-fold enhancement of the identification rate, reaching 35% of the theoretical proteome in that size range. This was achieved by optimization of common protocols for protein analysis with general applicability. LMW proteins were rapidly and effectively enriched by filter membrane centrifugation followed by tricine SDS-PAGE. Without staining and with significantly shortened digestion protocols, LMW proteins were identified using an FT-ICR mass spectrometer which allows reliable protein identification by MS3 of a single peptide. In addition to a series of technical challenges, small proteins may show low gene expression levels as suggested by their low average codon adaptation index. Twenty functionally uncharacterized proteins contain a characteristic DNA/RNA binding zinc finger motif which underlines the biological relevance of the small proteome and the necessity of their analysis for systems biology.

Original language	English
Journal	Journal of Proteome Research
Volume	6
Issue number	4
Pages (from-to)	1510-8
Number of pages	8
ISSN	1535-3893
DOIs	https://doi.org/10.1021/pr060634q
Publication status	Published - 2007
Externally published	Yes

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10.1021/pr060634q

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title = "The low molecular weight proteome of Halobacterium salinarum",

abstract = "Systematic investigation of low molecular weight proteins (LMW, below 20 kDa) in the archaeon Halobacterium salinarum resulted in a 6-fold enhancement of the identification rate, reaching 35% of the theoretical proteome in that size range. This was achieved by optimization of common protocols for protein analysis with general applicability. LMW proteins were rapidly and effectively enriched by filter membrane centrifugation followed by tricine SDS-PAGE. Without staining and with significantly shortened digestion protocols, LMW proteins were identified using an FT-ICR mass spectrometer which allows reliable protein identification by MS3 of a single peptide. In addition to a series of technical challenges, small proteins may show low gene expression levels as suggested by their low average codon adaptation index. Twenty functionally uncharacterized proteins contain a characteristic DNA/RNA binding zinc finger motif which underlines the biological relevance of the small proteome and the necessity of their analysis for systems biology.",

author = "Christian Klein and Michalis Aivaliotis and Olsen, {Jesper Velgaard} and Michaela Falb and H{\"u}seyin Besir and Beatrix Scheffer and Birgit Bisle and Andreas Tebbe and Kosta Konstantinidis and Frank Siedler and Friedhelm Pfeiffer and Matthias Mann and Dieter Oesterhelt",

note = "Keywords: Amino Acid Sequence; Archaeal Proteins; Codon; Electrophoresis, Polyacrylamide Gel; Glycine; Halobacterium salinarum; Molecular Sequence Data; Molecular Weight; Proteome; RNA-Binding Proteins; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Transcription Factors",

year = "2007",

doi = "10.1021/pr060634q",

language = "English",

volume = "6",

pages = "1510--8",

journal = "Journal of Proteome Research",

issn = "1535-3893",

publisher = "American Chemical Society",

number = "4",

}

TY - JOUR

T1 - The low molecular weight proteome of Halobacterium salinarum

AU - Klein, Christian

AU - Aivaliotis, Michalis

AU - Olsen, Jesper Velgaard

AU - Falb, Michaela

AU - Besir, Hüseyin

AU - Scheffer, Beatrix

AU - Bisle, Birgit

AU - Tebbe, Andreas

AU - Konstantinidis, Kosta

AU - Siedler, Frank

AU - Pfeiffer, Friedhelm

AU - Mann, Matthias

AU - Oesterhelt, Dieter

N1 - Keywords: Amino Acid Sequence; Archaeal Proteins; Codon; Electrophoresis, Polyacrylamide Gel; Glycine; Halobacterium salinarum; Molecular Sequence Data; Molecular Weight; Proteome; RNA-Binding Proteins; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; Transcription Factors

PY - 2007

Y1 - 2007

N2 - Systematic investigation of low molecular weight proteins (LMW, below 20 kDa) in the archaeon Halobacterium salinarum resulted in a 6-fold enhancement of the identification rate, reaching 35% of the theoretical proteome in that size range. This was achieved by optimization of common protocols for protein analysis with general applicability. LMW proteins were rapidly and effectively enriched by filter membrane centrifugation followed by tricine SDS-PAGE. Without staining and with significantly shortened digestion protocols, LMW proteins were identified using an FT-ICR mass spectrometer which allows reliable protein identification by MS3 of a single peptide. In addition to a series of technical challenges, small proteins may show low gene expression levels as suggested by their low average codon adaptation index. Twenty functionally uncharacterized proteins contain a characteristic DNA/RNA binding zinc finger motif which underlines the biological relevance of the small proteome and the necessity of their analysis for systems biology.

AB - Systematic investigation of low molecular weight proteins (LMW, below 20 kDa) in the archaeon Halobacterium salinarum resulted in a 6-fold enhancement of the identification rate, reaching 35% of the theoretical proteome in that size range. This was achieved by optimization of common protocols for protein analysis with general applicability. LMW proteins were rapidly and effectively enriched by filter membrane centrifugation followed by tricine SDS-PAGE. Without staining and with significantly shortened digestion protocols, LMW proteins were identified using an FT-ICR mass spectrometer which allows reliable protein identification by MS3 of a single peptide. In addition to a series of technical challenges, small proteins may show low gene expression levels as suggested by their low average codon adaptation index. Twenty functionally uncharacterized proteins contain a characteristic DNA/RNA binding zinc finger motif which underlines the biological relevance of the small proteome and the necessity of their analysis for systems biology.

U2 - 10.1021/pr060634q

DO - 10.1021/pr060634q

M3 - Journal article

SN - 1535-3893

VL - 6

SP - 1510

EP - 1518

JO - Journal of Proteome Research

JF - Journal of Proteome Research

IS - 4

ER -

The low molecular weight proteome of Halobacterium salinarum

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