Novel Phage Discovery and Phagelet Functional Analysis

Bacteriophage, viruses that infect bacteria, are a subject of intense scientific interest for their diverse clinical, ecological, and synthetic applications. There have been numerous large-scale efforts to capture the genetic diversity of phage and to describe novel phage systems. This thesis explores a novel phage satellite system, wherein a group of satellites, mobile genetic elements that cannot replicate and infect independently, called “phagelets” are hypothesized to parasitize the helper phage, HerbertWM. Genome annotation and comparison reveals that these 13 phagelet genomes, each approximately 11 kbp in length, fall into three distinct clusters with high homology within and across clusters. Genes shared across clusters include a terminase, a serine integrase, a tape measure protein, and a major capsid protein. Putative partial antirepressor genes were uncovered and investigated further as a set of candidate genes which might be responsible for the induction and subsequent parasitization of HerbertWM. Plasmids were created to express these genes and measure for prophage induction. It was found that the putative partial antidepressants were not sufficient to induce the prophage HerbertWM. Further, a novel phage in Cupriavidus gilardii was discovered from environmental samples. This phage’s genome is approximately 38 kbp in length. It shares similarities to Mu-like phages, and may be packaging host DNA into its capsid due to its transposase gene.