UC San Diego

The overall theme of this dissertation is the use post-translational modification (PTM)-tolerant approaches to investigate infectious diseases. Chapter 1 contains background information regarding quantitative proteomics, PTMs and infectious disease, particularly the anti-microbial resistant pathogen, Staphylococcus aureus. This information is provided to introduce the reader with the fundamentals of the biology and the main techniques used during the doctoral studies. The following chapters describe primary author works (published or under review) completed by the author of this dissertation.

Chapter 2 describes the discovery and characterization of modified microproteins produced by Staphylococcus aureus. These microproteins were discovered using an unbiased peptidogenomic approach and characterized using in vitro and in vivo assays. One of the new microproteins functions similarly to previously described virulence factors, while to other appears to have distinct mechanisms of action in the skin. The further investigation of these microproteins may provide a more comprehensive understanding of the host-pathogen interaction.

Chapter 3 introduces a computational tool, PTMphinder, created by the author of the dissertation. This tool enables the high-throughput localization of phospho-sites in full length proteins and the extraction of flanking sequences. The utility of this tool is demonstrated by applying it to gain a more comprehensive view of the in vivo host response to infection in a chronic Chagas disease model. Kinase-substrate pairs and drug targets are predicted from phospho-proteomic data, providing numerous hypotheses to further interrogate.

Chapter 4 aims to set a new standard in the biomarker research field. By employing a multi-omic approach, >10,000 features were quantified from >200 S. aureus bacteremia (SaB) patient samples, including abundant post-translational modifications (PTMs). A model was constructed from the multi-omic data which provides the best predictive ability for mortality from any infection to date. Further, the host response to infection was detailed and used to predict treatment strategies, which were substantiated using animal models. Overall, Chapter 4 details a comprehensive molecular view of the early host response to infection.

Lastly, Chapter 5 details experiments to further develop the research described in Chapter 4. This includes the development of a multi-marker immunoassay-based tool for the prediction of SaB outcomes and experiments to further understand detailed mechanisms of the host response to S. aureus bacteremia.