Designer Microbes Expand Life's Genetic Alphabet

DNA 2.0. By adding a new base pair, X and Y, to DNA's A-T and G-C pairs, researchers will enable organisms to build proteins from as many as 172 different amino acids.

DNA 2.0. By adding a new base pair, X and Y, to DNA's A-T and G-C pairs, researchers will enable organisms to build proteins from as many as 172 different amino acids.

Adapted from Synthorx

From bacteria to basketball players, all life as we know it encodes genetic information using two pairs of DNA letters. Not anymore. Now, along with the double helix’s two natural pairs—A bound to T and G bound to C—a bacterium growing in a California lab can incorporate and copy a third, artificial pair of letters. For now, the artificial bases—call them X and Y—don’t code for anything, unlike natural DNA base pairs, which in various combinations code for the 20 different amino acids that make up proteins. But the newly expanded genetic code opens the door for synthetic biologists to create microbes capable of building their proteins out of as many as 172 different amino acids, both natural and artificial—a potential boon to drug and materials developers.

“This is an amazing enabling technology,” says Ross Thyer, a molecular biologist at the University of Texas, Austin, who was not involved in the work, reported in this week’s issue of Nature. Not only does the feat open the way to a universe of new proteins, but it also gives researchers a new platform for investigating how DNA evolved and why all life is limited to just five bases. (In RNA, T is replaced with U.)

Creating synthetic superbacteria might sound ominous. But Eric Kool, a biological chemist at Stanford University in California, says the risks are low. “These organisms cannot survive outside the laboratory,” Kool says. In fact, they can’t even build X and Y (more formally known as d5SICS and dNaM) themselves: Researchers synthesize the bases and feed them to the bacteria. “Personally, I think it’s a less dangerous way to modify DNA” than existing genetic engineering, Kool says.

Over the decades, synthetic biologists trying to expand life’s genetic alphabet have come up with a handful of alternative genetic letters. A few teams, including one led by Floyd Romesberg, a biological chemist at the Scripps Research Institute in San Diego, California, have even managed to get DNA replication proteins called DNA polymerases to copy DNA strands incorporating alternative letters. But that was achieved in test tubes, not inside living cells.

Getting live bacteria to replicate altered DNA was another challenge entirely. The bacteria would need either to synthesize the new genetic letters themselves or to import them from the surrounding culture medium. In algae, Romesberg and his colleagues identified a protein that grabs nucleotide bases and pulls them into the cell. They spliced the gene for this transporter protein into Escherichia coli bacteria and found it enabled the bacteria to pull in presynthesized X and Y bases as well. The team had also engineered their E. coli to harbor small rings of DNA called plasmids carrying X-Y pairs. When the bacteria copied those plasmids, they used the newly imported X and Y bases—yet the engineered cells grew just as well as their native cousins.

Next, Romesberg says he hopes to use his expanded genetic alphabet to create designer proteins. Scripps biochemist Peter Schultz and others have already engineered bacteria to build proteins with dozens of amino acids beyond nature’s standard 20. But those experiments use natural DNA to code for unnatural amino acids. The newly expanded genetic alphabet, Thyer says, should yield a vastly more diverse menu of proteins with a wide variety of new chemical functions, such as medicines better able to survive in the body and protein-based materials that assemble themselves. Romesberg says forays into that new world of proteins are already under way.