Molecular mechanisms of recovery of stalled DNA replication fork

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An assay measuring synchronized, processive DNA replication by Escherichia coli DNA polymerase III holoenzyme (Pol III HE) was used to reveal replacement of Pol III by the specialized lesion bypass Pol IV when the replicative polymerase is stalled. When idled replication is restarted, a rapid burst of Pol III-catalyzed synthesis accompanied by 〜7-kb full-length products is strongly inhibited by the presence of Pol IV. The production of slower-forming shorter-length DNA reflects a rapid takeover of DNA synthesis by Pol IV. We demonstrated that Pol IV rapidly (<15 sec) obstructs the stable interaction between Pol III^* and the beta damp (the lifetime of the complex >5 min), causing the removal of Pol III^* from template DNA. We propose that the rapid replacement of Pol III^* on the beta damp with Pol IV is mediated by two processes, an interaction between Pol IV and the beta clamp and a separate interaction between Pol IV and Pol III^*. This newly discovered property of Pol IV facilitates a dynamic exchange between the two free polymerases at the primer terminus. Our study suggests a model in which the interaction between Pol III^* and the beta clamp is mediated by Pol IV to ensure that DNA replication proceeds with minimal interruption.