Editing the Genetic Code of Living Bacteria

Recoder ring: The colored spikes around this ring represent the number of codons that have been replaced in E.coli.
Credit: Farren Isaacs

A new method for making genomewide changes to organisms could lead to better ways of producing useful new drugs and chemicals.

Researchers at Harvard Medical School have come up with a find-and-replace tool for editing the genetic code of living bacteria. The technique offers a more powerful way to manipulate living organisms, and could eventually be used to make industrial microbes that are safer, more robust, and produce new kinds of drugs and chemicals.
Most of the genes that make up an organism's genetic code are essentially design plans for making proteins. Each gene consists of a long strand of molecules, called nucleotides. Three such nucleotides—a group known as a codon—tell a cell which amino acids it should use while building a protein.
Cells can use 22 naturally occuring amino acids as building blocks to make proteins, but chemists have synthesized over a hundred so-called "unnatural amino acids" in the lab using the tools of chemistry, not biology. Naturally occuring organisms can't make or build with these chemicals. Organisms that could build proteins using these amino acids would open up new possibilities, particularly in drug development. But normal cells lack the necessary genetic code to work with these unnatural amino acids.
A team at Harvard, led by George Church, has developed a tool for editing genes that could change this. To make microbes capable of building proteins that incorporate unnatural amino acids, researchers need to be able to both edit all of certain codons in the genome, and to manipulate the cell machinery that reads those codons. The new tool lets them do the first part.

Church says he hopes to achieve three goals with the approach. First, he wants to build bacteria that can produce new drugs and other chemicals. Second, he wants to genetically engineer bacteria that cannot live outside the lab because they need unnatural amino acids to survive—a feat that could prevent the environmental damage that might result from such bacteria being let loose in the world. And third, he wants to make bacteria that are immune to viruses, since viruses can cause problems in industrial production. "The way to achieve all these things is to change the [meaning of the] genetic code of your favorite organism," says Church.
Thursday, in the journal Science, Church's group described how it deleted all 314 instances of a particular codon in the genome of living E. coli and replaced them with another codon. The work was co-led by Farren Isaacs, now assistant professor of molecular biology at Yale University. The process involves making small-scale genetic changes in multiple strains of E. coli, then combining them.
Researchers at the J. Craig Venter Institute have previously demonstrated a different to edit a whole genome. This is the same group that made the first "synthetic living cell" last year. The Venter group edits the genome on a computer, and then synthesizes the entire thing using a combination of machinery and yeast cells; after that, the genome is transplanted into a recipient cell.
Church's method introduces changes in living cells. He believes the advantage of this approach is that it's possible to correct mistakes as they happen on the way toward making larger changes. Church hopes his latest work will convince other researchers of the value of "genome-scale" engineering. Both his method and that developed at the Venter Institute involve using DNA synthesizer machines to make large amounts of DNA for the engineered cells to take up. DNA synthesis is still expensive. And the time involved in both techniques, though it's getting shorter, is another expense. "We need to bring costs down, and think about ease of use," he says.
Making proteins with unnatural components is so useful that biologists have been doing it, albeit inefficiently, for decades, says David Tirrell, professor of chemical engineering at Caltech. Tirrell is not affiliated with the Harvard group.
Two companies—Allozyme, which Tirrell is associated with, and Ambrix—are both making protein drugs that incorporate unnatural amino acids. In both cases, they have engineered bacteria that can make proteins that include just one unnatural amino acid. Making organisms that can use more of these unnatural chemicals to produce new kinds of molecules would open up new frontiers for protein drugs, he says. Proteins with unnatural components might also be able to cross barriers in the body that are not easily breached today, such as the blood-brain barrier. Church's group is beginning a collaboration with Ambrix.