Determination and Comparison of the Baseline Proteomes of the Versatile Microbe Rhodopseudomonas palustris under its Major Metabolic States

Journal Article · Sun Jan 01 00:00:00 EST 2006 · Journal of Proteome Research

DOI:https://doi.org/10.1021/pr0503230· OSTI ID:978060

Verberkmoes, Nathan C ^[1]; Shah, Manesh B ^[1]; Lankford, Patricia K ^[1]; Pelletier, Dale A ^[1]; Strader, Michael B ^[1]; Tabb, Dave L ^[1]; McDonald, W Hayes ^[1]; Barton, John W ^[1]; Hauser, Loren John ^[1]; Davison, Brian H ^[1]; Beatty, Thomas ^[2]; Harwood, Caroline S ^[3]; Tabita, F Robert ^[4]; Larimer, Frank W ^[1]

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1. ORNL
2. University of British Columbia, Vancouver
3. University of Washington, Seattle
4. Ohio State University

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.

• Research Organization: Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
• Sponsoring Organization: USDOE Office of Science (SC)
• DOE Contract Number: DE-AC05-00OR22725
• OSTI ID: 978060
• Journal Information: Journal of Proteome Research, Vol. 5, Issue 2
• Country of Publication: United States
• Language: English

Related Subjects

59 BASIC BIOLOGICAL SCIENCES
54 ENVIRONMENTAL SCIENCES
99 GENERAL AND MISCELLANEOUS//MATHEMATICS, COMPUTING, AND INFORMATION SCIENCE
CARBON
CENTRIFUGATION
CHROMATOGRAPHY
DIGESTION
FRACTIONATION
GENES
MASS SPECTROSCOPY
METABOLISM
NITROGEN
NITROGEN FIXATION
PEPTIDES
PROTEINS
RHODOPSEUDOMONAS
SOILS
STRAINS
TRYPSIN
WATER