Papers In Press, published online ahead of print February 28, 2008
J. Biol. Chem, 10.1074/jbc.M709689200
Submitted on November 27, 2007
Revised on February 25, 2008
Accepted on February 28, 2008
A dynamic polymerase exchange with Escherichia coli pol IV replacing pol III on the sliding clamp
Asako Furukohri, Myron F. Goodman, and Hisaji Maki
Molecular Biology, Nara Institute of Science and Technology, Graduate School of Biological Sciences, Ikoma, Nara 630-0192
Corresponding Author: maki{at}bs.naist.jp
An assay that measures 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. Here we demonstrate that Pol IV rapidly (<15 sec) obstructs the stable interaction between Pol III* and the ß clamp (the lifetime of the complex is >5 min), causing the removal of Pol III* from template DNA. We propose that the rapid replacement of Pol III* on the ß clamp with Pol IV is mediated by two processes, an interaction between Pol IV and the ß 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 ß clamp is mediated by Pol IV to ensure that DNA replication proceeds with minimal interruption.