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Research Highlights

May 2008

Protein Research Uncovers Surprising Similarities in Diverse Bacteria

Scientists use proteomics to reveal proteins commonly present in 17 different bacteria

Results: Diverse bacteria have more in common than previously thought. Bacteria as diverse as ocean-dwelling Pelagibacter ubique and bubonic plague-causing Yersinia pestis produce identical proteins, according to scientists from the Pacific Northwest National Laboratory. Called the "core proteome," this research represents 6 years of gathering and evaluating proteomics measurements.

Why it matters: Knowing what proteins lie outside of the core proteome, and thus are unique to a bacteria, may present an opportunity to identify proteins that signal environmental stress and to identify targets to treat infectious diseases. For example, with the core proteome data, the team created a list of potential therapeutic targets for the disease-causing Salmonella typhimurium.

The research was published in the February 6 issue of PLoS ONE and was highlighted in the May 2008 issue of the Journal of Proteome Research.

Methods: For the study, the team identified a core genome, 144 genes that were found in each of the bacteria. Next, the proteins produced by the bacteria were extracted and digested into peptides by trypsin. The peptides were separated into fractions using ion exchange chromatography and identified using reversed-phase high-pressure liquid chromatography coupled online to an ion trap mass spectrometer housed. The work was done in the Department of Energy's Environmental Molecular Sciences Laboratory, a national scientific user facility at PNNL.

The resulting spectra were analyzed against sequenced genomes and the resulting peptides and proteins identified, with the assistance of database that contains approximately 967,000 peptides linked to specific protein information. With the proteins identified, the core proteome or common protein set was determined.

Originally, the team did not expect to see many proteins in the core proteome, because of the differences in the evolution and preferred growth environments of each bacteria. They found, however, more than they expected. In the core proteome, slightly over half of the proteins are involved in protein synthesis activities, however, about 7% of the core proteome is composed of proteins whose function is unknown.

What's next: The team plans to study a broader range of organisms in the future.

Acknowledgments: This research was funded by the Department of Energy Office of Biological and Environmental Research, the National Institute of Health's National Institute of Allergy and Infectious Diseases, and the NIH National Center for Research Resources.

This research was performed in the U.S. Department of Energy's Environmental Molecular Sciences Laboratory, a national scientific user facility at PNNL.

This work was done by Stephen J. Callister, Lee Ann McCue, Joshua E. Turse, Matthew E. Monroe, Kenneth J. Auberry, Richard D. Smith, Joshua N. Adkins, and Mary S. Lipton at Pacific Northwest National Laboratory. This work is part of PNNL's contributions to achieving predictive understanding of multi-cellular biological systems.

Citation: Callister SJ, LA McCue, JE Turse, ME Monroe, KJ Auberry, RD Smith, JN Adkins, and MS Lipton. 2008. "Comparative Bacterial Proteomics: Analytics of the Core Genome Concept." PLoS ONE 3(2):e1542.

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