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Issue 11, 2012
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The identification of global patterns and unique signatures of proteins across 14 environments using outer membrane proteomics of bacteria

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Abstract

We test the hypothesis that organisms sourced from different environments exhibit unique fingerprints in macromolecular composition. Experimentally, we followed proteomic changes with 14 different sub-lethal environmental stimuli in Escherichia coli at controlled growth rates. The focus was on the outer membrane sub-proteome, which is known to be extremely sensitive to environmental controls. The analyses surprisingly revealed that pairs of proteins belonging to very different regulons, such as Slp and OmpX or FadL and OmpF, have the closest patterns of change with the 14 conditions. Fe-limited and cold-cultured bacteria have the most distinct global patterns of spot changes, but the patterns with fast growth and oxygen limitation are the closest amongst the 14 environments. These unexpected but statistically robust results suggest that we have an incomplete picture of bacterial regulation across different stress responses; baseline choices and growth-rate influences are probably underestimated factors in such systems-level analysis. In terms of our aim of getting a unique profile for each of the 14 investigated environments, we find that it is unnecessary to compare all the proteins in a proteome and that a panel of five proteins is sufficient for identification of environmental fingerprints. This demonstrates the future feasibility of tracing the history of contaminating bacteria in hospitals, foods or industrial settings as well as for released organisms and biosecurity purposes.

Graphical abstract: The identification of global patterns and unique signatures of proteins across 14 environments using outer membrane proteomics of bacteria

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Publication details

The article was received on 29 May 2012, accepted on 16 Aug 2012 and first published on 17 Aug 2012


Article type: Paper
DOI: 10.1039/C2MB25212K
Citation: Mol. BioSyst., 2012,8, 3017-3027
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    The identification of global patterns and unique signatures of proteins across 14 environments using outer membrane proteomics of bacteria

    M. Schliep, B. Ryall and T. Ferenci, Mol. BioSyst., 2012, 8, 3017
    DOI: 10.1039/C2MB25212K

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