DNA gyrase on the bacterial chromosome: possibility of two levels of action.

In previous studies we have shown that oxolinic acid, a specific inhibitor of the A subunit of DNA gyrase, induces DNA cleavage at 100,000-base-pair intervals on the Escherichia coli chromosome. At subsaturating drug concentrations, cleavage is induced at a fraction of these sites and DNA synthesis is partially inhibited. This partial inhibition is surprisingly rapid even when few sites have been inactivated. We now report kinetic measurements suggesting that inactivation of 100,000-base-pair gyrase sites by oxolinic acid does not inhibit DNA synthesis by simply producing barriers to replication fork movement. Slowing the rate of fork movement, thus increasing the time for a fork to reach a barrier, fails to proportionately slow inhibition of DNA synthesis. Moreover, the initial, rapid phase of inhibition is followed by a slower decline that is not accelerated by increasing the frequency of barriers by raising drug concentrations. These data, when added to the observation that additional oxolinic acid-induced cleavage occurs in replicating regions of the chromosome, suggest that gyrase may function at replication forks as well as at 100,000-base-pair intervals on the chromosome.