Image: Christine Daniloff
Institute of Technology (MIT) and Harvard
have developed technologies that could be used to rewrite the genetic code of a
living cell, allowing them to make large-scale edits to the cell’s genome. Such
technology could enable scientists to design cells that build proteins not
found in nature, or engineer bacteria that are resistant to any type of viral
technology, described in an issue
of Science, can overwrite specific DNA sequences throughout the
genome, similar to the find-and-replace function in word-processing programs.
Using this approach, the researchers can make hundreds of targeted edits to the
genome of E. coli, apparently without
disrupting the cells’ function.
did get some skepticism from biologists early on,” says Peter Carr, senior
research staff at MIT’s Lincoln Laboratory (and formerly of the MIT Media Laboratory),
who is one of the paper’s lead authors. “When you’re making so many intentional
changes to the genome, you might think something’s got to go wrong with that.”
new paper is the result of a seven-year collaboration between researchers in
the lab of Joseph Jacobson, associate professor in the Media Lab, and George
Church, professor of genetics at Harvard
Editing DNA’s code
DNA consists of long strings of “letters” that code for specific amino acids.
Every organism uses the same genetic code to translate those letters into amino
acids, which are then strung together into proteins.
make that translation, nearly all living cells use the same genetic code, which
has 64 codons—three-letter DNA “words.” While most of them specify an amino acid,
there are also a few codons that tell the cell when to stop adding amino acids
to a protein chain. The MIT and Harvard researchers targeted one of these “stop” codons, which consists of the letters TAG. With just 314 occurrences,
the TAG stop codon is the rarest in the E.
coli genome, making it a prime target for replacement.
make their edits, the researchers combined a technique they previously unveiled
in 2009, called multiplex automated genome engineering (MAGE), with a new
technology dubbed conjugative assembly genome engineering (CAGE).
which has been called an “evolution machine” for its ability to accelerate
targeted genetic change in living cells, locates specific DNA sequences and
replaces them with a new sequence as the cell copies its DNA. This allows
scientists to precisely control the types of genetic changes that occur in
cells: The targets are replaced, while the rest of the genome is left
this case, the researchers replaced the TAG codon with another stop codon, TAA,
in living E. coli cells. To make the
process more manageable, the researchers first used MAGE to engineer 32 strains
of E. coli, each of which has 10 TAG
combine those strains and eventually end up with one that has all 314 edits,
the researchers then developed CAGE, which allows them to precisely control a
naturally occurring process that bacteria use to exchange genetic material. One
bacterium builds an extension to a neighboring cell and then passes a piece of
genetic material—in this case, TAA codons—to its neighbor.
researchers set up a playoff-like system in which each strain shares its DNA
with one other strain. After the first round of CAGE, the researchers had 16
strains, each of which had double the number of TAG edits that it started with.
Those 16 strains then went into a second round of CAGE, producing eight
this point, the researchers have four strains, each of which has about
one-quarter of the possible TAG substitutions; they believe they are on track
to produce the single combined strain with all 314 of the substitutions, Carr says.
‘Plug and play’
Because the alterations were done in living cells, the researchers have been
able to monitor any potential harmful effects as they appear. Preliminary
characterization suggests that the altered bacteria still behave normally, and
can survive and reproduce.
all the TAG stop codons are deleted, the researchers’ next step is to delete
the cell machinery that reads the TAG codon—freeing it up for a completely new
purpose, such as encoding a novel amino acid. That kind of “plug-and-play” slot
would give scientists great flexibility in designing cells that produce new
proteins, Carr says.
altering the genetic code, scientists could also engineer bacteria that are
resistant to multiple viruses. In industries that cultivate bacteria viruses
affect up to 20% of cultures, with a huge impact on productivity. However,
those viruses can only infect a cell if the bacterial and viral genetic codes
are the same.
the genetic code of industrial bacteria could also create a “genetic firewall”
that would prevent engineered bacteria from spreading their genes to natural
bacteria in the environment, or from allowing such bacteria to survive in the
wild, Carr says.