Regulating DNA replication and mutagenesis in Bacillus subtilis

Thesis (Ph.D.)--University of Washington, 2018All organisms must control the timing of DNA replication to maintain their genomic stability. In bacteria, this is achieved through tightly controlling the frequency of replication initiation. Though it is well established that DNA topology is important for replication initiation, it was unclear whether the enzymes that modulate supercoiling are important for regulating this process. The work presented in this dissertation identifies a novel role for the essential topoisomerase, DNA gyrase, as a negative regulator of the replication initiator, DnaA. We find that gyrase activity is required for proper binding of DnaA to oriC and controls replication initiation frequency in the model Gram-positive bacterium, Bacillus subtilis. Based on the conservation of both gyrase and DnaA across all bacteria, and the importance of DNA topology for all stages of DNA replication, it is unlikely that this regulatory mechanism is unique to B. subtilis, and likely reflects a general strategy widely utilized by prokaryotes. Creating genetic variability within bacterial populations is important for adaptation and survival. Therefore, cells must balance the need for high fidelity DNA replication with the need for genetic variability. They promote fidelity by accurately copying their DNA and repairing damaged DNA. Cells can increase variability by inducing pathways that introduce mutations. In particular, genome architecture and transcription levels together dictate mutation rates as a result of collisions between DNA replication forks and RNA polymerase. In support of previous work, I found that transcription-coupled nucleotide excision repair facilitates the increased mutation rates of highly transcribed genes in B. subtilis. Furthermore, I found that this mutagenesis is dependent on the activity of DNA polymerase I and the translesion synthesis polymerases YqjH and YqjW. My work contributes to our understanding of transcription-associated mutagenesis