UC Berkeley

Parasitism is a common evolutionary strategy present in many branches of life, and the study of parasitism has contributed substantially to evolutionary theory. Bacteriophages, viruses that infect bacteria, are one group of parasites that have been particularly valuable models of study. Study of bacteriophages, or phages as they are also known, has vastly improved our understanding of molecular biology. The study of bacterial systems that defend against phages has provided incredibly useful tools for genetic research such as restriction enzymes and CRISPR-Cas. A particularly interesting form of anti-phage defense is hyperparasitism, parasitism of a parasite, by bacteriophage satellites that are endogenous to the bacterial genome. Bacteriophage satellites rely on bacteriophage infection for horizontal mobility while reducing or restricting production of progeny bacteriophage. This allows them to function as immune systems for the cellular populations that encode them. Within this thesis, we identify mechanisms of parasitism and bacteriophage interference by the phage inducible chromosomal island-like element or PLE, a bacteriophage satellite found within some strains of Vibrio cholerae. Using deep sequencing approaches, we have outlined DNA replication and transcriptional programs for both the PLE, and the phage it parasitizes, ICP1. Molecular and phenotypic approaches were also applied to establish how PLE parasitizes ICP1 for its own genome replication and what effect this has on the life cycle of ICP1. We have found that PLE requires ICP1 not just for induction of gene expression, but also for replication of the PLE genome. Consistent with relying on ICP1 machinery for replication and mobilization, PLE does not broadly interfere with ICP1 transcription. The sole exception to this is repression of ICP1 capsid morphogenesis genes, consistent with the PLE remodeling ICP1 virions to fit its smaller genomes. The experiments presented here, along with other recent data, suggest that PLE inhibits ICP1 through multiple mechanisms which have dual functions of also boosting PLE reproduction and mobilization. This thesis provides a foundation for understanding the parasitism strategies of ICP1 and PLE, as well as the mechanisms through which PLE restricts ICP1. Our results suggest that PLE has adapted to interfere with the replication program of ICP1 only to an extent that is beneficial to the PLE, and fit within a context pattern of pathogen and parasite evolutionary patterns.