Comparative Proteomics Reveals Core vs. Unique Molecular Signatures for Dissimilatory Metal Reducing Bacteria Grown with Various Electron Acceptors

Dissimilatory metal reducing bacteria (DMRB) are probably one of the most respiratory versatile microorganisms on earth. Their ability to use metals as terminal electron acceptor allows them to survive in severe environments (e.g. radionuclide contaminated soil). In addition to metals, many other organic and inorganic substrates can be utilized as electron acceptors for DMRB respiration, including fumarate, nitrate, oxygen, etc. Genome information for many DMRB species is available, which reveals large numbers of c-type cytochrome encoding genes present in their genomes. For example, the genomes of three DMRBs, Anaeromyxobacter dehalogenans strain 2CP-C, Shewanella oneidensis strain MR-1, and Geobacter daltonii strain FRC-32, contain 69, 40, and 72 putative c-type cytochrome genes, respectively. Although mutagenesis techniques have determined the respiratory roles of several c-type cytochromes, gene disruption for majorities of the putative c-type cytochromes does not generate visible phenotypical alterations, and is not able to functionally link them to specific respirational activities. Thus, comprehensive proteome characterization for DMRBs is needed to elucidate the molecular mechanisms underlying their respirational versatilities. In this dissertation, a mass spectrometry-based proteomics approach was used to interrogate the proteomes of A. dehalogenans strain 2CP-C, S. oneidensis strain MR-1, and G. daltonii strain FRC-32. The proteomic responses of DMRBs to a wide range of electron acceptors were tested in this dissertation, including soluble and insoluble ferric iron, manganese oxide, fumarate, nitrate, oxygen, and nitrous oxide. The in-depth proteomic characterizations comparatively revealed the c-type cytochrome profiles of DMRBs, providing evidence for the identities and expressions of putative c-type cytochromes, and established the linkage between specific electron acceptor and individual c-type cytochromes. The entire proteome complements of DMRBs were also characterized, generating metabolic maps reflecting pathway-level activities responding to various electron acceptors. The results identified the core proteome carrying out the essential cellular machineries for each tested DMRB, and demonstrated clearly elevated energy metabolism for A. dehalogenans strain 2CP-C during respiration of metal electron acceptors. Comparative proteomics analysis between tested DMRB strains revealed the commonalities and differences of proteomic phenotypes displayed by different strains, and shed light into deeper understandings for DMRB metabolic activities.