Synthetic biology garnered national headlines in May 2010 when a team led by J. Craig Venter announced it had created the world’s first “synthetic cell." The group used computers to copy an entire bacterial genome that, when inserted into a cell whose own genome had been removed, "booted up" the cell, which then passed the synthesized genome to its offspring.
This accomplishment was no small feat but the new genome, although man-made, was almost entirely a replication of one that already existed in nature. Now, a new study published January 4 in PLoS One has shown that DNA sequences designed in the laboratory and distinct from any found in nature can, when inserted into cells missing genes necessary for survival, "rescue" some of those cells.
They were not random sequences, explains Michael Hecht, a professor of chemistry at Princeton University who led the research. Instead they were intentionally patterned to code for amino acid arrangements, which can fold into relatively crude three-dimensional protein structures that are distinct from any natural proteins. In the past three decades scientists have refined methods for designing entirely new proteins from scratch, and they have shown that some can even catalyze reactions. "Since proteins are basically molecular machines that work in cells," Hecht says, the next logical question was: "Can you get one that you design from scratch to work in a cell?"
To find the answer, Hecht and his colleagues employed 27 Escherichia coli strains, each of which lacked a gene that, given the nutrient-poor medium on which they were growing, should have left them unable to survive. The researchers then introduced to the cells more than one million synthetic DNA sequences, each known to code for a previously designed protein. Explains Hecht: "If we give them an opportunity to pick up one of our genes, and if that gene allows them to survive under these selective conditions, then that cell will form a colony where all of its neighbors have died."
Sure enough, after several days of incubation, four separate experimental strains formed colonies, whereas cells in a control group all perished. To assure the surviving cells had done so because they had incorporated a novel gene, and that survival was not the result of adaptive mutations on the original chromosomes, the researchers purified the DNA from these new colonies and inserted it into new cells with the same original gene deletion. "We transferred it over and over again to make sure that the phenotype—survival—transferred with the genotype, which was the piece of DNA that we put in," Hecht explains. "With something as shocking as this, you don’t believe it until you’ve done a lot of controls."
How did this happen? That is still not exactly clear, Hecht says. Whereas the new proteins could have replaced the catalytic activity of the missing ones, they could also have sustained the cells through an entirely separate, still unknown mechanism. Hecht adds that experiments aimed at elucidating the mechanisms are underway and are "really, really important."
Benjamin Davis, a professor of organic chemistry at the University of Oxford in England who was not part of the research group but studies artificial proteins in his own lab, says Hecht and his team performed a "very clean experiment," adding that they "are very clear that there are lots of unanswered questions about this. But they are great unanswered questions."
Specifically, even though certain processes have evolved in nature, they are not necessarily the only processes that can work, Davis explains. "There are so many possibilities that nature has not surveyed."
As the authors of the new study point out, the DNA and amino acid sequences that have emerged in nature represent only a "minuscule fraction of the theoretical sequence space that is possible for genes and proteins."
"Evolution does not work in a way that tries to map out everything—it can't. It's not possible," Davis says. Therefore, if Hecht's group's new proteins are not replacing the exact catalytic activity that was deleted, "there could be umpteen different ways they are working," he says, and investigations into those possibilities "are exactly the types of experiments we should be doing in synthetic biology."
In the meantime, does the new result bring scientists any closer to creating artificial life? Only very slightly, if at all, Hecht says. "If you imagine a toolbox that sustains life, we've replaced a few screwdrivers. The question with artificial genomes is: Could you sustain life with an entirely new toolbox? And we are nowhere near that point."