Major Professor:  Adina Howe

Co-Major Professor:  Walter Moss

Home Department:  Agricultural and Biosystems Engineering

Title:  CRISPR-Cas: Functional Specialization and Evolutionary Outcomes

Clustered Regularly Interspaced Palindromic Repeats (CRISPR) and CRISPR-associated (Cas) proteins form the constituent parts of heritable adaptive immune systems present in bacteria and archaea. These systems employ an RNA-guided nuclease to cut nucleic acids like phages and mobile genetic elements that might otherwise threaten cell fitness. Because these nucleases are guided by a small RNA sequence, they can easily be manipulated to target specific genetic sequences with existing biotechnology. As a result of their adaptability, a plethora of research has been performed that shows how CRISPR-Cas systems can be employed to solve biological issues. However, despite the heavy focus on CRISPR-Cas systems, the impact of how CRISPR-Cas systems affect bacterial ecology is mostly limited to research within specific types or subtypes of CRISPR-Cas systems in only one or two species. Such studies have revealed important characteristics and unique functions of individual systems. These findings have limited interpretation across multiple species because it is unclear where findings can be applied across the wide diversity that exists in these systems. In this dissertation, I explore three characteristics of these systems across multiple species and identify evolutionary patterns. Those three characteristics are the conservation of secondary structure of the guide-RNA, how CRISPR-Cas evolution affects bacterial genome content, and differences in expression of CRISPR-Cas proteins in response to in-feed antibiotic application.