Dynamics of chromosome organization in a minimal bacterial cell

Benjamin R Gilbert; Zane R Thornburg; Troy A Brier; Jan A Stevens; Fabian Grünewald; John E Stone; Siewert J Marrink; Zaida Luthey-Schulten

doi:10.3389/fcell.2023.1214962

Dynamics of chromosome organization in a minimal bacterial cell

Front Cell Dev Biol. 2023 Aug 9:11:1214962. doi: 10.3389/fcell.2023.1214962. eCollection 2023.

Authors

Benjamin R Gilbert¹, Zane R Thornburg¹, Troy A Brier¹, Jan A Stevens², Fabian Grünewald², John E Stone^{3

4}, Siewert J Marrink², Zaida Luthey-Schulten^{1

4

5}

Affiliations

¹ Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
² Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands.
³ NVIDIA Corporation, Santa Clara, CA, United States.
⁴ NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States.
⁵ NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States.

Abstract

Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication and inheritance of genetic material. By creating a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics, we investigate changes in chromosome organization during replication and extend the applicability of an existing whole-cell model (WCM) for a genetically minimal bacterium, JCVI-syn3A, to the entire cell-cycle. To achieve cell-scale chromosome structures that are realistic, we model 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 circular DNA must avoid overlapping with ribosomes identitied in cryo-electron tomograms. 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 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 analyze ribosome diffusion under the influence of the chromosome and calculate in silico chromosome contact maps that capture inter-daughter interactions. Finally, we present a methodology to map the polymer model of the chromosome to a Martini coarse-grained representation to prepare molecular dynamics models of entire Syn3A cells, which serves as an ultimate means of validation for cell states predicted by the WCM.

Keywords: Martini model; brownian dynamics; chromosome replication; chromosome segregation; smc proteins; topoisomerase; whole-cell modeling.

Grants and funding

BG, ZT, TB, and ZL-S: we acknowledge partial support from NSF MCB 1818344 and 2221237, and “The Physics of Living Systems Student Research Network” NSF PHY 2014027. JAS, FG, and SM: we acknowledge funding from the ERC with the Advanced grant 101053661 (“COMP-O-CELL”) and from NWO through the NWA grant “The limits to growth: The challenge to dissipate energy” and BaSyc (“Building a Synthetic Cell”) consortium. JES: Visual Molecular Dynamics (VMD) was developed by the NIH Center for Macromolecular Modeling and Bioinformatics at the Beckman Institute at UIUC, with support from NIH P41-GM104601 and R24-GM145965.