Bacteria and bacteriophages (bacterial viruses) have evolved a sophisticated arsenal of defensive and offensive molecular weaponry targeted against each other. Phages are ten times more abundant than their bacterial hosts in every environment tested, and thus they profoundly impact the bacterial communities in all environments. Although much research is currently focused on investigating bacterial defense systems in isolation, research activities in this project will examine whether bacterial immune systems act with other cellular processes to maximize the efficiency of defense. In this project, Staphylococcus bacteria and their phages, both abundant residents of human skin, will be used as a model host-virus system. Educational activities designed to stimulate interest in science will provide hands-on research experiences to undergraduates and high school students through a phage discovery course. Undergraduates will also gain early exposure to cutting-edge genome editing tools and techniques. The research has the potential to inspire novel biotechnologies and the educational activities are expected to promote participation of underrepresented groups in STEM careers.
The overarching goal of this project is to gain fundamental insight into defense and counter-defense mechanisms in S. epidermidis and its phages as a model system. CRISPR-Cas are an important class of adaptive defense systems that use small RNAs and Cas nucleases to destroy invading phages. Many staphylococci naturally possess Type III (CRISPR-Cas10) systems, which are among the most widespread in nature. Although recent research has shed light on the canonical immunity pathway of the model CRISPR-Cas10 system in S. epidermidis, the question of whether or not CRISPR-Cas10 relies upon other (non-Cas) pathways to carry out defense was never posed. Preliminary work in the PIs lab has discovered unexpected interactions between CRISPR-Cas10 and two conserved cellular pathways previously considered unrelated to immunity. These observations support the central hypothesis that CRISPR-Cas10 integrates with other cellular pathways, including other immune systems in S. epidermidis, to carry out defense. This integration in turn impacts the corresponding phage-encoded mechanisms of counter-defense. Research in this project will test this hypothesis by using a combination of biochemistry, genetic, and molecular biology approaches to 1) characterize molecular interactions between CRISPR-Cas10 and other cellular pathways, 2) determine the molecular mechanisms by which newly discovered immune system(s) operate, and 3) characterize phage-encoded mechanisms that counter these defenses. The new insights gained by this research are expected to form the basis for biotechnologies that can be used to shape and control natural Staphylococcus communities.
