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。细菌染色体是环状的，复制总是导致相互连接的子染色体的形成。需要无错误的解链以确保在细胞分裂时的适当分离和稳定的质粒遗传。II型拓扑异构酶解除复制链的连接。在大肠杆菌中，在缺乏拓扑异构酶IV（一种II型拓扑异构酶，与染色体解联有关）的情况下，位点特异性重组系统XerCD介导姐妹染色体解联。这种反应在分裂隔膜处被一种强大的移位酶FtsK激活，该移位酶协调染色体分离的最后阶段。XerCD-FtsK复合物简化DNA拓扑结构的机制尚不清楚。所提出的研究的主要目的是使用结理论，低维拓扑结构和计算机模拟的XerCD-FtsK系统的DNA解链的拓扑机制的特征。 有证据表明，在被FtsK激活后，XerCD酶以逐步的方式解除DNA的连接。缠结的方法将被用来寻找可能的拓扑路径的DNA解结和解链的位点特异性重组的小基板上。DNA重组的计算机模型将被开发，适用于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。该研究是高度跨学科的，涉及与日本，加拿大和英国的团体密切合作。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普通公众传播，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，繁殖开始于染色体复制成两个相同的子分子，随后是新复制的染色体的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解链通常由酶topoIV介导，topoIV是喹诺酮类抗微生物剂的重要药物靶标。了解DNA解链的Xer重组，除了提供一个更完整的图片染色体分离过程，是高度相关的药物设计。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，这些工具将被用来描述所有的解链途径，并揭示Xer解链的机制。教育目标是开发新的和有效的方法来传播有关DNA拓扑结构及其生物学意义的知识，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。拟议的计划包括在旧金山弗朗西斯科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。这将导致在加州科学院博物馆为公众制作一个关于DNA拓扑结构的展览。

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.