Self-organisation as the basis of bacterial chromosomal segregation

染色体复制和分离是所有细胞生命的关键过程。细菌染色体的复制始于一个称为起始点或ORI的独特位置，并沿着每个染色体臂双向进行。在大肠杆菌和其他细菌中，ORI专门定位于细胞内。在新生的细胞中，它位于细胞中部，在那里开始复制。复制的ORI随后被分割到相反的四分之一位置，在那里它们在细胞周期的剩余部分保持不变。虽然这些动力学已经得到了很好的研究，但其潜在的机制尚不清楚。我们最近提供了一种新的解释，基于SMC(染色体的结构维护)复合体的自组织，SMC(染色体的结构维护)复合体是一个普遍存在的蛋白质家族，参与染色体组织。MukBEF，大肠杆菌SMC按照上述ORI模式在细胞内形成动态簇。提出了MukBEF是一个自组织、自定位的系统，并给出了基于随机模式形成的数学模型。在这个模型的基础上，我们认为自组织的MukBEF对ORI进行了隔离和定位。我们已经证明了MukBEF和ORI之间的特定相互作用导致了双向吸引，导致了ORI的准确定位和划分。后者是系统的紧急属性，源于ORI不是简单地向上移动MukBEF梯度，而是以一种不平凡的方式与其交互。该模型得到了新的和已发表的实验数据的支持。在这个项目中，我们的目标是揭开组织大肠杆菌染色体的生物和物理机制。我们的第一个目标是将我们的空间随机模型与时移荧光显微镜数据进行严格的定量比较。为此，我们将开发一个图像分析管道和一个分布式计算和贝叶斯推理框架。这将使我们能够对照实验数据来检验生物物理假说。我们将使用这种方法来探索MukBEF和ORI之间相互作用的确切性质。最后，我们将研究另一个重要的基因组区域-复制末端的定位及其与MukBEF的相互作用，该区域也在决定未来的分裂位置中发挥作用。通过建立第一个大肠杆菌中染色体分离的定量模型，这项工作将为了解细菌细胞周期最基本的方面之一提供基本的生物学和物理学方面的见解。此外，将成像数据与时空随机模型进行比较的贝叶斯推理方法将对其他细胞生物学过程的研究感兴趣，而该模型本身将更广泛地吸引模式形成社区。

Chromosome replication and segregation are critical processes for all cellular life. Replication of bacterial chromosomes initiates at a unique site called the origin, or ori, and proceeds bi-directionally down each chromosomal arm. In Escherichia coli and other bacteria, the ori is specifically positioned within the cell. In new-born cells, it is found at the cell middle, where replication is initiated. Duplicated ori are subsequently partitioned to opposite quarter positions where they remain for the remainder of the cell cycle. While these dynamics been very well studied, the underlying mechanisms are unknown.We have recently provided a novel explanation based on self-organisation of SMC (Structural Maintenance of Chromosomes) complexes, a ubiquitous family of proteins involved in chromosome organisation. MukBEF, the E. coli SMC forms dynamic clusters inside cells following the pattern of ori, described above. We have proposed that MukBEF is a self-organising and self-positioning system and presented a mathematical model based on stochastic pattern formation. Building on this model, we argue that self-organising MukBEF segregates and positions ori. We have shown that a specific interaction between MukBEF and ori leads to bidirectional attraction, resulting in accurate positioning and partitioning of ori. The latter is an emergent property of the system, arising from the fact that ori do not simply move up the MukBEF gradient but rather interact with it in a non-trivial way. The model is supported by both new and published experimental data.In this project, we aim to unravel the biological and physical mechanism organising the E. coli chromosome. Our first goal is a rigorous quantitative comparison of our spatial stochastic model with time-lapse fluorescence microscopy data. For this, we will develop an image analysis pipeline and a distributed computing and Bayesian inference framework. This will give us the ability to test biophysical hypotheses against the experimental data. We will use this approach to explore the precise nature of the interaction between MukBEF and ori. Lastly, we will examine the positioning and interaction with MukBEF of another important genomic region, the replication terminus, which also plays a role in determining the future division site.By developing the first quantitative model of chromosome segregation in E. coli, this work will provide fundamental biological and physical insights into one of the most fundamental aspects of the bacterial cell cycle. Furthermore, the Bayesian inference approach for comparing imaging data to a spatio-temporal stochastic model will be of interest for the study of other cell biological processes, while the model itself will appeal more broadly to the pattern formation community.