Bacterial communities that inhabit the human body play essential roles in health and disease. Therefore, it is of utmost importance to continually expand our mechanistic understanding of the major pathways that control their survival and evolution. One such pathway is called CRISPR-Cas (Clustered regularly interspaced short palindromic repeat-CRISPR-associated). CRISPR-Cas constitutes a class of prokaryotic adaptive immune systems that use small CRISPR RNAs (crRNAs) and Cas nucleases to detect and destroy bacterial viruses (phages). They also present an effective barrier against other modes of horizontal gene transfer (HGT) through mobile genetic elements such as conjugative plasmids. Considering the fact that HGT is a major driving force behind bacterial evolution, these systems profoundly impact the survival and evolution of the organisms that harbor them. CRISPR-Cas systems fall into two broad classes and six distinct Types (I-VI). Type III systems, known as CRISPR-Cas10, are the second-most abundant in nature and found in important human-associated bacteria such as staphylococci and mycobacteria. Recent work on a model CRISPR-Cas10 system in Staphylococcus epidermidis has demonstrated that CRISPR-Cas10, unlike other CRISPR-Cas types, exhibits such robust immunity that it can drive a phage population to extinction. Therefore, this system can be considered the ultimate anti-phage protection. However, by the same token, it appears to be the greatest detriment to bacterial evolution as it poses an almost impenetrable barrier to the horizontal transfer of potentially useful genetic information. Although recent work has made remarkable strides toward understanding its three-step mechanism of immunity, almost nothing is known about possible regulatory pathways that control CRISPR-Cas10. This research will build on preliminary work funded by an NIH K22 award and test the hypothesis that the cell employs diverse mechanisms to control CRISPR-Cas10 expression and function in the model S. epidermidis system. Using an innovative blend of molecular, genetic and analytical chemistry approaches, this research will 1) Characterize genetic circuit(s) that regulate crRNA expression, 2) Determine the role(s) for epigenetic machinery in CRISPR-Cas10 function, and 3) Create a complete map of crRNA chemical modifications in this model system. Crucial insights into CRISPR-Cas10 regulatory mechanisms will offer great intrinsic value for basic science and also inform the development of therapeutic strategies that promote or restrict the growth of specific bacterial species in the context of the human microbiome.
The bacterial communities that reside within and on us impact our physiology in health and disease. Research in this proposal will investigate regulatory mechanisms of a bacterial immune system called CRISPR-Cas10, which controls the exchange of genetic information amongst human-associated bacteria. In the long-term, findings from this research will constitute the basis for therapeutic strategies that can be used to promote the survival of beneficial bacteria and deter the pathogenic strains.