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Oct 30, 2014
Evolution in a test tube may have recapitulated an evolutionary phase dating back to the very origins of life. During this phase, a simpler, pre-DNA time known as “RNA world,” life acquired one of its chemical prerequisites—the ability to self-replicate. That is, RNA strands started to assemble copies of themselves. Yet it has been unclear how this could have happened.
Virtually all the RNA we know has just one chirality, or handedness. But self-replicating RNA in the RNA world most likely had to contend with both left- and right-handed RNA nucleotide building blocks. Any strand of RNA that gathered stray nucleotides onto itself would have eventually incorporated an RNA nucleotide of the opposite handedness—which would have blocked further assembly of that copy.
One way life could have solved this conundrum, suggests researchers at The Scripps Research Institute (TSRI), would have been a cross-chiral RNA polymerase ribozyme. It would, as expected, have used an original RNA strand as a reference or template from which to knit together a copy strand of RNA. However, the copy would have opposite handedness. That is, the copy would not have been identical to the original. It would have been mirrored the original, rather like a left hand appears to mirror a right hand.
No one had ever made or even tried to make a ribozyme that worked cross-chirally, on opposite-handed RNA. But that did not deter researchers led by Gerald F. Joyce, Ph.D., professor in TSRI’s Departments of Chemistry and Cell and Molecular Biology and director of the Genomics Institute of the Novartis Research Foundation. These researchers synthesized such a ribozyme by using a technique called “test-tube evolution.”
A postdoc in Dr. Joyce’s group named Jonathan T. Sczepanski started with a soup of about a quadrillion (1015) short RNA molecules. Their sequences were essentially random, and all were of right-handed chirality. “We set it up so that the molecules that could catalyze a joining reaction with left-handed RNA could be pulled out of solution and then amplified.” Dr. Sczepanski said.
After just 10 of these selection-and-amplification rounds, the researchers had a strong candidate ribozyme. They then expanded the size of its core region, put it through six more selection rounds and trimmed the extraneous nucleotides. The result: an 83-nucleotide ribozyme that was only moderately sequence-specific and could reliably knit a test segment of left-handed RNA to a template—about a million times faster than would have happened without enzyme assistance.
The team also showed that the new ribozyme could work without hindrance even when same-handed RNA nucleotides were present. In a last test, the new ribozyme successfully catalyzed the assembly of 11 segments of RNA to make a complete copy of its left-handed counterpart ribozyme, which in turn was able to join segments of right-handed RNA.
The researchers are now working to put the right-handed ribozyme (and by implication its left-handed partner) through more selection rounds, so that it can mediate the full replication of RNA, with essentially no sequence-dependence. That would make it a true general-purpose RNA-replication enzyme, capable in principle of turning a primordial nucleotide soup into a vast biosphere.
The scientists reported their results October 29 in Nature, in an article entitled, “A cross-chiral RNA polymerase ribozyme.”
“Cross-chiral replication does not require the D- and L-enzymes to have the same sequence, and even if initiated with enzymes of the same sequence, the two would probably soon drift apart,” the authors wrote. “If early life did entail the cross-chiral polymerization of RNA, then there would have been an era when both sides of the mirror were indispensable. Subsequently, however, a key evolutionary innovation may have arisen on one side of the mirror, for example, the invention of instructed L-polypeptide synthesis by D-RNA. Then the other side of the mirror could go dark, leaving biology to follow a homochiral path.”
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