Pathogens and host immunity in the ancient human oral cavity.

Calcified dental plaque (dental calculus) preserves for millennia and entraps biomolecules from all domains of life and viruses. We report the first, to our knowledge, high-resolution taxonomic and protein functional characterization of the ancient oral microbiome and demonstrate that the oral cavity has long served as a reservoir for bacteria implicated in both local and systemic disease. We characterize (i) the ancient oral microbiome in a diseased state, (ii) 40 opportunistic pathogens, (iii) ancient human-associated putative antibiotic resistance genes, (iv) a genome reconstruction of the periodontal pathogen Tannerella forsythia, (v) 239 bacterial and 43 human proteins, allowing confirmation of a long-term association between host immune factors, 'red complex' pathogens and periodontal disease, and (vi) DNA sequences matching dietary sources. Directly datable and nearly ubiquitous, dental calculus permits the simultaneous investigation of pathogen activity, host immunity and diet, thereby extending direct investigation of common diseases into the human evolutionary past

Membrane proteins and protein-protein interactions in marine cyanobacteria

Thesis by publication.Includes bibliographic references.Chapter 1. Introduction -- Chapter 2. Comparative membrane proteomics reveal contrasting adaptation strategies for coastal and oceanic marine Synechococcus cyanobacteria -- Chapter 3. Protein-protein interactions of Synechococcus phosphatases and response regulators -- Chapter 4. Defining the protein-protein interaction network of protein phosphatases in marine cyanobacteria -- Chapter 5. Conclusions and future perspectivesMarine cyanobacteria Synechococcus are globally distributed in the world oceans. They play a vital role in primary production and the carbon biogeochemical cycles, as well as significant ecological roles in the ocean ecosystem. The cell membrane is the primary permeability barrier for ions, molecules and/or substrates enter/leave a cell. A comparative membrane proteomic study was conducted on 4 different marine Synechococcus namely CC9311 (Clade I), CC9605 (Clade II), WH8102 (Clade III) and CC9902 (Clade IV) representing the 4 most abundant Synechococcus clades in the world oceans to investigate adaptation strategies of marine cyanobacteria in nutrient acquisition. Comparative membrane proteomic analyses revealed distinct adaptation strategies among the 4 marine Synechococcus in nutrient acquisition. One protein annotated as protein phosphatase 2C was detected to be highly expressed in the coastal mesotrophic strains Synechococcus sp. CC9311 and CC9902. This suggests a pivotal, but as yet undefined, functional role for this protein phosphatase in cyanobacteria. The high expression level of this putative protein phosphatase in coastal Synechococcus sparked an interest in further investigation of the functional roles of protein phosphatases in marine cyanobacteria. Therefore, a total of nine putative protein phosphatases including serine/threonine, tyrosine and histidine phosphatases identified in marine Synechococcus sp. CC9311 were chosen for a protein-protein interaction study to investigate the proteins that interact with phosphatases and elucidate their functional roles. Pull-down assay was conducted on phosphatases and response regulators, the potential interacting proteins with phosphatases. For the 9 protein phosphatases and 17 response regulators, their genes were PCR amplified, cloned and transformed to test for protein expression and solubility. Two of the phosphatase proteins namely Sync_1857 and Sync_2828, and 9 response regulators were successfully purified to conduct in vitro pull-down assays. The pull-down assay coupled with mass spectrometry analysis shows that 7 out of the 9 response regulators interact with both of the phosphatases. Both purified phosphatase proteins were used to conduct a protein-protein interaction study against the cytoplasmic lysate of Synechococcus sp. CC9311 using an affinity purification mass spectrometry approach. Mass spectrometry analyses show that the protein phosphatase Sync_1857 interacts with a periplasmic urea ABC transporter, suggesting phosphorylation modification may be crucial for the activation of the transport of urea in marine cyanobacteria. Additionally, a broad range of proteins were found to interact with Sync_1857 including proteins involved in amino acid metabolism and translation suggesting it may play a broad role in cell signalling regulation. Meanwhile, Sync_2828 was found to interact with a range of stress-related proteins, suggesting a potential role in stress response regulation in cyanobacterial cells -- abstract.Mode of access: Internet.1 online resource (xx, 226 pages