For the first time, researchers have simulated almost every chemical reaction in a living bacterial cell. This simulation models how a bacterial cell copies its DNA and divides into two. Understanding these processes could help explain how the mix of proteins, nucleic acids, fats, and other molecules within a cell leads to life, according to Zane Thornburg, a computational biophysicist at the University of Illinois.
To study bacterial life, Thornburg focused on a simple example: a bacterial cell with a minimal genome called JCVI-Syn3a. This organism was created by reducing the genome of the parasite Mycoplasma mycoides to just 493 essential genes.
Thornburg developed a three-dimensional simulation that included the cell’s DNA and other vital molecules. The simulation used actual measurements to simulate the interactions between molecules, like a DNA-copying enzyme that acted when partners came close together. However, some aspects were simplified because dozens of JCVI-Syn3a genes are still not fully understood.
The goal was to simulate the time it takes for the cell to copy its DNA and divide, known as the cell cycle. Initial attempts faced issues, such as the genome breaking apart too quickly. After adjustments, the simulation ran over the US Thanksgiving break in November, revealing a complete cell cycle upon their return, which marked a significant breakthrough.
The simulation accurately reflected how the cell swells and elongates during division. It took 105 minutes for the virtual cell to divide, a duration similar to real cells, but the simulation required six days on a supercomputer, highlighting the complexity involved. Bernhard Palsson, a bioengineer, noted that capturing all these cellular processes coherently during the cell cycle is a significant achievement.
