A history of the RNA world hypothesis

by Jessie Nessa van de Velde

Our genetic material is kept safe in the form of deoxyribonucleic acid (DNA). However, evidence reveals that the first primitive molecules might have been made of and used ribonucleic acid (RNA) to replicate themselves^1,2. Scientists have been speculating for over 50 years about RNA’s role at the beginning of life³. They debate that before depending on DNA, primitive cells relied on RNA^4,5. This so-called RNA world would have existed some 4 billion years ago, approximately 11 billion years after the big bang, and is thought to be the first time a molecule could self-replicate^6,7. Could primitive molecules have depended on RNA before DNA?

When looking at the chemical structure of RNA and DNA, one difference makes RNA a more potent candidate as a primal (or original) nucleotide. RNA contains the sugar ribose, while DNA contains deoxyribose. Ribose and deoxyribose differ at the second carbon by one hydroxyl group (oxygen atom covalently bound to a hydrogen atom) (Figure 1). Ribose has two hydroxyl groups next to each other, making RNA inertly unstable. The oxygen in the hydroxyl group pulls the electron from the hydrogen enabling the oxygen to bond with positively charged atomic nuclei⁸. As a result, the oxygen atom on the second carbon can participate in catalytic reactions giving RNA a multi-talented ability compared to DNA and its more prone to mutation. Other differences are that RNA and DNA have four possible nucleotides, of which three are in common: adenosine, cytosine, and guanine; DNA has thymine and RNA uracil. Lastly, RNA is “usually” single-stranded, while DNA is double-stranded⁸.

Leading to the RNA world hypothesis

The RNA World hypothesis states that RNA was responsible for carrying our genetic information and catalysing chemical reactions inside the cell before DNA and proteins had this responsibility^14,22. A series of discoveries throughout the 20th century led to this hypothesis. In 1956 Alexander Rich discovered that RNA could form double helices⁹, and in 1957, he discovered that RNA could even form a triple helix¹⁰. From here on, he proposed that primitive polynucleotide chains of RNA could act as a template, and he suggested that RNA could have enzymatic activity. As such, it could be reasonable to assume that RNA was a primary agent in the origin of life⁴. In 1967 and 1968, Woese¹¹, Orgel¹², and Crick¹³ continued hypothesizing about RNA as a primordial nucleotide and the evolution based on RNA replication before protein synthesis, laying the foundation for The RNA World hypothesis^3,14–16. Then in the early 1980s, Thomas Cech and Sydney Altman discovered enzymatic RNAs named ribozymes^17,18. These two simultaneous discoveries were a breakthrough in the RNA world hypothesis, and in 1989, both received a Nobel Prize for their discovery of the catalytic properties of RNA¹⁹. Subsequently, in 1986, the phrase “The RNA World” was coined by Walter Gilbert⁵. Scientists continued pondering about RNA’s abilities as a catalyst in replication and the origins of life^20,21.

Is it possible that life began with RNA? Is RNA versatile enough to have functioned as a genetic carrier and, at the same time, as an executioner? Did DNA and proteins evolve to substitute multiple functions of RNA?

Evidence for the RNA world hypothesis

RNA based molecules

Compelling evidence for the hypothesis is found in numerous RNA-based molecules like ribocytes²³, riboswitches²⁴, ribozymes²⁵, and ribosomes²⁶ (Figure 2). These RNA molecules are allegedly fossils of the RNA world^8,12,16. Ribocytes are RNA-based primitive cells and presumably the ancestors of modern-day cells. Another class of miraculous RNA molecules are riboswitches; these RNA sequences control the translation of the mRNA in which they are embedded²⁴. Ribozymes are RNA enzymes with catalytic functions, they resemble protein enzymes in many ways, and their discovery led to The RNA World hypothesis¹². Tom Cech discovered a self-splicing RNA sequence in an intron; and named the RNA molecule a ribozyme^17,27. During that same period, Sidney Altman discovered a ribozyme that cleaved off an additional nucleotide sequence of transfer RNAs (tRNAs) named ribonuclease P (RNase P)¹⁸. Well-known ribozymes are ribosomes²⁶; these RNA-protein complexes form peptide bonds between amino acids. The catalytic centre of ribosomes is almost entirely made of RNA, and the exterior of the ribosome is protein-based⁸. All these molecules highlight the essential catalytic function RNA still has today in our cells, and according to Robertson and Joyce, it is the smoking gun to the The RNA World hypothesis¹⁴.

The versatility of RNA

Though RNA resembles DNA in many ways, RNA can perform tasks that today are collectively performed by DNA and proteins¹². RNA serves seven functions: transport of genetic information, storage of genetic information, catalytic, scaffolding, structural, recognition, and a template function. The transport of genetic information is RNAs most well-known function, which we know as messenger RNA (mRNA). The function of genetic information storage still exists in some viruses, which contain only RNA. In our eukaryotic cells, the role of genetic information storage was taken over by DNA. The catalytic function implies the enzymatic ability; it can cause a chemical reaction without being used. For example, riboswitches can change shape when binding to a ligand, enabling gene expression. Ribosomes can make polypeptides as an enzyme without themselves being consumed. Scaffolding means RNA can be used as a platform or frame to build on larger complexes. The structural function refers to a specific shape RNA needs to have to interact with other molecules. The recognition function means RNA can base pair with other RNA or DNA molecules⁸. For example, RNA can silence and affect gene expression with short non-coding RNAs¹⁵. RNA is also used as a template, as in the enzyme telomerase RNA, and acts as a primer⁸. The versatility of RNA’s functions is most basic to cellular life, and this vast list of extraordinary abilities of RNA speaks in support of The RNA World hypothesis¹².

The replicative abilities of RNA

Self-replication is important to The RNA World hypothesis. The RNA molecule must function as an RNA-dependent RNA polymerase, meaning it must be able to replicate and elongate other RNA molecules to produce additional copies, by creating consecutive phosphodiester bonds from a template¹⁴. The discovery of Thomas Cech in 1982 showed that RNA could ligate itself by making new phosphodiester bonds¹⁷. Elongation relies on the same biochemical principle as ligation, namely, forming a phosphodiester bond⁸.

Thus, could RNA replicate, meaning elongate an RNA sequence from a template? To answer this question, Bartel and Szostak performed an experiment in 1993. They showed that some random RNA sequences could ligate and elongate RNA sequences from an RNA template¹. They used an in vitro selection and amplification method named “systematic evolution of ligands by exponential enrichment” (SELEX) to mimic early RNA-based molecules. The SELEX experiment relies on the evolution mechanisms of variation, selection, and replication²⁸. The idea was that if one would synthesize and incubate enough random RNA sequences, some RNA sequences could have catalytic abilities. If those RNA sequences were selected, isolated, and further mutated, some RNA sequences might evolve to be able to replicate RNA from a template⁸. The SELEX experiment showed that, indeed, similar steps could have occurred during evolution, and their experiment increased the support for The RNA World hypothesis^1,8.

In summary, there are many arguments in favour of the RNA World hypothesis. Among these are its chemical structure, its many functions and the applications RNA still has today, not to forget the findings of the SELEX replicability experiment²⁰.

The question remained – how did RNA evolve into DNA, protein, and cells with membranes? In 1962 Alexander Rich hypothesized that the earliest RNA catalyst might have only catalyzed their own replication. They probably would have created membranes to keep “freeloader” molecules from trying to get their molecules replicated and to increase their concentration for faster replication. This might have generated the first membrane-enclosed molecules^4,23. In 1986 Walter Gilbert suggested that after RNA had acquired catalytic activities, it could have evolved in a self-replicative manner. The synthesis of proteins by RNAs would likely then have followed⁵. Proteins are much more stable than RNA and are built up from 20 amino acids instead of four nucleotides^7. This makes them more selective, versatile, and potent catalysts. Thus, proteins probably took over many of RNA’s initial functions and eventually dominated. Finally, DNA emerged and dominated the genetic storage of genes, due to its chemical stability making it safer for storing our genetic information longer-term⁵.

The RNA World hypothesis remains a topic of debate among scientists. Some believe that RNA and proteins evolved together, requiring the simultaneous evolution of RNA, proteins, replication, and translation²⁹. Others argue that it is much more likely that only one type of molecule evolved through mutation, rather than two types of molecules evolving simultaneously¹⁵. By this logic, it is plausible that RNA may have evolved into proteins and DNA^20,15. Unfortunately, it is impossible to be certain about the events that transpired around 4 billion years ago. As a result, The RNA World hypothesis remains for now the most likely explanation of how primitive nucleotides and cells have evolved. 

About the author

Further reading:

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2. E. H. Ekland, J. W. Szostak, and D. P. Bartel, “Structurally complex and Highly active RNA ligases derived from random RNA sequences,” Science (1979), vol. 269, pp. 364–370, 1995.
3. C. Tuerk et al., “The ‘strong’ RNA world hypothesis: fifty years old.,” Astrobiology, vol. 4, no. 4, pp. 391–403, 2013, doi: 10.1089/ast.2012.0868.
4. A. Rich, “On the problems of evolution and biochemical information transfer,” Horizons in Biochemistry, pp. 103–126, 1962.
5. Gilbert Walter, “The RNA world,” Nature, vol. 319, p. 618, 1986.
6. N. Lehman, “The RNA world: 4,000,000,050 years old,” Life, vol. 5, no. 4, pp. 1583–1586, 2015, doi: 10.3390/life5041583.
7. A. Bruce et al., Molecular Biology of the Cell Garland sciences. 2018.
8. D. Elliot and M. Ladomery, Molecular biology of RNA, Second. Oxford: Oxford University Press, 2015.
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11. C. R. Woese, “The Fundamental Nature of the Genetic Code :,” pp. 110–117, 1967.
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