Student Theses and Dissertations
Date of Award
2024
Document Type
Thesis
Degree Name
Doctor of Philosophy (PhD)
RU Laboratory
Marraffini Laboratory
Abstract
Viruses parasitize every known life form on the planet for their propagation and spread. To deal with this constant assault, organisms across all domains of life ave evolved immune strategies in the form of genetically encoded systems to defend themselves. Immunity can be conceptualized as occurring in three fundamental stages. First, the immune system must identify an invading pathogen—either directly via recognition of a pathogen-associated molecular pattern (PAMP), or indirectly by sensing the perturbation of homeostasis during the process of infection(“guard hypothesis”). Second, this information must be converted into molecular signals to be transmitted to the appropriate compartment within the cell or organism and to amplify downstream immune responses. Third,effect or programs must been acted to interfere with the virus’ ability to replicate and parasitize the host.Arising from these fundamental properties, immune systems are composed of multiple distinct components with specialized functions(e.g. the “innate” and “adaptive” arms of immunity in vertebrates)and involve a complex network of interactions. A viable immune response must therefore be able to optimally integrate multiple branches within this network in order to operate effectively—that is, to simultaneously enable robust immunity against any invading pathogen while limiting autoimmunity. Bacteriophages (phages)are viruses infecting bacteria that are thought to outnumber their hosts by a factor of ten to one in most environments. They are by far the most ubiquitous biological entities,estimated to exceed a staggering quantity of 1031 phage particles on the planet. As a result of this host-parasite conflict over billions of years, bacteria have evolved many diverse mechanisms of anti-bacteriophage defense, including many different“innate” systems as well as the“adaptive” CRISPR-Cas systems. In the last five years, dozens of new genes that confer bacterial immunity against bacteriophages have been identified through bioinformatic searches and more recently, functional screens. Many of these anti-bacteriophage defense systems have subsequently been validated and the details of their modes of activity have been revealed through experimental approaches.Although the mechanistic details of how these newly discovered defense genes interfere with bacteriophage propagation are rapidly being uncovered, there is a major gap in our understanding of how these systems sense bacteriophage infection in order to initiate immunity. Furthermore, it has only recently been recognized that within a single cell,bacteria commonly harbor many different defense systems—on average,five to seven distinct systems.Therefore, our understanding of how different defense systems interact with one another and the consequences of this crosstalk for the immune response and bacterial evolution remains in its infancy.In this thesis, I investigate these two fundamental, but nascent areas of the burgeoning field of bacterial immunology using staphylococci and staphylococcal phages as a powerful model system to study host-virus interactions. In the first part of my thesis (Chapters 1 and 2), I provide a broad introduction to the evolutionary conflict between bacteria and their phages, with a particular focus on staphylococci, a widespread taxon of bacteria with the utmost medical importance.I also discuss a conceptual framework for understanding how a successful immune response is generated in response to infection, with a focus on the current state of understanding of how bacterial defense systems are triggered by invading phages.In the second part of my thesis (Chapters 3 and 4), I demonstrate that a newly discovered defense system called CBASS, the bacterial homolog to the cGAS-STING innate immune pathway in eukaryotes, confers anti-viral defense in staphylococci.Specifically, a minimal type I CBASS operon from Staphylococcus schleiferi that is also broadly present in other species,including Staphylococcus aureus,can provide immunity against some, but not all, staphylococcal phages. I then detail our discovery and characterization of the CBASS-activating bacteriophage RNA (cabRNA), which we propose to be a phage-specific cue during infection that triggers the initiation of CBASS-mediated immunity.In the third part of my thesis (Chapters 5, 6, and 7), I focus on the current state of knowledge on “immune crosstalk” in prokaryotes, with a focus on how these interactions impact the strength and durability of immunity. Specifically, I explore the complex tripartite interactions between bacteriophages,S. aureus pathogenicity islands (SaPIs), and CRISPR-Cas systems and detail our discovery that SaPI-mediated parasitism of phages can stimulate the development of CRISPR-Cas adaptive immunity through the production of immunizing defective viral particles. In the last part of my thesis (Chapter 8), I discuss the many unanswered questions that remain and the exciting avenues of inquiry that extend from my research. I further discuss the mechanistic insights gleaned from these experimental studies and the implications that this work has on understanding the interactions between bacteria and bacteriophages.In conclusion,the research described in this thesis collectively reveals novel molecular mechanisms underlying the sensing o fbacteriophage infection by CBASS—the bacterial counterpart to cGAS—and the synergistic interactions between S. aureus pathogenicity islands and adaptive CRISPR-Cas immune systems in staphylococci.This work touches upon two fundamental features of every immune response across all domains of life: sensing and synergy. Furthermore, this work provides a foundation for future studies that will continue to uncover the details of how various anti-bacteriophage defense systems are activated during viral infection and additional modes of immune crosstalk in bacteria.
Recommended Citation
Banh, Dalton Van, "Molecular Mechanisms of Sensing and Synergy by Anti-Bacteriophage Immune Systems in Staphylococcus" (2024). Student Theses and Dissertations. 751.
https://digitalcommons.rockefeller.edu/student_theses_and_dissertations/751
Comments
A Thesis Presented to the Faculty of The Rockefeller University in Partial Fulfillment of the Requirements for the degree of Doctor of Philosophy