Characterization of UNO-SLW2 infection of Pseudomonas fluorescens using bioinformatics analyses

Despite their widespread nature, Pseudomonas bacteriophages are poorly understood. Accordingly, using novel Podoviruses (UNO-SLW1-4) that have been isolated in our laboratory and the Pseudomonas fluorescens host, we seek to clarify the mechanisms and functions of their “hypothetical” genes and gene products. RNA sequencing will especially shed light on gene expression changes during viral infection, illuminating the phage genes previously unrecognized during infection of P. fluorescens over time and as they induce an oxidative stress response. These genes are initially found using high throughput sequencing methods and functionally annotated for characterization of phylogenetic homology using whole genome sequences. Computerized analysis of Pseudomonas bacteria will be used to identify genomic regions that correlate with virus pathogenicity, thus clarifying the utility of such aforementioned genetic heterogeneity. Moreover, by mapping the course of gene expression in conjunction with infection progress of P. fluorescens and its bacteriophage, we learn more about the genes and gene products expressed at specific stages of growth, for both the host and virus. Initial analyses have already identified proteins involved in this infection mechanism. Overall, using such bioinformatics temporal gene expression analyses, we validate a genetic surveillance workflow. This methodology elucidates virulence factors of common nosocomial Pseudomonas bacteriophages, and how they dysregulate the growth of Pseudomonas bacteria. This will provide greater insight into bacteria in the Pseudomonas genus, including those that cause human disease