Proteomics of foodborne bacterial pathogens

Authors: Fagerquist, Clifton - Keith

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 1/1/2009
Publication Date: 2/1/2011
Citation: Fagerquist, C.K. 2011. Proteomics of foodborne bacterial pathogens. In: Wiedman, M.; Zhang, W., editors of: Genomics of foodborne bacterial pathogens. New York, NY: Springer. p. 343-402.

Interpretive Summary: The proteomics of microorganisms, and in particular foodborne pathogens, is a relatively new area of research. Proteomics is only one component of systems biology (genomics/transcriptomics/proteomics/metabolomics), however it plays a critical role in the understanding of microorganisms and their response to their environment through changes in protein expression and post-translational processing. Proteomics is now widely utilized for global proteome and subproteome investigations of foodborne pathogens. The rapid development of mass spectrometry-based proteomics and the parallel development of protein microarrays suggest that this field will continue to evolve with the emergence of new proteomics technologies and improvements in existing proteomics platforms. As future outbreaks of microbially-linked foodborne illness occur, proteomics will undoubtedly continue to focus on issues related to antibiotic resistance, biofilm formation, virulence and pathogenicity, microbial forensics, microbial persistence in the environment, pathogen/host interactions, lateral gene transfer, bacterial communities, quorum sensing and vaccine development. This chapter is intended to be a relatively brief overview of proteomics techniques currently in use for the identification and analysis of microorganisms with a special emphasis on foodborne pathogens.

Technical Abstract: This chapter focuses on recent research on foodborne bacterial pathogens that use mass spectrometry-based proteomic techniques as well as protein microarrays. Mass spectrometry ionization techniques (e.g. electrospray ionization and matrix-assisted laser desorption/ionization), analyzers (e.g. ion trap, time-of-flight, ion cyclotron resonance, Orbitrap, ion mobility, hybrid instruments, etc.) and dissociation techniques (e.g. collision-induced dissociation, post-source decay, electron capture/transfer dissociation, etc.) are discussed within the context of proteomic applications. Various proteomic strategies are also discussed (i.e. "bottom-up", "top-down", "middle-down", etc.) as well as labeling (or label-free) techniques for quantifying changes in protein expression. Proteomics software is also highlighted: commercial versus open-source search engines, de novo sequencing software, sub-cellular localization software and software for identification of protein post-translational modifications. A brief summary of protein microarray technology is also provided. Finally, a number of recent studies of foodborne pathogens are highlighted that utilize proteomic techniques to address specific biological questions, e.g. the increased virulence and pathogenicity of specific strains, the effect of environmental conditions (pH, temperature, oxidation) on bacterial stress response, the emergence of antibiotic resistance strains, etc.