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Harju J, Broedersz CP. Physical models of bacterial chromosomes. Mol Microbiol 2024. [PMID: 38578226 DOI: 10.1111/mmi.15257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 03/12/2024] [Accepted: 03/18/2024] [Indexed: 04/06/2024]
Abstract
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can be theoretically challenging. In this minireview, we discuss how connecting experimental observations to biophysical theory and modeling can give rise to new insights on bacterial chromosome organization. We consider three flavors of models of increasing complexity: simple polymer models that explore how physical constraints, such as confinement or plectoneme branching, can affect bacterial chromosome organization; bottom-up mechanistic models that connect these constraints to their underlying causes, for instance, chromosome compaction to macromolecular crowding, or supercoiling to transcription; and finally, data-driven methods for inferring interpretable and quantitative models directly from complex experimental data. Using recent examples, we discuss how biophysical models can both deepen our understanding of how bacterial chromosomes are structured and give rise to novel predictions about bacterial chromosome organization.
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Affiliation(s)
- Janni Harju
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
| | - Chase P Broedersz
- Department of Physics and Astronomy, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands
- Department of Physics, Arnold Sommerfeld Center for Theoretical Physics and Center for NanoScience, Ludwig-Maximilian-University Munich, Munich, Germany
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2
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Wasim A, Bera P, Mondal J. Development of a Data-Driven Integrative Model of a Bacterial Chromosome. J Chem Theory Comput 2024; 20:1673-1688. [PMID: 37083406 DOI: 10.1021/acs.jctc.3c00118] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/22/2023]
Abstract
The chromosome of archetypal bacteria E. coli is known for a complex topology with a 4.6 × 106 base pairs (bp) long sequence of nucleotides packed within a micrometer-sized cellular confinement. The inherent organization underlying this chromosome eludes general consensus due to the lack of a high-resolution picture of its conformation. Here we present our development of an integrative model of E. coli at a 500 bp resolution (https://github.com/JMLab-tifrh/ecoli_finer), which optimally combines a set of multiresolution genome-wide experimentally measured data within a framework of polymer based architecture. In particular the model is informed with an intragenome contact probability map at 5000 bp resolution derived via the Hi-C experiment and RNA-sequencing data at 500 bp resolution. Via dynamical simulations, this data-driven polymer based model generates an appropriate conformational ensemble commensurate with chromosome architectures that E. coli adopts. As a key hallmark of the E. coli chromosome the model spontaneously self-organizes into a set of nonoverlapping macrodomains and suitably locates plectonemic loops near the cell membrane. As novel extensions, it predicts a contact probability map simulated at a higher resolution than precedent experiments and can demonstrate segregation of chromosomes in a partially replicating cell. Finally, the modular nature of the model helps us devise control simulations to quantify the individual role of key features in hierarchical organization of the bacterial chromosome.
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Affiliation(s)
- Abdul Wasim
- Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana 500046, India
| | - Palash Bera
- Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana 500046, India
| | - Jagannath Mondal
- Tata Institute of Fundamental Research Hyderabad, Hyderabad, Telangana 500046, India
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3
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Li C, Chen Q, Ding M. Escape dynamics of active ring polymers in a cylindrical nanochannel. SOFT MATTER 2024; 20:1719-1724. [PMID: 38284326 DOI: 10.1039/d3sm01524f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2024]
Abstract
We explore the escape dynamics of active ring polymers confined in a cylindrical nanochannel using Brownian dynamics. Our simulation results show that the escape time decreases with the increase of the Péclet number, which is not noticeable between the two stages of the escape process, based on whether the center of mass of the polymer is inside or outside the nanochannel. However, the monomer motion trajectory of the active polymer is very different from that of the passive polymer, similar to the snake-like motion with uniform velocity. The passive polymer, however, is in constant fugitive motion with increased velocity at the tail end of the escape. Our work is vital for understanding the escape dynamics of active ring polymers in the confined nanochannel, which provides new perspectives on their characterization and analysis.
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Affiliation(s)
- Chuqiao Li
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Qiaoyue Chen
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
| | - Mingming Ding
- Xinjiang Laboratory of Phase Transitions and Microstructures in Condensed Matter Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, China
- School of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, China.
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Gilbert BR, Luthey-Schulten Z. Replicating Chromosomes in Whole-Cell Models of Bacteria. Methods Mol Biol 2024; 2819:625-653. [PMID: 39028527 DOI: 10.1007/978-1-0716-3930-6_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Computational models of cells cannot be considered complete unless they include the most fundamental process of life, the replication of genetic material. In a recent study, we presented a computational framework to model systems of replicating bacterial chromosomes as polymers at 10 bp resolution with Brownian dynamics. This approach was used to 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 modeled the chromosome as a self-avoiding homopolymer with bending and torsional stiffnesses that capture the essential mechanical properties of dsDNA in Syn3A. Additionally, the polymer interacts with ribosomes distributed according to cryo-electron tomograms of Syn3A. The polymer model was further augmented by computational models of loop extrusion by structural maintenance of chromosomes (SMC) protein complexes and topoisomerase action, and the modeling and analysis of multi-fork replication states.
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Affiliation(s)
- Benjamin R Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
- NSF Science and Technology Center for Quantitative Cell Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA.
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Gilbert BR, Thornburg ZR, Brier TA, Stevens JA, Grünewald F, Stone JE, Marrink SJ, Luthey-Schulten Z. Dynamics of chromosome organization in a minimal bacterial cell. Front Cell Dev Biol 2023; 11:1214962. [PMID: 37621774 PMCID: PMC10445541 DOI: 10.3389/fcell.2023.1214962] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
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.
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Affiliation(s)
- Benjamin R. Gilbert
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Zane R. Thornburg
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Troy A. Brier
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Jan A. Stevens
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Fabian Grünewald
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - John E. Stone
- NVIDIA Corporation, Santa Clara, CA, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
| | - Siewert J. Marrink
- Molecular Dynamics Group, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, Netherlands
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, IL, United States
- NSF Center for the Physics of Living Cells, Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, United States
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Rehel DA, Polson JM. Equilibrium behaviour of two cavity-confined polymers: effects of polymer width and system asymmetries. SOFT MATTER 2023; 19:1092-1108. [PMID: 36625101 DOI: 10.1039/d2sm01413k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
Experiments using nanofluidic devices have proven effective in characterizing the physical properties of polymers confined to small cavities. Two recent studies using such methods examined the organization and dynamics of two DNA molecules in box-like cavities with strong confinement in one direction and with square and elliptical cross sections in the lateral plane. Motivated by these experiments, we employ Monte Carlo and Brownian dynamics simulations to study the physical behaviour of two polymers confined to small cavities with shapes comparable to those used in the experiments. We quantify the effects of varying the following polymer properties and confinement dimensions on the organization and dynamics of the polymers: the polymer width, the polymer contour length ratio, the cavity cross-sectional area, and the degree of cavity elongation for cavities with rectangular and elliptical cross sections. We find that the tendency for polymers to segregate is enhanced by increasing polymer width. For sufficiently small cavities, increasing cavity elongation promotes segregation and localization of identical polymers to opposite sides of the cavity along its long axis. A free-energy barrier controls the rate of polymers swapping positions, and the observed dynamics are roughly in accord with predictions of a simple theoretical model. Increasing the contour length difference between polymers significantly affects their organization in the cavity. In the case of a large linear polymer co-trapped with a small ring polymer in an elliptical cavity, the small polymer tends to lie near the lateral confining walls, and especially at the cavity poles for highly elongated ellipses.
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Affiliation(s)
- Desiree A Rehel
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada.
| | - James M Polson
- Department of Physics, University of Prince Edward Island, 550 University Ave., Charlottetown, Prince Edward Island, C1A 4P3, Canada.
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