title: Determination and comparison of the baseline proteomes of the versatile microbe Rhodopseudomonas palustris under its major metabolic states.
abstract: 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.
authors.affiliation: Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA. verberkmoesn@ornl.gov
authors.forename: Nathan C
authors.initials: NC
authors.lastname: VerBerkmoes
authors.forename: Manesh B
authors.initials: MB
authors.lastname: Shah
authors.forename: Patricia K
authors.initials: PK
authors.lastname: Lankford
authors.forename: Dale A
authors.initials: DA
authors.lastname: Pelletier
authors.forename: Michael B
authors.initials: MB
authors.lastname: Strader
authors.forename: David L
authors.initials: DL
authors.lastname: Tabb
authors.forename: W Hayes
authors.initials: WH
authors.lastname: McDonald
authors.forename: John W
authors.initials: JW
authors.lastname: Barton
authors.forename: Gregory B
authors.initials: GB
authors.lastname: Hurst
authors.forename: Loren
authors.initials: L
authors.lastname: Hauser
authors.forename: Brian H
authors.initials: BH
authors.lastname: Davison
authors.forename: J Thomas
authors.initials: JT
authors.lastname: Beatty
authors.forename: Caroline S
authors.initials: CS
authors.lastname: Harwood
authors.forename: F Robert
authors.initials: FR
authors.lastname: Tabita
authors.forename: Robert L
authors.initials: RL
authors.lastname: Hettich
authors.forename: Frank W
authors.initials: FW
authors.lastname: Larimer
mesh_terms: 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
chemical_list: D001426:Bacterial Proteins; D020543:Proteome