Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools.
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.
Berven
Frode S
FS
Department of Molecular Biology, University of Bergen, Thormøhlensgate 55, N-5020, Bergen, Norway. frodeb@ii.uib.no
Karlsen
Odd André
OA
Straume
Anne Hege
AH
Flikka
Kristian
K
Murrell
J Colin
JC
Fjellbirkeland
Anne
A
Lillehaug
Johan R
JR
Eidhammer
Ingvar
I
Jensen
Harald B
HB
D001425:Bacterial Outer Membrane Proteins / Q000737:chemistry / Q000235:genetics*; D019921:Biotinylation; D002254:Carbonates; D019295:Computational Biology / Q000379:methods*; D015180:Electrophoresis, Gel, Two-Dimensional / Q000379:methods; D016680:Genome, Bacterial / Q000235:genetics; D020619:Methylococcus capsulatus / Q000737:chemistry / Q000235:genetics*; D040901:Proteomics / Q000379:methods*; D012995:Solubility
D001425:Bacterial Outer Membrane Proteins; D002254:Carbonates