Insights into the physiology of Methylotenera mobilis as revealed by metagenome-based shotgun proteomic analysis.
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.
Bosch
Gundula
G
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.
Wang
Tiansong
T
Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
Latypova
Ekaterina
E
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.
Kalyuzhnaya
Marina G
MG
Department of Microbiology, University of Washington, Seattle, WA 98195, USA.
Hackett
Murray
M
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.
Chistoserdova
Ludmila
L
Department of Chemical Engineering, University of Washington, Seattle, WA 98195, USA.