On the trail of a core proteome for bacteria

LC/MS/MS is used to determine common genes expressed in a variety of bacteria.

STEPHEN CALLISTER

A core genome of 144 genes is predicted by comparing the genomes of 17 bacteria. Of the 144 core genes, 105 were verified by protein observations; these represent the core proteome for the set of bacteria.

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Although scientists can identify genes that are common to all of the variants of a particular species, they generally do not check whether the proteins encoded by a core genome are expressed. For the first time, researchers at Pacific Northwest National Laboratory (PNNL) have validated the expression of the common genes and defined a core proteome shared by multiple species of bacteria (PLoS ONE 2008, 3, e1542). To verify their proposed set of conserved bacterial genes, Stephen Callister, Joshua Adkins, Mary Lipton, and their colleagues have used LC/MS/MS to identify the proteins expressed by the genes conserved across 17 different types of bacteria. The "study advances the application of proteomics beyond the paradigms of single organism versus multiple conditions or wild-type versus mutant comparisons," says Callister.

An ortholog is a gene found in two or more species that can be traced to a common ancestor. To discover the core genome, the team used algorithms to find 144 orthologs present in all 17 bacteria. Then, the authors searched their extensive database of LC/MS/MS data for bacterial proteins expressed by the core genome and present in two or more types of bacteria. A minimum of two peptides was needed to identify each protein.

Because the bacteria have different evolutionary paths and preferred growth environments, the researchers did not expect to see many proteins in the core proteome. However, they found that 74% of the core genes express proteins in all 17 bacteria. Of the proteins in this core proteome, 55% are involved in protein synthesis, and ~7% have a general characterization or unknown functions. "I personally was surprised that there are proteins that are part of . . . the observed core proteome as small as YbeB, ~12 kDa, that are poorly characterized in the literature," says Adkins.

Jeremy Nicholson of Imperial College London writes that this work is significant because it "translates the core genome concept to something potentially more useful—a functional classification of bacteria and their biological potentials (to act within an environment)—based on the similarity of their core proteomes." However, he adds that a limitation of all proteomic techniques is the inability to directly assay functional activity, which depends on protein conformation and location and, for enzymes, cofactors, substrates, and the absence of inhibitors.

Although the group concluded that the core proteome is likely to be independent of culture conditions, they suggested that the study of orthologs that are unique to closely related organisms could help scientists determine the proteome that is associated with a given growth environment and identify therapeutic targets. For example, the authors generated a list of potential therapeutic targets against a particular Salmonella species by identifying orthologs that were uniquely expressed in one species but not in the other.

The team is quick to credit the many collaborators who enabled the acquisition of such a large and varied data set. Adkins says, "In general, we are pushing to make as much of our data [publicly] available as possible. Currently, a substantial amount of data for Salmonella typhimurium and Salmonella typhi are available in raw form at http://omics.pnl.gov."

Ron Beavis of the University of British Columbia (Canada) points out that most labs discard data irrelevant to their hypotheses, and this situation leads to "a curious form of scientific Alzheimer's: even the most well-known proteomics laboratories cannot leverage their previous measurements to act as a guide to the design of new experiments in any systematic fashion." Beavis looks to the PNNL paper to "mark the turning point where proteomics changes from being simply a series of 'one-off' experiments into a field in which new experiments can be tested and placed into the context of previous results."

According to Callister, the specific applications of their research include the identification of environmental markers for monitoring biological processes and, to some extent, the basal components of bacterial life. Lipton says the group plans to study a broader range of organisms. "When we understand the core set of genes, we understand the essentiality of life itself and what is necessary for life. . . . Understanding these relationships will give us a deeper understanding of the relationship between biological organisms and evolution."

—Christine Piggee