An enzyme made of RNA selectively recognizes a chemical mark that characterizes broken strands and attaches additional RNA to them. The discovery strengthens the possibility that ancient life in the RNA world could have preserved genetic information even without repair proteins.
How could the first life forms preserve their genetic information, at a time when sophisticated proteins for repairing damage were not yet available? A new ribozyme developed by researchers at the University of Notre Dame suggests a possible mechanism: a molecule RNA Capable of recognizing a characteristic end of broken RNA and catalyzing its joining to another RNA strand.
Ribozyme—an enzyme made of RNA rather than protein—developed through in vitro evolution. It looks for a phosphate group at the 3′ end of an RNA strand, a feature that may appear after the molecule has been cleaved. It has little or no response to intact strands that end in a normal hydroxyl group. The ability to distinguish between the two types of ends makes it a candidate for an ancient damage-detection mechanism. ([ScienceCast][1])
The study was published in the journal Nature Communications and was led by Anisha Biswas and Dr. Saurja Das Gupta from the University of Notre Dame, in collaboration with Zoe Weiss and Nobel Prize laureate in Chemistry Jack Shostak.
“Our results suggest that the molecular tools needed to preserve an RNA-based genetic code and pass it on to future generations could have been provided by RNA alone, without the need for proteins,” said Das Gupta.
The chicken-and-egg problem of early life
In modern cells, the division of labor is relatively clear. DNA stores most of the genetic information, while proteins replicate it, repair damage, and carry out much of its instructions. However, the proteins themselves are manufactured according to information stored in DNA.
This situation raises a familiar question in research. The source of life: What appeared first – the genetic information or the protein machinery that handles it?
Hypothesis The world of RNA suggests a possible way out of the loop. According to the hypothesis, before the advent of DNA and proteins, there were systems in which RNA played both roles: it stored information and also catalyzed chemical reactions. Even in modern cells, catalytic RNA molecules, called Ribozymes.
Das Gupta's lab is investigating how the structure, function, and evolution of RNA may explain the chemistry that preceded modern cells. In the lab, researchers are developing RNA enzymes with activities that are not currently known in nature but may have been essential for the origins of life. ([Department of Chemistry & Biochemistry][2])
Why was a correction mechanism needed?
RNA is a relatively sensitive molecule. Heat, acidic or basic conditions, radiation, and chemical reactions can break its backbone. In a world where the genome itself was made of RNA, any such breakage could erase some of the information needed for survival and reproduction.
“Modern organisms have mechanisms for repairing broken DNA,” Das Gupta explained. “If early life carried its genes in RNA, a similar repair process would have been required. Otherwise, inevitable damage to the RNA genome would have resulted in permanent loss of genetic information.”
The ribozyme discovered is not proof that this mechanism actually existed about four billion years ago. The researchers do not have RNA molecules from that period, and the catalyst tested was created in the laboratory. The result mainly shows that, chemically speaking, RNA is capable of developing an activity that recognizes breakdown products – a task that until now was generally attributed mainly to protein enzymes.
A discovery they weren't looking for
The researchers did not initially plan to create ribosomes forRNA repairTheir goal was to modify an existing ribozyme so that it could bind RNA molecules with an end containing three phosphate groups.
To do this, they used in vitro evolution: starting with a huge population of different RNA molecules, selecting the ones that succeed in performing a certain action, replicating them, and repeating the process in several cycles. In this way, sequences that fit the selection conditions set by the researchers gradually accumulate.
Previous work by the group has shown that the substrate preferences of ribozymes can be altered through in vitro evolution. During the transition, the molecule may develop a new structure, while still retaining some activity through a series of intermediate mutations. ([pnas.org][3])
However, during the current experiment, unexpected results emerged. Instead of ignoring them and continuing to look for only the activity they had planned, the researchers examined the unusual molecules and discovered that they require a phosphate group at the 3′ end of the RNA to which they bind.
“The existence of this ribosome has interesting implications for understanding the origin of life, and we stumbled upon it while we were looking for something else,” Das Gupta said. “What surprises me most is that it hasn’t been found before.”
A chemical bond that is not the usual bond
Chemically, the ribozyme catalyzes a reaction in which the hydroxyl group at the 2′ position of the broken RNA strand attacks the 5′-triphosphate end of another RNA. The phosphate group at the 3′ end does not participate directly in bond formation, but probably serves as part of the substrate recognition mechanism.
The result is a 2′–5′ phosphodiester bond, rather than the 3′–5′ bond that typically makes up the backbone of modern RNA. Therefore, this is not yet a system that accurately restores an entire genetic strand to its original state.
However, even unconventional splicing could have been useful in an ancient system, for example to prevent loss of an RNA segment, to keep two adjacent segments together, or to provide an intermediate step before further processing. The researchers suggest that the selectivity for damaged ends is reminiscent of mechanisms present in protein-based RNA repair pathways in modern cells. ([ScienceCast][1])
A possible tool for disease research
The discovery may also have contemporary biotechnological applications. Broken RNA strands are formed during viral infections, immune responses, and conditions of cellular dysfunction, including some types of cancer.
Acceptable methods forRNA sequencing are generally adapted to molecules with normal ends. As a result, some of the cleavage products do not receive the chemical markers needed to prepare them for paving, and remain virtually invisible.
In laboratory experiments, the ribozymes were able to selectively bind to RNA fragments with a 3′ phosphate at the end, even in diverse mixtures of cellular RNA. This ability could be used in the future to isolate and enrich cleavage products before sequencing, allowing researchers to better map where and how RNA is broken in cells. ([Biorexiv][4])
The group is now working to improve the efficiency of the reaction and expand the range of target molecules that the ribozyme can recognize. The road to diagnostic application is still a long one, but this experiment provides an extraordinary bridge between two questions: how genetic information is preserved early in life, and how we can now identify damaged RNA in diseased cells.
The original article: A ribozyme ligase that requires a terminal 3′-phosphate on its RNA substrate, Nature Communications, DOI: 10.1038/s41467-026-74622-8.
Questions and Answers
What is ribozyme? A ribozyme is an RNA molecule capable of catalyzing a chemical reaction, similar to a protein enzyme. Natural ribozymes still participate in key processes in cells today.
Have researchers discovered an ancient repair mechanism that has survived to this day? No. They created ribozymes in the lab that demonstrate that RNA can recognize broken ends and join other RNA to them. This is proof of chemical feasibility, not a molecular fossil of early life.
How does ribozyme recognize broken RNA? It requires a phosphate group at the 3′ end of the substrate. Intact RNA strands usually end with a hydroxyl group, so ribozyme prefers ends that may be formed by cleavage.
Why is the discovery important for biotechnology? The selectivity for broken RNA may allow the isolation of cleavage products that are not well detected by standard sequencing methods, and aid in the study of viral infections and diseases associated with RNA damage.
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