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Microbiology. 2009 Apr;155(Pt 4):1103-10. doi: 10.1099/mic.0.024968-0.

Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis.

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  • 1Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.

Abstract

While the shotgun proteomics approach is gaining momentum in understanding microbial physiology, it remains limited by the paucity of high-quality genomic data, especially when it comes to poorly characterized newly identified phyla. At the same time, large-scale metagenomic sequencing projects produce datasets representing genomes of a variety of environmental microbes, although with lower sequence coverage and sequence quality. In this work we tested the utility of a metagenomic dataset enriched in sequences of environmental strains of Methylotenera mobilis, to assess the protein profile of a laboratory-cultivated strain, M. mobilis JLW8, as a proof of principle. We demonstrate that a large portion of the proteome predicted from the metagenomic sequence (approx. 20 %) could be identified with high confidence (three or more peptide sequences), thus gaining insights into the physiology of this bacterium, which represents a new genus within the family Methylophilaceae.

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