Ribozyme May Hint At The Origin Of Life

Researchers have developed the first cross-chiral biocatalyst—a right-handed (d) RNA enzyme that catalyzes the linkage of left-handed (l) RNA nucleotides into l-RNA chains. No other RNA or protein enzymes of one chirality are known to use substrates of the opposite chirality to produce biopolymers.

Such ribozymes could be useful for creating novel compounds, such as nuclease-resistant l versions of conventional d-RNA bioactive agents. Their development also gives a boost to the RNA world hypothesis—the idea that there may have once been living systems in which RNA did most of the work and that this RNA world may have evolved into today’s more complex RNA/DNA/protein world.

No known modern-day RNA-based enzyme can assemble RNA from a racemic soup of left- and right-handed RNA building blocks, the form in which RNA likely would have existed prior to the origin of an RNA world. To develop such a ribozyme, chemical biologist Gerald F. Joyce and postdoc Jonathan T. Sczepanski of Scripps Research Institute California used directed evolution. Like modern RNAs, the new ribozyme has d chirality. But unlike them, it catalyzes the template-directed poly­merization of RNAs of opposite handedness, the joining together of l-RNA building blocks bound to an l-RNA template (Nature 2014, DOI: 10.1038/nature13900). It ignores d-RNA building blocks that may be around.

The d-enzyme’s activity was sufficient to catalyze the assembly of a full-length l version of itself by the templated joining of 11 l-RNA oligomers. In a Nature commentary, Sandip A. Shelke and Joseph A. Piccirilli of the University of Chicago describe the work as “a remarkable first demonstration of an enzyme (RNA or protein) being synthesized by its own enantiomer.” The l-ribozyme product can then use d-RNA building blocks to reconstruct the d-ribozyme that created it.

This trick makes the cross-chiral ribozyme “a molecular incarnation of M. C. Escher’s famous woodcut ‘Drawing Hands,’ ” which depicts right and left hands drawing each other, says RNA evolution specialist Irene Chen of the University of California, Santa Barbara. “It will be exciting to see where further evolution takes this system.”

The ribozyme’s ability to use RNA substrates and templates of opposite chirality from itself stems from the non-sequence-specific interactions it uses to bind those substrates and templates. Those interactions resemble the ones modern protein-based enzymes use to recognize RNA substrates and templates—not the base-pairing strategies RNA or DNA enzymes typically use to recognize substrates and templates of the same chirality as the enzymes’. The new ribozyme’s “ability to recognize substrates without base-pairing to them could lead to the development of the types of generalized catalytic activity that would have been needed early in evolution,” says RNA specialist David Bartel of Massachusetts Institute of Technology. He points out that the Scripps researchers “are still at a very early stage”—the ribozyme isn’t as versatile as might have been needed in an RNA world. “But they have a new approach for eventually achieving that.”

RNA catalysis researcher Peter J. Unrau of Simon Fraser University, in Burnaby, British Columbia, also commends the study but points out that it does not directly address how a cross-chiral ribozyme that itself has pure chirality “could have emerged de novo from an achiral mix of nucleotides.”

“This is a brilliant paper that opens up many new and fascinating lines of investigation and elegantly addresses some vexing problems of RNA self-replication,” says Philipp Holliger, a nucleic acid replication expert with the Medical Research Council Laboratory of Molecular Biology, in Cambridge, England. However, he notes that early-world cross-chiral systems “would at some point have to transition to today’s homochiral systems” and that it is difficult to envisage how that could occur.

Joyce says he and his coworkers are continuing to evolve the enzyme to expand its catalytic properties. “I would hope that others will take the cue and devise other cross-chiral enzymes, including protein enzymes, such as a d-protease that acts on l-polypeptides,” he says.