The low molecular weight proteome of Halobacterium salinarum.
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.
Klein
Christian
C
Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
Aivaliotis
Michalis
M
Olsen
Jesper V
JV
Falb
Michaela
M
Besir
Hüseyin
H
Scheffer
Beatrix
B
Bisle
Birgit
B
Tebbe
Andreas
A
Konstantinidis
Kosta
K
Siedler
Frank
F
Pfeiffer
Friedhelm
F
Mann
Matthias
M
Oesterhelt
Dieter
D
D000595:Amino Acid Sequence; D019843:Archaeal Proteins / Q000032:analysis*; D003062:Codon / Q000235:genetics; D004591:Electrophoresis, Polyacrylamide Gel; D005998:Glycine / Q000031:analogs & derivatives / Q000737:chemistry; D019617:Halobacterium salinarum / Q000378:metabolism*; D008969:Molecular Sequence Data; D008970:Molecular Weight; D020543:Proteome / Q000032:analysis* / Q000235:genetics; D016601:RNA-Binding Proteins / Q000032:analysis*; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D014157:Transcription Factors / Q000032:analysis*
D019843:Archaeal Proteins; D003062:Codon; D020543:Proteome; D016601:RNA-Binding Proteins; D014157:Transcription Factors; D005998:Glycine; C100184:tricine