Eukaryotic type IA topoisomerases are important for the normal function of the cell, and in some cases essential for the organism, although their role in DNA metabolism remains to be elucidated. In this study, we cloned Drosophila melanogaster topoisomerase (topo) III␣ from an embryonic cDNA library and expressed and purified the protein to >95% homogeneity. This enzyme partially relaxes a hypernegatively supercoiled plasmid substrate consistent with other purified topo IIIs. A novel, covalently closed bubble substrate was prepared for this study, which topo III␣ fully relaxed, regardless of the handedness of the supercoils. Experiments with the bubble substrate demonstrate that topo III␣ has much different reaction preferences from those obtained by plasmid substrate-based assays. This is presumably due to the fact that solution conditions can affect the structure of plasmid based substrates and therefore their suitability as a substrate. A mutant allele of the Top3␣ gene, Top3␣ 191, was isolated through imprecise excision mutagenesis of an existing P-element inserted in the first intron of the gene. Top3␣ 191 is recessive lethal, with most of the homozygous individuals surviving to pupation but never emerging to adulthood. Whereas this mutation can be rescued by a Top3␣ transgene, ubiquitous overexpression of D. melanogaster topo III␤ cannot rescue this allele.DNA topoisomerases are ubiquitous enzymes found in all cells and some viruses that regulate the topology of DNA in such cellular processes as replication, transcription, and recombination (1, 2). These enzymes work by making a transient covalent bond to the phosphodiester backbone of the DNA, creating a protein mediated DNA gate, which allows another strand (or strands) of DNA to pass through this reversible break. Type II topoisomerases create double-stranded breaks, and double strand passage, whereas type I topoisomerases break a single strand of DNA. The type I topoisomerases are further divided into the IA and IB subfamilies, based on structural and mechanistic differences (3, 4). Topoisomerase III (topo III) 1 is a member of the type IA subfamily that is conserved from bacteria to humans.Topo III was originally purified by following superhelical relaxation activity from extracts of Escherichia coli containing a deletion for topo I (5). This enzyme was also independently purified based on its decatenating abilities in an assay utilizing plasmid DNA replication intermediates (6). Despite the strong sequence homology that this protein shares with E. coli topo I (7), purified topo III shows a weak ability to relax negatively supercoiled DNA (5). The relaxation activity of Topo III is strongly inhibited by single-stranded DNA (ssDNA) (5), and the enzyme was subsequently shown to preferentially bind ssDNA. The decatenase activity of topo III also depends on the presence of single-stranded regions in the catenated DNA (6). Recently, Nurse et al. showed that topo III serves as a decatenase in vivo by removing precatenanes that arise during replication of ci...

The topoisomerase (topo) III enzymes are found in organisms ranging from bacteria to humans, yet the precise cellular function of these enzymes remains to be determined. We previously found that Drosophila topo III␤ can relax plasmid DNA only if the DNA is first hypernegatively supercoiled. To investigate the possibility that topo III␤ requires a single-stranded region for its relaxation activity, we formed R-loops and D-loops in plasmids. In addition to containing a single-stranded region, these R-loops and D-loops have the advantage of being covalently closed and supercoiled, thus allowing us to assay for supercoil relaxation. We found that topo III␤ preferentially cleaves, rather than relaxes, these substrates. The cleavage of the R-loops and D-loops, which is primarily in the form of nicking, occurs to a greater extent at a temperature that is lower than the optimal temperature for relaxation of hypernegatively supercoiled plasmid. In addition, the cleavage can be readily reversed by high salt or high temperature, and the products fail to enter the gel in the absence of proteinase K treatment and are not observed with an active-site Y332F mutant of topo III␤, indicating that the cleavage is mediated by a topoisomerase. We mapped the cleavage to the unpaired strand within the loop region and found that the cleavage occurs along the length of the unpaired strand. These studies suggest that the topo III enzyme behaves as a structure-specific endonuclease in vivo, providing a reversible DNA cleavage activity that is specific for unpaired regions in the DNA.C ellular processes such as replication, transcription, and recombination rely on the action of topoisomerases to relieve the accompanying flexural and torsional stress these processes impart upon the DNA (reviewed in refs. 1 and 2). The topoisomerases act through a simple, yet elegant, mechanism whereby the active-site tyrosine covalently attaches to the DNA phosphodiester backbone, thereby introducing a transient break into the DNA. Passage of an additional strand (or strands) of DNA through this break, followed by religation of the break, produces a change in the overall topology of the DNA. While much has been discovered about the in vitro and in vivo activities of the topoisomerase (topo) I and topo II enzymes, much less is known about the activities of topo III.The topo III enzymes are ubiquitous in nature, having been found in organisms ranging from bacteria to humans. Interestingly, it has been suggested that these enzymes may play a role in some aspect of nucleic acid metabolism other than the regulation of DNA supercoiling. This suggestion is based both upon the weak in vitro relaxation activity of topo III (3-5) and upon genetic information gained by mutations made in bacteria and yeast (6 -9). Relative to its ability to relax DNA, bacterial topo III has a much greater activity in decatenation (3), but it can also knot and unknot single-stranded circles of RNA as well (10).Insight into the biological function(s) of topo III comes through the identif...

Drosophila topoisomerase (topo) III␤ is a member of the type IA family of DNA topoisomerases, which generates a single-stranded break to form a covalent complex with the 5-end of DNA. We show here that a purified preparation of topo III␤ is able to convert a hypernegatively supercoiled substrate into primarily nicked, but also linear, DNA at enzyme/DNA molar ratios of 5:1 or greater. Although the optimal temperature for the relaxation activity is between 37 and 45°C, maximal cleavage occurs between 23 and 30°C, a temperature range that is more physiologically relevant for fruit flies. The cleavage products require protease treatment to enter the gel, they are stable over time, they are reversible, and they are not observed with a Y332F active site mutant, which further supports the idea that topo III␤ possesses an endonucleolytic cleavage activity. This cleavage activity appears to be specific for highly unwound, or single strand-containing substrates. Southern blot analysis of the cleavage products demonstrates that the topo III␤ cleavage activity is concentrated primarily in highly A/T-rich regions. These results suggest that topo III␤ may function as a reversible endonuclease in vivo by recognizing and cleaving/rejoining DNA structures with single-stranded character.Processes such as replication, transcription, chromosome segregation, and recombination require the activities of a class of enzymes called topoisomerases (topos).1 Topoisomerases are classified as either type I or type II enzymes, depending on overall structure and mechanism (reviewed in Refs. 1-3). These enzymes work by going through two cycles of transesterification. The first one is initiated by the active-site tyrosine to form a phosphodiester bond with the 5Ј-or 3Ј-DNA phosphate at the transient break site, and the second one is the reversal in which the 3Ј-or 5Ј-hydroxyl at the break reforms the DNA backbone bond, thus regenerating the free tyrosine in the enzyme. The type I enzymes are usually monomers that work by making a reversible single-stranded break in the DNA backbone, whereas type II enzymes are dimeric in structure and thus can introduce a transient double-stranded break. Passage of an intact strand(s) through the broken strand(s) followed by religation of the broken ends completes the topoisomerase reaction cycle and affects the topological transformation in DNA. The type I enzymes are further divided into the IA and IB families, with the Escherichia coli protein as the prototypical type IA enzyme (4, 5). The first eukaryotic type IA topoisomerase was discovered in yeast through a genetic screen for suppression of recombination among repeated sequences (6), and more type IA enzymes (the topo III enzymes) subsequently have been identified in other higher eukaryotes (7-11). Prokaryotes like E. coli and lower eukaryotes such as yeast each possess one topo III enzyme, whereas the metazoans like worms, fruit flies, mice, and humans contain two topo III isoforms, designated topo III␣ and topo III␤.Although much is known about topo I a...