A Glimpse into the Proteome of Phototrophic Bacterium Rhodobacter capsulatus

  • Ozlem Onder
  • Semra Aygun-Sunar
  • Nur Selamoglu
  • Fevzi Daldal
Conference paper
Part of the Advances in Experimental Medicine and Biology book series (AEMB, volume 675)


A first glimpse into the proteome of Rhodobacter capsulatus revealed more than 450 (with over 210 cytoplasmic and 185 extracytoplasmic known as well as 55 unknown) proteins that are identified with high degree of confidence using nLC–MS/MS analyses. The accumulated data provide a solid platform for ongoing efforts to establish the proteome of this species and the cellular locations of its constituents. They also indicate that at least 40 of the identified proteins, which were annotated in genome databases as unknown hypothetical proteins, correspond to predicted translation products that are indeed present in cells under the growth conditions used in this work. In addition, matching the identification labels of the proteins reported between the two available R. capsulatus genome databases (ERGO-light with RRCxxxxx and NT05 with NT05RCxxxx numbers) indicated that 11 such proteins are listed only in the latter database.


Major Metabolic Pathway Acclaim PepMap100 Tryptic Peptide Mixture Comprehensive Proteome Analysis Predict Translation Product 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.



This work is supported by grants from DOE ER9120053 and NIH GM38237 to F.D.


  1. Bendtsen JD, Nielsen H, von Heijne G et al (2004) Improved prediction of signal peptides: SignalP 3.0. J Mol Biol 340:783–795PubMedCrossRefGoogle Scholar
  2. Daldal F, Cheng S, Applebaum J et al (1986) Cytochrome c (2) is not essential for photosynthetic growth of Rhodopseudomonas capsulata. Proc Natl Acad Sci USA 83:2012–2016PubMedCrossRefGoogle Scholar
  3. Du X, Callister SJ, Manes NP et al (2008) A computational strategy to analyze label-free temporal bottom-up proteomics data. J Proteome Res 7:2595–604Google Scholar
  4. Gardy JL, Laird MR, Chen F et al (2005) PSORTb v.2.0: expanded prediction of bacterial protein subcellular localization and insights gained from comparative proteome analysis. Bioinformatics 21:617–623PubMedCrossRefGoogle Scholar
  5. Hunter NC, Daldal F, Thurnauer MC, Beatty JT (eds) (2009) The purple phototrophic bacteria. Springer, DordrechtCrossRefGoogle Scholar
  6. Myllykallio H, Jenney FE Jr, Moomaw CR et al (1997) Cytochrome c(y) of Rhodobacter capsulatus is attached to the cytoplasmic membrane by an uncleaved signal sequence-like anchor. J Bacteriol 179:2623–2631PubMedGoogle Scholar
  7. Neuhoff V, Stamm R, Pardowitz I et al (1990) Essential problems in quantification of proteins following colloidal staining with coomassie brilliant blue dyes in polyacrylamide gels, and their solution. Electrophoresis 11:101–117PubMedCrossRefGoogle Scholar
  8. Onder O, Turkarslan S, Sun D et al (2008) Overproduction or absence of the periplasmic protease DegP severly compromises bacterial growth in the absence of the dithiol:disulfide oxidoreductase DsbA. Mol Cell Proteomics 7:875–890PubMedCrossRefGoogle Scholar
  9. Onder O, Yoon H, Naumann B et al (2006) Modifications of the lipoamide-containing mitochondrial subproteome in a yeast mutant defective in cysteine desulfurase. Mol Cell Proteomics 5:1426–1436PubMedCrossRefGoogle Scholar
  10. Park SJ, Lee SY, Cho J et al (2005) Global physiological understanding and metabolic engineering of microorganisms based on omics studies. Appl Microb Biotechnol 68: 567–79Google Scholar
  11. Ren Q, Thony-Meyer L (2001) Physical interaction of CcmC with heme and the heme chaperone CcmE during cytochrome c maturation. J Biol Chem 276:32591–32596PubMedCrossRefGoogle Scholar
  12. Wasinger V (2006) Holistic biology of microorganisms: genomics, transcriptomics, and proteomics. Methods Biochem Anal 49:3–14PubMedGoogle Scholar
  13. Zannoni D (1995) Aerobic and anaerobic electron transport chains in anoxygenic phototrophic bacteria. In: Blankenship RE, Madigan MT, Bauer CE (eds) Anoxygenic photosynthetic bacteria. Kluwer Academic, Dordrecht, pp 949–971Google Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Ozlem Onder
    • 1
  • Semra Aygun-Sunar
    • 1
  • Nur Selamoglu
    • 1
  • Fevzi Daldal
    • 1
  1. 1.Department of BiologyUniversity of PennsylvaniaPhiladelphiaUSA

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