Mechanistic Dissection of DNA Repair Pathways in Bacillus subtilis.

All cells must accurately copy and maintain their DNA to ensure the faithful transmission of their genetic material to the next generation. Organisms ranging from bacteria to humans contain a suite of DNA repair pathways dedicated to the specific recognition and repair of the myriad of damaged or incorrect bases that occur throughout the lifetime of a cell. Here, I study the mechanisms of Bacillus subtilis mismatch repair and homologous recombination that maintain DNA integrity in the complex environment of a living cell. I. Mismatch repair increases the fidelity of DNA replication by identifying and correcting replication errors. Although Mismatch repair has been thoroughly studied in vitro, little is known about how its central components, MutS and MutL, identify replication errors and orchestrate their repair within a living cell. Here, I investigate how the B. subtilis processivity clamp DnaN aids mismatch detection by MutS in vivo. I found that DnaN serves as an essential platform for mismatch detection, targeting the MutS search for mismatches to nascent DNA. II. Following mismatch detection, MutS recruits MutL to the mismatch by an unknown mechanism. I identified a discrete site composed of two adjacent phenylalanine residues on MutS that binds MutL. Disruption of this site renders MutS defective in binding MutL in vitro and in vivo, while eliminating mismatch repair in vivo. Analysis of MutS repair complexes defective in MutL recruitment revealed a continuous loading response by MutS, revealing an intermediate step in the repair process. III. The recombinase RecA is required for homologous recombination and stabilization of stalled replication forks in many bacteria, yet the polypeptides important for RecA loading remains unclear in organisms lacking RecBCD. Here, I find that RecA loading is dependent on the presence of RecOR; proteins that associate with the SSB DNA maintenance hub, ensuring that RecA loading localizes to active replication forks. Furthermore, we find that RecF is not required for RecA loading; however, provides an enhancement in either RecA filament nucleation or elongation.PhDMolecular, Cellular, and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/107185/1/coldnjl_1.pd