Editing the genome

Jul 14, 2011

The power to edit genes is as revolutionary, immediately useful and unlimited in its potential as was Johannes Gutenberg's printing press. And like Gutenberg's invention, most DNA editing tools are slow, expensive, and hard to use—a brilliant technology in its infancy. Now, Harvard researchers developing genome-scale editing tools as fast and easy as word processing have rewritten the genome of living cells using the genetic equivalent of search and replace—and combined those rewrites in novel cell strains, strikingly different from their forebears.

"The payoff doesn't really come from making a copy of something that already exists," said George Church, a professor of genetics at Harvard Medical School who led the research effort in collaboration with Joe Jacobson, an associate professor at the Media Lab at the Massachusetts Institute of Technology. "You have to change it—functionally and radically."

Such change, Church said, serves three goals. The first is to add functionality to a cell by encoding for useful new amino acids. The second is to introduce safeguards that prevent cross-contamination between modified organisms and the wild. A third, related aim, is to establish multi-viral resistance by rewriting code hijacked by viruses. In industries that cultivate bacteria, including pharmaceuticals and energy, such viruses affect up to 20 percent of cultures. A notable example afflicted the biotech company Genzyme, where estimates of losses due to viral contamination range from a few hundred million dollars to more than $1 billion.

In a paper scheduled for publication July 15 in Science, the researchers describe how they replaced instances of a codon — a DNA "word" of three nucleotide letters — in 32 strains of E. coli, and then coaxed those partially-edited strains along an evolutionary path toward a single cell line in which all 314 instances of the codon had been replaced. That many edits surpasses current methods by two orders of magnitude, said Harris Wang, a research fellow in Church's lab at the Wyss Institute for Biologically Inspired Engineering who shares lead-author credit on the paper with Farren Isaacs, an assistant professor of molecular, cellular and developmental biology at Yale University and former Harvard research fellow, and Peter Carr, a research scientist at the MIT Media Lab.

In the genetic code, most codons specify an amino acid, a protein building block. But a few codons tell the cell when to stop adding amino acids to a protein chain, and it was one of these "stop" codons that the Harvard researchers targeted. With just 314 occurrences, the TAG stop codon is the rarest word in the E. coli genome, making it a prime target for replacement. Using a platform called multiplex automated genome engineering, or MAGE, the team replaced instances of the TAG codon with another stop codon, TAA, in living E. coli cells. (Unveiled by the team in 2009, the MAGE process has been called an evolution machine for its ability to accelerate targeted genetic change in living cells.)

While MAGE, a small-scale engineering process, yielded cells in which TAA codons replaced some but not all TAG codons, the team constructed 32 strains that, taken together, included every possible TAA replacement. Then, using bacteria's innate ability to trade through a process called conjugation, the researchers induced the cells to transfer genes containing TAA codons at increasingly larger scales. The new method, called conjugative assembly genome engineering, or CAGE, resembles a playoff bracket—a hierarchy that winnows 16 pairs to eight to four to two to one—with each round's winner possessing more TAA codons and fewer TAG, explains Isaacs, who invokes "March Madness."

"We're testing decades-old theories on the conservation of the genetic code," Isaacs said. "And we're showing on a genome-wide scale that we're able to make these changes."

Eager to share their enabling technology, the team published their results as CAGE reached the semifinal round. Results suggested that the final four strains were healthy, even as the team assembled four groups of 80 engineered alterations into stretches of the chromosome surpassing 1 million base pairs. "We encountered a great deal of skepticism early on that we could make so many changes and preserve the health of these cells," Carr said. "But that's what we've seen."

The researchers are confident that they will create a single strain in which TAG codons are completely eliminated. The next step, they say, is to delete the cell's machinery that reads the TAG gene — freeing up the codon for a completely new purpose, such as encoding a novel amino acid.

"We're trying to challenge people," Wang said, "to think about the as something that's highly malleable, highly editable."

Explore further: Researchers uncover secrets of internal cell fine-tuning

More information: "Precise Manipulation of Chromosomes in Vivo Enables Genome-wide Codon Replacement," Science, July 15, 2011

Related Stories

Viruses evolve to play by host rules

Mar 03, 2008

Biologists at the University of Pennsylvania and Harvard University have examined the complete genomes of viruses that infect the bacteria E. coli, P. aeruginosa and L. lactis and have found that many of these viral genomes ...

Recommended for you

Researchers uncover secrets of internal cell fine-tuning

12 hours ago

New research from scientists at the University of Kent has shown for the first time how the structures inside cells are regulated – a breakthrough that could have a major impact on cancer therapy development.

Microscopic rowing—without a cox

13 hours ago

Many different types of cell, including sperm, bacteria and algae, propel themselves using whip-like appendages known as flagella. These protrusions, about one-hundredth of a millimetre long, function like ...

Illuminating the dark side of the genome

19 hours ago

Almost 50 percent of our genome is made up of highly repetitive DNA, which makes it very difficult to be analysed. In fact, repeats are discarded in most genome-wide studies and thus, insights into this part ...

User comments : 8

Adjust slider to filter visible comments by rank

Display comments: newest first

Waterdog
1 / 5 (6) Jul 14, 2011
This is a case (and I don't often feel this way) where the question should be "Should we?" not "Can we?"

I'm really not sure we understand this well enough to be attempting this at this stage. Let's study the genome for a few decades (or centuries) and when we are sure we know exactly what it does, then we can start thinking about changing it.

This really smacks of playing God and I'm not a very religious man
jscroft
4 / 5 (5) Jul 14, 2011
That's a little bit like suggesting we study the chemical elements for a few centuries before we risk reacting them with one another. You just removed our most effective learning tool from the game.
Waterdog
1 / 5 (1) Jul 14, 2011
The stakes are very high. I think the atomic bomb development is a more comparable analogy. I work in the nuclear safety industry and I know how different things might have been if peaceful uses had been studied before development of the bomb. For one thing, it is unlikely that the Fukishima Reactor design would have been a model developed for commercial use. There were several potential models that would have been intrinsically safer that did not recieve much development money because they didn't support the development of the bomb or military reactor designs.

I would just like to see a more thorough understanding of what we are handling before we introduce a change into the genome of ourselves or something else that will come back to haunt us a generation or two from now.
Waterdog
1 / 5 (3) Jul 14, 2011
I'm not saying that we shouldn't study this, I'm saying let's go slower. We have time to understand what we are changing. A generation ago we barely knew what DNA was much less what it was for. Changing something is easy, but it's really hard to put the genie back into the bottle, and there is always someone out there who will make the worst possible use of the most well intentioned discoveries.
Deesky
5 / 5 (4) Jul 14, 2011
We have time to understand what we are changing.

How do you understand something without changing and testing it?

Your refrain is similar to those that say humanity is not ready for so-and-so, we should wait until we're more 'wise'. That's a nonsense argument. If we did that, we would never do anything at all.

By doing, we learn, and yes, we also learn from our mistakes and what doesn't work. That's the nature of knowledge acquisition as opposed to navel gazing.
Avitar
not rated yet Jul 15, 2011
The big difference here is that we have the Sorcerer II ship out sequencing thousands of genome every month from the bottom of the Ocean. The commercial demand is at least as powerful as steam power was in the nineteenth century. We already have a vast library of material that is growing every day of proteins that do things that nobody has ever seen done. This is dangerous technology but understanding it as quickly as possible is probably as safe as we can be.
I too cannot imagine the stupid selections that the Government drive forced on the Nuclear Industry and on the Space industry. We do want to avoid the same committee charted negative paths. But there is going to be demands to use this technology. It is too powerful and our needs are too great. So any thoughts about developing it safely at speed should be presented because "Go Slow" is a nonstarter.
DavidMcC
not rated yet Jul 15, 2011
The biggest problem might turn out to be due to the fact that editing the genome of a given somatic cell type is not exactly equivalent to editing the genome of a germ-line cell in the corresponding way.

erplus
not rated yet Jul 17, 2011
not as original as it sounds since every mol.biology student has to learn that organisms use stop codons already in some instances to encode the 21st and the 22nd amino-acids: selenocysteine and pyrrolysine.

so all the useful ideas here are already in the natural examples...

plus ca change plus these harvard frauds try to appear non-plus-ultrish...