The RNA World on Ice: A New Scenario for the Emergence of RNA Information

The RNA world hypothesis refers to a hypothetical era prior to coded peptide synthesis, where RNA was the major structural, genetic, and catalytic agent. Though it is a widely accepted scenario, a number of vexing difficulties remain. In this review we focus on a missing link of the RNA world hypothesis—primitive miniribozymes, in particular ligases, and discuss the role of these molecules in the evolution of RNA size and complexity. We argue that prebiotic conditions associated with freezing, rather than “warm and wet” conditions, could have been of key importance in the early RNA world.[Reviewing Editor: Dr. Niles Lehman]     

The chemical origins of life and its early evolution: an introduction

Can we look at contemporary biology and couple this with chemical insight to propose some plausible mechanisms for the origin of life on the planet? In what follows, we examine some promising chemical reactions by which the building blocks for nucleic acids might have been created about a billion years after the Earth formed. This could have led to self-assembling systems that were based on an all-RNA metabolism, where RNA is both catalytic and informational. We consider the breadth of RNA enzymes presently existing in biology, and to what extent these might have covered a wider range of chemistry in the RNA world. Ultimately, the RNA world would probably have given way to protein-based life quite quickly, and the origins of peptidyl transferase activity are discussed below.     

The RNA World and Its Evolution

This paper develops Belozersky’s early idea of the precedence of RNA in the origin of life on the Earth. Based on the current knowledge of the functional omnipotence of RNA, three new mechanisms are considered that could be critical for the origin and evolution of the ancient RNA world: (1) the reaction of spontaneous transesterification of polyribonucleotides in aqueous media, which has been recently discovered by A.B. Chetverin and colleagues and could result in elongation of short initial oligoribonucleotides and generate sequence variants for further selection; (2) compartmentation of functional RNA ensembles in the form of mixed molecular colonies on moist mineral surfaces, in the absence of membranes and other envelopes; and (3) systematic exponential enrichment of an RNA population with “ functionally the best” molecules due to alternating dissolution of the colonies upon flooding and formation of new colonies upon drying in ancient pools (“primordial natural SELEX”).__________Translated from Molekulyarnaya Biologiya, Vol. 39, No. 4, 2005, pp. 550–556.Original Russian Text Copyright © 2005 by Spirin.     

Question 5: On the Chemical Reality of the RNA World

The discovery of catalytic RNA has revolutionised modern molecular biology and bears important implications for the origin of Life research. Catalytic RNA, in particular self-replicating RNA, prompted the hypothesis of an early “RNA world” where RNA molecules played all major roles such information storage and catalysis. The actual role of RNA as primary actor in the origin of life has been under debate for a long time, with a particular emphasis on possible pathways to the prebiotic synthesis of mononucleotides; their polymerization and the possibility of spontaneous emergence of catalytic RNAs synthesised under plausible prebiotic conditions. However, little emphasis has been put on the chemical reality of an RNA world; in particular concerning the chemical constrains that such scenario should have met to be feasible. This paper intends to address those concerns with regard to the achievement of high local RNA molecules concentration and the aetiology of unique sequence under plausible prebiotic conditions. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

Ice And The Origin Of Life

Sea ice occurs abundantly at the polar caps of the Earth and, probably, of many other planets. Its static and dynamic properties that may be important for prebiotic and early biotic reactions are described. It concentrates substrates and has many features that are important for catalytical actions. We propose that it provided optimal conditions for the early replication of nucleic acids and the RNA world. We repeated a famous prebiotic experiment, the poly-uridylic acid-instructed synthesis of polyadenylic acid from adenylic acid imidazolides in artificial sea ice, simulating the dynamic variability of real sea ice by cyclic temperature variation. Poly(A) was obtained in high yield and reached nucleotide chain lengths up to 400 containing predominantly 3′→ 5′ linkages.     

Introns: Mighty Elements from the RNA World

The discovery of RNA-based enzymatic activity by Thomas Cechs and Sidney Altmans laboratories was a momentous event that led Walter Gilbert to the concept of an RNA world—a primitive ancient stage of life that existed before the appearance of DNA and protein molecules. A year later, Gilbert formulated the exon theory of genes, which hypothesized that introns are very ancient genetic elements present at the earliest stages of life in the RNA world. This theory has been fiercely debated and still has vigorous supporters and opponents. In this communication, we explore peculiarities in the RNA-protein world and their effect on intron–exon structures. We demonstrate that these peculiarities, which exist in the absence of DNA, could shed light on introns original functions as well as the important role they might have played in the origin of life. For ancient DNA-lacking cells, a crucial problem existed in distinguishing two distinct subsets of RNAs: those messenger molecules coding for proteins and those heritable genetic molecules complementary to messenger RNAs that propagate the genetic information through generations. We propose that ancient introns could act as markers of RNA subsets, directing them to different functions.Reviewing Editor: Dr. Manyuan Long     

Creative catalysis: pieces of the RNA world jigsaw

Novel ribozymes produced by in vitro selection techniques provide insights into the possible mechanisms of protein synthesis evolution. The availability of such ribozymes also paves the way for experiments to explore the evolution of RNA–protein enzymes.     

Coenzymes, viruses and the RNA world

The results of a detailed bioinformatic search for ribonucleotidyl coenzyme biosynthetic sequences in DNA- and RNA viral genomes are presented. No RNA viral genome sequence available as of April 2011 appears to encode for sequences involved in coenzyme biosynthesis. In both single- and double-stranded DNA viruses a diverse array of coenzyme biosynthetic genes has been identified, but none of the viral genomes examined here encodes for a complete pathway. Although our conclusions may be constrained by the unexplored diversity of viral genomes and the biases in the construction of viral genome databases, our results do not support the possibility that RNA viruses are direct holdovers from an ancient RNA/protein world. Extrapolation of our results to evolutionary epochs prior to the emergence of DNA genomes suggest that during those early stages living entities may have depended on discontinuous genetic systems consisting of multiple small-size RNA sequences.     

The Prebiotic Synthesis of Modified Purines and Their Potential Role in the RNA World

Modified purines are found in all organisms in the tRNA, rRNA, and even DNA, raising the possibility of an early role for these compounds in the evolution of life. These include N ⁶-methyladenine, 1-methyladenine, N ⁶,N ⁶-dimethyladenine, 1-methylhypoxanthine, 1-methylguanine, and N ²-methylguanine. We find that these bases as well as a number of nonbiological modified purines can be synthesized from adenine and guanine by the simple reaction of an amine or an amino group with adenine and guanine under the concentrated conditions of the drying-lagoon or drying-beach model of prebiotic synthesis with yields as high as 50%. These compounds are therefore as prebiotic as adenine and guanine and could have played an important role in the RNA world by providing additional functional groups in ribozymes, especially for the construction of hydrophobic binding pockets. Received: 7 August 1998 / Accepted: 31 December 1998     

Effect of Inhibitors on the Montmorillonite Clay-Catalyzed Formation of RNA: Studies on the Reaction Pathway

The Langmuir adsorption isotherms of the phosphoroimidazolides of adenosine (ImpA) and uridine (ImpU), dA^5'ppdA and N⁶, N⁶-dimethyladenine binding on montmorillonite are consistent with their forming a monolayer on the clay surface. This suggests the condensation of ImpA and ImpU to oligomers proceeds on the surface of the clay and not in groups of monomers stacked on the clay surfaces. The binding and reactions of ImpU and ImpA on montmorillonite are blocked by N⁶, N⁶-dimethyladenine and dA^5'ppdA. dA^5'ppdA is a better inhibitor of oligomer formation than N⁶, N⁶-dimethyladenine because both adenine rings of dA^5'ppdA bind to the clay surface and block adjacent catalytic sites. An upper limit of 5–10 × 10¹⁵catalytic sites on 50 mg of clay was estimated from the binding of ImpU and the inhibition of oligomer formation by dA^5'ppdA.     

RNA的历史与未来

核酶的发现使得人们有理由相信生命起源于RNA,通过试管演化实验获得的各种各样的催化性RNA更使人们对地球历史早期的RNA世界有了越来越多的了解。同时,随着RNA结构和功能上非凡的多样性的日益被揭示．RNA在未来的临床应用研究中所具有的巨大潜力也正逐渐显现出来。     

Relics from the RNA World

An RNA world is widely accepted as a probable stage in the early evolution of life. Two implications are that proteins have gradually replaced RNA as the main biological catalysts and that RNA has not taken on any major de novo catalytic function after the evolution of protein synthesis, that is, there is an essentially irreversible series of steps RNA → RNP → protein. This transition, as expected from a consideration of catalytic perfection, is essentially complete for reactions when the substrates are small molecules. Based on these principles we derive criteria for identifying RNAs in modern organisms that are relics from the RNA world and then examine the function and phylogenetic distribution of RNA for such remnants of the RNA world. This allows an estimate of the minimum complexity of the last ribo-organism—the stage just preceding the advent of genetically encoded protein synthesis. Despite the constraints placed on its size by a low fidelity of replication (the Eigen limit), we conclude that the genome of this organism reached a considerable level of complexity that included several RNA-processing steps. It would include a large protoribosome with many smaller RNAs involved in its assembly, pre-tRNAs and tRNA processing, an ability for recombination of RNA, some RNA editing, an ability to copy to the end of each RNA strand, and some transport functions. It is harder to recognize specific metabolic reactions that must have existed but synthetic and bio-energetic functions would be necessary. Overall, this requires that such an organism maintained a multiple copy, double-stranded linear RNA genome capable of recombination and splicing. The genome was most likely fragmented, allowing each ``chromosome' to be replicated with minimum error, that is, within the Eigen limit. The model as developed serves as an outgroup to root the tree of life and is an alternative to using sequence data for inferring properties of the earliest cells. Received: 14 January 1997 / Accepted: 19 May 1997     

The roads to and from the RNA world

The historical existence of the RNA world, in which early life used RNA for both genetic information and catalytic ability, is widely accepted. However, there has been little discussion of whether protein synthesis arose before DNA or what preceded the RNA world (i.e. the pre-RNA world). We outline arguments of what route life may have taken out of the RNA world: whether DNA or protein followed. Metabolic arguments favor the possibility that RNA genomes preceded the use of DNA as the informational macromolecule. However, the opposite can also be argued based on the enhanced stability, reactivity, and solubility of 2-deoxyribose as compared to ribose. The possibility that DNA may have come before RNA is discussed, although it is a less parsimonious explanation than DNA following RNA.     

Use of a coenzyme by the glmS ribozyme-riboswitch suggests primordial expansion of RNA chemistry by small molecules

The glmS ribozyme-riboswitch is the first known example of a naturally occurring catalytic RNA that employs a small molecule as a coenzyme. Binding of glucosamine-6-phosphate (GlcN6P) activates self-cleavage of the bacterial ribozyme, which is part of the mRNA encoding the metabolic enzyme GlcN6P-synthetase. Cleavage leads to negative feedback regulation. GlcN6P binds in the active site of the ribozyme, where its amine could function as a general acid and electrostatic catalyst. The ribozyme is pre-folded but inactive in the absence of GlcN6P, demonstrating it has evolved strict dependence on the exogenous small molecule. The ribozyme showcases the ability of RNA to co-opt non-covalently bound small molecules to expand its chemical repertoire. Analogue studies demonstrate that some molecules other than GlcN6P, such as l-serine (but not d-serine), can function as weak activators. This suggests how coenzyme use by RNA world ribozymes may have led to evolution of proteins. Primordial cofactor-dependent ribozymes may have evolved to bind their cofactors covalently. If amino acids were used as cofactors, this could have driven the evolution of RNA aminoacylation. The ability to make covalently bound peptide coenzymes may have further increased the fitness of such primordial ribozymes, providing a selective pressure for the invention of translation.     

On the structural repertoire of pools of short, random RNA sequences

A detailed knowledge of the mapping between sequence and structure spaces in populations of RNA molecules is essential to better understand their present-day functional properties, to envisage a plausible early evolution of RNA in a prebiotic chemical environment and to improve the design of in vitro evolution experiments, among others. Analysis of natural RNAs, as well as in vitro and computational studies, show that certain RNA structural motifs are much more abundant than others, pointing out a complex relation between sequence and structure. Within this framework, we have investigated computationally the structural properties of a large pool (10⁸ molecules) of single-stranded, 35 nt-long, random RNA sequences. The secondary structures obtained are ranked and classified into structure families. The number of structures in main families is analytically calculated and compared with the numerical results. This permits a quantification of the fraction of structure space covered by a large pool of sequences. We further show that the number of structural motifs and their frequency is highly unbalanced with respect to the nucleotide composition: simple structures such as stem-loops and hairpins arise from sequences depleted in G, while more complex structures require an enrichment of G. In general, we observe a strong correlation between subfamilies—characterized by a fixed number of paired nucleotides—and nucleotide composition. Our results are compared to the structural repertoire obtained in a second pool where isolated base pairs are prohibited.     

An RNA replisome as the ancestor of the ribosome

Summary The ribosome is proposed to have evolved from an earlier RNA-replisome, which synthesized RNA. Ancestral tRNA molecules originally were loaded with trinucleotide sequences and donated them to growing RNA chains. The enzymatic addition of the C-C-A trinucleotide to presentday transfer RNA molecules is a carryover from this function. The strategies of reading RNA sequences by triplet codons and of housing information genetically in special repository molecules predates the origin of protein and DNA. These latter two polymers arose together at the time when the RNA replisome was converted to a ribosome.     

A possible circular RNA at the origin of life

The increasing volume of sequenced genomes and the recent techniques for performing in vitro molecular evolution have rekindled the interest for questions on the origin of life. Nevertheless, a gap continues to exist between the research on prebiotic chemistry and molecule generation, on one hand, and the study of molecular fossils preserved in genomes, on the other. Here we attempt to fill this gap by using some assumptions about the prebiotic scenario (including a strong stereochemical basis for the genetic code) to determine the RNA sequences more likely to appear and subsist. A set of minimal RNA rings is exhaustively determined; a subset of them is then selected through stability arguments, and a particular ring (AL ring) is finally singled out as the most likely winner of this prebiotic game. The rings happen to have several structural and statistical properties of modern genes: a repeated AUG codon appears spontaneously (and is thus made available for becoming a start signal), the form AUG/STOP emerges, and frequency patterns resemble those of present genes. The whole set of rings was also compared to a database of tRNAs, considering the conserved positions (located in the free parts of the molecule, essentially the loops); the ring that most closely matched tRNA sequences-and matched, in fact, the consensus of tRNA at all the aligned positions-was AL, the same ring independently selected before. The unselected emergence of gene-like features through two simple selection steps and the close similarity between the finally selected ring and tRNA (including some remarkable features of the resulting alignment) suggest a possible link between the prebiotic world and the first biological molecules, which is amenable for experimental testing. Even if our scenario is partially wrong, the unlikely coincidences should provide useful hints for other efforts.     

The dawn of the RNA World: Toward functional complexity through ligation of random RNA oligomers

A main unsolved problem in the RNA World scenario for the origin of life is how a template-dependent RNA polymerase ribozyme emerged from short RNA oligomers obtained by random polymerization on mineral surfaces. A number of computational studies have shown that the structural repertoire yielded by that process is dominated by topologically simple structures, notably hairpin-like ones. A fraction of these could display RNA ligase activity and catalyze the assembly of larger, eventually functional RNA molecules retaining their previous modular structure: molecular complexity increases but template replication is absent. This allows us to build up a stepwise model of ligation-based, modular evolution that could pave the way to the emergence of a ribozyme with RNA replicase activity, step at which information-driven Darwinian evolution would be triggered.     

The origin of life-a review of facts and speculations

Three popular hypotheses attempt to explain the origin of prebiotic molecules: synthesis in a reducing atmosphere, input in meteorites and synthesis on metal sulfides in deep-sea vents. It is not possible to decide which is correct. It is also unclear whether the RNA world was the first biological world or whether some simpler world preceded it.     

Analysis of Evolutionarily Independent Protein-RNA Complexes Yields a Criterion to Evaluate the Relevance of Prebiotic Scenarios

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