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

细胞(尤其是细菌)在一系列环境条件下生存并茁壮成长，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，因为许多过程都在半稳定状态下运行。这意味着许多过程可以这样或那样进行，这取决于一个临界点(或操作点)，该临界点(或操作点)在激活时会引导细胞沿着正确的路径前进。因此，细胞过程必须建立正确的操作点，以便稳健地执行功能，同时，敏感地使这一点适应不断变化的环境线索。这个项目的首要目标是阐明细胞如何控制接近临界点的操作，以确保细胞过程的保真度。该项目将使用计算建模和实验相结合的方法来研究细菌中的遗传分割，以揭示细胞如何在不断变化的条件下分离DNA。该项目将阐明进化如何塑造这一重要细胞过程的操作点，以确保遗传物质被高保真地分割。该项目将包括对本科生和研究生研究人员的培训，促进代表不足的少数群体的学术代表性的社区外联努力，以及创建一门新课程，即“细胞生物学的机械建模”，该课程强调如何有意义地将建模与实验相结合。还将举办一次关于新出现的专题的年度讲习班，要求与会者开始制定基本程序的合理模式。细菌中的低拷贝质粒分割提供了一个非常适合的范例来提炼基因组分割保真度背后的基本原理。大多数低拷贝质粒被保守的三方ParABS系统沿着类核主动分离。在复制时，姐妹质粒总是以大约一半的类核长度分离，确保高保真地分割成两个子细胞。由于质粒分裂与细胞周期无关，类核在细胞分裂前不断延长，当亲本细胞开始分裂时，姊妹质粒可能在类核上的任何地方。这就产生了一个关键的悬而未决的问题：ParABS介导的分配如何忠实地将质粒分离距离调整为类核长度的一半，以确保质粒分配的保真度。该项目团队建立了：1)细菌低拷贝质粒通过布朗棘轮机制进行分割，其中质粒通过在类核上创建并遵循对位浓度梯度来“自我驱动”；以及2)体内的这种棘轮在参数空间的临界点附近运行。该项目将有两个具体的目标：1)确定对位介导的分配如何灵敏地适应延长的类核的长度，以及2)确定对位介导的分配如何确保质粒分离的稳健性。该项目将阐明准时空调控如何控制这种接近临界点的操作，并确保基因组分割的保真度不受随机波动(例如，准水平的变化)的影响。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来忠实地测量细胞尺度的距离？这个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。这一奖项反映了NSF的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.