Attention:The NSF Public Access Repository (PAR) system and access will be unavailable from 11:00 PM ET on Thursday, October 15th until 12:00 AM ET on Friday, October 16th due to maintenance. We apologize for the inconvenience.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


  • NSF Public Access
  • Search Results
  • Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps
Title: Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps
JCVI-syn3A is a genetically minimal bacterial cell, consisting of 493 genes and only a single 543 kbp circular chromosome. Syn3A’s genome and physical size are approximately one-tenth those of the model bacterial organism Escherichia coli ’s, and the corresponding reduction in complexity and scale provides a unique opportunity for whole-cell modeling. Previous work established genome-scale gene essentiality and proteomics data along with its essential metabolic network and a kinetic model of genetic information processing. In addition to that information, whole-cell, spatially-resolved kinetic models require cellular architecture, including spatial distributions of ribosomes and the circular chromosome’s configuration. We reconstruct cellular architectures of Syn3A cells at the single-cell level directly from cryo-electron tomograms, including the ribosome distributions. We present a method of generating self-avoiding circular chromosome configurations in a lattice model with a resolution of 11.8 bp per monomer on a 4 nm cubic lattice. Realizations of the chromosome configurations are constrained by the ribosomes and geometry reconstructed from the tomograms and include DNA loops suggested by experimental chromosome conformation capture (3C) maps. Using ensembles of simulated chromosome configurations we predict chromosome contact maps for Syn3A cells at resolutions of 250 bp and greater and compare them to the experimental maps. Additionally, the spatial distributions of ribosomes and the DNA-crowding resulting from the individual chromosome configurations can be used to identify macromolecular structures formed from ribosomes and DNA, such as polysomes and expressomes.  more » « less
Award ID(s):
1818344 1840320 1430124 1840301 1920374
PAR ID:
10279307
Author(s) / Creator(s):
; ; ; ; ; ; ;
Date Published:
Journal Name:
Frontiers in Molecular Biosciences
Volume:
8
ISSN:
2296-889X
Format(s):
Medium: X
Sponsoring Org:
National Science Foundation
More Like this
  1. ; ; ; ; ; ; ; (, Frontiers in Cell and Developmental Biology)
    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 calculatein silicochromosome 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. 
    more » « less
  2. ; ; (, Protein Science)
    Abstract Minimal bacterial cells such as JCVI‐Syn3A provide a powerful system for uncovering the essential mechanisms of chromosome organization and segregation. Lacking canonical systems such as Min and ParABS, JCVI‐Syn3A relies primarily on structural maintenance of chromosomes (SMC) protein complexes for partitioning. Here, we investigate a four‐dimensional (4D; three spatial dimensions plus time) polymer‐based model of the JCVI‐Syn3A chromosome (543 kbp) that captures replication and partitioning dynamics across the full cell cycle. Our simulations reproduce chromosome segregation mediated by SMC‐driven loop extrusion and reveal how segregation depends on the number of SMC complexes, their translocation speed, and their dwell time on DNA. A systematic parameter scan shows that segregation is strongly predicted by the effective loop coverage, which represents the expected fraction of the chromosome extruded into loops. We generate contact maps for stationary‐phase cells to directly connect our simulations with 3C experiments, and for replicating chromosomes throughout the cell cycle to provide new, testable predictions for synchronized cell populations. Our results suggest that SMC protein complexes and topoisomerases can drive chromosome segregation in minimal cells without additional partitioning systems provided loop extrusion achieves sufficient genomic coverage. 
    more » « less
  3. ; ; ; ; ; ; ; ; (, Science Advances)
    Chromosome architecture plays a crucial role in bacterial adaptation, yet its direct impact remains unclear. Different bacterial species and even strains within the same species exhibit diverse chromosomal configurations, including a single circular or linear chromosome, two circular chromosomes, or a circular-linear combination. To investigate how these architectures shape bacterial behavior, we generated near-isogenic strains representing each configuration inAgrobacterium tumefaciensC58, an important soil bacterium widely used for plant genetic transformation. Strains with a single-chromosome architecture, whether linear or circular, exhibited faster growth, enhanced stress tolerance, and greater interstrain competitiveness. In contrast, bipartite chromosome strains showed higher virulence gene expression and enhanced transient plant transformation efficiency, suggesting a pathogenic adaptation. Whole-transcriptome analysis revealed architecture-dependent gene expression patterns, underscoring the profound impact of chromosome organization onAgrobacteriumfitness and virulence. These findings highlight how chromosome structure influences bacterial adaptation and shapes evolutionary trajectories. 
    more » « less
  4. ; ; (, Trends in Cell Biology)
    Genomically minimal cells, such as JCVI-syn3.0 and JCVI-syn3A, offer an empowering framework to study relationships between genotype and phenotype. With a polygenic basis, the fundamental physiological process of cell division depends on multiple genes of known and unknown function in JCVI-syn3A. A physical description of cellular mechanics can further understanding of the contributions of genes to cell division in this genomically minimal context. We review current knowledge on genes in JCVI-syn3A contributing to two physical parameters relevant to cell division, namely, the surface-area-to-volume ratio and membrane curvature. This physical view of JCVI-syn3A may inform the attribution of gene functions and conserved processes in bacterial physiology, as well as whole-cell models and the engineering of synthetic cells. 
    more » « less
  5. ; ; ; ; (, bioRxiv)
    Bacterial chromosome segregation, ensuring equal distribution of replicated DNA, is crucial for cell division. During fast growth, replication and segregation co-occur. Overlapping cycles of DNA replication and segregation require efficient segregation of the origin of replication (Ori), which is known to be orchestrated by the protein families SMC and ParAB. We used data-driven physical modeling to study the roles of these proteins in Ori segregation. Developing a polymer model of the Bacillus subtilis genome based on Hi-C data, we analyzed chromosome structures in wild-type cells and mutants lacking SMC or ParAB. Wild-type chromosomes showed clear Ori segregation, while the mutants lacked faithful segregation. The model suggests that the dual role of ParB proteins, loading SMCs near the Ori and interacting with ParA, is crucial for Ori segregation. ParB-loaded SMCs compact individual Ori and introduce an effective inter-sister repulsion that regulates the ParAB-activity to avoid the detrimental scenario of pulling both Ori to the same pole. The model makes testable predictions for sister-chromosome-resolved Hi-C experiments and proposes that replicated sister chromosomes segregate via mechanistic cooperation of SMC and ParAB activity. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Text Encoded Conversion
  • XML
  • Save / Share this Record
  • Send to Email