Prebiotically Plausible ‘Patching’ of RNA Backbone Cleavage Through a 3′-5′ Pyrophosphate Linkage

ABSTRACTAchieving multiple cycles of RNA replication within a model protocell would be a critical step towards demonstrating a path from prebiotic chemistry to cellular biology. Any model for early life based on an ‘RNA world’ must account for RNA strand cleavage and hydrolysis, which would degrade primitive genetic information and lead to an accumulation of truncated, phosphate-terminated strands. We show here that cleavage of the phosphodiester backbone is not an endpoint for RNA replication. Instead, 3′ -phosphate terminated RNA strands are able to participate in template-directed copying reactions with activated ribonucleotide monomers. These reactions form a pyrophosphate linkage, the stability of which we have characterized in the context of RNA copying chemistry. We found that the pyrophosphate bond is relatively stable within an RNA duplex and in the presence of chelated magnesium. Under these conditions, pyrophosphate-RNA can act as a temporary ‘patch’ to template the polymerization of canonical ribonucleotides, suggesting a plausible non-enzymatic pathway for the salvage and recovery of genetic information following strand cleavage.

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Mini-ribozymes and freezing environment: a new scenario for the early RNA world

Biogeosciences Discussions ◽

10.5194/bgd-2-1719-2005 ◽

2005 ◽

Vol 2 (6) ◽

pp. 1719-1737 ◽

Cited By ~ 2

Author(s):

A. V. Vlassov

Keyword(s):

Genetic Information ◽

Life Form ◽

Catalytic Properties ◽

Rna World ◽

Catalytic Rna ◽

Rna Molecules ◽

Phosphodiester Backbone ◽

World Hypothesis ◽

Rna World Hypothesis

Abstract. The RNA World hypothesis states that the present-day life, which is based on DNA genomes and protein enzymes, was preceded by a simpler life form based primarily on RNA. During this era, the genetic information resided in the sequence of RNA molecules and the phenotype derived from the catalytic properties of RNA. Though it is a widely accepted scenario, a number of problems remain unsolved. One of the biggest questions is how complex RNAs could evolve, survive and replicate under typically assumed ''warm and wet'' conditions, taking into account that the RNA phosphodiester backbone is chemically unstable under these conditions. We suggest that prebiotic conditions associated with freezing could have been of key importance in the early RNA World, and discuss the role of primitive catalytic RNA in the evolution of RNA size and complexity.

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Cofactors are Remnants of Life’s Origin and Early Evolution

Journal of Molecular Evolution ◽

10.1007/s00239-020-09988-4 ◽

2021 ◽

Vol 89 (3) ◽

pp. 127-133 ◽

Cited By ~ 1

Author(s):

Aaron D. Goldman ◽

Betul Kacar

Keyword(s):

Genetic Information ◽

Evolutionary Biology ◽

Active Sites ◽

Rna World ◽

Genetic System ◽

Early Evolution ◽

Modern Biology ◽

Iron Sulfur Cluster ◽

Adenosyl Methionine ◽

Precursor Rna

AbstractThe RNA World is one of the most widely accepted hypotheses explaining the origin of the genetic system used by all organisms today. It proposes that the tripartite system of DNA, RNA, and proteins was preceded by one consisting solely of RNA, which both stored genetic information and performed the molecular functions encoded by that genetic information. Current research into a potential RNA World revolves around the catalytic properties of RNA-based enzymes, or ribozymes. Well before the discovery of ribozymes, Harold White proposed that evidence for a precursor RNA world could be found within modern proteins in the form of coenzymes, the majority of which contain nucleobases or nucleoside moieties, such as Coenzyme A and S-adenosyl methionine, or are themselves nucleotides, such as ATP and NADH (a dinucleotide). These coenzymes, White suggested, had been the catalytic active sites of ancient ribozymes, which transitioned to their current forms after the surrounding ribozyme scaffolds had been replaced by protein apoenzymes during the evolution of translation. Since its proposal four decades ago, this groundbreaking hypothesis has garnered support from several different research disciplines and motivated similar hypotheses about other classes of cofactors, most notably iron-sulfur cluster cofactors as remnants of the geochemical setting of the origin of life. Evidence from prebiotic geochemistry, ribozyme biochemistry, and evolutionary biology, increasingly supports these hypotheses. Certain coenzymes and cofactors may bridge modern biology with the past and can thus provide insights into the elusive and poorly-recorded period of the origin and early evolution of life.

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Enzymatic RNA Production from NTPs Synthesized from Nucleosides and Trimetaphosphate

10.26434/chemrxiv.13875842 ◽

2021 ◽

Author(s):

Fabio Chizzolini ◽

Alexandra Kent ◽

Luiz F. M. Passalacqua ◽

Andrej Lupták

Keyword(s):

Rna Synthesis ◽

Rna World ◽

Rna Replication ◽

High Energy ◽

Rna Degradation ◽

T7 Rna Polymerase ◽

Nucleotide Synthesis ◽

Enthalpy Of Activation ◽

Rna Polymerization ◽

Synthetic Approaches

A mechanism of nucleoside triphosphorylation would have been critical in an evolving “RNA world” to provide high-energy substrates for reactions such as RNA polymerization. However, synthetic approaches to produce ribonucleoside triphosphoates (rNTPs) have suffered from conditions such as high temperatures or high pH that lead to increased RNA degradation, as well as substrate production that cannot sustain replication. We demonstrate that cyclic trimetaphosphate (cTmp) can react with nucleosides to form rNTPs under mild, prebiotically-relevant conditions, with second-order rate constants ranging from 1.7 x 10–6 to 6.5 x 10–6 M–1 s–1. The ATP reaction shows a linear dependence on pH and Mg2+, and an enthalpy of activation of 88 ± 4 kJ/mol. At millimolar nucleoside and cTmp concentrations, the rNTP production rate is sufficient to facilitate RNA synthesis by both T7 RNA polymerase and a polymerase ribozyme. We suggest that the optimized reaction of cTmp with nucleosides may provide a viable connection between prebiotic nucleotide synthesis and RNA replication.

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The effect of adenine protonation on RNA phosphodiester backbone bond cleavage elucidated by deaza-nucleobase modifications and mass spectrometry

Nucleic Acids Research ◽

10.1093/nar/gkz574 ◽

2019 ◽

Vol 47 (14) ◽

pp. 7223-7234 ◽

Cited By ~ 4

Author(s):

Elisabeth Fuchs ◽

Christoph Falschlunger ◽

Ronald Micura ◽

Kathrin Breuker

Keyword(s):

Mass Spectrometry ◽

Gas Phase ◽

Vibrational Excitation ◽

Bond Cleavage ◽

Low Energy ◽

Biological Processes ◽

Phosphodiester Backbone ◽

Collisionally Activated Dissociation ◽

Rna Backbone ◽

Ionic Hydrogen Bonds

Abstract The catalytic strategies of small self-cleaving ribozymes often involve interactions between nucleobases and the ribonucleic acid (RNA) backbone. Here we show that multiply protonated, gaseous RNA has an intrinsic preference for the formation of ionic hydrogen bonds between adenine protonated at N3 and the phosphodiester backbone moiety on its 5′-side that facilitates preferential phosphodiester backbone bond cleavage upon vibrational excitation by low-energy collisionally activated dissociation. Removal of the basic N3 site by deaza-modification of adenine was found to abrogate preferential phosphodiester backbone bond cleavage. No such effects were observed for N1 or N7 of adenine. Importantly, we found that the pH of the solution used for generation of the multiply protonated, gaseous RNA ions by electrospray ionization affects phosphodiester backbone bond cleavage next to adenine, which implies that the protonation patterns in solution are at least in part preserved during and after transfer into the gas phase. Our study suggests that interactions between protonated adenine and phosphodiester moieties of RNA may play a more important mechanistic role in biological processes than considered until now.

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Adding levels of complexity enhances robustness and evolvability in a multilevel genotype–phenotype map

Journal of The Royal Society Interface ◽

10.1098/rsif.2017.0516 ◽

2018 ◽

Vol 15 (138) ◽

pp. 20170516 ◽

Cited By ~ 8

Author(s):

Pablo Catalán ◽

Andreas Wagner ◽

Susanna Manrubia ◽

José A. Cuesta

Keyword(s):

Protein Folding ◽

Regulatory Networks ◽

Phenotypic Expression ◽

Point Mutations ◽

Skewed Distribution ◽

Cellular Biology ◽

Folding Model ◽

Number Of Genes ◽

Genotype Space ◽

The Stability

Robustness and evolvability are the main properties that account for the stability and accessibility of phenotypes. They have been studied in a number of computational genotype–phenotype maps. In this paper, we study a metabolic genotype–phenotype map defined in toyLIFE , a multilevel computational model that represents a simplified cellular biology. toyLIFE includes several levels of phenotypic expression, from proteins to regulatory networks to metabolism. Our results show that toyLIFE shares many similarities with other seemingly unrelated computational genotype–phenotype maps. Thus, toyLIFE shows a high degeneracy in the mapping from genotypes to phenotypes, as well as a highly skewed distribution of phenotypic abundances. The neutral networks associated with abundant phenotypes are highly navigable, and common phenotypes are close to each other in genotype space. All of these properties are remarkable, as toyLIFE is built on a version of the HP protein-folding model that is neither robust nor evolvable: phenotypes cannot be mutually accessed through point mutations. In addition, both robustness and evolvability increase with the number of genes in a genotype. Therefore, our results suggest that adding levels of complexity to the mapping of genotypes to phenotypes and increasing genome size enhances both these properties.

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Formation of Abasic Oligomers in Nonenzymatic Polymerization of Canonical Nucleotides

Life ◽

10.3390/life9030057 ◽

2019 ◽

Vol 9 (3) ◽

pp. 57

Author(s):

Chaitanya V. Mungi ◽

Niraja V. Bapat ◽

Yayoi Hongo ◽

Sudha Rajamani

Keyword(s):

Information Transfer ◽

Rna World ◽

Purine Nucleotides ◽

Abasic Sites ◽

Glycosidic Bonds ◽

Product Characterization ◽

Acid Catalyzed ◽

The Stability ◽

High Degree ◽

Do So

Polymerization of nucleotides under prebiotically plausible conditions has been a focus of several origins of life studies. Non-activated nucleotides have been shown to undergo polymerization under geothermal conditions when subjected to dry-wet cycles. They do so by a mechanism similar to acid-catalyzed ester-bond formation. However, one study showed that the low pH of these reactions resulted in predominantly depurination, thereby resulting in the formation of abasic sites in the oligomers. In this study, we aimed to systematically characterize the nature of the oligomers that resulted in reactions that involved one or more of the canonical ribonucleotides. All the reactions analyzed showed the presence of abasic oligomers, with purine nucleotides being affected the most due to deglycosylation. Even in the reactions that contained nucleotide mixtures, the presence of abasic oligomers was detected, which suggested that information transfer would be severely hampered due to losing the capacity to base pair via H-bonds. Importantly, the stability of the N-glycosidic linkage, under conditions used for dry-wet cycling, was also determined. Results from this study further strengthen the hypothesis that chemical evolution in a pre-RNA World would have been vital for the evolution of informational molecules of an RNA World. This is evident in the high degree of instability displayed by N-glycosidic bonds of canonical purine ribonucleotides under the same geothermal conditions that otherwise readily favors polymerization. Significantly, the resultant product characterization in the reactions concerned underscores the difficulty associated with analyzing complex prebiotically relevant reactions due to inherent limitation of current analytical methods.

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Behaviour of RNA under hydrothermal conditions and the origins of life

International Journal of Astrobiology ◽

10.1017/s1473550405002284 ◽

2004 ◽

Vol 3 (4) ◽

pp. 301-309 ◽

Cited By ~ 26

Author(s):

Kunio Kawamura

Keyword(s):

High Temperatures ◽

Open Systems ◽

Rna World ◽

Enzymatic Reaction ◽

Reaction Rates ◽

Extensive Literature ◽

Hydrothermal Conditions ◽

Phosphodiester Bond ◽

Rna Molecules ◽

The Stability

The RNA world hypothesis and the hydrothermal origin of life hypothesis are contradictory to each other. Although it is considered that RNA molecules are too labile to maintain life-like systems at high temperatures and there is extensive literature on nucleic acid hydrolysis, the stability and the chemical evolution of RNA have not been sufficiently analysed from the viewpoint of hydrothermal reactions. Based on our experimental data concerning the stability and the prebiotic formation of RNA at high temperatures, two different aspects seem to be important for evaluating whether RNA molecules are too labile. First, the stability of RNA molecules should be evaluated from the comparison of the rate of formation and the rate of degradation of RNA in open systems. Our prebiotic reaction models of phosphodiester bond formation suggest that at high temperatures the accumulation of RNA may be possible. However, an RNA world entirely consisting of RNA molecules is unlikely to occur because the biologically important interactions are not effective for the bare RNA molecules at high temperatures. Second, since enzymes presently mediate most biological reactions, evaluation of the accumulation of RNA should be based on the comparison between the enzymatic and non-enzymatic reaction rates. Hence, the evaluation of the primitive enzymatic reaction rates at high temperatures has been attempted. There is a large difference between the present enzymatic reaction rates at 25–90 °C and the non-enzymatic reaction rates at high temperatures of 200–300 °C. It is thus possible that prebiotic enzyme-like assemblies could have facilitated the accumulation of RNA molecules at hydrothermal vent temperatures.

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Prebiotic Chemistry and the Origin of the RNA World

Critical Reviews in Biochemistry and Molecular Biology ◽

10.1080/10409230490460765 ◽

2004 ◽

Vol 39 (2) ◽

pp. 99-123 ◽

Cited By ~ 633

Author(s):

Orgel Leslie E.

Keyword(s):

Prebiotic Chemistry ◽

Rna World

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Nucleic acids: function and potential for abiogenesis

Quarterly Reviews of Biophysics ◽

10.1017/s0033583517000038 ◽

2017 ◽

Vol 50 ◽

Cited By ~ 32

Author(s):

Falk Wachowius ◽

James Attwater ◽

Philipp Holliger

Keyword(s):

Nucleic Acids ◽

Prebiotic Chemistry ◽

Molecular Level ◽

Rna World ◽

Information Storage ◽

Molecular Systems ◽

Rna Molecules ◽

Functional Potential ◽

Self Replication ◽

Uniform Composition

AbstractThe emergence of functional cooperation between the three main classes of biomolecules – nucleic acids, peptides and lipids – defines life at the molecular level. However, how such mutually interdependent molecular systems emerged from prebiotic chemistry remains a mystery. A key hypothesis, formulated by Crick, Orgel and Woese over 40 year ago, posits that early life must have been simpler. Specifically, it proposed that an early primordial biology lacked proteins and DNA but instead relied on RNA as the key biopolymer responsible not just for genetic information storage and propagation, but also for catalysis, i.e. metabolism. Indeed, there is compelling evidence for such an ‘RNA world’, notably in the structure of the ribosome as a likely molecular fossil from that time. Nevertheless, one might justifiably ask whether RNA alone would be up to the task. From a purely chemical perspective, RNA is a molecule of rather uniform composition with all four bases comprising organic heterocycles of similar size and comparable polarity and pKa values. Thus, RNA molecules cover a much narrower range of steric, electronic and physicochemical properties than, e.g. the 20 amino acid side-chains of proteins. Herein we will examine the functional potential of RNA (and other nucleic acids) with respect to self-replication, catalysis and assembly into simple protocellular entities.

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