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

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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 β-barrel outer membrane proteins (OMPs) and OM lipoproteins were compared to proteins identified experimentally. BOMP (http://www.bioinfo.no/tools/bomp) predicted 43 β-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.

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Abbreviations

OMP:

Outer membrane protein

ICM:

Intra-cytoplasmic membrane system

IM:

Inner membrane

OM:

Outer membrane

PTF:

Peptide mass fingerprint

CHAPS:

3[(3-cholamidopropyl)-dimethyl-ammonio]-1-propanesulfonate

GRAVY:

Grand average hydropathy

TFA:

Trifluoroacetic acid

LC:

Liquid chromatography

TM:

Transmembrane

ORF:

Open reading frame

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Acknowledgements

This work was supported in part by grants from the Norwegian Research Council [SUP 140785/420 (GABI); FUGE/CBU-151899/ISO], the Meltzer Foundation, University of Bergen, and the National Programme for Research in Functional Genomics (FUGE) in The Research Council of Norway.

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Authors and Affiliations

  1. Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway

    Frode S. Berven, Odd André Karlsen, Anne Hege Straume, Anne Fjellbirkeland, Johan R. Lillehaug & Harald B. Jensen

  2. Computational Biology Unit, Bergen Centre for Computational Science, Coventry, England

    Kristian Flikka

  3. Department of Biological Sciences, University of Warwick, Coventry, England

    J. Colin Murrell

  4. Department of Informatics, University of Bergen, Bergen, Norway

    Ingvar Eidhammer

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  1. Frode S. Berven
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  2. Odd André Karlsen
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  9. Harald B. Jensen
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Correspondence to Frode S. Berven.

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Berven, F.S., Karlsen, O.A., Straume, A.H. et al. Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Arch Microbiol 184, 362–377 (2006). https://doi.org/10.1007/s00203-005-0055-7

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  • DOI: https://doi.org/10.1007/s00203-005-0055-7

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