Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states.
Rhodopseudomonas palustris is a purple nonsulfur anoxygenic phototrophic bacterium that is ubiquitous in soil and water. R. palustris is metabolically versatile with respect to energy generation and carbon and nitrogen metabolism. We have characterized and compared the baseline proteome of a R. palustris wild-type strain grown under six metabolic conditions. The methodology for proteome analysis involved protein fractionation by centrifugation, subsequent digestion with trypsin, and analysis of peptides by liquid chromatography coupled with tandem mass spectrometry. Using these methods, we identified 1664 proteins out of 4836 predicted proteins with conservative filtering constraints. A total of 107 novel hypothetical proteins and 218 conserved hypothetical proteins were detected. Qualitative analyses revealed over 311 proteins exhibiting marked differences between conditions, many of these being hypothetical or conserved hypothetical proteins showing strong correlations with different metabolic modes. For example, five proteins encoded by genes from a novel operon appeared only after anaerobic growth with no evidence of these proteins in extracts of aerobically grown cells. Proteins known to be associated with specialized growth states such as nitrogen fixation, photoautotrophic, or growth on benzoate, were observed to be up-regulated under those states.
VerBerkmoes
Nathan C
NC
Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. verberkmoesn@ornl.gov
Shah
Manesh B
MB
Lankford
Patricia K
PK
Pelletier
Dale A
DA
Strader
Michael B
MB
Tabb
David L
DL
McDonald
W Hayes
WH
Barton
John W
JW
Hurst
Gregory B
GB
Hauser
Loren
L
Davison
Brian H
BH
Beatty
J Thomas
JT
Harwood
Caroline S
CS
Tabita
F Robert
FR
Hettich
Robert L
RL
Larimer
Frank W
FW
D000332:Aerobiosis / Q000502:physiology; D000693:Anaerobiosis / Q000502:physiology; D001426:Bacterial Proteins / Q000378:metabolism*; D002853:Chromatography, Liquid; D015964:Gene Expression Regulation, Bacterial; D008027:Light; D009586:Nitrogen Fixation; D020543:Proteome; D012241:Rhodopseudomonas / Q000378:metabolism*; D021241:Spectrometry, Mass, Electrospray Ionization
D001426:Bacterial Proteins; D020543:Proteome