Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps

Abstract

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.

Molecular dynamics simulation of an entire cell

“…The nucleoid structure of Syn3A was previously modeled by Gilbert et al (2021) based on the ribosome distribution and cell boundary determined by cryo-electron tomography. A Monte Carlo (MC) method grew the chromosome, modeled by a self-avoiding polygon, on a lattice inside the cell boundary.…”

“…Data from CryoET images [Image from EMD-23661 by Lam and Villa ref. ( Gilbert et al, 2021 )], Cryo-EM protein structures and -Omics experiments are incorporated into our cell models. The second stage in the workflow concerns mesoscale modeling.…”

“…The initial step consists of collecting experimental data to inform the in silico modeling. Data from CryoET images [Image from EMD-23661 by Lam and Villa ref (Gilbert et al, 2021)…”

Integrative illustration of a JCVI-syn3A minimal cell

“…The illustration builds extensively on recent experimental and modeling work on Syn3A, including systems biology modeling of metabolic and genetic networks and structural modeling with LatticeMicrobes [ 7 , 20 ], [ 21 ], [ 22 ]. That work reconciles the identity and abundance of gene products found in the proteome study [ 7 ], and provided a touchstone throughout researching and creating the illustration to define the molecular composition of the cell.…”

“…Briefly, style sheets for all molecules were created at a consistent magnification and used to develop a full sketch of the foreground of the scene. Abundances were approximated in the following manner: ribosomes were added first based on distribution in cryoEM images [ 21 ] and the nucleoid sketched around them; multiple copies of abundant translation factors, tRNA, chaperones, and metabolic enzymes were then added; the remaining space was filled with one or two copies of less abundant proteins to complete the proteome. This foreground sketch was transferred to Arches 300 lb Rough Natural White paper using carbon paper.…”