The RNA world

by Sidney Altman
1989 Nobel Prize laureate in chemistry

The phrase “The RNA World” was coined by Walter Gilbert in 1986 in a commentary on the then recent observations of the catalytic properties of various RNAs. The RNA World referred to an hypothetical stage in the origin of life on Earth. During this stage, proteins were not yet engaged in biochemical reactions and RNA carried out both the information storage task of genetic information and the full range of catalytic roles necessary in a very primitive self-replicating system. Gilbert pointed out that neither DNA nor protein were required in such a primitive system if RNA could perform as a catalyst. At that time, it had only been demonstrated that RNA could cleave or ligate phosphodiester bonds. Nevertheless, as is a frequent occurrence in science, a general hypothesis was constructed from a few specific instances of a phenomenon. This hypothesis proved to be very effective in stimulating thought about the origin of life on Earth. Ensuing discoveries of other natural catalytic RNAs that could cleave and ligate phosphodiester bonds, and the very recent observation that the region surrounding the peptidyl transferase center of a bacterial 50S ribosomal subunit contains RNA and no protein, further buttress the hypothesis. Finally, the so-called “evolution in vitro” methodology, which is able to scan an enormous number of nucleic acid sequences in vitro for any given function, has revealed that RNA, indeed, can have many different catalytic functions as so can, presumably, DNA.

On further reflection, many doubts have been raised about whether or not the original genetic/catalytic material could have been RNA as we know it today because extreme conditions on the primitive Earth might have led to the rapid chemical degradation of RNA. Nevertheless, even if the precise chemical nature of the early genetic/catalytic material differed from present-day RNA, it seems reasonable to conclude that the RNA World did exist at some time. If very primitive life on Earth did not arise until about 3.5 billion years ago, there was, perhaps, a period of 0.5 billion years in which to sample many polymer sequences that originally arose through non-biochemical mechanisms and that ultimately evolved directed the first self-replicating systems.

My involvement in the discovery of the first catalytic RNA began in innocence during a study of tRNA biosynthesis in Escherichia coli. I was fortunate enough to isolate and characterize a precursor tRNA, one of the intermediates in the metabolic pathway leading to the synthesis of mature tRNA. As in all biochemical pathways, if one has an intermediate compound, there must be an intra-cellular enzyme that acts on this intermediate to take it to the next step in the pathway. This enzyme, ribonuclease P (RNase P), was readily identifiable. Its function was to cleave a phosphodiester bond at the start of the mature tRNA nucleotide sequence, thereby releasing the upstream extra or “precursor” nucleotides.

The total purification of RNase P proved to be a very difficult task. However, a perceptive and hard-working graduate student, Ben Stark, noticed that an RNA copurified with the protein in the enzyme preparation. He then devised a test to see if the RNA molecule was essential for the function of the enzyme. This test used the same strategy that Avery, MacLeod and McCarty had used to prove that DNA was the essential ingredient in bacterial transformation. In Stark’s experiment, the test showed that the RNA was essential for RNase P function. This result explained why the purification, which had been designed to isolate a proteinaceous complex, was so difficult. It also led to much disbelief in the community of enzymologists.

We soon suggested that the RNA subunit of RNase P was part of the active center of the enzyme, by analogy to the then current picture of the ribosome. A few years later, however, Cecilia Guerrier-Takada, a postdoctoral fellow, demonstrated that this RNA, itself, was a true enzyme in vitro. At that time, Tom Cech had recently and independently observed phosphoester bond cleavage and ligation by a different RNA molecule. Cech’s observation and ours, while still greeted skeptically by some members of the enzymological community, were soon universally accepted and within a few years other catalytic RNAs derived from plant pathogens and the human delta RNA were also found.

The chemical details of catalysis by RNase P remain to be fully worked out although a rough picture of this reaction is now available. A fascinating aspect of the RNase P “problem” is the vast difference in chemical make-up of subunits and catalytic mechanism of this enzyme as it is found in eukaryotes (e.g., the RNA subunit is not active in vitro) compared to these properties in prokaryotes. Evolution has presented us with contemporary versions of this enzyme that undoubtedly will someday tell us an interesting story of its progression from an RNA to various complexes of RNA and protein.

References

Orgel, L. E., The origin of life on the Earth. Scientific American, October 1994, Volume 271, pages 76-83.

Orgel, L. E., The origin of life – a review of facts and speculations, Trends in Biochemical Sciences, December 1998, Volume 2-3, pages 491-495.