A handful of bacterial genes crucial to survival were successfully replaced by artificial ones in a new synthetic-biology experiment.
It’s not clear how the synthetic genes rescued the doomed E. coli bacteria, which had several important sequences of DNA knocked out of its genome. But scientists think synthetic proteins produced by the new genes replaced the missing natural versions.
“To enable life you need genes and proteins, which are information and machines,” said molecular biologist Michael Hecht of Princeton University, co-author of the study published online in PLoS ONE. “These evolved over a very long period of time, but we wanted to ask, ‘Are they really special, or can we make stuff like them from scratch?’ It seems we can.”
One of synthetic biology’s primary goals is to create customizable organisms able to produce food, fuel or pharmaceuticals; clean toxins from the environment; or even function as computers.
Most synthetic-biology experiments, including the J. Craig Venter Institute’s recent creation of a synthetic life form, rely on existing genes in nature. In the new experiment, however, Hecht and his team engineered a semi-random library of 1.5 million made-from-scratch genes.
Genes contain instructions for building proteins, which are made of units called amino acids. There are 20 different amino acids a protein can be made of, and some sequencesmake a protein fold into three dimensions. Each gene in Hecht’s synthetic library calls for proteins made of 102 amino acids. Yet, instead of randomly filling each spot, the genes included sequences prompting them fold into four-helix structures (right).
“Folding in three dimensions [is required for functionality] when it comes to proteins, so the library isn’t completely randomized,” Hecht said. “You might think of it as a targeted shotgun of randomness instead of a bomb of it.”
Twenty-seven strains of E. coli, each missing one gene critical for survival, individually mingled with the synthetic-gene library. Four strains of bacteria incorporated a synthetic gene into their DNA and grew on Petri dishes that contained only the bare nutrients for survival. Without the new genes, the four strains didn’t grow at all.
Taking the rescue of doomed microbes further, Hecht’s team made a strain of E. coli missing all four genes from the previous experiments. When the synthetic replacement genes from the library were added, the microbe was rescued.
“I think this is a very interesting start to some more research,” said biotechnologist Andrew Ellington of the University of Texas at Austin, who was not involved with the experiments. “I’d like to see more proof that these proteins are doing what [Hecht] says they’re doing…. There may be some weird things going on.”
Hecht said “it would be nice” to untangle the biochemistry of his genetic rescues, adding that the synthetic genes weren’t exactly optimum replacements for nature’s versions that were chiseled over billions of years of evolution. But he said that’s not the biggest takeaway from the experiment.
“We know which specific genetic sequences rescue the strains, even if we don’t yet know how they work,” Hecht said.
In addition to following up on the biochemistry of the genes that revived the bacteria, Hecht’s laboratory plans to engineer more-complex libraries and knock out even-more-crucial genes.
“‘How far can you go with this?’ is what we want to know. Could you knock out 100 genes and rescue all of them? Eventually a whole genome?” Hecht said.
By Dave Mosher