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

DNA拓扑学是研究环状DNA分子的打结、连接和超螺旋的学科。细菌的染色体是环形的，复制总是会导致相互关联的子染色体的形成。为了确保细胞分裂时的正确分离和稳定的质粒遗传，需要无差错的解链。II型拓扑异构酶解链复制链接。在大肠杆菌中，在没有Topo IV(一种被认为是导致染色体解链的II型拓扑异构酶)的情况下，定点重组系统XerCD介导姐妹染色体的解链。这种反应在分裂隔膜被一种强大的转位酶FtsK激活，该转位酶协调染色体分离的最后阶段。XerCD-FtsK复合体简化DNA拓扑结构的机制尚不清楚。本研究的主要目的是利用纽结理论、低维拓扑学和计算机模拟来表征XerCD-FtsK系统解链DNA的拓扑机制。有证据表明，在被FtsK激活后，XerCD酶以一种循序渐进的方式将DNA解链。缠绕法将被用来寻找DNA在小底物上通过定点重组解结和解链的可能的拓扑路径。将开发一个适合Xer-FtsK系统的DNA重组的计算机模型，并将其与分析结果结合起来分析从Sherratt实验室获得的实验数据。这项研究是高度跨学科的，涉及到与日本、加拿大和英国的团体的密切合作。这样的合作将促进最先进的学生交叉培训。有关DNA拓扑学的基本信息将向公众传播，包括小学生和加州科学院的参观者。DNA复制是生物遗传的基础。在细菌中，繁殖始于将染色体复制到两个相同的子代分子中，然后分离新复制的染色体，并将亲本细胞分裂为两个子代细胞。在环形染色体中，DNA连接过程中的缠绕问题使染色体分离过程复杂化。在大肠杆菌中，DNA解链通常是由topoIV酶介导的，topoIV是喹诺酮类抗菌药物的重要药物靶点。了解通过Xer重组来解链DNA，除了提供更完整的染色体分离过程图外，还与药物设计高度相关。数学和计算工具对于研究改变DNA拓扑结构的酶的作用非常有用。在这个项目中，这些工具将被用来表征所有的解链途径，并揭示Xer解链的机制。教育目标是开发新的有效方法来传播与DNA拓扑学及其生物学意义有关的知识，并提高公众对数学在理解生物过程中的关键作用的认识。拟议的计划包括在旧金山为小学生创建数学圈，并与加州科学院合作开发一系列供公众消费的教育材料。这将在加州科学院博物馆为普通公众制作一场关于DNA拓扑学的展览。

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.