Spatial-temporal control over tipping-point operation defines fidelity of genome partition

对临界点操作的时空控制定义了基因组分区的保真度

• 批准号: 2105837
• 负责人: Jian Liu
• 金额: $ 108.6万
• 依托单位: Johns Hopkins University
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-07-01 至 2025-06-30
• 项目状态: 未结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=2105837&HistoricalAwards=false
• 关键词: Spatial; temporal; control; over; tipping

Cells (especially bacteria) exist and thrive under a range of environmental conditions and they must alter various functions to adapt to changing conditions. This is challenging because many processes operate in a semi-stable state. This means that many processes can go one way or another, depending upon a tipping point (or operating point) which upon activation leads the cell down the proper path. Thus, cellular processes must establish the right operating point to robustly execute function and at the same time,¬ sensitively adapt this point to changing environmental cues. The overarching goal of this project is to elucidate how cells control the near-tipping-point operation to ensure the fidelity of cellular processes. This project will examine genetic partitioning in bacteria using a combined computational modeling and experimental approach to reveal how cells segregate DNA under changing conditions. The project will shed important light on how evolution shapes the operating point of this important cellular process to ensure genetic material is partitioned with high fidelity. The project will include training of undergraduate and graduate student researchers, community outreach efforts promoting the academic representation of underrepresented minorities, and creating a new course, “Mechanistic modeling of cell biology”, which emphasizes how to meaningfully integrate modeling with experiments. An annual workshop on the emerging topics will also be developed and will challenge participants to begin developing reasonable models of essential processes. Low-copy plasmid partitioning in bacteria provides a well-suited paradigm to distill the fundamental principles underlying the fidelity of genome partitioning. Most low-copy plasmids are actively segregated along the nucleoid by the conserved tripartite ParABS system. Upon replication, the sister plasmids always segregate by about half of the nucleoid length, ensuring high fidelity partitioning into the two daughter cells. As plasmid partitioning is not coupled to cell cycle and the nucleoid keeps elongating before cell division, the sister plasmids can be anywhere along the nucleoid when the parental cells starts to divide. This precipitates the key unanswered question of how the ParABS-mediated partition faithfully adapts the plasmid segregation distance to half of the nucleoid length to ensure plasmid partition fidelity. The project team established: 1) bacterial low-copy plasmid partitions via a Brownian ratchet mechanism where the plasmid “self-drives” by creating and following the ParA concentration gradient on nucleoid, and; 2) this ratcheting in vivo operates near a tipping point in the parameter space. The project will have two specific aims: 1) determine how ParA-mediated partition sensitively adapts to the length of the elongating nucleoid, and 2) establish how ParA-mediated partition ensures robustness of plasmid segregations. The project will elucidate how the ParA spatial-temporal regulation controls this near-tipping-point operation and ensures the fidelity of genome partition against stochastic fluctuations (e.g., the variations in ParA level). The basic principles distilled from this project would help address one fundamental question in cell biology: How do cells faithfully measure cellular-scale distance by using only molecular-scale interactions? This project is partially supported by the Genetic Mechanisms cluster in the Division of Molecular and Cellular Biosciences.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

细胞（特别是细菌）在一系列环境条件下生存和繁衍，它们必须改变各种功能以适应不断变化的条件。 这是具有挑战性的，因为许多过程在半稳定状态下操作。 这意味着许多过程可以以这样或那样的方式进行，这取决于在激活时将细胞沿着正确路径引导的临界点（或操作点）。因此，细胞过程必须建立正确的操作点以稳健地执行功能，同时敏感地使该点适应变化的环境线索。这个项目的首要目标是阐明细胞如何控制近临界点操作，以确保细胞过程的保真度。该项目将使用计算建模和实验方法相结合的方法来研究细菌中的遗传分配，以揭示细胞如何在变化的条件下分离DNA。该项目将揭示进化如何塑造这一重要细胞过程的操作点，以确保遗传物质以高保真度分配。该项目将包括培训本科生和研究生研究人员，开展社区外联工作，促进代表性不足的少数群体的学术代表性，并开设一门新课程“细胞生物学的机械建模”，该课程强调如何将建模与实验有意义地结合起来。 还将举办一个关于新出现的专题的年度讲习班，要求参加者开始制定基本进程的合理模式。细菌中的低拷贝质粒分配提供了一个非常适合的范例，以提取基因组分配的保真度的基本原则。大多数低拷贝质粒通过保守的三部分ParABS系统沿类核沿着分离。在复制时，姐妹质粒总是以大约一半的类核长度分离，确保高保真地分配到两个子细胞中。由于质粒分配不与细胞周期偶联，并且类核在细胞分裂前保持伸长，因此当亲本细胞开始分裂时，姐妹质粒可以沿着类核的任何位置。这沉淀了关键的未回答的问题，即Parabs介导的分区如何忠实地将质粒分离距离调整为类核长度的一半，以确保质粒分区的保真度。项目小组建立了：1）细菌低拷贝质粒通过布朗棘轮机制进行分配，其中质粒通过在类核上产生和遵循帕拉浓度梯度而“自驱动”，和; 2）这种体内棘轮作用在参数空间中的临界点附近操作。该项目将有两个具体目标：1）确定ParA介导的分区如何敏感地适应延长类核的长度，以及2）确定ParA介导的分区如何确保质粒分离的稳健性。该项目将阐明帕拉时空调控如何控制这种接近临界点的操作，并确保基因组分区对随机波动的保真度（例如，帕拉水平的变化）。从这个项目中提炼出的基本原理将有助于解决细胞生物学中的一个基本问题：细胞如何通过仅使用分子尺度的相互作用忠实地测量细胞尺度的距离？ 该项目得到了分子和细胞生物科学部遗传机制组的部分支持。该奖项反映了NSF的法定使命，并通过使用基金会的知识价值和更广泛的影响审查标准进行评估，被认为值得支持。