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M600882200v1
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Papers In Press, published online ahead of print April 21, 2006
J. Biol. Chem, 10.1074/jbc.M600882200
Submitted on January 30, 2006
Revised on April 14, 2006
Accepted on April 21, 2006

The AddAB helicase/nuclease forms a stable complex with its cognate chi sequence during translocation

Frédéric Chédin, Naofumi Handa, Mark S. Dillingham, and Stephen C. Kowalczykowski

Section of Microbiology, UC Davis, Davis, CA 95616

Corresponding Author: sckowalczykowski{at}ucdavis.edu

The Bacillus subtilis AddAB enzyme possesses ATP-dependent helicase and nuclease activities, which result in the unwinding and degradation of double-stranded DNA (dsDNA) upon translocation. Similar to its functional counterpart, the Escherichia coli RecBCD enzyme, it also recognizes and responds to a specific DNA sequence, referred to as Chi (chi . Recognition of chi triggers attenuation of the 3’ to 5’ nuclease, which permits the generation of recombinogenic 3’-overhanging, single-stranded DNA (ssDNA), terminating at chi . While the RecBCD enzyme briefly pauses at chi , no specific binding of RecBCD to chi during translocation has been documented. Here, we show that the AddAB enzyme transiently binds to its cognate chi sequence (chi Bs;5’-AGCGG-3’) during translocation. The binding of AddAB enzyme to the 3’-end of the chi Bs-specific ssDNA results in protection from degradation by Exonuclease I. This protection is gradually reduced with time and lost upon phenol extraction, showing that the binding is non-covalent. Addition of AddAB enzyme to processed, chi Bs-specific ssDNA that had been stripped of all protein does not restore nuclease protection, indicating that AddAB enzyme binds to chi Bs with high affinity only during translocation. Finally, protection of chi Bs-specific ssDNA is still observed when translocation occurs in the presence of competitor chi Bs-carrying ssDNA, showing that binding occurs in cis. We suggest that this transient binding of AddAB to chi Bs is an integral part of the AddAB-chi Bs interaction and propose that this molecular event underlies a general mechanism for regulating the biochemical activities and biological functions of RecBCD-like enzymes.


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