Thoughts on RNA World

One of the most important questions facing the study of the origins of life is the nature of the first genetic material. A very thin boundary between the non-living and living biological entities was formed once the transition to accumulating and replicating of the genetic material in the primitive environment occurred. Nowadays, RNA is widely accepted as one of the first informational polymers to evolve and is being of the utmost importance in the origins of life.

The definition of the RNA World was proposed by Gilbert (1986), who was mainly interested in how catalytic RNA might have ushered in the exon-intron structure of genes. Woese (1967), Crick (1968), and Orgel (1968) have proposed RNA as a primordial molecule decades ago. The RNA world hypothesis is an appealingly simple model for early life forms, as it allows the complex array of biochemical interactions among proteins, DNAm and RNA to evolve gradually.

The “RNA world” hypotheses usually include three essential assumptions:

• At some point the evolution of life employed solely the replication of RNA for genetic continuity. RNA played a role of both a molecule that carried forth the genetic information and was its own biocatalyst. And indeed RNA can perform the RNA replication chemistry on its own as well as execute some functions of DNA and proteins (Cech 1986). It is also important to understand, that a single type of molecule that can replicate itself would have been more advantageous to evolve than two allot two molecules for that purpose. Such as nucleic acids and a protein to replicate them.
• Genetically encode proteins were not employed as catalysts. They also had an extremely limited ability to transmit information.
• Watson-Crick base-pairing was the key to replication.

There are more arguments in favor of an RNA world.

• Ribosomes utilized RNA catalysis to perform the key activity of protein synthesis in all extant organisms, therefore it must have done so in the last universal common ancestor.
• There were studies using SELEX ("Systematic Evolution of Ligands by Exponential Enrichment", also referred to as in vitro selection and in vitro evolution is a Combinatorial_chemistry technique in Molecular_biology for producing oligonucleotides of either single-stranded DNA or RNA that specifically bind to a target ligand or ligands) that showed that RNA had the catalytic activities, that are absent in modern RNAs.
• It has been thoroughly established that, RNA had appeared before DNA, due to a greater number of enzymes that are responsible for the biogenesis of the ribonucleotide precursors of RNA, whereas the synthesis of deoxyribonucleotide precursors requires only two additional enzymatic activities and is a deriviative of ribonucleotide synthesis.
• The baffling complexity of the contemporary ribosome might be explained by gradual addition of  RNA domains.

Crick (1968) suggested that, “the primitive ribosome could have been made entirely of RNA”. Most likely, smaller functional units capable of carrying out different translational steps such as peptydil transferase, decoding and so on evolved first. Then the smaller RNA units merged and formed a larger complex. The molecular evolution then incrementally incorporated additional elements into the structure. One of the evidences to support this idea, might be the fact that when small RNAs, are excised from their parental larger RNA structure, they retain their local functions, unlike for example peptides. RNAs lack hydrophobic cores that are essential for their folding. IT makes then possible to assemble a large functional RNA complex out of pre-existing smaller units and preserve their original function untouched. RNAs have an ability to form complexes by tertiary interactions and not only by base-pairing. A thorough study on 23S rRNA by Bokov and Steinberg (2009) strongly supports these conjectures. They demonstrated that 23S rRNA evolved through the gradual addition of RNA domains to the catalytic core with the help of A-minor interactions. Multiple copies of new functional RNAs then would appear because the constructed RNA becomes its own gene and the cycle would repeat, selecting for better ribosome-like function, along with ribosome-binding peptides that are formed during the process.

Our current natural world no longer uses RNA enzymes to carry out the biological functions, so we have to rely on proxies, like engineered RNA “ribozymes” that would have catalytic functions without the need for proteins, just like in the primordial conditions. One study by Aniela Wochner has successfully demonstrated the synthesis of ribozyme tC19Z from RNA polymerase ribozyme R18. The synthesized ribozyme had a catalytic activity, as it was able to cleave an RNA substrate at the expected location in the sequence. Thus giving even more evidence, that such RNA enzymes could have existed in early Earth. Self-sustained replication of an RNA enzyme was later realized by Joyce (2009), who managed to create a cross-catalytic system involving two RNA enzymes that were capable of catalyzing each other’s synthesis from a total of four component substrates.

While the RNA world hypothesis is a convenient explanation of the origins of the first self-replicating biological entities, and has an attractive feature of continuity, it is not clear how such a sophisticated self-replicating system could have been supplanted by RNA based on completely unrelated chemistry. So the question rises, whether there was some even more ancient ancestral molecule preceding RNA or it was formed by random prebiotic chemical reactions (“The Prebiotic Chemis’s Nightmare”). Many researchers attempted to address this vital question, that could help us better understand the true origins of life. There was some optimism planted into the supporters of “RNA-first” hypothesis by Powner (2009), who successfully managed to synthesize activated pyrimidine ribonucleotides in prebiotic plausible conditions from just cyanamide, cyanoacetylene, glycolaldehyde, glyceraldehydes and inorganic phosphate, which plausibly could have been formed in early-Earth conditions. The study was further corroborated by Raines and Sutherland (2010), who suggested that a key step during the synthesis of an activated ribonucletide from the mentioned prebiotic feedstock could be facilitated by a stereoelectronic effect.  However, another study by Joyce (2010) suggested that the chiral purity of modern RNA makes it hard to imagine that RNA could have arisen de novo. But if we surmise that the ancient RNA had predecessors we need to realize that evolution has to have a path that has a probable functional logic. So what could have been a primordial replicator even before RNA?

Yarus suggested that AMP-containing enzymatic cofactors are the modern descendant of the initial Darwinian ancestor. The idea is that such ubiquitous complexes as e.g NAD, FAD, CoA have been conserved amongst all living systems with their ancient metabolic uses and have the nicotinamide, which can be easily reached by several synthetic routes with prebiotic chemicals, like ethylene and ammonia or aspartate and dihydroxyacetone phosphate. It is quiet frequent that free modern cofactors display diminished version of the chemical activity, that they have when together with a protein enzyme. It is credible to consider nicotinamide-containing cofactors an early participant in biochemistry, before the rise of RNA catalysts. The cofactors suggest that genotype/phenotype junction could exist in a small system of two complementary two-nucleotide entities. Such ancestral molecules would be selected for both replication and activation and therefore would have undergone Darwinian evolution, because their biochemistry would have improved via their own replication.

Small regulatory RNAs are components of small RNA pathways that are found in all domains of life. They play the key roles in responding to the exogenous nucleic acids pathogens, such as viruses and have the genome defense as their ancestral function. Small RNAs can also work as self-cleavers and turn into multiple-turnover RNA-cleaving enzymes, which plausibly could have existed in a primordial ribo-organism. There is also an evidence of the RNA world that can be seen in structural and functional similarities between group II intron self-splicing and spliceosomal splicing of mRNA introns.

The RNA can bind specifically to small metabolites like guanine or lysine and use the binding energy to alter the RNA structure, they are called riboswitches. These structures can be found in bacteria and plants as gene expression regulators and are one of the most ancient ones as well.

The low levels of prebiotic deoxyribose could have been another factor for the RNA to rule and, hence prebiotic and early synthetic pathways for deoxyribose should be investigated. The presence of ribose as a component of many coenzymes is a powerful argument for the importance of RNA monomers and dimmers early in evolution.

Scrum et al (2010) for the first time managed to achieve a replication of simple nucleic acid-like polymers within liquid envelopes. The liposomes that they created were capable of dividing and passing on newly replicated nucleic acids. This may shed some light on how the first ribo-organsims might have looked like and function.