Proteomics in Pathogen Target Discovery

Like cultured cell lines, unicellular organisms offer the opportunity to study pathogenesis in a controlled and uniform laboratory environment, allowing for more precise measurements of protein/cell input and greater reproducibility in proteomic systems. In an attempt to characterize the adaptation of Pseudomonas aeruginosa to airway epithelia in cystic fibrosis, Guina et al. (62) carried out a full proteomic analysis of the organism using an in vitro model of the adaptive response, demonstrating the induction of an entire metabolic pathway affecting the homoserine lactone signaling pathway. The elucidation of the genomic structure and sequence of the malarial parasite Plasmodium falciparum paved the way for a thorough proteomic investigation of proteins expressed at each stage of its lifecycle. Using MudPIT, 2400 different proteins were annotated with correlation to the developmental stage and included some new findings relevant to pharmaceutical or immunological intervention (63). Cell surface interactions are considered to be important in pathogenicity, and proteomic studies have also focused on the identification of proteins extracted from in vitro biotinylated whole organisms, such as Helicobacter pylori (64).

Protein-based assays have been used for some time to detect pathogens. These can either be the direct detection of pathogen antigens or, in the case of many viral infections, detection of the antibodies naturally generated against them. The discovery of this type of antigen and antibody marker is well suited to proteomic studies because the induced protein profile changes can be absolute (i.e., presence versus absence of a particular protein), and the induction of an immune response could allow the use of such technologies as SEREX (42) to define pathogen antigens. These and many other studies indicate the potential to discover new markers for early identification of infections, or for the monitoring of infectious stages, through to novel antibiotic targets.

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