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Microbiology 155 (2009), 1103-1110; DOI  10.1099/mic.0.024968-0
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Microbiology 155 (2009), 1103-1110; DOI  10.1099/mic.0.024968-0
© 2009 Society for General Microbiology

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

Gundula Bosch1, Tiansong Wang2, Ekaterina Latypova1, Marina G. Kalyuzhnaya2, Murray Hackett1 and Ludmila Chistoserdova1

1 Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA
2 Department of Microbiology, University of Washington, Seattle, WA 98195, USA

Correspondence
Ludmila Chistoserdova
milachis{at}u.washington.edu

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.

Abbreviations: GS/GOGAT, glutamine synthetase/glutamate synthase; RMP, ribulose monophosphate

A supplementary table is available with the online version of this paper.






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