Life is complicated. Even the smallest cells contain an astonishing assortment of chemical reactions that allow them to thrive in a chaotic environment.
If we want to know where to draw the line between life and the bubbles of an old-fashioned organic broth, it helps to strip out unnecessary additives to expose essential ingredients, and then map out how each works.
This has been the goal of biochemists for a number of years, who, over the years, have succeeded in designing some amazing basic organisms that barely cling to life in the lab.
Now, scientists from the J. Craig Venter Institute, the University of Illinois Urbana-Champaign in the US and Technische Universität Dresden in Germany have taken the next step and built a detailed simulation of the latest simple microbe.
“What’s new here is that we have developed a fully dynamic, 3D kinematic model of a small living cell that simulates what happens in the actual cell,” says Zaida Luthy Schulten, a chemist at the University of Illinois.
Luthey-Schulten led a team of researchers analyzing the diverse genetic, metabolic and structural changes that occur in a repeat culture of a synthetic bacteria called JCVI-syn3A.
Simulate the work of the simplest living organisms, such as types mycoplasma Or the common microbe Escherichia coli, still requires some mathematical fudge operators to model the operations of many subsystems on a large scale. It would not have been possible to woven a whole host of detailed descriptions of everything from genes to nutrients, even for this relatively simple bacteria.
In the early 2000s, researchers at the J. Craig Venter Institute removed as many genes as possible Mycoplasma mycoids, leaving the copy that was about to survive.
This artificial life form, called JCVI-syn1.0, was soon replaced by something more basic. JCVI-syn3.0.
This updated version contains only 531,000 bases split over 473 genes. With all of its nutritional needs the lab provides, the genome of bare bones is left to take care of reproduction, growth, and a bit of other stuff.
However, JCVI-syn3.0 is not completely consistent in its growth, resulting in a bewildering diversity of polymorphs in its progeny. Some genes appeared again, giving rise to the newest version of the small cell: JCVI-syn3A.
Its creators have a solid idea of what genes their artificial cell contains, although they’re still working on determining exactly what each one does.
To make things even more difficult, it is crucial to know how each atom and molecule propagates through the cell, a description that would require heavy-handed computing power to simulate.
“We have developed a fully 3D kinetic and dynamic model of a small living cell,” says Luthey-Schulten.
“Our model opens a window into the inner workings of the cell, showing us how all components interact and change in response to internal and external signals. This model—and other more complex models to come—will help us better understand the basic principles of life.”
The simulations confirmed some doubts, such as the fact that most of the energy of the miniature cell went toward pulling core materials across the membranes.
He also provided an accurate description of the timescales of genetic and metabolic interactions, explaining the relationships between the rate of production of lipids and proteins in the membrane and changes in cell shape.
Since JCVI-syn3A are essentially shortened versions of a naturally occurring organism, they are just one example of how biology functions can be minimized. Life is nothing if not creative in how to overcome obstacles to survive.
Now that we have a proven model to simulate JCVI-syn3A’s growth and development, researchers can build its complexity again to determine how different genes add to its function.
We may expect not only new “light” versions M. mycoides, but other organisms in the near future. If not entirely new artificial life forms.
Life may still be complicated, but studying just got a lot easier.
This research was published in cell.