Proteogenomic Strategies Help in Refining Plague Genome
Strains of bacteria from the genus Yersinia are pathogenic and have a wide virulence range. For example, Y. pseudotuberculosis causes intestinal distress, while Y. pestis causes plague. To better understand and potentially design ways to mitigate the effects of Yersinia on human health, a research team from the University of Texas Medical Branch, J. Craig Venter Institute, Pacific Northwest National Laboratory, and Environmental Molecular Sciences Laboratory (EMSL), a DOE scientific user facility in Richland, Washington, took on the task of refining the genome maps of three Yersinia strains. The team used one of EMSL’s mass spectrometers to obtain proteomic data and combined these data with microarray data to annotate both the proteome and transcriptome of the three Yersinia strains. The data confirmed the validity of nearly 40% of the computationally predicted genes and resulted in the discovery of 28 novel proteins expressed under conditions relevant to infections. In addition, 68 previously identified protein coding sequences were shown to be invalid. This new multi-faceted approach layers several types of evidence and substantially improves the genome annotation process. Importantly, the team’s work established refined genome annotations that provide essential information needed for a better understanding of how the plague functions, may provide new targets for therapeutics, and should speed the characterization of other pathogenic bacteria.
Schrimpe-Rutledge, A. C., M. B. Jones, S. Chauhan, S. O. Purvine, J. Sanford, M. E. Monroe, H. M. Brewer, S. H. Payne, C. Ansong, B. C. Frank, R. D. Smith, S. Peterson, V. L. Motin, and J. N. Adkins. 2012. “Comparative Omics-Driven Genome Annotation Refinement: Application Across Yersiniae,” PLoS One 7(3), e33903. DOI:10.1371/journal.pone.0033903.