Now, scientists led by the Scripps Research Institute in La Jolla, Calif., have added two extra, artificial letters to the ancient alphabet of A, C, G and T. And the E. coli living with this unusual six-letter, three-base-pair alphabet are, by the account published Monday in the Proceedings of the National Academy of the Sciences, capable of surviving tough laboratory conditions.
In 2014, the synthetic biologists announced they had achieved something unprecedented in the history of DNA. They went beyond remixing the DNA music, mashing it up with an alien beat. It was the genetic equivalent of Danger Mouse’s “Grey Album”: Where other bands simply covered John, Paul, George and Ringo, someone figured out how to thread in Jay Z.
The biologists added two new letters to the four-letter DNA alphabet within E. coli bacteria. The scientists called the novel base units dNaM and d5SICS (a newer, improved version of the bases were named dNaM and dTPT3). You can think of these unnatural nucleobases as X and Y. Years down the line, microbes with increased genetic information could present exciting and lucrative scientific possibilities: bacteria capable of churning out therapeutic human proteins, or altered bugs that hoover up environmental spills.
But, in 2014, there was a problem with X and Y.
Specifically, the method of incorporating X and Y into the bacterial DNA proved toxic. E. coli that had the extra base pairs were weaker than those without them. The population of semi-synthetic E. coli microbes, within a few days, lost the X and Y bases; they reverted to a natural, two-base-pair state. To The Washington Post by phone on Monday, Scripps researcher Floyd E. Romesberg likened the 2014 success as a proof-of-concept lightbulb capable of a single flash. It was as though the scientists sent electricity coursing through a filament to a bulb — to see light just for a moment, before the bulb winked out forever.
On Monday, Romesberg and his colleagues announced they had created a stable version of their semi-synthetic microbe. They threw the switch, and the light stayed on.
“It is not an incremental improvement,” Romesberg told The Post. “It is a wonderful experience to bathe in the light of a lightbulb that does not go out.”
A decade ago, Ian Paulsen, an expert on microbial genomes at Australia’s Macquarie University, would have scoffed at the idea that biologists could create stable microorganisms with an additional DNA base-pair.
The new study marked an impressive first step “on a very long journey to make designer life, for want of a better phrase,” said Paulsen, who was not involved with the research, via phone to The Post early Tuesday. “It’s a very elegant, very clever piece of work.”
Three developments enabled the scientists to create these always-on microbes. The bacteria cannot produce X and Y themselves; a ring of DNA called a plasmid transported the bases, supplied by the researchers, into the bacteria. “We fixed the toxicity of the transporter,” Romesberg said. “They grow better, they’re much healthier.” The researchers also tweaked the chemical composition of Y so that it better partnered with X.
The third improvement involved the powerful, and scientifically fashionable, technique known as CRISPR-Cas9. Though CRISPR is frequently described in the context of human genetic editing, it first belonged to bacteria. As part of a microbial immune system, the seek-and-snip protein eliminates foreign genetic material introduced by viruses. The Scripps researchers used Cas9 like an eraser on a pencil to blot out any E. coli DNA that lacked X and Y.
It seemed to do the trick. “The use of CRISPR is a clever application,” Paulsen said.
These semi-synthetic microbes were much more robust than their 2014 precursors. The biologists subjected the bacteria to what Romesberg described as a “horrendously demanding” growth regimen in the lab, one that would not have been possible three years ago.
Yes, these bacteria were hearty. And, yes, they were semi-synthetic and unlike anything found in nature. But Romesberg took pains to allay any worries of the Steven Spielberg variety.
“This isn’t like ‘Jurassic Park,’ ” he said, referring to the 1993 blockbuster in which genetically-engineered dinosaurs terrorize a tropical island. Even “Jurassic Park,” as far-fetched as it was, reshuffled natural DNA. X and Y do not exist in nature. The microbes cannot produce X or Y on their own; there does not exist a wild supply of synthetic base pairs that the germs could somehow ingest. And to synthesize the artificial nucleoside triphosphates on their own, the bacteria would have to suddenly develop two entire cellular pathways heretofore absent from evolutionary history.
Survival outside of a laboratory, Romesberg said, “is so far outside the realm of possibility that, as a scientist, I feel comfortable calling it zero.”
Paulsen agreed. “I have zero concerns of it breaking out of the lab.”
But when it came to future applications of these alien base pairs, the Australian scientist displayed more hesitation. The unnatural base pairs were stable, but they functionally did not add anything to the E. coli. The “downstream dreams,” Paulsen said, would include bacteria that could create unnatural amino acids. (There are 20 standard amino acids; a six-letter DNA alphabet, in theory, could support many more.)
“I think that’s still — as of today, at least — science fiction,” Paulsen said.
Romesberg envisioned a future in which the bugs produce medically useful proteins, similar to therapeutic insulin. And beyond tweaking the smaller protein scale, this synthetic DNA technique might one day allow researchers to create bacteria that possess new traits or abilities as entirely new organisms. “This represents a nice step toward our long-term goal,” Romesberg said, “the creation of semi-synthetic life.”
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