Genomic, Proteomic and Computational Approaches to the Study of Host-Microbe Systems
Abstract
Host-microbe systems are core to some of biology's most consequential interactions, from the pathogens that drive infectious disease to intracellular symbionts mitigating vector-borne disease transmission. Yet unlike the model organisms that have driven most of modern molecular biology, the microbes at the center of these interactions are rarely genetically tractable. Many intracellular bacteria cannot be cultured outside a host, resist standard tools for genetic manipulation, and are annotated largely by homology to distantly related free-living relatives. This dissertation develops genomic, proteomic, and computational methods to work around this lack of infrastructure and contribute techniques and tools to the study and further understanding of host-microbe systems. Using Wolbachia cultured in Drosophila melanogaster cell lines, I demonstrate that chemical mutagenesis can be used to perturb intracellular genomes leaving a detectable mutational signal. I employ a low error rate sequencing technique to record and model the mutational landscape left by the mutagen ethyl methanesulfonate (EMS) demonstrating its use for mutagenesis screens of intracellular bacteria. I next utilize structural proteome datasets to screen host-microbe proteomes for strong candidates of molecular mimicry, microbe proteins that have coevolved a eukaryotic-like domain or structure and suggest use for host manipulation or microbe survival in the host environment. Building off of this screen for novel effectors through structural alignments I develop and test a distributed computing system for performing large scale systematic literature reviews. Altogether these projects represent generalizable approaches to the study of host-microbe systems reaching from classically studied and thoroughly understood to novel and non-model systems.