RNA world

The RNA world describes a hypothetical epoch in the evolutionary trajectory of life on Earth, characterized by the proliferation of self-replicating RNA molecules preceding the development of DNA and proteins. This term also denotes the hypothesis that postulates the occurrence of this particular stage. Alexander Rich initially advanced the concept of the RNA world in 1962, and Walter Gilbert subsequently coined the term in 1986.

Several intrinsic properties of RNA suggest its foundational role in early life, notably:

• RNA, akin to DNA, possesses the capacity to store and replicate genetic information. Although RNA exhibits significantly greater fragility than DNA, it is hypothesized that some ancient RNA molecules may have acquired the ability to methylate other RNAs for protective purposes. The simultaneous emergence of all four RNA building blocks provides additional corroboration for this hypothesis.
• Ribozymes, which are enzymes composed of RNA, are capable of catalyzing chemical reactions fundamental to life. Therefore, it is conceivable that in an RNA world, ribozymes could have emerged prior to protein-based enzymes.
• Numerous coenzymes critical for cellular functions, such as acetyl-CoA, NADH, FADH, and F420, display striking structural similarities to RNA. This resemblance suggests they may constitute surviving remnants of covalently bound coenzymes from an RNA world.

• The ribosome, a fundamental cellular constituent, is primarily composed of RNA.

While alternative chemical pathways for the emergence of life have been proposed, and RNA-based life may not have represented the earliest form of existence, the RNA world hypothesis is currently considered the most favored abiogenesis paradigm. However, even its proponents concede that definitive evidence to entirely falsify other paradigms and hypotheses remains elusive. Irrespective of its prebiotic plausibility, the RNA world offers a valuable model system for investigating the origin of life.

Should the RNA world have existed, it was likely succeeded by a period defined by the evolution of ribonucleoproteins (the RNP world), which subsequently initiated the era of DNA and more elaborate proteins. The enhanced stability and durability of DNA compared to RNA may elucidate its adoption as the predominant molecule for genetic information storage. Protein enzymes might have superseded RNA-based ribozymes as biocatalysts, owing to the greater abundance and diversity of their constituent monomers, which confers increased versatility. Considering that some cofactors possess both nucleotide and amino-acid characteristics, it is conceivable that amino acids, peptides, and ultimately proteins initially served as cofactors for ribozymes.

History

A primary challenge in the study of abiogenesis arises from the fact that the reproductive and metabolic systems employed by all extant life involve three distinct and interdependent macromolecules: DNA, RNA, and proteins. None of these can function or reproduce autonomously, presenting a classic chicken-and-egg paradox. This complexity suggests that life could not have originated in its current form, prompting researchers to hypothesize mechanisms through which the present system might have evolved from a simpler precursor. The American molecular biologist Alexander Rich was the first to propose a coherent hypothesis concerning the origin of nucleotides as precursors to life. In a 1962 article, he elucidated how the primitive Earth's environment could have generated RNA molecules (polynucleotide monomers) that eventually acquired enzymatic and self-replicating functions.

Additional references to RNA as a primordial molecule are present in publications by Francis Crick and Leslie Orgel, and in Carl Woese's 1967 book, The Genetic Code. In 1972, Hans Kuhn delineated a plausible process through which the contemporary genetic system might have originated from a nucleotide-based precursor. This work subsequently led Harold White, in 1976, to note that numerous cofactors indispensable for enzymatic function are either nucleotides or demonstrably derived from them. White advanced a scenario positing that the critical electrochemistry of enzymatic reactions would have necessitated the retention of specific nucleotide moieties from the original RNA-based enzymes performing these reactions. Simultaneously, the remaining structural components of these enzymes were gradually substituted by protein, until only these nucleotide cofactors, termed "fossils of nucleic acid enzymes," persisted from the original RNAs.

Properties of RNA

The conceptual plausibility of the RNA world hypothesis stems from RNA's inherent properties, although its widespread acceptance as the definitive explanation for life's origins still necessitates additional empirical support. RNA is recognized for its capacity to function as an effective catalyst, and its structural resemblance to DNA underscores its capability for information storage. Nevertheless, scholarly perspectives diverge regarding whether RNA represented the inaugural autonomous self-replicating system or evolved from a preceding molecular framework. One proposed variant of the hypothesis posits that an alternative nucleic acid, designated as pre-RNA, initially emerged as the self-reproducing molecule, subsequently superseded by RNA. Conversely, the 2009 finding that activated pyrimidine ribonucleotides can be synthesized under credible prebiotic conditions indicates that it is premature to disregard scenarios prioritizing RNA's initial role. Proposed 'simple' pre-RNA nucleic acids encompass peptide nucleic acid (PNA), threose nucleic acid (TNA), and glycol nucleic acid (GNA). Despite their structural simplicity and attributes comparable to RNA, the chemically feasible synthesis of these "simpler" nucleic acids under prebiotic conditions remains unproven.

RNA's Enzymatic Function

During the 1980s, researchers identified RNA structures possessing self-processing capabilities, notably the RNA component of ribonuclease P, which functions as its catalytic subunit. These catalytic RNA molecules, termed RNA enzymes or ribozymes, are present in contemporary DNA-based organisms and may represent examples of living fossils. Ribozymes fulfill crucial biological functions, exemplified by their role within the ribosome. Specifically, the large ribosomal subunit contains an rRNA molecule that mediates the peptidyl transferase activity essential for peptide bond formation during protein synthesis. Numerous other ribozyme activities have been documented; for instance, the hammerhead ribozyme executes self-cleavage, while an RNA polymerase ribozyme can synthesize a short RNA strand utilizing a primed RNA template.

Key enzymatic properties considered significant for the emergence of life include:

Self-Replication

The capacity for self-replication or the synthesis of other RNA molecules is a critical attribute; relatively short RNA molecules capable of synthesizing others have been successfully generated in laboratory settings. The smallest such molecule measured 165 bases in length, although it is hypothesized that only a segment of this molecule was essential for its function.

• A particular variant, comprising 189 bases, exhibited an error rate of merely 1.1% per nucleotide during the synthesis of an 11-nucleotide RNA strand from primed template strands. This 189-base pair ribozyme demonstrated the ability to polymerize a template up to 14 nucleotides in length, a span insufficient for complete self-replication but representing a promising avenue for continued research. The maximum primer extension achieved by a ribozyme polymerase was 20 bases.
• In 2016, a research team documented the application of in vitro evolution to significantly enhance the activity and broad applicability of an RNA polymerase ribozyme. This was achieved by selecting variants capable of synthesizing functional RNA molecules from an RNA template. Each RNA polymerase ribozyme was specifically designed to remain covalently attached to its newly synthesized RNA strand, thereby enabling the isolation of effective polymerases. These isolated RNA polymerases were subsequently subjected to additional rounds of evolutionary selection. Following multiple rounds of evolution, the researchers successfully developed an RNA polymerase ribozyme, designated 24-3, which demonstrated the capacity to replicate nearly any other RNA, ranging from small catalytic molecules to extensive RNA-based enzymes. Specific RNA sequences were amplified by up to 10,000-fold, marking the initial RNA-based iteration of the polymerase chain reaction (PCR).

The prevailing hypothesis suggests that life originated from inorganic matter over 3.5 billion years ago, as a rudimentary abiogenetic process progressively developed into an autocatalytic system capable of template-driven replication. Based on experimentally demonstrable RNA reactions catalyzed by a ribozyme, it has been posited that life's emergence was likely a gradual phenomenon encompassing the evolutionary characteristics of variation, heredity, and reproduction, which ultimately facilitated Darwinian evolution.

Recent investigations have sought to demonstrate RNA replication under conditions simulating early evolutionary environments, specifically those with plausible nucleotide intermediates and environmental factors conducive to alternating RNA strand replication and separation. One study successfully demonstrated high-fidelity RNA copying through 2',3'-cyclic phosphate ligation, enabling polynucleotide synthesis under conditions also compatible with strand separation. Another investigation revealed that ribozyme-mediated RNA synthesis and replication are feasible within a model oscillating Hadean environment, which is thought to have been prevalent during early evolution.

Catalysis

Catalysis of simple chemical reactions would facilitate the synthesis of RNA building blocks, thereby promoting the formation of additional RNA strands. Laboratory experiments have successfully synthesized relatively short RNA molecules exhibiting such catalytic capabilities. Recent research indicates that nearly any nucleic acid can evolve into a catalytic sequence under suitable selective pressures. For example, an arbitrarily selected 50-nucleotide DNA fragment, encoding for Bos taurus (cattle) albumin mRNA, underwent in vitro evolution to yield a catalytic DNA (deoxyribozyme or DNAzyme) possessing RNA-cleavage activity. Within a few weeks, a DNAzyme with substantial catalytic activity emerged. Generally, DNA exhibits greater chemical inertness compared to RNA, rendering it more resistant to acquiring catalytic properties. Consequently, if in vitro evolution is effective for DNA, it is expected to occur with greater ease for RNA. In 2022, Nick Lane and colleagues demonstrated through computational simulation that short RNA sequences might have catalyzed CO₂ fixation, thereby supporting protocell replication and growth.

Amino acid-RNA ligation

This refers to the capacity to ligate an amino acid to the 3'-end of an RNA molecule, either to utilize its chemical groups or to introduce a long-branched aliphatic sidechain. Hypotheses propose that amino acids initially functioned as cofactors with RNA molecules, augmenting or diversifying their enzymatic functions, prior to their evolution into more intricate peptides. Presently, this phenomenon is most frequently observed in aminoacyl-tRNA.

Peptide bond formation

This refers to the capacity to catalyze the formation of peptide bonds between amino acids, leading to the synthesis of short peptides or longer proteins. In contemporary cells, this process is executed by ribosomes, which are complexes comprising multiple ribosomal RNA (rRNA) molecules and numerous proteins. The enzymatic activity of ribosomes is attributed to rRNA molecules, given that no amino acid residues are located within 18Å of the enzyme's active site. Furthermore, even after the stringent removal of most amino acid residues from the ribosome, the remaining structure fully retained its peptidyl transferase activity, demonstrating its complete ability to catalyze peptide bond formation between amino acids.

• The observation of pseudo-twofold symmetry in the region surrounding the peptidyl transferase center (PTC) has given rise to the Proto-Ribosome hypothesis, suggesting that a remnant of an ancient dimeric molecule from the RNA world operates within the ribosome. To investigate this hypothesis, an RNA molecule derived from the 23S ribosomal RNA sequence corresponding to this region was synthesized in the laboratory in 2022. This synthetic molecule demonstrated the capacity to dimerize and form peptide bonds.
• In 1999, a significantly shorter RNA molecule capable of forming peptide bonds was synthesized in the laboratory, leading to the hypothesis that rRNA evolved from a similar ancestral molecule.
• It is hypothesized that tRNA also evolved from RNA molecules that initiated the catalysis of amino acid transfer. Furthermore, the contemporary core of the ribosome, the PTC, might have originated from the concatenation of five proto-tRNAs.
  • One hypothesis, characteristic of an RNP world model, posits that the tRNA acceptor stem and the catalytic domain of aminoacyl-tRNA synthetases (aaRS) predated the genetic code and the PTC.

Cofactors

Many protein enzymes, while catalyzing diverse chemical reactions, require cofactors to enhance and broaden their catalytic functions. These cofactors are biologically crucial, primarily comprising nucleotides rather than amino acids. Ribozymes utilize nucleotide cofactors for metabolic processes, employing either non-covalent binding or covalent attachment. Directed evolution has successfully demonstrated both strategies, enabling the creation of RNA analogs that mimic protein-catalyzed reactions. Lorsch and Szostak conducted research on ribozymes capable of autophosphorylation, utilizing ATP-γS as a substrate. Nevertheless, only one of the seven identified ribozyme classes exhibited measurable ATP affinity, suggesting a diminished capacity for ATP binding. Furthermore, NAD⁺-dependent redox ribozymes underwent evaluation. The chosen ribozyme demonstrated a catalytic rate enhancement exceeding 10⁷-fold and was shown to catalyze the reverse reaction, specifically the reduction of benzaldehyde by NADH. Given the widespread use of adenosine as a cofactor in contemporary metabolism and its probable prevalence in the RNA world, these findings are critical for understanding the evolution of metabolism during that era.

The Role of RNA in Information Storage

RNA shares substantial structural similarity with DNA, differing primarily in two chemical aspects: its backbone incorporates ribose instead of deoxyribose, and its nucleobases include uracil rather than thymine. The macroscopic structures of RNA and DNA are remarkably alike, allowing a single strand of DNA to hybridize with an RNA strand to form a double helix. Consequently, RNA can store genetic information through mechanisms highly analogous to those employed by DNA. Nevertheless, RNA exhibits reduced stability and increased susceptibility to hydrolysis, a characteristic attributed to the hydroxyl group located at the 2' position of its ribose sugar.

Structural Comparison of DNA and RNA

A primary distinction between RNA and DNA lies in the presence of a hydroxyl group at the 2'-position of the ribose sugar in RNA. This hydroxyl group diminishes the molecule's stability; when not confined within a double helix, the 2' hydroxyl can nucleophilically attack the adjacent phosphodiester bond, leading to the cleavage of the phosphodiester backbone. Furthermore, this hydroxyl group compels the ribose sugar to adopt a C3'-endo conformation, contrasting with the C2'-endo conformation observed in the deoxyribose sugar of DNA. Consequently, an RNA double helix deviates from a B-DNA structure, instead adopting a conformation that more closely approximates A-DNA.

RNA employs a distinct set of nitrogenous bases compared to DNA, specifically adenine, guanine, cytosine, and uracil, as opposed to adenine, guanine, cytosine, and thymine. Chemically, uracil closely resembles thymine, with the sole distinction being a methyl group, and its biosynthesis demands less energy. Regarding base pairing, this difference is inconsequential. Adenine forms stable associations with both uracil and thymine. Nevertheless, uracil can arise from the deamination of cytosine, rendering RNA especially vulnerable to mutations that could substitute a GC base pair with either a GU (wobble) or a AU base pair.

The sequential arrangement of RNA and DNA within biosynthetic pathways suggests that RNA predates DNA evolutionarily. Deoxyribonucleotides, the fundamental components of DNA, are synthesized from ribonucleotides—the building blocks of RNA—through the enzymatic removal of the 2'-hydroxyl group. Therefore, cellular machinery must possess the capacity for RNA synthesis prior to DNA synthesis.

Constraints on Information Storage in RNA

The inherent chemical characteristics of RNA render large RNA molecules intrinsically labile, making them susceptible to facile degradation into their constituent nucleotides via hydrolysis. While these limitations do not preclude the utilization of RNA for information storage, they necessitate significant energy expenditure for the repair or replacement of damaged RNA molecules and increase susceptibility to mutations. Consequently, although RNA is ill-suited for contemporary 'DNA-optimized' life forms, it might have been adequate for more rudimentary biological systems.

RNA as a Regulatory Molecule

Riboswitches function as crucial regulators of gene expression, primarily observed in bacteria, but also present in plants and archaea. Their regulatory mechanism involves altering their secondary structure upon the binding of a specific metabolite. Notably, riboswitch classes exhibit highly conserved aptamer domains across a wide range of organisms. The binding of a target metabolite to the aptamer domain induces conformational changes, which subsequently modulate the expression of genes encoded by messenger RNA (mRNA). These structural alterations manifest within an expression platform, situated downstream from the aptamer. Such structural modifications can either lead to the formation or disruption of a transcriptional terminator, thereby truncating or permitting transcription, respectively. Furthermore, riboswitches can influence gene expression by binding to or occluding the Shine–Dalgarno sequence, which impacts translation. A hypothesis posits their origin within an RNA-based world. Complementing this, RNA thermometers also regulate gene expression, specifically in response to temperature fluctuations.

Evidence and Challenges

The RNA world hypothesis gains support from RNA's multifaceted capabilities, encompassing the storage, transmission, and duplication of genetic information, akin to DNA, alongside the execution of enzymatic reactions, similar to protein-based enzymes. Given its capacity to perform functions currently attributed to both proteins and DNA, RNA is theorized to have independently sustained life forms in early evolutionary stages. Notably, certain viruses utilize RNA as their genetic material instead of DNA. Although nucleotides were not detected in experiments replicating the Miller-Urey conditions, their synthesis under prebiotically plausible circumstances was reported in 2009. For instance, the purine base adenine is structurally a pentamer of hydrogen cyanide. Significantly, adenine serves as a ubiquitous energy carrier within cells, with adenosine triphosphate (ATP) being universally preferred over guanosine triphosphate, cytidine triphosphate, uridine triphosphate, or even deoxythymidine triphosphate, despite their potential equivalence, except for their role as nucleic acid building blocks. Furthermore, studies involving fundamental ribozymes, such as Bacteriophage Qβ RNA, have demonstrated that rudimentary self-replicating RNA structures can endure substantial selective pressures, including those imposed by opposite-chirality chain terminators.

A significant challenge arises from the absence of known abiogenic chemical pathways for synthesizing nucleotides from the pyrimidine nucleobases cytosine and uracil under prebiotic conditions, leading some researchers to hypothesize that early nucleic acids might not have incorporated these specific nucleobases found in contemporary life. The nucleoside cytosine exhibits a relatively short half-life in isolation: 19 days at 100 °C (212 °F) and 17,000 years in freezing water. This instability is considered by some to be insufficient for its accumulation over geological timescales. Furthermore, questions have been raised regarding the stability of ribose and other backbone sugars, questioning their viability as components of the original genetic material. A critical concern is the requirement for all ribose molecules to possess the same enantiomeric form, given that nucleotides with incorrect chirality function as chain terminators.

Prebiotic synthesis of pyrimidine ribonucleosides and their corresponding nucleotides has been achieved through a reaction sequence that circumvents free sugars, instead assembling these molecules stepwise via nitrogenous and oxygenous chemical pathways. John Sutherland and his research group at the University of Manchester's School of Chemistry have published a series of studies detailing high-yield synthetic routes to cytidine and uridine ribonucleotides. These syntheses utilize small two- and three-carbon fragments, including glycolaldehyde, glyceraldehyde, glyceraldehyde-3-phosphate, cyanamide, and cyanoacetylene. A crucial step in this sequence permits the isolation of enantiopure ribose aminooxazoline when the enantiomeric excess of glyceraldehyde reaches 60% or higher, a finding potentially significant for understanding biological homochirality. This process can be conceptualized as a prebiotic purification, wherein the specified compound spontaneously crystallizes from a mixture of other pentose aminooxazolines. Aminooxazolines subsequently react with cyanoacetylene in a mild and highly efficient manner, regulated by inorganic phosphate, to generate cytidine ribonucleotides. Photoanomerization employing UV light facilitates inversion at the 1' anomeric center, yielding the correct beta stereochemistry; however, a challenge associated with this chemistry is the selective phosphorylation of alpha-cytidine at the 2' position. Nevertheless, in 2009, the team demonstrated that the same fundamental building blocks could directly produce 2',3'-cyclic pyrimidine nucleotides, known precursors for RNA polymerization, through phosphate-controlled nucleobase elaboration. Organic chemist Donna Blackmond characterized this discovery as "strong evidence" supporting the RNA world hypothesis. Conversely, John Sutherland clarified that while his team's research indicates an early and central role for nucleic acids in the origin of life, it does not necessarily endorse the RNA world hypothesis in its strict interpretation, which he described as a "restrictive, hypothetical arrangement."

The 2009 publication by the Sutherland group additionally emphasized the potential for photo-sanitization of pyrimidine-2',3'-cyclic phosphates. A notable limitation of these synthetic pathways is the requirement for generating enantioenriched glyceraldehyde or its 3-phosphate derivative, given that glyceraldehyde predominantly exists as its keto tautomer, dihydroxyacetone.

On August 8, 2011, a report based on NASA investigations of meteorites discovered on Earth proposed that fundamental RNA building blocks, including adenine, guanine, and related organic molecules, might have originated in outer space. Subsequent research in 2017, employing a numerical model, posited that an RNA world could have emerged in warm ponds on the early Earth, with meteorites serving as a plausible and probable source of RNA constituents such as ribose and nucleic acids for these environments. Furthermore, on August 29, 2012, astronomers at Copenhagen University announced the detection of glycolaldehyde, a specific sugar molecule, within a distant star system. This molecule was identified around the protostellar binary IRAS 16293-2422, situated 400 light-years from Earth. Given glycolaldehyde's necessity for RNA formation, this discovery implies that complex organic molecules may develop in stellar systems prior to planetary formation, subsequently being delivered to nascent planets during their early developmental stages. Nitriles, recognized as crucial molecular precursors within the RNA World scenario, represent one of the most abundant chemical families in the universe, having been observed in molecular clouds at the Milky Way's center, various protostars, meteorites, comets, and the atmosphere of Titan, Saturn's largest moon.

A 2001 investigation demonstrated that nicotinic acid and its precursor, quinolinic acid, can be generated with yields up to 7% through a six-step nonenzymatic pathway originating from aspartic acid and dihydroxyacetone phosphate (DHAP). The biosynthesis of ribose phosphate could have yielded DHAP and other three-carbon compounds, while aspartic acid might have been accessible from prebiotic synthesis or through the ribozyme-mediated synthesis of pyrimidines. This evidence supports the hypothesis that NAD could have originated within the RNA world. Furthermore, RNA sequences of varying lengths—specifically 30, 60, 100, and 140 nucleotides—were shown to catalyze the synthesis of three ubiquitous coenzymes: CoA, NAD, and FAD, from their respective precursors: 4'-phosphopantetheine, NMN, and FMN.

Prebiotic RNA synthesis

Nucleotides constitute the foundational molecules that polymerize to form RNA, each comprising a nitrogenous base covalently linked to a sugar-phosphate backbone. RNA polymers consist of extended sequences of specific nucleotides, where the arrangement of their bases encodes genetic information. The RNA world hypothesis posits the presence of free-floating nucleotides within the primordial environment. These nucleotides frequently formed transient bonds, which often dissociated due to minimal energy changes. Nevertheless, particular sequences of base pairs possess catalytic attributes that reduce the activation energy required for chain formation, thereby promoting their stability and extended persistence. As these chains elongated, they more rapidly attracted complementary nucleotides, leading to a net increase in chain formation rate over dissociation.

Some theories propose these early RNA chains as the initial, rudimentary forms of life. Within an RNA world scenario, distinct ensembles of RNA strands would have exhibited varying replication efficiencies, consequently influencing their population frequencies through a process analogous to natural selection. As the most robust RNA molecular sets proliferated, advantageous novel catalytic properties arising from mutations, which enhanced their survival and propagation, could become established within the population. An autocatalytic system of ribozymes, demonstrating self-replication within approximately one hour, has been experimentally identified. This system emerged from molecular competition, specifically through in vitro evolution of prospective enzyme mixtures.

Inter-RNA competition might have fostered the development of cooperative interactions among diverse RNA chains, potentially facilitating the genesis of the earliest protocells. Subsequently, RNA chains evolved catalytic capabilities that promoted the linkage of amino acids, a process known as peptide-bonding. These amino acids, in turn, could contribute to RNA synthesis, thereby conferring a selective advantage upon RNA chains functioning as ribozymes. The capacity to catalyze a specific stage in protein synthesis, namely the aminoacylation of RNA, has been experimentally observed in a concise RNA segment comprising five nucleotides.

In 2014, researchers successfully synthesized all four constituent components of RNA by simulating an asteroid impact under primordial environmental conditions. In March 2015, NASA scientists announced the unprecedented laboratory formation of complex organic compounds essential for DNA and RNA, including uracil, cytosine, and thymine. This synthesis occurred under conditions characteristic of outer space, utilizing precursor chemicals such as pyrimidine, which are present in meteorites. Scientists hypothesize that pyrimidine, similar to polycyclic aromatic hydrocarbons (PAHs), may have originated within red giant stars or in interstellar dust and gas clouds. During the same month, another research team synthesized over 50 distinct amino acids in a laboratory environment, employing only hydrogen sulfide, hydrogen cyanide (hypothesized to form from the reaction of extraterrestrial meteorites with atmospheric nitrogen), and ultraviolet radiation.

In 2018, investigators at the Georgia Institute of Technology identified three molecular candidates for the nucleobases that could have constituted an early form of proto-RNA: barbituric acid, melamine, and 2,4,6-triaminopyrimidine (TAP). These three molecules represent simpler analogues of the four bases found in contemporary RNA, potentially existing in higher concentrations and exhibiting forward compatibility with them. However, they might have been superseded during evolution in favor of more optimal base pairing configurations. Specifically, TAP demonstrates the capacity to form nucleotides with a diverse array of sugars. Both TAP and melamine are capable of base pairing with barbituric acid. Furthermore, all three compounds spontaneously generate nucleotides when combined with ribose.

A study conducted in 2026 reported the synthesis of a 45-nucleotide polymerase ribozyme, identified from random sequence libraries, which catalyzes general RNA-templated RNA synthesis. This ribozyme is capable of synthesizing both its complementary strand and an accurate self-copy. The authors propose that polymerase ribozymes may be more prevalent within the RNA sequence space than previously estimated.

The Evolution of DNA

The RNA world hypothesis faces the challenge of elucidating the transitional pathway from an RNA-based system to a DNA-based one. Research by Geoffrey Diemer and Ken Stedman at Portland State University in Oregon may offer a potential resolution. Their survey of viruses in a hot acidic lake within Lassen Volcanic National Park, California, revealed evidence that a rudimentary DNA virus had acquired a gene from an entirely distinct RNA-based virus. Concurrently, virologist Luis Villareal from the University of California Irvine posits that viruses capable of converting RNA-based genes into DNA and subsequently integrating them into more intricate DNA-based genomes were likely prevalent in the viral ecosystem during the RNA-to-DNA transition approximately four billion years ago. This discovery strengthens the proposition of information transfer from the RNA world to the nascent DNA world prior to the emergence of the last universal common ancestor. The diversity observed in this ancient viral realm persists into the present.

Viroids

Further support for the RNA world concept stems from investigations into viroids, which constitute the initial exemplars of a distinct category of "subviral pathogens." Viroids primarily infect plants, often acting as pathogens, and are characterized by short, highly complementary, circular, single-stranded, non-coding RNA molecules devoid of a protein coat. These entities are remarkably diminutive, spanning 246 to 467 nucleobases, in stark contrast to the smallest known infectious viruses, which possess genomes approximately 2,000 nucleobases long.

In 1989, plant biologist Theodor Diener proposed that viroids, owing to their distinctive characteristics, represent more compelling living relics of the RNA world than introns and other RNA molecules then considered as candidates. Ricardo Flores's research group subsequently expanded Diener's hypothesis, which achieved wider recognition in 2014 following the publication of a popularized account by a New York Times science writer.

The attributes of viroids cited as consistent with an RNA world include their compact size, elevated guanine and cytosine content, circular configuration, structural periodicity, absence of protein-coding capacity, and, in certain instances, ribozyme-catalyzed replication. A key point of contention raised by critics of this hypothesis is that angiosperms, the sole known hosts of all extant viroids, emerged billions of years after the RNA world's hypothesized replacement. This temporal discrepancy suggests that viroids might have originated through later evolutionary processes unrelated to the RNA world, rather than persisting through a cryptic host over such an extensive duration. Regardless of their precise origin, whether ancient relics or more recent developments, their autonomous function as naked RNA is considered analogous to the proposed characteristics of an RNA world.

Origin of Sexual Reproduction

Eigen et al. and Woese hypothesized that the genomes of primordial protocells consisted of single-stranded RNA, with individual genes corresponding to discrete RNA segments rather than being linearly concatenated as observed in contemporary DNA genomes. A haploid protocell, possessing only one copy of each RNA gene, would exhibit susceptibility to damage, as a singular lesion within any RNA segment could prove lethal to the protocell (e.g., by impeding replication or suppressing the function of a vital gene).

The susceptibility to damage could be mitigated by preserving multiple copies (two or more) of each RNA segment within every protocell, thereby establishing diploidy or polyploidy. Genomic redundancy would enable the replacement of a compromised RNA segment through an additional replication of its homologous counterpart. Nevertheless, for such rudimentary organisms, the fraction of available resources allocated to genetic material would constitute a substantial portion of the overall resource budget. In environments with constrained resources, the protocell's reproductive rate would probably inversely correlate with its ploidy level. The fitness of the protocell would consequently diminish due to the expenditures associated with redundancy. Therefore, addressing damaged RNA genes while simultaneously minimizing the costs of redundancy likely presented a foundational challenge for early protocells.

A comprehensive cost-benefit analysis was conducted, evaluating the expenses associated with maintaining genetic redundancy against the potential costs incurred from genome damage. This investigation concluded that, across a broad spectrum of conditions, the optimal strategy for protocells would involve a haploid state, punctuated by periodic fusions with other haploid protocells to form a transient diploid entity. The maintenance of the haploid state is crucial for maximizing growth rates. Conversely, these periodic fusions enable the mutual reactivation of protocells that would otherwise suffer lethal damage. The formation of viable progeny is contingent upon the presence of at least one undamaged copy of each RNA gene within the transient diploid. To produce two viable daughter cells, rather than just one, an additional replication of the intact RNA gene homologous to any pre-division damaged RNA gene within the fused protocell would be necessary. This cyclical process, encompassing haploid reproduction, intermittent fusion into a transient diploid state, and subsequent division back into the haploid state, represents the most rudimentary form of a sexual cycle. Without this sexual cycle, haploid protocells sustaining damage to an essential RNA gene would inevitably perish.

This proposed model for the nascent sexual cycle, while hypothetical, exhibits significant parallels with the established sexual behaviors observed in segmented RNA viruses, which are recognized as some of the simplest known organisms. The influenza virus, characterized by a genome comprising eight physically distinct single-stranded RNA segments, exemplifies this viral category. In segmented RNA viruses, a form of "mating" can transpire when a host cell is simultaneously infected by a minimum of two viral particles. Should these viruses each possess an RNA segment with lethal damage, a multiple infection scenario can facilitate reactivation, provided that at least one undamaged copy of every viral gene is present within the infected cell. This phenomenon is termed "multiplicity reactivation." Reports indicate that multiplicity reactivation occurs in influenza virus infections following the induction of RNA damage by both UV-irradiation and ionizing radiation.

Subsequent Research and Theoretical Advances

Patrick Forterre has advanced a novel hypothesis, designated "three viruses, three domains," which posits that viruses played a pivotal role in the evolutionary transition from RNA to DNA and in the diversification of Bacteria, Archaea, and Eukaryota. He theorizes that the last universal common ancestor was RNA-based and gave rise to RNA viruses. Subsequently, some of these viruses evolved into DNA viruses, a mechanism for safeguarding their genetic material from degradation. The evolution of the three domains of life is proposed to have occurred through the process of viral infection into host organisms.

Another compelling proposition suggests that RNA synthesis may have been driven by temperature gradients, a process referred to as thermosynthesis. Furthermore, individual nucleotides have demonstrated the capacity to catalyze various organic reactions.

Steven Benner has posited that the chemical conditions prevalent on Mars, including the presence of boron, molybdenum, and oxygen, might have been more conducive to the initial formation of RNA molecules than those found on Earth. If this premise holds true, then molecules suitable for life, originating on Mars, could have subsequently migrated to Earth through mechanisms such as panspermia or analogous processes.

Alternative Theoretical Frameworks

The theoretical framework of an RNA world does not preclude the existence of a "Pre-RNA world," a preceding era where a metabolic system based on a distinct nucleic acid is hypothesized to have predated RNA. Peptide nucleic acid (PNA), which utilizes simple peptide bonds to link nucleobases, is considered a potential candidate for such an ancestral nucleic acid.

An alternative, or potentially complementary, theory regarding the origin of RNA is presented by the PAH world hypothesis, which proposes that polycyclic aromatic hydrocarbons (PAHs) mediated the synthesis of RNA molecules. PAHs constitute the most prevalent and abundant known polyatomic molecules in the observable Universe and are considered a probable component of the primordial sea. Both PAHs and fullerenes, which are also implicated in abiogenesis, have been detected within nebulae.

The challenges associated with the terrestrial production of precursors are circumvented by another alternative or complementary theory for their origin: panspermia. This hypothesis explores the possibility that the earliest forms of life on Earth were transported from elsewhere in the galaxy, potentially via meteorites akin to the Murchison meteorite. Notably, sugar molecules, including ribose, have been identified in meteorites.

Coevolution of RNA and Peptides

An alternative hypothesis posits that the contemporary dual-molecule system, requiring a nucleotide-based molecule for protein synthesis and a peptide-based (protein) molecule for nucleic acid polymer formation, reflects the primordial life form. This concept, termed RNA-peptide coevolution or the Peptide-RNA world, provides a potential explanation for the swift development of efficient RNA replication, given the catalytic nature of proteins. However, it necessitates the simultaneous emergence of two intricate molecules: an enzyme (derived from peptides) and RNA (from nucleotides). Within this Peptide-RNA World framework, RNA would have encoded life's instructions, while peptides (simple protein enzymes) would have accelerated crucial chemical reactions to execute these instructions. The precise mechanism by which these rudimentary systems achieved self-replication remains an open question, a challenge neither the RNA World hypothesis nor the Peptide-RNA World theory can fully address without invoking the involvement of polymerases (enzymes that rapidly assemble RNA molecules).

In March 2015, a research initiative led by the Sutherland group demonstrated that a reaction network, initiated by hydrogen cyanide and hydrogen sulfide in UV-irradiated aqueous environments, could generate the chemical constituents of proteins, lipids, and RNA. The investigators designated this reaction network as 'cyanosulfidic.' Subsequently, in November 2017, a team at the Scripps Research Institute identified reactions involving diamidophosphate, which could have facilitated the linkage of these chemical components into short peptide and lipid chains, as well as nascent RNA-like nucleotide chains.

Implications

Should the RNA world hypothesis prove accurate, it carries significant implications for both the definition and the genesis of life. For a substantial period following Franklin, Watson, and Crick's elucidation of DNA structure in 1953, life was predominantly conceptualized through the lens of DNA and proteins. These macromolecules were perceived as the primary constituents of living cells, with RNA merely serving as an intermediary in protein synthesis from the DNA blueprint.

The RNA world hypothesis positions RNA as a central player in the origin of life. This hypothesis is substantiated by observations demonstrating that ribosomes function as ribozymes, where the catalytic site is composed of RNA, and proteins primarily serve minor structural or peripheral functional roles. This understanding was corroborated by the deciphering of the ribosome's three-dimensional structure in 2001. Notably, the formation of peptide bonds, which link amino acids to form proteins, is now recognized as being catalyzed by an adenine residue within the ribosomal RNA (rRNA).

RNAs are also recognized for their involvement in other cellular catalytic processes, particularly in directing enzymes to specific RNA sequences. Within eukaryotes, the processing of pre-mRNA and RNA editing occurs at locations dictated by the base pairing between the target RNA and the RNA components of small nuclear ribonucleoproteins (snRNPs). This enzyme targeting mechanism also underlies gene downregulation via RNA interference (RNAi), where an enzyme-associated guide RNA specifically targets messenger RNA (mRNA) for selective degradation. Similarly, in eukaryotes, telomere maintenance involves the replication of an RNA template, which is an integral part of the telomerase ribonucleoprotein enzyme. Furthermore, the cellular organelle known as the vault contains a ribonucleoprotein component, though its precise function is yet to be fully elucidated.

GADV-protein world hypothesis

• GADV-protein world hypothesis
• The Major Transitions in Evolution
• RNA-based evolution
• Protocell or Pre-cell, the primordial version of a cell which confined RNA and later, DNA
• First universal common ancestor (FUCA)
• Origin of DNA

References

• "Understanding the RNA World." Exploring Life's Origins. Exploring Origins Project.Ferris, James P. "The Formation of the RNA World." The New York Center for Studies of the Origins of Life, Rensselaer Polytechnic Institute. Archived from the original on March 1, 2012.Altman, Sidney (2001). "The RNA World." NobelPrize.org. Nobel Media.Kuska, Robert (June 2002). "A World Apart" (PDF). HHMI Bulletin. Howard Hughes Medical Institute. pp. 14–19. Archived (PDF) from the original on 2004-05-22.Cech, Thomas R. (2004). "Exploring the New RNA World." NobelPrize.org. Nobel Media.Sutherland, J. D. (April 2010). "Ribonucleotides." Cold Spring Harbor Perspectives in Biology, §34§(4): a005439. doi:10.1101/cshperspect.a005439. PMC 2845210. PMID 20452951."The Origins of the RNA World." YouTube. Library of Congress, August 5, 2016.Source: TORIma Academy Archive