Laboratory “Theme Park” Re-creates RNA World for Study

CAMBRIDGE, Mass. — People love theme parks, giant playgrounds that usually offer patchwork renditions of either an evocative historical moment or a particular future vision. Rarely, if ever, are theme parks built around a biological theme—and never do such parks fit inside a test tube. Almost never. Scientist David Bartel is hard at work on what might seem an impossibility—a microscopic theme park whose motif, the origins of life, is of equal interest to both scientists and philosophers.

Bartel, a researcher at Whitehead Institute for Biomedical Research, pursues a theory of early evolution called the “RNA-world hypothesis,” which maintains that, in the beginning, long before DNA or protein existed, RNA performed both DNA’s job of encoding information and protein’s job of catalyzing replication. Because RNA replication is far simpler than protein replication, and because RNA participates in central cellular functions, researchers postulate a primitive, yet elegant, system in which RNA made RNA.

Central to this hypothesis is an RNA enzyme that replicates other RNA molecules. Unfortunately, no such molecule currently exists in nature. To demonstrate the feasibility of this hypothesis, researchers must re-create certain aspects of this RNA world in the lab. Hence Bartel’s RNA theme park. According to Bartel, the micro exhibits in his lab are “artificial and fragmented when compared with the real thing, but still well worth a visit.”

So far, Bartel has developed some impressive displays. In a paper published in the journal Science in 2001, his lab demonstrated one of the first pieces of hard evidence that such a world is at least possible. But this landmark paper also revealed that Bartel’s RNA molecules didn’t yet perform to the degree that the RNA world would have required. In a July 2003 follow-up in the journal Biochemistry, Bartel and doctoral student Michael Lawrence published research pinpointing the exact reason for this, findings Bartel claims are “an important step toward figuring out how to improve the efficiency of these RNA replicating molecules.”

Re-evolving evolution

Today, cellular machinery coordinates a sophisticated process that involves proteins, DNA, and RNA all working in concert, with proteins typically serving as enzymes to catalyze reactions, and DNA and RNA storing and processing genetic information. If, as the RNA-world hypothesis states, RNA once was in the business of replicating RNA, then enzymes once were composed entirely of RNA and not amino acids—the building blocks of protein. The first step then, in creating an RNA-world theme park, is to create RNA enzymes from scratch. To do this, Bartel employs a process developed with Harvard Medical School’s Jack Szostak: in vitro evolution—or evolution in a test tube.

Workers in Bartel’s lab fill tubes with anywhere from 1 trillion to 1 quadrillion RNA molecules, selecting for those that can expand by forming chemical bonds with other RNAs. The molecules that can do this are isolated; the rest are discarded. These new, bigger RNAs are multiplied, returned to the tube and tested again for the same ability. Again, losers are removed, and winners multiplied. As this cycle repeats, slight mutations often appear in the RNAs, some of which create molecules superior to the parent molecule. Says Bartel, “Really, we end up selecting for the survival of the best molecules, and then propagating those survivors”—Darwinian natural selection.

So far, Bartel’s lab has demonstrated that these new RNA molecules can act as enzymes: In this case, they can bind to an RNA template molecule that serves as the pattern for producing, one nucleotide at a time, another RNA. The Science paper reported both good and cautionary news. The good news was that these RNA enzymes are flexible and robust enough to bind to just about any kind of template regardless of its sequence – findings that eluded earlier experiments. The more sobering news was that these new sequences of RNA are at most 14 nucleotides long, which, while still a major achievement, is far short of the roughly 200-nucleotide goal. As reported in Biochemistry, Bartel and Lawrence have now learned the reason for this: The actual process of assembling the new RNA is fast and efficient once binding occurs, but the binding doesn’t last long enough to produce a complete replicate. “What we really need now,” says Bartel, “is to work on the binding.”

Life was a garbage bag

Less than four decades old, the RNA-world hypothesis has garnered widespread support within the scientific community. However, some researchers subscribe to an alternate view often called the “metabolism first” theory. This idea, in contrast to the RNA world’s “information first” thesis, posits that a chaotic soup of small, random molecules led to chance metabolic reactions that evolved into modern cellular life.

Stuart Kauffman, a biologist and RNA-world skeptic affiliated with the nonprofit research center Santa Fe Institute, believes the RNA hypothesis is narrow and fails to take into account the possibility that other polymeric molecules may be able to self-reproduce without making a copy of a template. He theorizes that life originated from a complex mixture of such polymers that eventually yielded autocatalytic reactions.

A similar notion is Freeman Dyson’s “garbage bag” hypothesis. Dyson, a physicist at the Institute for Advanced Studies in Princeton, N.J., believes that primordial soup was filled with membranes (garbage bags) that contained random chemicals not nearly as complex as RNA or DNA. These chemicals began catalyzing reactions in each other, some of which eventually caused the cell-like garbage bags to divide and thus evolve.

Proponents of this view claim the key factor in early evolution is the garbage bag rather than the molecule. For University of California, Santa Cruz, chemistry professor David Deamer, it’s inconceivable that RNA could have catalyzed and evolved outside the barrier of a cell membrane without just drifting off.

Bartel, rather than countering these critics, takes seriously the need for some kind of cell-like barrier—or garbage bag. “If our lab is able to demonstrate that RNA can replicate RNA, a next step would be to synthesize a self-replicating system that can also evolve,” he says. “To do this would require membranes, or some other type of compartmentalization.”

Harvard’s Szostak, a prominent advocate of the RNA world, counters that he can’t imagine a system as complex as cell formation and division not being preceded by some sort of informational transmission, such as RNA creating RNA. However, he adds that the RNA-world hypothesis isn’t without its problems. “The big question,” he says, “is whether RNA arose as the first genetic polymer from some prebiotic chemistry that we don’t understand, or whether there were one or more progenitors of RNA. People are looking at many possible candidates for being a progenitor for RNA.”

Szostak looks not to a world of random metabolism, but rather to threose nucleic acid, or TNA, a molecule that, while not existing in nature, has been successfully synthesized in the lab. Szostak believes that TNA’s relatively simple composition make it a likely candidate to have spawned RNA in a prebiotic world.

In spite of the various theories, most researchers readily admit that, like the proverbial blind men trying to describe an elephant, each approach may have captured only one angle of life’s origins. “We’ll never really know the whole story of how life got started,” says Bartel, “but every insight that we can discover is important. This is one of the most significant and fundamental questions in science, right up there with ‘how does the mind work?’ or ‘how did the universe begin?’”

Meanwhile, Bartel and his team continue working toward their goal of developing an RNA enzyme that can fully replicate other RNAs. “We’re designing these RNAs as well as we can,” Bartel says, “and what we can’t design, we evolve.”

The more successful this re-evolving, the closer he gets to his theme park’s grand opening.

The research was supported by the National Institutes of Health.

Citation

Lawrence, M. S., & Bartel, D. P. (2003). Processivity of ribozyme-catalyzed RNA polymerization. Biochemistry, 42(29), 8748-8755.

Johnston, W. K., Unrau, P. J., Lawrence, M. S., Glasner, M. E., & Bartel, D. P. (2001). RNA-catalyzed RNA polymerization: accurate and general RNA-templated primer extension. Science, 292(5520), 1319-1325.