Skip to main content
eScholarship
Open Access Publications from the University of California

UC San Diego

UC San Diego Electronic Theses and Dissertations bannerUC San Diego

Defining the role of bacteriophage in mucosal immunity

  • Author(s): Benler, Sean
  • Advisor(s): Rohwer, Forest
  • et al.
Abstract

Since their discovery over one hundred years ago, bacteriophages (phages) play a central role in the ongoing molecular biology revolution. As such, model phages like Lambda and T4 are perhaps the most genetically well-understood biological entities. Yet, critical aspects regarding the life histories of these phages, nevertheless non-model phages, remain unaddressed. This dissertation examines the life history of T4 and non-model phages. In chapter 2, the steps involved in the morphogenesis of T4-like phages were reevaluated. During the final stages of morphogenesis, T4 packages DNA into an empty head that is subsequently joined with a tail to make a mature virion. Bioinformatic analysis of one gene involved in this head-to-tail joining process, gene 4 (gp4), identified a previously unrecognized nuclease motif. Biochemical analysis confirmed the DNA-cutting capabilities of gp4. The nuclease function of gp4 is shown to be conserved in T4-like phages. In aggregate, the data contained in chapter 2 of this dissertation suggests gp4 plays a role in the termination of genome packaging to enable head-tail joining. Chapter 3 is dedicated to the analysis of non-model phages, focusing on those that contain diversity-generating retroelements (DGRs). DGRs are genetic cassettes that introduce sequence variation into target genes. Few isolated phages possess a DGR, yet metagenomic analyses reveal their presence in uncultured viral communities. In chapter 3, a survey identified 92 DGRs that were only found in phages exhibiting a temperate lifestyle. One novel temperate phage that possesses a DGR cassette targeting a gene of unknown function was isolated from Bacteroides dorei. This phage, here named Hankyphage, exhibits broad host-range and is capable of infecting at least 13 different Bacteroides species. Sequencing reads from whole-community metagenomes and viromes were recruited to the Hankyphage genome, highlighting the global distribution of Hankyphage. The results in chapter 3 suggest that targeted hypervariation by temperate phages, such as Hankyphage, may be a ubiquitous mechanism underlying phage-bacteria interaction in the human microbiome.

Main Content
Current View