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Open Access Publications from the University of California

Scholarly Works (2 results)

  • Thesis
  • Peer Reviewed
UC San Diego Electronic Theses and Dissertations (2023)

Diverse and widespread populations of bacteriophages infect and co-evolve with their bacterial hosts. Although the process of host recognition and infection occurs within microbiomes, the molecular mechanisms underlying host-phage interactions within the context of a community remain poorly studied. The biofilms, or rinds, of cheese, contain taxonomically diverse microbial communities that follow reproducible growth patterns and can be manipulated under laboratory conditions. Our lab has previously used a model Brie community to demonstrate specific microbe-microbe interactions occurring within a community. Using this system, we are investigating how host-phage interactions and co-evolution influence other community members, and vice versa. The work outlined here described our efforts to use cheese as a model for studying phage-microbe interactions by identifying and characterizing a tractable host-phage pair co-occurring within this system. We successfully isolated lytic bacteriophage TS33 that kills Hafnia strain JB232, a member of a model Brie community. TS33 is easily propagated in the lab and naturally co-occurs in the cheese with its Hafnia host and other members of the Brie community, rendering it a prime candidate for the study of host-phage interactions. We used Random Barcode Transposon Sequencing (RB-TnSeq) experiments to identify candidate host factors that contribute to TS33 infectivity, many of which are critical to the integrity of the lipopolysaccharide (LPS) layer of the host cell. Notably, disruption of these genes results in decreased susceptibility to infection by phage TS33, while simultaneously exhibiting a significant negative effect on the fitness of Hafnia strain JB232 in the presence of its fungal partners, Geotrichum candidum and Penicillium camemberti. Therefore, LPS mutations may have pleiotropic effects on the interactions between JB232 and the rest of the Brie community. Ongoing and future studies aim to unearth the molecular mechanisms by which the LPS of JB232 mediates its interactions with its viral and fungal partners.

    • Article
    • Peer Reviewed
    UC San Diego Previously Published Works (2023)
    We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.
      Cover page: Identifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY
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