The RNA world is a hypothetical stage in the evolutionary history of life on Earth in which self-replicating RNA molecules proliferated before the evolution of DNA and proteins. The term also refers to the hypothesis that posits the existence of this stage. Alexander Rich first proposed the concept of the RNA world in 1962, and Walter Gilbert coined the term in 1986.
Among the characteristics of RNA that suggest its original prominence are that: Like DNA, RNA can store and replicate genetic information. Although RNA is considerably more fragile than DNA, some ancient RNAs may have evolved the ability to methylate other RNAs to protect them. The concurrent formation of all four RNA building blocks further strengthens the hypothesis. Enzymes made of RNA (ribozymes) can catalyze (start or accelerate) chemical reactions that are critical for life, so it is conceivable that in an RNA world, ribozymes might have preceded enzymes made of protein. Many coenzymes that have fundamental roles in cellular life, such as acetyl-CoA, NADH, FADH, and F420, are structurally strikingly similar to RNA and so may be surviving remnants of covalently bound coenzymes in an RNA world. One of the most critical components of cells, the ribosome, is composed primarily of RNA.
Although alternative chemical paths to life have been proposed, and RNA-based life may not have been the first life to exist, the RNA world hypothesis seems to be the most favored abiogenesis paradigm. However, even proponents agree that there is still not conclusive evidence to completely falsify other paradigms and hypotheses. Regardless of its plausibility in a prebiotic scenario, the RNA world can serve as a model system for studying the origin of life.
If the RNA world existed, it was probably followed by an age characterized by the evolution of ribonucleoproteins (RNP world), which in turn ushered in the era of DNA and longer proteins. DNA has greater stability and durability than RNA, which may explain why it became the predominant information storage molecule. Protein enzymes may have replaced RNA-based ribozymes as biocatalysts because the greater abundance and diversity of the monomers of which they are built makes them more versatile. As some cofactors contain both nucleotide and amino-acid characteristics, it may be that amino acids, peptides, and finally proteins initially were cofactors for ribozymes.
History One of the challenges in studying abiogenesis is that the system of reproduction and metabolism utilized by all extant life involves three distinct types of interdependent macromolecules (DNA, RNA, and proteins), none of which can function and reproduce without the others, the classic chicken-and-egg paradox. This suggests that life could not have arisen in its current form, which has led researchers to hypothesize mechanisms whereby the current system might have arisen from a simpler precursor system. American molecular biologist Alexander Rich was the first to posit a coherent hypothesis on the origin of nucleotides as precursors of life. In a 1962 article he explained that the primitive Earth's environment could have produced RNA molecules (polynucleotide monomers) that eventually acquired enzymatic and self-replicating functions.
Other mentions of RNA as a primordial molecule can be found in papers by Francis Crick and Leslie Orgel, as well as in Carl Woese's 1967 book The Genetic Code. Hans Kuhn in 1972 laid out a possible process by which the modern genetic system might have arisen from a nucleotide-based precursor, and this led Harold White in 1976 to observe that many of the cofactors essential for enzymatic function are either nucleotides or could have been derived from nucleotides. He proposed a scenario whereby the critical electrochemistry of enzymatic reactions would have necessitated retention of the specific nucleotide moieties of the original RNA-based enzymes carrying out the reactions, while the remaining structural elements of the enzymes were gradually replaced by protein, until all that remained of the original RNAs were these nucleotide cofactors, "fossils of nucleic acid enzymes".
Properties of RNA The properties of RNA make the idea of the RNA world hypothesis conceptually plausible, though its general acceptance as an explanation for the origin of life requires further evidence. RNA is known to form efficient catalysts, and its similarity to DNA makes clear its ability to store information. Opinions differ, however, as to whether RNA constituted the first autonomous self-replicating system or was a derivative of a still-earlier system. One version of the hypothesis is that a different type of nucleic acid, termed pre-RNA, was the first one to emerge as a self-reproducing molecule, to be replaced by RNA only later. On the other hand, the discovery in 2009 that activated pyrimidine ribonucleotides can be synthesized under plausible prebiotic conditions suggests that it is premature to dismiss the RNA-first scenarios. Suggestions for 'simple' pre-RNA nucleic acids have included peptide nucleic acid (PNA), threose nucleic acid (TNA) or glycol nucleic acid (GNA). Despite their structural simplicity and possession of properties comparable with RNA, the chemically plausible generation of "simpler" nucleic acids under prebiotic conditions has yet to be demonstrated.
RNA as an enzyme
In the 1980s, RNA structures capable of self-processing were discovered, with the RNA moiety of ribonuclease P acting as its catalytic subunit. These catalytic RNAs – referred to as RNA enzymes, or ribozymes – are found in today's DNA-based life and could be examples of living fossils. Ribozymes play vital roles, such as that of the ribosome. The large subunit of the ribosome includes an rRNA responsible for the peptide bond-forming peptidyl transferase activity of protein synthesis. Many other ribozyme activities exist; for example, the hammerhead ribozyme performs self-cleavage and an RNA polymerase ribozyme can synthesize a short RNA strand from a primed RNA template.
Among the enzymatic properties important for the beginning of life are: Self-replication The ability to self-replicate or synthesize other RNA molecules; relatively short RNA molecules that can synthesize others have been artificially produced in the lab. The shortest was 165 bases long, though it has been estimated that only part of the molecule was crucial for this function. One version, 189 bases long, had an error rate of just 1.1% per nucleotide when synthesizing an 11-nucleotide long RNA strand from primed template strands. This 189-base pair ribozyme could polymerize a template of at most 14 nucleotides in length, which is too short for self-replication, but is a potential lead for further investigation. The longest primer extension performed by a ribozyme polymerase was 20 bases. In 2016, researchers reported the use of in vitro evolution to improve dramatically the activity and generality of an RNA polymerase ribozyme by selecting variants that can synthesize functional RNA molecules from an RNA template. Each RNA polymerase ribozyme was engineered to remain linked to its new, synthesized RNA strand; this allowed the team to isolate successful polymerases. The isolated RNA polymerases were again used for another round of evolution. After several rounds of evolution, they obtained one RNA polymerase ribozyme called 24-3 that was able to copy almost any other RNA, from small catalysts to long RNA-based enzymes. Particular RNAs were amplified up to 10,000 times, a first RNA version of the polymerase chain reaction (PCR). Life is thought to have emerged from inanimate matter more than 3.5 billion years ago when a rudimentary abiogenesis process gradually evolved into an autocatalytic process capable of template-based replication. It was proposed on the basis of experimentally feasible RNA reactions catalyzed by a ribozyme, that the emergence of life was likely a gradual process involving the evolutionary properties of variation, heredity and reproduction, ultimately allowing for Darwinian evolution. Recent efforts have been directed at trying to demonstrate RNA replication under conditions that assume the presence during early evolution of plausible nucleotide intermediates and plausible environmental conditions that could favor strand replication alternating with strand separation. One such effort was the demonstration of high fidelity RNA copying using 2′,3′-cyclic phosphate ligation to allow polynucleotide synthesis under conditions also compatible with strand separation. In another study, it was shown that in a model oscillating Hadean environment likely to have been abundant during early evolution, that ribozyme-mediated RNA synthesis and replication can occur. Catalysis The ability to catalyze simple chemical reactions—which would enhance creation of molecules that are building blocks of RNA molecules (i.e., a strand of RNA that would make creating more strands of RNA easier). Relatively short RNA molecules with such abilities have been artificially formed in the lab. A recent study showed that almost any nucleic acid can evolve into a catalytic sequence under appropriate selection. For instance, an arbitrarily chosen 50-nucleotide DNA fragment encoding for the Bos taurus (cattle) albumin mRNA was subjected to test-tube evolution to derive a catalytic DNA (a deoxyribozyme, also called a DNAzyme) with RNA-cleavage activity. After only a few weeks, a DNAzyme with significant catalytic activity had evolved. In general, DNA is much more chemically inert than RNA and hence much more resistant to obtaining catalytic properties. If in vitro evolution works for DNA it will happen much more easily with RNA. In 2022, Nick Lane and coauthors showed in a computational simulation that short RNA sequences could have been capable of catalyzing fixation which supported protocell replication and growth. Amino acid-RNA ligation The ability to conjugate an amino acid to the 3′-end of an RNA in order to use its chemical groups or provide a long-branched aliphatic sidechain. It has been suggested that amino acids may have initially been involved with RNA molecules as cofactors enhancing or diversifying their enzymatic capabilities, before evolving into more complex peptides. In today's world, this is most commonly seen in the form of aminoacyl-tRNA. Peptide bond formation The ability to catalyse the formation of peptide bonds between amino acids to produce short peptides or longer proteins. This is done in modern cells by ribosomes, a complex of several RNA molecules known as rRNA together with many proteins. The rRNA molecules are thought responsible for its enzymatic activity, as no amino-acid residues lie within 18Å of the enzyme's active site, and, when the majority of the amino-acid residues in the ribosome were stringently removed, the resulting ribosome retained its full peptidyl transferase activity, fully able to catalyze the formation of peptide bonds between amino acids. A pseudo 2 fold symmetry of the region surrounding the peptidyl transferase center (PTC) led to the hypothesis of the Proto-Ribosome, that a vestige of an ancient dimeric molecule from the RNA world is functioning within the ribosome. An RNA molecule derived from the 23S ribosomal RNA sequence for this region has been synthesized in the lab in 2022 to test the proto-ribosome hypothesis. It was able to dimerize and to form peptide bonds. A much shorter RNA molecule has been synthesized in the laboratory in 1999 with the ability to form peptide bonds, and it has been suggested that rRNA has evolved from a similar molecule. tRNA is suggested to have also evolved from RNA molecules that began to catalyze amino acid transfer (also see the discussion of amino acid-RNA ligation above). The current core of the ribosome, the PTC, may also have evolved from the concatenation of five proto-tRNAs.