Scientists went full Frankenstein mode and resurrected ‘dead’ bacterial cells by replacing their defunct DNA with functional DNA from another species. This feat can advance gene engineering, as whole genomes can be transferred from one bacterium to another and customized to confer useful properties, such as the ability to produce drugs or biofuels.
Genome transfers such as this, which give rise to ‘zombie cells’, have so far been possible only between species within a single bacterial class. Scientists hope to routinely make zombies from other bacteria to test engineered genomes from more commonly studied species, like the model bacterium Escherichia coli.
Over 15 years ago, scientists created the first synthetic cell by chemically synthesizing a 1.1-million-base-pair genome of the bacterium Mycoplasma mycoides and transplanting it into a living Mycoplasma capricolum cell. Later, in a 2016 study, scientists successfully transplanted genomes between species of the same class of bacteria as Mycoplasma, called Mollicutes.
The team that worked on the first synthetic cell included some researchers from the latest study, who added a gene to the synthetic M. mycoides genome that imparted resistance to the antibiotic tetracycline. Antibiotic resistance is the property that nullifies an antibiotic’s effects on bacteria. After the synthetic genome is transplanted into M. capricolum, these recipient cells will grow and survive in the presence of tetracycline, which would otherwise be fatal.
As of now, efforts to transplant genomes more widely have been unsuccessful, and false positives in the results were often seen as success, which they weren’t. Genomes of the recipient cells incorporated the antibiotic resistance gene via homologous recombination, the process of sharing genetic information between identical DNA strands. This means that the recipient cells would survive even if they didn’t absorb the entire donor genome.
What stands out as different in the first experiment with M. capricolum is that it could not have given false positives because it cannot recombine, meaning it had to absorb the entire synthetic genome to become tetracycline resistant. In search of a way to transplant genomes without worrying about false positives, the scientists went a step further. They inactivated the genomes of recipient cells using a DNA-damaging chemotherapy drug called mitomycin C, leaving the cells unable to replicate (form a new DNA strand from pre-existing DNA) and hence, functionally dead. This also prevents recombination and the uptake of foreign DNA.
When engineered M. mycoides genomes were transferred into dead M. capricolum cells, a small fraction of the recipient cells survived. Co-author Zumra Peksaglam Seidel, a synthetic biologist at the J. Craig Venter Institute (JCVI) in La Jolla, California, and her colleagues call these survivors ‘zombie cells’.
Researchers haven’t yet explained why genome transplantation—with or without zombie recipients—occurs efficiently between Mycoplasma species. However, scientists hope to expand the process and eventually make zombies from other bacterial species.
Tom Ellis, a synthetic biologist at Imperial College London, suggests that identifying bacteria that have acquired large chunks of DNA doesn’t necessarily require a selection marker such as an antibiotic-resistance gene. Instead, Eliis and his team used the CRISPR gene-editing system to incise recipient DNA sequences they are replacing. John Glass, a synthetic biologist at JCVI and the author of the synthetic cell study, and his team acknowledge that CRISPR can be used to silence undesirable genes in recipient cells, such as those involved in homologous recombination.
Zombie cells are the perfect chassis for testing microbial genomes designed by AI tools. Olivier Borkowski, a synthetic biologist at the French National Research Institute for Agriculture, Food and Environment (INRAE) and Paris-Saclay University, says, “If robust zombie-cell protocols can be established for E. coli or other model organisms, the approach could become a general-purpose platform for synthetic biology.”
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