Profiles of infection

Potential perils from bioterrorism to bird flu are increasingly pushing proteomics researchers to identify molecules involved in the infection process. Often stymied in characterizing all the proteins of a single organism, investigators must now contend with the complexities inherent in characterizing two intertwined, antagonistic organisms: host and pathogen. “There’s really just not a whole lot of proteomic work published yet” on host-pathogen interactions, says Sandra L. McCutchen-Maloney, biodefense proteomics group leader at Lawrence Livermore National Laboratory in Livermore, Calif., who recently coauthored a review of the literature. Prospects for such research are improving, however, thanks to technical advances and increased funding. If presentations at meetings are any indication, significant papers should emerge within a year, predicts Philip C. Hanna, an associate professor of microbiology and immunology at the University of Michigan Medical School in Ann Arbor.

Hanna directs one of seven biodefense proteomics research centers (BPRCs) that the US National Institute of Allergy and Infectious Diseases funded in 2004 for $81 million. Joseph J. Breen, the NIAID program officer who oversees the centers, describes their goal as generating targets for diagnostics, therapeutics, and vaccines. To attain it, some BPRC investigators are trying a bold new approach – monitoring host and pathogen proteomes simultaneously. Earlier studies, in contrast, identified proteins in either host or pathogen. McCutchen-Maloney, for example, separately explored proteomes of the plague bacterium Yersinia pestis and of the human cells it infects.

Most projects to date have focused on the pathogen’s proteome, which is simpler than the host’s and easier to manipulate genetically in follow-up studies. Findings about bacteria, in particular, are “more easily interpreted” because microbes regulate protein expression much more strictly than hosts do, says Eustache Paramithiotis, head of the BPRC at Caprion Pharmaceuticals in Montreal. But a pathogen-centered approach requires that a bacterium, virus, or parasite be able to thrive on its own or be extricable from its host. Otherwise, the host’s proteome can swamp the pathogen’s.

A host-centered approach, on the other hand, benefits from this imbalance, which renders host proteins easier to identify. But the most abundant – albumin in plasma, for example – must be selectively removed, or else they can mask the rarer signaling molecules thought to be crucial to the host’s response to infection. Moreover, large discrepancies seem to occur between protein sets expressed by hosts of the same species. In an unpublished study of 12 people, McCutchen-Maloney found that about 200 plasma proteins varied enough to differentiate one subject from another. Joshua N. Adkins, who manages the BPRC at Pacific Northwest National Laboratory in Richland, Wash., is initially focusing on the bacterium Salmonella typhimurium, though he eventually plans to scrutinize the macrophages that it infects. Adkins has cultured the pathogen in LB broth, which promotes its growth, and in magnesium-minimal medium (MgM), which mimics its intracellular environment.
He has already cataloged more than 2,400 proteins, 200 of which are unique to the MgM condition. In a related project, his team is seeking to purify the intracellular vacuole that contains the bacteria and to examine the pathogen and host proteins there. Adkins reports that in early experiments, vacuole isolates have been contaminated by host-cell mitochondria, which are “about the same size and similar in structure.”

The Scientist
December 20, 2005

Original web page at The Scientist