Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools

Arch Microbiol. 2006 Feb;184(6):362-77. doi: 10.1007/s00203-005-0055-7. Epub 2005 Nov 26.


High-resolution two-dimensional gel electrophoresis and mass spectrometry has been used to identify the outer membrane (OM) subproteome of the Gram-negative bacterium Methylococcus capsulatus (Bath). Twenty-eight unique polypeptide sequences were identified from protein samples enriched in OMs. Only six of these polypeptides had previously been identified. The predictions from novel bioinformatic methods predicting beta-barrel outer membrane proteins (OMPs) and OM lipoproteins were compared to proteins identified experimentally. BOMP ( ) predicted 43 beta-barrel OMPs (1.45%) from the 2,959 annotated open reading frames. This was a lower percentage than predicted from other Gram-negative proteomes (1.8-3%). More than half of the predicted BOMPs in M. capsulatus were annotated as (conserved) hypothetical proteins with significant similarity to very few sequences in Swiss-Prot or TrEMBL. The experimental data and the computer predictions indicated that the protein composition of the M. capsulatus OM subproteome was different from that of other Gram-negative bacteria studied in a similar manner. A new program, Lipo, was developed that can analyse entire predicted proteomes and give a list of recognised lipoproteins categorised according to their lipo-box similarity to known Gram-negative lipoproteins ( ). This report is the first using a proteomics and bioinformatics approach to identify the OM subproteome of an obligate methanotroph.

Publication types

  • Evaluation Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Bacterial Outer Membrane Proteins / chemistry
  • Bacterial Outer Membrane Proteins / genetics*
  • Biotinylation
  • Carbonates
  • Computational Biology / methods*
  • Electrophoresis, Gel, Two-Dimensional / methods
  • Genome, Bacterial / genetics
  • Methylococcus capsulatus / chemistry
  • Methylococcus capsulatus / genetics*
  • Proteomics / methods*
  • Solubility


  • Bacterial Outer Membrane Proteins
  • Carbonates