Early RNA may have used isolation strategy to defeat useless mutants

Long before modern cells were around to house genetic material, tiny water droplets might have protected the first self-replicating molecules from parasitic mutants. New experimental evidence shows that such temporary compartments can help RNA molecules resist takeover by shorter, faster-replicating mutants, researchers report in the Dec. 9 Science.

“We have a lot of theoretical papers that sort of hint at how parasites could have been fought off, but here we have a lab-based study that shows a potential mechanism,” says Niles Lehman, a chemist at Portland State University in Oregon who wasn’t part of the study.

A crucial step in the emergence of life on Earth was the appearance of molecules that could copy themselves. Many scientists believe the first self-replicating molecules might have been rudimentary versions of today’s RNA, which carries instructions to make proteins. But as that RNA replicated, mutations would inevitably sneak in. And mutations that shortened the molecule (even at the expense of its function) would have a selective advantage.

“Fitness means number of offspring per unit time,” says Lehman. “When you strip away all the biology and get down to the pure chemistry, it’s just the rate of the reaction.” So shorter, snappier mutants that could copy themselves quickly and produce more offspring would soon push out longer RNA molecules that carried more information. These mutants are molecular parasites: They reproduce very quickly, but they’ve lost their instruction manual to do anything else.

Mathematical models had suggested that compartmentalization could help solve the parasite problem — that is, having RNAs replicating in many discrete populations instead of one giant pool. Just by chance, some pockets would end up with fewer parasites. And in those compartments, the longer RNA might be able to get a foothold.

Compartments with fewer parasites could produce a lot of longer, functional RNA, boosting its representation in the population as a whole, says study coauthor Eörs Szathmáry, an evolutionary biologist at the Parmenides Foundation in Munich.

To test the idea in the lab, Szathmáry and his colleagues took a piece of RNA from a bacteriophage and pasted in a ribozyme, a piece of RNA that can catalyze a chemical reaction. Then they let the RNA duplicate under different conditions — either freely in a vial or distributed through a million microscopic water droplets in oil. The droplets acted as temporary containers: They held populations of RNA molecules together for short periods of time before breaking, letting the RNA all mix together again, and then reforming with a different set of RNA inside.

The researchers could test the catalytic activity of individual droplets to see how well the original RNA was resisting the parasitic RNA. When the RNA got shorter, it dropped the instructions to catalyze chemical reactions. So a droplet that couldn’t catalyze very well probably contained a lot of parasitic RNA.

After four generations, catalytic RNA that wasn’t compartmentalized in any way had been completely overrun by parasitic RNA. Random compartmentalization inside droplets slowed the speed at which parasites took over, but the original RNA still disappeared by the seventh generation. “Within compartments, there’s selection for the parasites,” says Szathmáry — the shorter mutants still have the edge.

But in competition between compartments, the advantage flips: A compartment with too many parasites won’t fare well. Take, for instance, a cell — a compartment that’s a little more complicated than a droplet. A cell with RNA that couldn’t catalyze chemical reactions would probably die.

The researchers mimicked that type of selection between the droplets by removing the ones filled with parasitic RNAs after each generation. With selection, the cheaters no longer dominated the population in the same way. After nine generations, a substantial amount of the functioning RNA still remained.

In nature, temporary compartments like aerosolized droplets could have provided the separation necessary for self-replicating molecules to get going, Szathmáry says. Or RNA populations brewing inside different pores inside rocks could have acted like distinct populations. Those rudimentary compartments were less elegant than the cells that make up all life today, but on the most basic level, they did a similar job.

It’s becoming increasingly clear that compartmentalization helped to shape the emergence of life, says Brian Paegel, a chemist at the Scripps Research Institute in Jupiter, Fla. “Cellularity might not have been something that just happened because it was cool. It might have been totally central to life as we know it today.”