CAREER: Topological mechanism of DNA unlinking by the XerCD-FtsK system

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DNA topology is the study of knotting, linking and supercoiling of circular DNA molecules. The bacterial chromosome is circular and replication invariably results in the formation of interlinked daughter chromosomes. Error-free unlinking is required to ensure proper segregation at cell division and stable plasmid inheritance. Type II topoisomerases unlink replication links. In Escherichia coli, in the absence of topo IV (a type II topoisomerase credited with chromosome unlinking), the site-specific recombination system XerCD mediates sister chromosome unlinking. This reaction is activated at the division septum by a powerful translocase FtsK, which coordinates the last stages of chromosome segregation. The mechanism by which the XerCD-FtsK complex simplifies the topology of DNA remains unclear. The main objective of the proposed studies is to characterize the topological mechanism of DNA unlinking by the XerCD-FtsK system using knot theory, low-dimensional topology, and computer simulations. There is evidence that after being activated by FtsK, the enzymes XerCD unlink DNA in a stepwise manner. The tangle method will be used to find possible topological pathways of DNA unknotting and unlinking by site-specific recombination on small substrates. A computer model of DNA recombination will be developed, adapted to the Xer-FtsK system, and combined with the analytical results to analyze experimental data obtained from the Sherratt lab. The research is highly interdisciplinary and involves close collaboration with groups in Japan, Canada and the UK. Such collaborations will facilitate state-of-the-art student cross-training. Basic information about DNA topology will be disseminated to the general public, including elementary school children and visitors to the California Academy of Sciences. DNA replication is the basis for biological inheritance. In bacteria, reproduction starts with replication of the chromosome into two identical daughter molecules, followed by segregation of the newly replicated chromosomes and division of the parent cell into two daughter cells. In circular chromosomes, problems of entanglement during DNA linking complicate the process of chromosome segregation. In Escherichia coli, DNA unlinking is typically mediated by the enzyme topoIV, which is an important drug target for quinolone antimicrobial agents. Understanding DNA unlinking by Xer recombination, in addition to providing a more complete picture of the chromosome segregation process, is highly relevant for drug design. Mathematical and computational tools are very useful for studying the action of enzymes that change the topology of DNA. In this project such tools will be used to characterize all unlinking pathways and to reveal the mechanism of unlinking by Xer. The educational goal is to develop new and effective ways to disseminate knowledge related to DNA topology and its biological significance, as well as to increase public awareness of the critical role of mathematics in understanding biological processes. The proposed plans include the creation of Math Circles for elementary school children in San Francisco and the development of a series of educational materials for public consumption in collaboration with the California Academy of Sciences. This will culminate in the production of an exhibit on DNA topology for the general public in the California Academy of Sciences Museum.