New Research Supports Concept of "RNA World"

Evolution, according to Charles Darwin, is “descent with modification.” DNA sequences contain genetic information that is copied and passed down from one generation to the next. However, this process needs to be somewhat adaptable so that new traits can eventually emerge from small variations in genes and enter the population.

But how did this whole thing start? Could a simpler version of this kind of evolution have occurred in the beginnings of life, long before there were cells, proteins, and DNA? From the 1960s, scientists Leslie Orgel, a Salk Fellow, postulated that the dynamics of Darwinian evolution were established during the “RNA World,” a fictitious period when tiny, stringy RNA molecules ruled the early Earth.

The Salk Institute’s most recent research offers new perspectives on the beginnings of life and strong evidence in favor of the RNA World theory. The research, published in the journal Proceedings of the National Academy of Sciences (PNAS), reveals an RNA enzyme that can replicate other functional RNA strands accurately and simultaneously permit the emergence of new RNA variants over time.

These extraordinary abilities imply that RNA might have undergone molecular evolution in its earliest forms.

The discoveries also advance scientists’ efforts to replicate RNA-based life in the lab. By creating these rudimentary environments in the laboratory, scientists can test theories regarding the origin of life on Earth or possibly other planets.

We are chasing the dawn of evolution, by revealing these novel capabilities of RNA, we are uncovering the potential origins of life itself, and how simple molecules could have paved the way for the complexity and diversity of life we see today.”

Gerald Joyce, Senior Author and President, Salk Institute

Utilizing DNA, scientists are able to follow the evolutionary path from the earliest single-celled organisms to the current flora and fauna. What preceded that, though, is still unknown. Helixes of double-stranded DNA are excellent genetic data storage materials.

In the end, many of those genes code for proteins, which are intricate molecular structures that perform a variety of tasks to maintain the viability of cells, because these molecules can do a little bit of both, RNA is special.

Like proteins, they are composed of lengthy nucleotide sequences, but they can also function as enzymes to speed up reactions. So, is it feasible that life has currently evolved from RNA?

For years, researchers like Joyce have been delving into this concept, concentrating especially on RNA polymerase ribozymes, which are RNA molecules capable of copying other RNA strands. Joyce and his colleagues have been working on RNA polymerase ribozymes in the lab for the past ten years.

They have created new versions of the enzymes that can replicate larger molecules through a process known as directed evolution. However, the majority have a fatal flaw in that they cannot accurately duplicate the sequences. The sequence is tainted with many errors over many generations and the resulting RNA strands have completely lost their function and no longer resemble the original sequence.

Thus far, several critical mutations in the most recent RNA polymerase ribozyme produced in the lab enable it to copy an RNA strand with significantly greater accuracy.

The RNA strand replicated in these experiments is a “hammerhead,” a tiny molecule that splits other RNA molecules into fragments. The RNA polymerase ribozyme not only successfully replicated functional hammerheads, but over time, new variants of the hammerheads started to appear, which surprised the researchers.

The performance of these new variants was similar. Still, they were easier to replicate due to their mutations, which improved their evolutionary fitness and eventually made them dominate the hammerhead population in the lab.

We have long wondered how simple life was at its beginning and when it gained the ability to start improving itself, this study suggests the dawn of evolution could have been very early and very simple. Something at the level of individual molecules could sustain Darwinian evolution, and that might have been the spark that allowed life to become more complex, going from molecules to cells to multicellular organisms.”

Nikolaos Papastavrou, Study First Author and Research Associate, Salk Institute

The results demonstrate how crucial replication fidelity is to the process of evolution. To preserve heritable information across several generations, the RNA polymerase's copying accuracy needs to be higher than a critical threshold, which would have increased as the size and complexity of the evolving RNAs increased.

To develop better-performing polymerases and eventually create an RNA polymerase capable of self-replication, Joyce's team is replicating this process in lab test tubes. They are doing this by applying increasing selective pressure to the system. This could potentially lead to the emergence of autonomous RNA life in the lab within the next ten years, according to the researchers.

The scientists are also curious about what else could happen when this little “RNA World” has more freedom.

We have seen that selection pressure can improve RNAs with an existing function, but if we let the system evolve for longer with larger populations of RNA molecules, can new functions be invented? We are excited to answer how early life could ratchet up its own complexity, using the tools developed here at Salk.”

David Horning, Study Co-Author and Staff Scientist, Salk Institute

Future research examining alternative theories regarding the origins of life, such as which environmental factors on Earth and other planets might have been most conducive to RNA evolution, is made possible by the techniques employed in the Joyce lab.