Methylococcus capsulatus: Difference between revisions
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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. | 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. | ||
===Reference=== | ===Reference=== | ||
Guengerich, F. P. (1991) J. Biol. Chem. 266, 10019-10022 | Guengerich, F. P. (1991) J. Biol. Chem. 266, 10019-10022 | ||
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Shet, M. S., Fisher, C. W., Holmans, P. L., and Estabrook, R. W. (1993) Proc. Natl. Acad. Sci. U. S. A | Shet, M. S., Fisher, C. W., Holmans, P. L., and Estabrook, R. W. (1993) Proc. Natl. Acad. Sci. U. S. A | ||
Bellamine, A., Mangla, A. T., Nes, W. D., and Waterman, M. R. (1999) Proc. Natl. Acad. Sci. U. S. A. | Bellamine, A., Mangla, A. T., Nes, W. D., and Waterman, M. R. (1999) Proc. Natl. Acad. | ||
Edited by Ting Yuan Feng, student of Rachel Larsen at UCSD.Sci. U. S. A. | |||
Revision as of 20:24, 3 May 2007
A Microbial Biorealm page on the genus Methylococcus capsulatus
Classification
Higher order taxa
Kingdom: Bacteria Domain: Proteobacteria Phylum: Gammaproteobacteria Class: Methylococcales Order: Methylococcaceae Family: Methylococcus
Species
- Genus: Methylococcus
- Species: capsulatus
Description and significance
Methylococcus capsulatus is a methylotrophic gram-negative bacterium with coccus shape, live in multiple habitate, however, oxygen is the necessity for such cell to survive. Methylococcus capsulatus is also a thermophilic microbe which optically live in the temperature of 45C.
Genome structure
"The genome of M. capsulatus (Bath) comprises a single circular molecule of 3,304,697 bp."
Methylocuccus capsulatus a Gram-Negative microbe with linear structure.
Cell structure and metabolism
"Methylococcus capsulatus is a methanotroph (Methane-oxidising bacteria.) Methanotrophs are ubiquitous Gram-negative bacteria that can use the greenhouse gas methane as a sole carbon and energy source for growth, thus playing major roles in global carbon cycles, and in particular, substantially reducing emissions of biologically generated methane to the atmosphere."
"Methanotrophs are also able to metabolize or co-metabolize xenobiotic compounds, including chlorinated solvents such as trichloroethylene, and hence have potential as bioremediation tools."
Ecology
"Methylococcus capsulatus (Bath) is the first complete genome sequence reported from an obligate methanotroph. Genome analysis suggests the ability of M. capsulatus to scavenge copper (including a previously unreported nonribosomal peptide synthetase) and to use copper in regulation of methanotrophy, but the exact regulatory mechanisms remain unclear."
Pathology
How does this organism cause disease? Human, animal, plant hosts? Virulence factors, as well as patient symptoms.
Application to Biotechnology
Does this organism produce any useful compounds or enzymes? What are they and how are they used?
Current Research
Arch Microbiol. 2005 Nov 26; :1-16 16311759
Analysing the outer membrane subproteome of Methylococcus capsulatus (Bath) using proteomics and novel biocomputing tools. Frode Berven , Odd Karlsen , Anne Straume , Kristian Flikka , J Murrell , Anne Fjellbirkeland , Johan Lillehaug , Ingvar Eidhammer , Harald Jensen 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.
Reference
Guengerich, F. P. (1991) J. Biol. Chem. 266, 10019-10022
Nelson, D. R., Koymans, L., Kamataki, T., Stegeman, J. J., Feyereisen, R., Waxman, D. J., Waterman, M. R., Gotoh, O., Coon, M. J., Estabrook, R. W., Gunsalus, I. C., and Nebert, D. W. (1996) Pharmacogenetics
Bird, C. W., Lynch, J. M., Pirt, F. J., Reid, W. W., Brooks, C. J. W., and Middleditch, B. S. (1971) Nature
Degtyarenko, K. N., and Archakov, A. I. (1993) FEBS Lett
Nakayama, N., Takemae, A., and Shoun, H. (1996) J. Biochem. (Tokyo)
Shet, M. S., Fisher, C. W., Holmans, P. L., and Estabrook, R. W. (1993) Proc. Natl. Acad. Sci. U. S. A
Bellamine, A., Mangla, A. T., Nes, W. D., and Waterman, M. R. (1999) Proc. Natl. Acad.
Edited by Ting Yuan Feng, student of Rachel Larsen at UCSD.Sci. U. S. A.
