Protein Filament Formation in Activating and Modulating Enzymatic DNA Cleavage Specificity

University Of Arizona, Tucson AZ

Investigators

Abstract

In this research project, the PI will investigate complex regulatory mechanisms employed by unique biological systems. These investigations will build a foundation for understanding such mechanisms that are only just becoming widely appreciated, and for prediction and manipulation of their behavior for biotechnological applications. The research and associated training activities in this project will benefit both the academic research community and as well as the biotechnology industry. The program will train junior scientists to develop and implement biophysical and biochemical based conceptual approaches to understand complex enzyme regulatory mechanisms, to become leaders in this multidisciplinary field. As a result of this project, new experimental measurements will be made available to be incorporated into the biological physics curriculum to allow direct "hands-on" analyses by junior scientists in training. The PI will continue to expand upon her outreach initiatives in an effort to encourage and train scientists from a diverse range of academic and social backgrounds. Phage-host systems are under intense evolutionary pressure, consequently they have developed remarkably ingenious mechanisms of attack and defense. This project investigates one such remarkable system: that found in Streptomyces griseus. Based on its biochemical activities, SgrAI, a nuclease from S. griseus, is postulated to be activated by binding to invading phage DNA, simultaneously expanding its DNA sequence cleavage specificity and forming polymers that may act to protect the host DNA from its resulting off-target cleavage activity. Enzyme mechanisms involving polymer or filament formation are exceedingly rare, although recent screens suggest this may be more common than previously thought. Being a potentially new paradigm for enzyme regulation, several fundamental questions arise that will be investigated in this research project, including the structure, kinetics, and biological role of the polymer. Biochemical data suggests that the polymer formed from activated SgrAI is a run-on oligomer, which has now been confirmed by the 8.6 Å cryo-electron microscopy structure. Although this structure shows how the SgrAI dimers bound to activating DNA associate in a repeating helical arrangement, fundamental questions such as how DNA cleavage is activated, how DNA sequence specificity is altered, and whether or not domain swapping (found in a crystal structure of two DNA bound SgrAI dimers) is present require higher resolution and therefore remain to be answered. Also important to understanding the function of the run-on oligomer is determining how formation of such an assembly, where the bound DNA appears critical for oligomer stability, accelerates rather than impedes multiple DNA cleavages. Finally, the biological role for run-on oligomer formation has been hypothesized to function in protecting the host DNA from dangerous off-target cleavages made possible via activation of SgrAI, by sequestering SgrAI on the invading phage DNA. This project will investigate the structure of the run-on oligomer using biochemical and x-ray crystallographic methods, measure kinetic steps involving polymer formation and dissociation in the reaction pathway using pre-steady state fluorescence methods, and test the postulated biological role of the polymer using in vitro and in vivo assays including phage infection challenges.