A team of scientists at Stanford University has publicly released its whole-cell model of the bacterium Mycoplasma genitalium, along with full data sets from more than 3,000 simulations of the single-celled microbe growing and dividing. The video below plays back data from one of those simulations through a visualization tool called WholeCellViz, which is also available online.
Six panels display different aspects of the cell’s physiology as it proceeds through its nine-hour life cycle.
The “Cell Shape” panel indicates the length, weight and volume of the cell as it expands and divides into two daughter cells.
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In the “Metabolism” panel the flashing arrows and circles represent the motions and changing concentrations of some of the more important biochemical and reactions that the cell uses for processing energy, nutrients and waste.
The “Gene Expression” visualization shows the levels at which RNA is transcribed from various genes in the DNA chromosomes (top block) and then translated into individual proteins (middle) and protein complexes (bottom).
Each circular shape in the bottom left panel represents one of the organism’s two chromosomes, which replicate at different times in the life cycle of the cell. The dark blue circles represent the DNA of the original (mother) cell; the light blue circles reflect the DNA copies that go into the new (daughter) cell. The colored lines that rise at various positions from the chromosomes reflect proteins that have bound to the DNA (green); methyl groups (affecting gene activity) attached to the DNA (orange); and damage that breaks one of the DNA strands (red), which is rare and thus difficult to see in this video.
“DNA replication” charts the position of the DNA polymerase protein on the chromosomes and shows how replication activity picks up beginning about two hours into the simulated life of the cell. DNA polymerase is the enzyme that makes copies of the DNA strands for use in the daughter cell.
A map of the protein-encoding genes in M. genitalium is presented in the bottom right panel. When a single ribosome attaches to pieces of RNA and begins translating them into protein, the block for the corresponding gene from which the RNA was transcribed changes from white to blue. When two or more ribosomes have attached to the RNA at once, the block changes to green. The switch to green is a sign that a protein is being made in abundance.
For more on how the cell simulator was developed, see “Scientists Successfully Model a Living Cell with Software,” by Markus W. Covert, in the January 2014 issue of Scientific American.