Functional synthetic enzyme could be catalyst for artificial life

In an iron-rich medium, E. coli bacteria colonies without the Fes enzyme have limited growth (the small red colonies), while those with the artificial enzyme Syn-F4 appear large, white and healthy, because they're able to access the iron(Credit: Ann Donnelly/Hecht Lab/Princeton University)

Not content with editing the genes of living organisms or creating ever-smarter AI, scientists may eventually be able to biologically engineer unique artificial lifeforms from scratch. A new study from Princeton has brought that future a step closer, by confirming that an artificial protein the team developed functions as an enzyme in living bacteria.

We mere mortals are making decent progress "playing God": in 2010 scientists created a synthetic organism from a computer-generated genome in a natural cell that could self-replicate. Then, about a year ago, the Scripps Institute announced it had created a bacteria with two completely new DNA nucleobases in its genome, and in November the same team reported that their creation had spawned a brand new protein.

Over the years, the Princeton team has created artificial proteins for E. coli, a simple bacteria species that's commonly used as a testbed for these kinds of experiments. To test their creations, the researchers removed certain genes that resulted in the bacteria being unable to produce the enzyme Fes, which cells use to obtain iron. Without that vital mineral, the bacteria wouldn't be able to survive, but the team then plugged in proteins that could replace the missing function, "rescuing" or resuscitating the bacteria.

In the new study, the researchers have identified just how their new proteins work. They discovered that two of them keep the E. coli alive by compensating for the missing enzymes, boosting the production of other processes in the cell. But another of the proteins solved the problem more directly.

"This artificial protein, Syn-F4, was actually an enzyme," says Ann Donnelly, lead author of the study. "That was an incredible and unbelievable moment for me – unbelievable to the point that I didn't want to say anything until I had repeated it several times."

Donnelly initially noticed that the cells were suddenly able to obtain iron, suggesting that Syn-F4 was an enzyme. After repeating the test a few more times to be sure, she brought it to the attention of the lab's lead researcher Michael Hecht.

"Biology is the system of biochemical reactions and catalysts," says Hecht. "Each step has an enzyme that catalyzes it, because otherwise those reactions wouldn't go fast enough for life to exist. An enzyme is a protein that is a catalyst. They're the best catalysts in the universe because evolution has spent billions of years selecting them. Enzymes can increase the speed of a reaction by many orders of magnitude."

While the researchers are still playing with the building blocks of life, a functional artificial enzyme is an important step towards developing truly synthetic biology. Not only could these lifeforms be designed to efficiently develop food, fuel or medicine, but they can help us understand how life could arise under other circumstances – say, on other planets.

"We're starting to code for an artificial genome," says Hecht. "We've rescued 0.1 percent of the E. coli genome. For now, it's a weird E. coli with some artificial genes that allow it to grow. Suppose you replace 10 percent or 20 percent. Then it's not just a weird E. coli with some artificial genes, then you have to say it's a novel organism."

Michael Hecht, lead researcher on the team that developed the artificial enzyme Syn-F4(Credit: Brian Wilson, Office of Communications, Princeton)

In an iron-rich medium, <em>E. coli </em>bacteria colonies without the Fes enzyme have limited growth (the small red colonies), while those with the artificial enzyme Syn-F4 appear large, white and healthy, because they're able to access the iron(Credit: Ann Donnelly/Hecht Lab/Princeton University)