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J Biol Chem, Vol. 273, Issue 14, 8447-8453, April 3, 1998

Replication Origin of the Broad Host Range Plasmid RK2
POSITIONING OF VARIOUS MOTIFS IS CRITICAL FOR INITIATION OF REPLICATION

Kelly S. Doran, Igor Konieczny^¶, and Donald R. Helinski

From the  Department of Biology, Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634 and the ^¶ University of Gdansk, Department of Molecular and Cellular Biology, 24 Kladki, PL-80822 Gdansk, Poland

The 393-base pair minimal origin, oriV, of plasmid RK2 contains three iterated motifs essential for initiation of replication: consensus sequences for binding the bacterial DnaA protein, DnaA boxes, which have recently been shown to bind the DnaA protein; 17-base pair direct repeats, iterons, which bind the plasmid encoded replication protein, TrfA; and A + T-rich repeated sequences, 13-mers, which serve as the initial site of helix destabilization. To investigate how the organization of the RK2 origin contributes to the mechanism of replication initiation, mutations were introduced into the minimal origin which altered the sequence and/or spacing of each particular region relative to the rest of the origin. These altered origins were analyzed for replication activity in vivo and in vitro, for localized strand opening and for DnaB helicase mediated unwinding. Mutations in the region between the iterons and the 13-mers which altered the helical phase or the intrinsic DNA curvature prevented strand opening of the origin and consequently abolished replication activity. Insertions of more or less than one helical turn between the DnaA boxes and the iterons also inactivated the replication origin. In these mutants, however, strand opening appeared normal but the levels of DnaB helicase activity were substantially reduced. These results demonstrate that correct helical phasing and intrinsic DNA curvature are critical for the formation of an open complex and that the DnaA boxes must be on the correct side of the helix to load DnaB helicase.

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