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

Benjamin R. Gilbert, Zane R. Thornburg, Vinson Lam, Fatema-Zahra M. Rashid, John I. Glass, Elizabeth Villa, Remus T. Dame, Zaida Luthey-Schulten

Research output: Contribution to JournalArticleAcademicpeer-review

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.
Original languageEnglish
Article number644133
JournalFrontiers in Molecular Biosciences
Volume8
DOIs
Publication statusPublished - 22 Jul 2021
Externally publishedYes

Funding

JG: Partial support from NSF MCB 1818344, 1840301 and 1840320. VL and EV: This work was supported by an NIH Director’s New Innovator Award 1DP2GM123494-01 (to EV) and NIH 5T32GM7240-40 (to VL). VL is also supported in part by NIH R35GM118290 awarded to Susan S. Golden. This work on Syn3A by VL and EV is also supported in part by NSF MCB 1818344. This work was supported by the National Science Foundation MRI grant (NSF DBI 1920374). We acknowledge the use of the UCSD Cryo-Electron Microscopy Facility which is supported by NIH grants to Dr Timothy S. Baker and a gift from the Agouron Institute to UCSD. Molecular graphics and analyses performed with UCSF Chimera, developed by the Resource for Biocomputing, Visualization, and Informatics at the University of California, San Francisco, with support from NIH P41-GM103311. BG, ZT, and ZL-S: We thank John Stone at the Beckman Institute at UIUC for his assistance in preparing scientific visualizations using VMD. F-ZR and RD: We thank Utrecht Sequencing Facility for providing sequencing service and data. Utrecht Sequencing Facility is subsidized by the University Medical Center Utrecht, Hubrecht Institute, Utrecht University and The Netherlands X-omics Initiative (NWO project 184.034.019). We thank Wouter de Laat and Amin Allahyar (Hubrecht Institute, The Netherlands) for discussions and assistance with data analysis. We thank Kim Wise at the J. Craig Venter Institute (JCVI) for providing JCVI-Syn3A cells and growth medium to the laboratories of EV and RD. BG, ZT, and ZL-S: Partial support from NSF MCB 1818344 and 1840320, The Center for the Physics of Living Cells NSF PHY 1430124, and The Physics of Living Systems Student Research Network NSF PHY 1505008. The cell figures in the workflow diagram and all lattice representations of ribosomes and DNA were prepared using Visual Molecular Dynamics (VMD), developed by the NIH Center for Macromolecular Modeling and Bioinformatics in the Beckman Institute at UIUC, with support from NIH P41-GM104601-28.

FundersFunder number
Center for the Physics of Living Cells NSFPHY 1430124, PHY 1505008
Hubrecht Institute
University Medical Center Utrecht
Wouter de Laat and Amin Allahyar
National Science Foundation1840301, NSF DBI 1920374, 1840320, MCB 1818344
National Institutes of HealthR35GM118290, 1DP2GM123494-01, 5T32GM7240-40
University of Illinois at Urbana-Champaign
Beckman Institute for Advanced Science and Technology, University of Illinois, Urbana-Champaign
Agouron Institute
Universiteit Utrecht
Nederlandse Organisatie voor Wetenschappelijk Onderzoek184.034.019

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