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. suggests that it is premature to dismiss the RNA-first scenarios. 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. :
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. 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 18
Å of the enzyme's
active site, :* 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. :** A
RNP world-type hypothesis is that the tRNA acceptor stem and the catalytic domain of the aaRS came earlier than the genetic code and the PTC.
Cofactors :Protein enzymes catalyze various chemical reactions, but over half of them incorporate cofactors to facilitate and diversify their catalytic activities. Cofactors are essential in biology, as they are based largely on nucleotides rather than amino acids. Ribozymes use nucleotide cofactors to create metabolism, with two basic choices: non-covalent binding or covalent attachment. Both approaches have been demonstrated using directed evolution to reinvent RNA dupes of protein-catalyzed processes. Lorsch and Szostak investigated ribozymes that could phosphorylate themselves and use
ATP-γS as a substrate. However, only one of the seven classes of selected ribozymes had detectable ATP affinity, indicating that the ability to bind ATP was compromised. NAD+- dependent redox ribozymes were also evaluated. The selected ribozyme had a rate of enhancement of more than 107 fold and was proven to catalyze the reverse reaction - benzaldehyde reduction by NADH. Since the usage of adenosine as a cofactor is prevalent in current metabolism and is likely to have been common in the RNA world, these discoveries are essential for the evolution of metabolism in the RNA world.
RNA in information storage RNA is a very similar molecule to DNA, with only two significant chemical differences (the backbone of RNA uses ribose instead of deoxyribose and its nucleobases include
uracil instead of
thymine). The overall structure of RNA and DNA are immensely similar—one strand of DNA and one of RNA can bind to form a double helical structure. This makes the storage of information in RNA possible in a very similar way to the storage of information in DNA. However, RNA is less stable, being more prone to hydrolysis due to the presence of a hydroxyl group at the ribose 2' position. group at the 2'-position.
Comparison of DNA and RNA structure The major difference between RNA and DNA is the presence of a
hydroxyl group at the 2'-position of the
ribose sugar in RNA (illustration, right). In terms of base pairing, this has no effect. Adenine readily binds uracil or thymine. Uracil is, however, one product of
damage to cytosine that makes RNA particularly susceptible to mutations that can replace a
GC base pair with a
GU (
wobble) or
AU base pair. RNA is thought to have preceded DNA, because of their ordering in the biosynthetic pathways. These limitations do not make use of RNA as an
information storage system impossible, simply energy intensive (to repair or replace damaged RNA molecules) and prone to mutation. While this makes it unsuitable for current 'DNA optimised' life, it may have been acceptable for more primitive life.
RNA as a regulator Riboswitches have been found to act as regulators of gene expression, particularly in bacteria, but also in plants and
archaea. Riboswitches alter their
secondary structure in response to the binding of a
metabolite. Riboswitch classes have highly conserved
aptamer domains, even among diverse organisms. When a target metabolite is bound to this aptamer, conformational changes occur, modulating the expression of genes carried by mRNA. These changes occur in an expression platform, located downstream from the aptamer. This change in structure can result in the formation or disruption of a
terminator, truncating or permitting transcription respectively. Alternatively, riboswitches may bind or occlude the
Shine–Dalgarno sequence, affecting translation. It has been suggested that these originated in an RNA-based world. In addition,
RNA thermometers regulate gene expression in response to temperature changes. == Support and difficulties ==