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Cells with lab-made DNA produce a new kind of protein, a ‘holy grail’ for synthetic biology

In San Diego, a microbe with lab-made DNA has synthesized proteins from molecules never before used by life. (Rachel Orr/Washington Post illustration; images from iStock)

Scientists in San Diego have achieved a major goal in the effort to craft artificial organisms: A microbe whose genetic material included some lab-made instructions was able to live, reproduce and synthesize proteins that included molecules never before used by life.

The development, described Wednesday in a paper in the journal Nature, is a step toward a world in which scientists can engineer organisms capable of producing highly specialized proteins that may be used to improve medicines, construct new materials and perhaps even change the functions of cells.

“It's wave front stuff; this is the edge of science,” said Andrew Ellington, a biochemist at the University of Texas at Austin who was not involved in the research. “We are better learning how to engineer living systems.”

For 4 billion years, the story of life on Earth has been written using a limited molecular alphabet. The rungs of DNA's twisting ladder are built from just four base units — adenine, which links with thymine, and cytosine, which pairs with guanine. These four “letters” — A, T, C and G — define the form and function of every organism on Earth, from a bacterium to an elephant, from photosynthesis to camouflage.

When those genetic instructions are transcribed and translated by cellular machinery, they enable the production of proteins — life's workhorses, which catalyze reactions, transmit signals, and make up tissues like cartilage and shells. The building blocks of proteins, called amino acids, are only slightly more varied than those of DNA; just 20 amino acids are used to synthesize the proteins needed for all life's functions.

In 2014, the San Diego scientists, led by chemist Floyd Romesberg of the Scripps Research Institute, rewrote the genetic material for a strain of E. coli to include a new pair of bases, dubbed dNaM and dTPT3 but informally known as X and Y. Though the resulting microbe population wasn't stable (they usually lost their X and Y bases after a few days) these were the first organisms in the history of life to include a new base pair in their DNA.

It was an entirely new kind of genetic engineering. Other gene editors tweak organisms' DNA using already-existing materials, like Shakespeare coming up with new idioms. But Romesberg and his colleagues were writing genetic instructions with molecules life had never seen before — the biological equivalent of Tolkien inventing Elvish.

In their latest experiment, Romesberg's team used that expanded genetic alphabet to instruct the cells to synthesize proteins from “noncanonical” amino acids — hundreds of molecules that can be found in nature or the lab but are not naturally used by organisms. The semi-synthetic cells were able to produce artificial proteins almost as efficiently as their unmodified parents.

“This last step of adding an unnatural base pair to add an unnatural amino acid into a protein is sort of the holy grail of what we’ve been trying to do the whole time,” said Yorke Zhang, a graduate student in Romesberg's lab who designed, performed and analyzed the experiment.

For decades, scientists have sought to add noncanonical amino acids to proteins in the hope of making these biological workhorses even more powerful. But they had a problem. Translation of genetic material into a protein product, which is carried out by RNA molecules, depends on three-letter sequences called “codons.” Each codon corresponds to a particular amino acid, so when the cell's machinery reads that sequence, it knows exactly which piece of protein to grab. Yet, with the existing genetic alphabet, all 64 possible codon combinations are already associated with a specific task. If researchers wanted the cell to perform a new function, they had no unique way to convey the demand.

Some scientists have tried to get around this obstacle by reprogramming one of the cell's “stop” codons — which carry instructions to halt the protein production process — to instead be associated with a new amino acid.

But Romesberg and his colleagues had grander ambitions. By adding just two new base units to a cell's genetic instructions, they would generate dozens of new codon possibilities — “more than we could possibly use” for any practical purposes, Romesberg said.

After testing hundreds of possible base pairs, they landed on dNaM and dTPT3. Not only were these units utterly foreign to life on Earth, they were chemically linked by a completely different bond than the one that connects A to T and G to C.

In an interview this week, astrobiologist Steve Benner, who led the first team to develop an artificial base pair nearly 30 years ago, expressed doubt that DNA could be fully functional with this unusual base pair bond. He suggested that the natural base pairs in Romesberg's E. coli might be “flanking” the lab-made ones — holding up the double helix despite the unnatural and uncomfortable insertions. The DNA was effectively damaged, he said, and the fact that the cells didn't die is just a testament to life's resiliency.

Romesberg disagreed, pointing out that the engineered cells in his latest experiment successfully used X and Y genetic material and a noncanonical amino acid to produce large amounts of glowing green protein without much loss of efficiency.

“In some sense the proof is in the pudding,” he said. The experiment worked, which would indicate that the synthetic DNA works, too. 

Because the microbes themselves can't produce the X and Y bases or the alien amino acid, the scientists had to continually “feed” these molecules into the cells. This is a feature, not a bug, Romesberg said. For one thing, it ensures that any microbe that escaped the lab would swiftly die — allaying fears of a Jurassic Park-style artificial life apocalypse.

Moreover, it suggests one possible application of these lab-made microbes: vaccines. “If you put it into a person the organism can’t survive any more,” Zhang said — making these cells a safe way to train the body to fight infection.

In 2014, Romesberg co-founded a biotechnology company, Synthorx, aimed at turning proteins made from noncanonical amino acids into medicine. In the near term, he said, scientists could harvest such proteins from synthetic cells and use them to assist with drug-delivery, or to make protein therapeutics, like insulin, more effective.

But an even more distant — and more enticing — application involves not just the proteins, but the lab-made microbes that produce them: “What if you allow the bacteria to harbor this unnatural information retrieve the protein and use it for something interesting?” Romesberg mused. “Could you develop organisms that have new properties” — like the ability to siphon up oil spills or eat cancer cells? “Could we develop cells that can do things their natural counterparts can't?”

Maureen McKeague, a synthetic biologist at the Swiss Federal Institute of Technology in Zurich, said this latest achievement is a synthesis of work that Romesberg and others have been chipping away at for a while. By now, several scientists have developed artificial base pairs and synthesized unnatural proteins, “but this demonstrates all the parts can come together, from encoding information and storing it to transcribing and translating it,” she said.

It also raises some interesting philosophical questions.

“One thing that scientists have always been questioning is whether the way biology has evolved is the only way,” McKeague said.

That Romesberg's artificial cells lived — and that they lived even with the unusual bond linking their added base pair — suggests that it's not. Perhaps, on some distant rocky planet or chilly ocean moon, organisms are following genetic instructions written in an alien alphabet according to chemistry utterly unlike our own. 

Scientists are just beginning to expand the language of life on Earth. But out in the universe, biology may follow an even stranger script.

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