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J Biol Chem, Vol. 274, Issue 25, 17918-17923, June 18, 1999

A Critical DnaA Box Directs the Cooperative Binding of the Escherichia coli DnaA Protein to the Plasmid RK2 Replication Origin

Kelly S. DoranDagger , Donald R. HelinskiDagger , and Igor KoniecznyDagger parallel

From the Dagger  Department of Biology, Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0322 and the parallel  Department of Molecular and Cellular Biology, Faculty of Biotechnology, University of Gdansk, 24 Kladki, PL-80822 Gdansk, Poland

The requirement of DnaA protein binding for plasmid RK2 replication initiation the Escherichia coli was investigated by constructing mutations in the plasmid replication origin that scrambled or deleted each of the four upstream DnaA boxes. Altered origins were analyzed for replication activity in vivo and in vitro and for binding to the E. coli DnaA protein using a gel mobility shift assay and DNase I footprinting. Most strikingly, a mutation in one of the boxes, box 4, abolished replication activity and eliminated stable DnaA protein binding to all four boxes. Unlike DnaA binding to the E. coli origin, oriC, DnaA binding to two of the boxes (boxes 4 and 3) in the RK2 origin, oriV, is cooperative with box 4 acting as the "organizer" for the formation of the DnaA-oriV nucleoprotein complex. Interestingly, the inversion of box 4 also abolished replication activity, but did not result in a loss of binding to the other boxes. However, DnaA binding to this mutant origin was no longer cooperative. These results demonstrate that the sequence, position, and orientation of box 4 are crucial for cooperative DnaA binding and the formation of a nucleoprotein structure that is functional for the initiation of replication.

Copyright © 1999 by The American Society for Biochemistry and Molecular Biology, Inc.
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