U.S. Department of Energy Office of Biological and Environmental Research

BER Research Highlights


Proteogenomic Strategies Help in Refining Plague Genome
Published: March 27, 2012
Posted: May 24, 2012

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.

Reference: 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. (Reference link)

Contact: Paul E. Bayer, SC-23.1, (301) 903-5324
Topic Areas:

  • Research Area: DOE Environmental Molecular Sciences Laboratory (EMSL)
  • Research Area: Genomic Analysis and Systems Biology
  • Research Area: Microbes and Communities
  • Research Area: Computational Biology, Bioinformatics, Modeling

Division: SC-23.1 Climate and Environmental Sciences Division, BER

 

BER supports basic research and scientific user facilities to advance DOE missions in energy and environment. More about BER

Recent Highlights

Aug 24, 2019
New Approach for Studying How Microbes Influence Their Environment
A diverse group of scientists suggests a common framework and targeting of known microbial processes [more...]

Aug 08, 2019
Nutrient-Hungry Peatland Microbes Reduce Carbon Loss Under Warmer Conditions
Enzyme production in peatlands reduces carbon lost to respiration under future high temperatures. [more...]

Aug 05, 2019
Amazon Forest Response to CO2 Fertilization Dependent on Plant Phosphorus Acquisition
AmazonFACE Model Intercomparison. The Science Plant growth is dependent on the availabi [more...]

Jul 29, 2019
A Slippery Slope: Soil Carbon Destabilization
Carbon gain or loss depends on the balance between competing biological, chemical, and physical reac [more...]

Jul 15, 2019
Field Evaluation of Gas Analyzers for Measuring Ecosystem Fluxes
How gas analyzer type and correction method impact measured fluxes. The Science A side- [more...]

List all highlights (possible long download time)