Direct Visualization of Translesion DNA Synthesis Polymerase IV at the Replisome

Abstract In bacterial cells, DNA damage tolerance is manifested by the action of translesion DNA polymerases that can synthesize DNA across template lesions that typically block the replicative DNA polymerase III. It has been suggested that one of these TLS DNA polymerases, DNA polymerase IV, can either act in concert with the replisome, switching places on the β sliding clamp with DNA polymerase III to bypass the template damage, or act subsequent to the replisome skipping over the template lesion in the gap in nascent DNA left behind as the replisome continues downstream. Evidence exists in support of both mechanisms. Using single-molecule analyses we show that DNA polymerase IV associates with the replisome in a concentration-dependent manner and remains associated over long stretches of replication fork progression under unstressed conditions. This association slows the replisome, requires DNA polymerase IV binding to the β clamp but not its catalytic activity, and is reinforced by the presence of the γ subunit of the β clamp-loading DnaX complex in the DNA polymerase III holoenzyme. Thus, DNA damage is not required for association of DNA polymerase IV with the replisome. We suggest that under stress conditions such as induction of the SOS response, the association of DNA polymerase IV with the replisome provides both a surveillance/bypass mechanism and a means to slow replication fork progression, thereby reducing the frequency of collisions with template damage and the overall mutagenic potential. Significance Damage to the nucleotide bases that make up the DNA in chromosomes creates a problem for their subsequent accurate duplication each time a cell divides. Typically, the cellular enzymatic machinery that replicates the DNA cannot copy a damaged base and specialized trans-lesion DNA polymerases, which are prone to making errors that result in mutations, are required to copy the damaged base, allowing replication to proceed. We demonstrate that the bacterial replisome, which is comprised of the enzymes required to replicate the chromosome, can associate with one of these specialized trans-lesion polymerases over long distances of replicated DNA. This association slows the speed of replication, thereby reducing the chance of mutations arising in the cell under conditions of stress.