Five years ago, researchers announced to great fanfare that they had engineered a stripped-down microbial cell able to survive with fewer genes than any known organism. But that “minimal cell” often divides abnormally. Now, by putting back only seven genes, a team has corrected the cells so they grow like the natural versions.
The discovery could sharpen scientists’ understanding of which functions are crucial for normal cells and what the many mysterious genes in these organisms are doing, says synthetic biologist Kate Adamala of the University of Minnesota, Twin Cities. “This is a significant step forward that maybe can help identify the functions of these unknown genes.”
Pinning down essential genes could also benefit synthetic biologists, who are working to craft cells or cell-like objects that could produce chemicals, sense environmental conditions, deliver drugs, and perform other tasks in industry and medicine. “We need to know what is the minimal parts list we need to put together to restore life,” says microbiologist Anthony Vecchiarelli of the University of Michigan, Ann Arbor. Minimal cells could also provide insight into the origin of life by illuminating which capabilities were essential for primordial cells.
Genome sequencing pioneer J. Craig Venter of the J. Craig Venter Institute (JCVI) and colleagues created the first minimal cells. They started with Mycoplasma microbes, parasites that are already pretty minimal—one variety gets by with 525 genes, compared with the roughly 4000 of the common intestinal bacterium Escherichia coli. In 2010, the team reported that replacing the 985-gene genome of one type of Mycoplasma with a 901-gene synthetic genome kept the cell, dubbed syn1.0, purring. The scientists continued to remove chunks of DNA from syn1.0’s genome, and in 2016, they unveiled an even sparer version, known as syn3.0, that could metabolize and reproduce with a measly 473 genes.
But this cell also has a quirk: Many of its progeny are misshapen. To check whether lab conditions might be stressing the delicate synthetic cells, a group led by synthetic biologist Elizabeth Strychalski of the National Institute of Standards and Technology cosseted the cells in chambers on microfluidic chips. These deluxe quarters shielded the cells from currents in the nutrient medium that might harm them and allowed the researchers to watch as they divided.
This gentle treatment didn’t make a difference, however. “When we looked at the individual cell level, it was absolute mayhem,” says Strychalski, who worked with colleagues from JCVI and three universities. The cells should have been small orbs, but some were behemoths about 25 times the normal girth. Others looked like threads or strings of pearls. Rough handling wasn’t the problem, the researchers concluded; instead, the problem stemmed from the removal of genes that help control reproduction and cell shape.
It wasn’t obvious which missing genes were to blame, but a clue was sitting in a lab freezer. To create syn3.0, Venter and colleagues had generated a variety of other strains of cells that lacked portions of syn1.0’s genome. When Strychalski and her team thawed one of these strains, which was missing 76 of syn1.0’s genes, it also produced abnormally shaped progeny. “It helped us narrow the genes from 400 to 76,” says co-author James Pelletier, a biophysicist at the Massachusetts Institute of Technology.
By adding back combinations of genes to determine whether the resulting cells divided normally, the researchers shrank the number required to 19 and then even further. Today in Cell, they report they could restore normal division by adding just seven genes to syn3.0.
Two of the genes were already known to play a role in cell division, but the involvement of the other five came as a surprise—and their roles in cleaving the microbes remain unknown. The corrected minimal cells could help elucidate this still-mysterious process, Strychalski says: “We still don’t know the mechanism by which these things divide. That blows my mind—it’s one of the basic aspects of life.”