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Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools
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UNSPECIFIED. (2006) Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. ARCHIVES OF MICROBIOLOGY, 184 (6). pp. 362-377. ISSN 0302-8933
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Official URL: http://dx.doi.org/10.1007/s00203-005-0055-7
Abstract
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 (http://www.bioinfo.no/tools/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 (http://www.bioinfo.no/tools/lipo). This report is the first using a proteomics and bioinformatics approach to identify the OM subproteome of an obligate methanotroph.
| Item Type: | Journal Article |
|---|---|
| Subjects: | Q Science > QR Microbiology |
| Journal or Publication Title: | ARCHIVES OF MICROBIOLOGY |
| Publisher: | SPRINGER |
| ISSN: | 0302-8933 |
| Date: | February 2006 |
| Volume: | 184 |
| Number: | 6 |
| Number of Pages: | 16 |
| Page Range: | pp. 362-377 |
| Identification Number: | 10.1007/s00203-005-0055-7 |
| Publication Status: | Published |
| URI: | http://wrap.warwick.ac.uk/id/eprint/34005 |
Data sourced from Thomson Reuters' Web of Knowledge
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