Topoisomerase I confers specificity in enzymatic replication of the Escherichia coli chromosomal origin.

Crude soluble enzyme fractions that initiate bidirectional replication from the unique Escherichia coli chromosomal origin (oriC) have been fractionated further to identify the components and mechanisms of this complex system. Among the necessary factors is a class of specificity proteins that suppress initiations on plasmids which lack the oriC sequence and which do not depend on dnaA protein. One such specificity factor has been identified as RNase H (Ogawa, T., Pickett, G. G., Kogoma, T., and Kornberg, A. (1984) Proc. Natl. Acad. Sci. U. S. A. 81, 1040-1044). Another, described here, has proved to be topoisomerase I. A protein was purified to near homogeneity based on assays of (i) inhibition of the replication of plasmids (and other supercoiled DNA) lacking oriC and (ii) conferral of dnaA protein dependence on the replication of an oriC plasmid. This specificity protein is indistinguishable from authentic E. coli topoisomerase I by several criteria: (i) molecular weight under denaturing conditions, (ii) relaxation activity on negatively supercoiled DNA, (iii) cleavage pattern of single-stranded DNA, (iv) specificity factor activity, and (v) neutralization of activity by antibody against topoisomerase I. One possible mechanism of the specificity action of topoisomerase I is destabilization of primers for replication except when they are preserved at an oriC sequence bound by dnaA protein and other replication proteins.