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Published October 1997 | public
Journal Article

Role of architectural elements in combinatorial regulation of initiation of DNA replication in Escherichia coli


Bending of DNA is a prerequisite of site-specific recombination and gene expression in many regulatory systems involving the assembly of specific nucleoprotein complexes. We have investigated how the uniquely clustered Dam methylase sites, GATCs, in the origin of Escherichia coli replication (oriC ) and their methylation status modulate the geometry of oriC and its interaction with architectural proteins, such as integration host factor (IHF), factor for inversion stimulation (Fis) and DnaA initiator protein. We note that 3 of the 11 GATC sites at oriC are strategically positioned within the IHF protected region. Methylation of the GATCs enhances IHF binding and alters the IHF-induced bend at oriC. GATC motifs also contribute to intrinsic DNA curvature at oriC and the degree of bending is modulated by methylation. The IHF-induced bend at oriC is further modified by Fis protein and IHF affinity for its binding site may be impaired by protein(s) binding to GATCs within the IHF site. Thus, GATC sites at oriC affect the DNA conformation and GATCs, in conjunction with the protein-induced bends, are critical cis-acting elements in specifying proper juxtapositioning of initiation factors in the early steps of DNA replication.

Additional Information

© 1997 Blackwell Science Ltd. Received 21 May 1997; revised 4 August 1997; accepted 5 August 1997. Article first published online: 7 Nov. 2003. We would like to thank Moselio Schaechter for support and critical reading of the manuscript. We thank Debabrata Raychaudhuri for valuable comments and extensive editorial help. We thank Howard Nash (National Institutes of Health) for the gift of IHF protein, David Bramhill (Merck), for DnaA and HU, Roger McMacken (Johns Hopkins) for HU and David Kowalski (Roswell Park) for pBTsAoriC plasmid. This work was carried out with the partial support of a National Institutes of Health Grant (GM34132) to Dr Moselio Schaechter, Tufts University, and with support of National Institutes of Health Grant GM25508 to J. L. C.

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