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Bringing the Genetically Minimal Cell to Life on a Computer in 4D

Thornburg, Z. R.; Maytin, A.; Kwon, J.; Brier, T. A.; Gilbert, B. R.; Fu, E.; Gao, Y.-L.; Quenneville, J.; Wu, T.; Li, H.; Long, T.; Pezeshkian, W.; Sun, L.; Glass, J.; Mehta, A.; Ha, T.; Luthey-Schulten, Z.

2025-06-15 biophysics
10.1101/2025.06.10.658899 bioRxiv
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We present a whole-cell spatial and kinetic model for the 100 minute cell cycle of the genetically minimal bacterium, JCVI-syn3A. This is the first simulation of a complete cell cycle in 4D including all genetic information processes, metabolic networks, growth, and cell division. Integrating hybrid computational methods, dynamics of the morphological transformations were achieved. Growth is driven by synthesis of lipids and membrane proteins and constrained by new fluorescence imaging data. Chromosome replication and segregation is controlled by essential SMC and topoisomerase proteins in Brownian dynamics simulations with replication rates responding to dNTP pools from metabolism. The model captures the origin to terminus ratio measured in our DNA sequencing and recovers other experimental measurements like doubling time, mRNA half-lives, protein distributions, and ribosome counts. Because of stochasticity, each replicate cell is unique. Not only do we predict average behavior for partitioning to daughter cells, we predict the heterogeneity among them.

Published in Cell · training set

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"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.