Genome-wide proteomics of Natronomonas pharaonis.
The aerobic, haloalkaliphilic archaeon Natronomonas pharaonis is able to survive in salt-saturated lakes of pH 11. According to genome analysis, the theoretical proteome consists of 2843 proteins. To reach further conclusions about its cellular physiology, the cytosolic protein inventory of Nmn. pharaonis has been analyzed using MS/MS on an ESI-Q-TOF mass spectrometer coupled on-line with a nanoLC system. The efficiency of this shotgun approach is illustrated by the identification of 929 proteins of which 886 are soluble proteins representing 41% of the cytosolic proteome. Cell lysis under denaturing conditions in water with subsequent separation by SDS-PAGE prior to nanoLC-MS/MS resulted in identification of 700 proteins. The same number (but a different subset) of proteins was identified upon cell lysis under native conditions followed by size fractionation (retaining protein complexes) prior to SDS-PAGE. Additional size fractionation reduced sample complexity and increased identification reliability. The set of identified proteins covers about 60% of the cytosolic proteins involved in metabolism and genetic information processing. Many of the identified proteins illustrate the high genetic variability among the halophilic archaea.
Konstantinidis
Kosta
K
Department of Membrane Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
Tebbe
Andreas
A
Klein
Christian
C
Scheffer
Beatrix
B
Aivaliotis
Michalis
M
Bisle
Birgit
B
Falb
Michaela
M
Pfeiffer
Friedhelm
F
Siedler
Frank
F
Oesterhelt
Dieter
D
D001105:Archaea / Q000378:metabolism; D002853:Chromatography, Liquid; D003062:Codon; D019295:Computational Biology / Q000379:methods; D003600:Cytosol / Q000378:metabolism; D004591:Electrophoresis, Polyacrylamide Gel; D016680:Genome, Bacterial; D006216:Halobacteriaceae / Q000378:metabolism*; D006863:Hydrogen-Ion Concentration; D005810:Multigene Family; D020543:Proteome; D040901:Proteomics / Q000379:methods*; D012492:Salts / Q000494:pharmacology; D021241:Spectrometry, Mass, Electrospray Ionization; D014867:Water / Q000378:metabolism
D003062:Codon; D020543:Proteome; D012492:Salts; D014867:Water