Viruses are generally considered to be agents of destruction that must be efficiently eliminated by the host for
self-preservation. However, viruses are also the largest reservoir of genetic diversity on the planet, and viral
infections (estimated 1023 infections per second) are a primary mechanism for delivering new genes to naïve
hosts. Thus, viruses have a complex role in the process of evolution, being both a major source of disease and
mortality, while simultaneously presenting the cellular community with new opportunities for genetic innovation.
In bacteria, viruses (i.e., phages) are major purveyors of genes that confer virulence and antibiotic resistance,
and thus play a major role in the evolution of bacterial pathogenesis. The long-term goal of our research is to
understand the impact of phage defense systems on the evolution and ecology of human-associated microbial
communities. We are interested in understanding the dynamic processes that balance host preservation
(defense from lethal infection) with the advantages of sampling foreign DNA for selectively advantageous traits.
Specifically, the work outlined in this proposal is aimed at determining the mechanisms of two evolutionarily
distinct immune systems that both rely on small RNA or small DNA guides for sequence-specific recognition of
invading genetic elements. The proposal is divided into two projects, with an eye toward developing new tools
for applications in molecular biology and medicine. Project 1 focuses on understanding the phylogenetic and
functional diversity of phage encoded anti-CRISPRs that suppress CRISPR-mediated adaptive immune
systems. Project 2 aims to understand the functional diversity of Argonaute proteins in bacteria and archaea.
Results from this research will provide mechanistic insights that contribute to our long-term goal and have
significance implications in the near-term application of these emerging tools for precise genome engineering.