Engineered Enzyme Repairs Broken RNA, Hinting at Life’s Origins

Modern cells rely on DNA to store genetic information and on proteins to replicate, repair and build from it, while proteins themselves require DNA’s instructions to be made. This chicken-and-egg problem has led some researchers, including Notre Dame biochemist Saurja DasGupta, to hypothesize that neither came first. DasGupta studies the chemical origins of life through RNA, a molecule that can both store genetic information and catalyze chemical reactions. In a study published today in Nature Communications, DasGupta and collaborator Jack W. Szostak of the University of Chicago describe an engineered enzyme, or ribozyme, that selectively recognizes and repairs broken RNA.

“Our results suggest that the molecular tools needed to preserve the RNA-based genetic code and pass it on to future generations could have been furnished by RNA alone—no proteins required,” DasGupta said.

The ribozyme pastes together pieces of RNA and targets a terminal phosphate group, a feature found at the end of broken RNA chains but not on intact strands, which end in a hydroxyl group instead. “The fact that this enzyme seeks out terminal phosphate groups in RNA—and, therefore, broken RNAs—while ignoring strands that end with standard hydroxyl groups suggests that it could have been important for primordial RNA repair,” DasGupta said.

This relates to the RNA World hypothesis, which proposes that early life forms nearly four billion years ago relied exclusively on RNA before DNA and proteins took over encoding genes and running cellular processes. “Modern organisms have repair mechanisms to mend broken DNAs; if early life forms carried their genes in RNA, then a similar repair process must have existed,” DasGupta said. “Otherwise, when heat, high pH or other stressors inevitably damaged the RNA genome, the genetic information would have been permanently lost, effectively stopping life in its tracks.”

The ribozyme was engineered through in vitro evolution, a process of selecting RNA catalysts with desired properties from trillions of molecules in test tubes. DasGupta’s team originally set out to modify an existing class of ribozymes but pursued unexpected results instead, leading to this discovery. “What I’m most surprised about, actually, is that it wasn’t found sooner,” he said.

The ribozyme also has biotechnology applications. Broken RNA, common in viral infections and certain cancers, is typically invisible to standard sequencing methods because the chemical tags used don’t attach to broken ends. Since the ribozyme targets broken RNA selectively, it could help make these strands detectable before sequencing. DasGupta’s group is now optimizing the ribozyme’s efficiency and expanding its range of molecular targets.