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Ftsk-Dependent Xercd-Dif Recombination Unlinks Replication Catenanes in a Stepwise Manner

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Ftsk-Dependent Xercd-Dif Recombination Unlinks Replication Catenanes in a Stepwise Manner FtsK-dependent XerCD-dif recombination unlinks replication catenanes in a stepwise manner Koya Shimokawaa, Kai Ishiharab, Ian Graingec, David J. Sherrattd, and Mariel Vazqueze,1 aDepartment of Mathematics, Saitama University, Saitama 380-8570, Japan; bFaculty of Education, Yamaguchi University, Yamaguchi 753-8512, Japan; cSchool of Environmental and Life Sciences, University of Newcastle, Callaghan, NSW 2308, Australia; dDepartment of Biochemistry, University of Oxford, Oxford OX1 3QU, United Kingdom; and eDepartment of Mathematics, San Francisco State University, San Francisco, CA 94132 Edited by De Witt Sumners, Florida State University, Tallahassee, FL, and accepted by the Editorial Board October 17, 2013 (received for review May 10, 2013) In Escherichia coli, complete unlinking of newly replicated sister In E. coli, XerCD-dif recombination plays an essential role in chromosomes is required to ensure their proper segregation at cell chromosome dimer resolution (reviewed in ref. 7). Furthermore, division. Whereas replication links are removed primarily by top- when coupled with FtsK, XerCD recombination at dif sites can oisomerase IV, XerC/XerD-dif site-specific recombination can me- unlink 2m-cats produced in vitro by λ-Integrase (3). These results diate sister chromosome unlinking in Topoisomerase IV-deficient suggested a potential in vivo role for XerCD–FtsK recombination, cells. This reaction is activated at the division septum by the DNA which was then hypothesized to work with TopoIV to unlink translocase FtsK, which coordinates the last stages of chromosome DNA links produced by DNA replication. To test this hypothe- segregation with cell division. It has been proposed that, after being sis, a pair of supercoiled linked plasmids, each with one dif site, activated by FtsK, XerC/XerD-dif recombination removes DNA links was produced in vivo by replication in TopoIV-deficient cells, in a stepwise manner. Here, we provide a mathematically rigorous and these were then incubated in vitro with XerCD–FtsK50C (4). characterization of this topological mechanism of DNA unlinking. The ATP-dependent reaction efficiently produced unlinked cir- We show that stepwise unlinking is the only possible pathway that cles. The ATP dependence of the reaction is likely twofold: firstly strictly reduces the complexity of the substrates at each step. Finally, the DNA translocase activity of FtsK relies upon ATP hydrolysis we propose a topological mechanism for this unlinking reaction. for movement, and in the absence of translocation there is no stimulation of recombination. Secondly, the energy from ATP DNA topology | tangle method | Xer recombination | band surgery | hydrolysis is also used to align the two recombining dif sites so topology simplification that subsequent recombination produces the observed stepwise reduction in complexity. In addition to right-handed (RH) torus – he Escherichia coli chromosome is a 4.6-Mbp circular double- links with parallel sites and with 2 14 crossings, unknotted Tstranded (ds) DNA duplex, in which the two DNA strands dimers and a few dimeric knots were also observed. The exper- are wrapped around each other ∼420,000 times. During repli- imental data suggested a stepwise reaction where crossings are cation, DNA gyrase acts to remove the majority of these strand removed one at a time, iteratively converting links into knots, crossings, but those that remain result in two circular sister into links, until two free circles are obtained (Fig. 1). A control – molecules that are nontrivially linked. This creates the topolog- experiment demonstrated that XerCD FtsK50C recombination ical problem of separating the two linked sister chromosomes to could convert knotted dimers (RH torus knots with two directly ensure proper segregation at the time of cell division. Unlinking repeated dif sites) to free circles. Separate experiments showed of replication links in E. coli is largely achieved by Topoisomerase that chromosome unlinking in E. coli can be accomplished in IV (TopoIV), a type II topoisomerase (1, 2). However, Ip et al. fi demonstrated that XerC/XerD-dif (XerCD-dif) site-specific re- Signi cance combination, coupled with action of the translocase FtsK, could resolve linked plasmid substrates in vitro and hypothesized that Newly replicated circular chromosomes are topologically linked. this system could work alongside, yet independently of, TopoIV XerC/XerD-dif (XerCD-dif)–FtsK recombination acts in the repli- during in vivo unlinking of replicative catenanes in the bacterial cation termination region of the Escherichia coli chromosome to chromosome (3). Grainge et al. then demonstrated that in- remove links introduced during homologous recombination and creased site-specific recombination could indeed compensate for replication, whereas Topoisomerase IV removes replication links a loss of TopoIV activity in unlinking chromosomes in vivo (4). only. Based on gel mobility patterns of the products of recombi- When the activity of TopoIV is blocked, the result is cell le- nation, a stepwise unlinking pathway has been proposed. Here, thality. We here propose a mathematically rigorous analysis to we present a rigorous mathematical validation of this model, a fi describe the pathway and mechanisms of unlinking of replication signi cant advance over prior biological approaches. We show fi links by XerCD–FtsK. This work places a fundamental biological de nitively that there is a unique shortest pathway of unlinking dif– process within a mathematical context. by XerCD- FtsK that strictly reducesthecomplexityofthe Site-specific recombination is a process of breakage and re- links at every step. We delineate the mechanism of action of union at two specific dsDNA duplexes (the recombination sites). the enzymes at each step along this pathway and provide a 3D When the DNA substrate consists of circular DNA molecules, interpretation of the results. the recombination sites may occur in a single DNA circle or in Author contributions: K.S., D.J.S., and M.V. designed research; K.S., K.I., and M.V. per- separate circles. Two sites are in direct repeat if they are in the formed research; K.S., K.I., I.G., D.J.S., and M.V. contributed new reagents/analytic tools; same orientation on one DNA circle (Fig. 1). The relative ori- K.S., K.I., I.G., D.J.S., and M.V. analyzed data; and K.S., I.G., D.J.S., and M.V. wrote the entation of the sites is harder to characterize when the two sites paper. are on separate DNA circles. In the case of simple torus links The authors declare no conflict of interest. with 2m crossings (also called 2m-catenanes, or 2m-cats) for an This article is a PNAS Direct Submission. D.W.S. is a guest editor invited by the Editorial Board. integer m > 1, the sites are said to be in parallel or antiparallel Freely available online through the PNAS open access option. orientation with respect to each other (Fig. 1). Site-specific re- See Commentary on page 20854. combination occurs in two steps (5, 6): first, the recombination 1To whom correspondence should be addressed. E-mail: [email protected]. sites are brought together (synapsis); second, each site is cleaved This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. and the DNA ends are exchanged, then rejoined. 1073/pnas.1308450110/-/DCSupplemental. 20906–20911 | PNAS | December 24, 2013 | vol. 110 | no. 52 www.pnas.org/cgi/doi/10.1073/pnas.1308450110 Downloaded by guest on October 2, 2021 biologically reasonable assumptions and using results from low- dimensional topology, one can show that the tangles involved are SEE COMMENTARY all rational (14, 15, 21). Therefore, all solutions to the XerCD– psi system of equations can be computed using tangle calculus. There are only three solutions consistent with the experimental data (15). It was further shown that these solutions can be seen as different projections of the same three-dimensional (3D) ob- Fig. 1. Proposed stepwise unlinking by XerCD-dif–FtsK recombination: Parallel ject, and a unique topological mechanism for XerCD at psi was RH 2m-cats [e.g., T(2,6)p] are converted to RH torus knots [e.g., T(2,5)] with proposed that incorporated all three solutions (15). directly repeated sites; such knots are converted to RH cats, and so on, In Grainge et al. (4), several systems of tangle equations were iteratively, until the reaction stops at two open circles. (In ref. 4, RH torus links with parallel sites and up to 14 crossings, also called parallel 2m-cats proposed for the pathway taking replication links to two open cir- cles (the unlink). Tangle calculus was used to solve each system. For and denoted by T(2,2m)p, were used as substrates of Xer recombination.) example, all possible systems of two equations converting a RH 6-cat with parallel sites into a knotted product with five or fewer vivo by multiple rounds of XerCD-dif or Cre-loxP site-specific crossings were considered. Using tangle calculus, only three bio- recombination. The reactions required DNA translocation by logically meaningful solutions were found, all of which produced the FtsK. Overexpression of FtsK50C in TopoIV-deficient cells was RH 5-crossing torus knot with directly repeated sites. The authors sufficient to drive the topology simplification. Furthermore, in proposed that the three solutions are equivalent by 3D rigid motion vivo XerCD activation by actively translocating FtsK is essential (i.e., the three solutions reflect different views of the same 3D to effectively unlink replication links (4). In the absence of FtsK, shape). This study concluded that the stepwise unlinking pathway of an active XerCD complex may produce complicated DNA knots Fig. 1 is the most likely pathway of XerCD–FtsK recombination and links, with a small yield of unlinks (8). Whereas Xer site-specific when acting on 2m-cats, and posited a stepwise mechanism of action. recombination on DNA plasmids in vitro has been well-characterized The mathematical study in ref.
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