Modeling Multi-fork Replication and Segregation of Bacterial Chromosomes

Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. In a series of projects detailed here, we describe efforts to create whole-cell models (WCMs) for a genetically minimal bacterium, JCVI-syn3A, with particular focus on modeling of the chromosome. In the earliest work, we developed a methodology to construct complete cellular architectures of Syn3A from cryo-electron tomography (cryo-ET) and generate static configurations of chromosomes using a self-avoiding polygon (SAP) lattice polymer model. The lattice model was formulated to ensure compatibility with spatially resolved WCM simulations using reaction-diffusion master equations, and showed agreement with the chromosome organization observed in chromosome conformation capture (3C) maps from 3C-seq experiments. The static nature of the lattice model rendered it insufficient for modeling dynamics processes such as chromosome replication and segregation. Furthermore, there was not an established methodology to describe nontrivial replication states of circular chromosomes, i.e. nested theta structures. Motivated these two deficiencies, we created a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics. Using this, we investigated changes in chromosome organization during replication and extended the applicability of an existing WCM for Syn3A to the entire cell cycle. To achieve cell-scale chromosome structures that are realistic, we modeled the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. In addition, the conformations of the chromosomes are constrained by the ribosomes identitied in cryo-ET and confined within mebrane morphologies that may be dynamically altered. While Syn3A lacks the complex regulatory systems known to orchestrate chromosome segregation in other bacteria, its minimized genome retains essential loop-extruding structural maintenance of chromosomes (SMC) protein complexes (SMC-scpAB) and strand-crossing topoisomerases. Through implementing the effects of these proteins in our simulations of replicating chromosomes, we find that they alone are sufficient for simultaneous chromosome segregation across all generations within nested theta structures. This supports previous studies suggesting loop-extrusion serves as a near-universal mechanism for chromosome organization within bacterial and eukaryotic cells. Furthermore, we calculate in silico chromosome contact maps that capture inter-daughter interactions as a function of the cell’s replication state. Beyond these analyses of the physical structure of the chromosome and the mechanisms by which it is modified, the novel description of the replication states of circular dsDNA molecules using binary trees enables simulations of cell cycles that include multi-fork replication and the partitioning of daughter chromosomes in nontrivial replication states into the daughter cells.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Chemistry

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2024

Author dc:creator

• Gilbert, Benjamin Robert

Contributors dc:contributor

• Luthey-Schulten, Zaida
• Gruebele, Martin
• Aksimentiev, Aleksei
• Kim, Sangjin

• Bacteria
• Whole-cell Modeling
• Chromosome Replication
• Chromosome Segregation
• Brownian Dynamics
• Dna Polymer Models

Statement dc:rights

• Copyright 2024 Benjamin R. Gilbert

Language dc:language

en, eng

Handle dc:identifier

https://hdl.handle.net/2142/125660

OAI record oai:identifier

https://www.ideals.illinois.edu/oai-pmh?verb=GetRecord&metadataPrefix=etdms&identifier=oai%3Awww.ideals.illinois.edu%3A2142%2F125660