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 nave 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.
RNA-guided nucleases that protect bacteria and archaea from infection by viruses are now being routinely repurposed for genome engineering in a wide variety of cell types and multicellular organisms. However, creative and safe application of these new tools requires a fundamental understanding of how these systems function. This proposal aims to elucidate the mechanisms of two nucleic acid guided defense systems in bacteria (Argonaute proteins and CRISPR-Cas systems), with an eye toward the development of new tools for molecular biology and medicine.