Mechanistic studies of type IA topoisomerases
Seminar Room 1, Newton Institute
Type I topoisomerases are enzymes that change the topology of DNA by breaking one DNA strand and passing another DNA strand through the break before resealing it. They are subdivided into three groups based on sequence, structural, and mechanistic similarities. Biochemical, biophysical, and structural studies have provided atomic level understanding of the mechanism of action of these enzymes but many unanswered questions regarding their mechanism of action remain. E. coli topoisomerases I and III (Topo I and Topo III) relax negatively supercoiled DNA and also catenate/decatenate DNA molecules. Although these enzymes share the same mechanism of activity and have similar structures, they participate in different cellular processes: Topo I helps maintain the topological state of DNA, whereas Topo III helps resolve recombination and replication intermediates. In bulk experiments Topo I is more efficient at DNA relaxation whereas Topo III is more efficient at catenation/decatenation. To understand the differences in activity by these two highly related type IA topoisomerases, single molecule magnetic tweezers studies were conducted on several different DNA substrates. The experiments show differences in the way the two proteins work at the single molecule level, while also recovering observations from the bulk experiments. Surprisingly, the experiments show that Topo III relaxes DNA very efficiently, but with long pauses between relaxation events, whereas Topo I relaxes DNA more steadily and slowly. The results provide insights into the mechanism of both proteins and suggest reasons why Topo I is more efficient than Topo III at relaxing negatively supercoiled DNA.