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、连接和超卷曲。细菌的染色体是圆形的，复制总是导致形成相互连接的子染色体。无错误解联是确保细胞分裂时正确分离和质粒稳定遗传的必要条件。II型拓扑异构酶解除复制链路。在大肠杆菌中，缺乏topo IV（一种II型拓扑异构酶，被认为与染色体解联有关），位点特异性重组系统XerCD介导姐妹染色体解联。这个反应在分裂间隔被一个强大的转位酶FtsK激活，它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。提出的研究的主要目的是利用结理论、低维拓扑和计算机模拟来表征XerCD-FtsK系统DNA解联的拓扑机制。有证据表明，在被FtsK激活后，XerCD酶以逐步的方式断开DNA的连接。缠结方法将用于寻找可能的拓扑途径的DNA解结和解连接的位点特异性重组在小底物上。将开发一个DNA重组的计算机模型，适应Xer-FtsK系统，并结合分析结果来分析从Sherratt实验室获得的实验数据。这项研究是高度跨学科的，涉及与日本、加拿大和英国的小组密切合作。这种合作将促进最先进的学生交叉培训。有关DNA拓扑结构的基本信息将向公众传播，包括小学生和加州科学院的访客。DNA复制是生物遗传的基础。在细菌中，繁殖开始于染色体复制成两个相同的子分子，接着是新复制的染色体分离和亲本细胞分裂成两个子细胞。在环状染色体中，DNA连接过程中的缠结问题使染色体分离过程复杂化。在大肠杆菌中，DNA解联通常由topoIV酶介导，topoIV酶是喹诺酮类抗菌剂的重要药物靶点。通过Xer重组了解DNA解链，除了提供染色体分离过程的更完整的图片外，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，这些工具将用于表征所有解联途径，并揭示Xer解联的机制。教育目标是开发新的和有效的方法来传播与DNA拓扑及其生物学意义有关的知识，以及提高公众对数学在理解生物过程中的关键作用的认识。拟议的计划包括为旧金山的小学生创建数学圈，并与加州科学院合作开发一系列供公众消费的教育材料。最终将在加州科学院博物馆为公众举办一个关于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.