RNA-catalyzed evolution of catalytic RNA

An RNA Condensate Model for the Origin of Life

The RNA World hypothesis predicts that self-replicating RNAs evolved before DNA genomes and coded proteins. Despite widespread support for the RNA World, self-replicating RNAs have yet to be identified in a natural context, leaving a key 'missing link' for this explanation of the origin of life. Inspired by recent work showing that condensates of charged polymers are capable of catalyzing chemical reactions, we consider a catalytic RNA condensate as a candidate for the self-replicating RNA. Specifically, we propose that short, low-complexity RNA polymers formed catalytic condensates capable of templated RNA polymerization. Because the condensate properties depend on the RNA sequences, RNAs that formed condensates with improved polymerization and demixing capacity would be amplified, leading to a 'condensate chain reaction' and evolution by natural selection. Many of the needed properties of this self-replicating RNA condensate have been realized experimentally in recent studies and our predictions could be tested with current experimental and theoretical tools. Our theory addresses central problems in the origins of life: (i) the origin of compartmentalization, (ii) the error threshold for the accuracy of templated replication, (iii) the free energy cost of maintaining an information-rich population of replicating RNA polymers. Furthermore, we note that the extant nucleolus appears to satisfy many of the requirements of an evolutionary relic for the model we propose. More generally, we suggest that future work on the origin of life would benefit from condensate-centric biophysical models of RNA evolution.

Emergent and Convergent Features in the Laboratory Evolution of Polymerase Ribozymes

In modern biology, molecular heredity is established by polymerase proteins that copy genetic information encoded in the sequence of nucleic acids. Prior to the emergence of coded protein synthesis, this role may have been filled by RNA polymerase ribozymes. Although such enzymes can no longer be found in extant life, ribozymes first evolved from random sequence populations have been progressively engineered in the laboratory to function as general RNA-dependent RNA polymerases. Polymerase ribozymes discovered in the past ten years can catalyze hundreds of sequential RNA synthesis reactions, match the complexity and catalytic sophistication of biological RNA enzymes, and employ many of the same strategies used by polymerase proteins to copy nucleic acids. This review describes the approaches to directed in vitro evolution that have led to the discovery of RNA enzymes that copy RNA molecules processively and accurately, and surveys how laboratory evolution has shaped biochemical and structural adaptations in these enzymes. The review then considers the challenges and opportunities that remain in the effort to propagate and evolve RNA genes with RNA catalysts alone.

A stepwise emergence of evolution in the RNA world

Building on experimental evidence and replicator theories, I propose a 3-stage scenario for a transition from autocatalysis into template-based replication of RNA, providing a pathway for the origin of life. In stage 1, self-reproduction occurs via autocatalysis using oligomer substrates, replicator viability relies on substrate-specificity, and heritable variations are mediated by structural interactions. In stage 2, autocatalysis coexists with the templated ligation of external substrates. This dual mode of reproduction combined with limited diffusion avoids the error catastrophe. In stage 3, template-based replication takes over and uses substrates of decreasing size, made possible by enhanced catalytic properties and compartmentalization. Structural complexity, catalytic efficiency, metabolic efficiency, and cellularization all evolve gradually and interdependently, ultimately leading to evolutionary processes similar to extant biology. Impact statement This perspective proposes a testable stepwise scenario for the emergence of evolution in an RNA origin of life. It shows how evolution could appear in a gradual manner, thanks to catalytic feedback among random mixtures of molecules. It highlights possible couplings between the different facets of molecular self-organization, which could bootstrap life.

On an RNA-Membrane Protogenome

Efficient evolution exists before DNA, else the DNA genome itself could not evolve. Current data suggest RNA-membranes for this role. Selected RNAs bind well to phospholipid bilayers; randomized sequences do not. No repeated sequences are evident in selected binding RNAs. This implies small and varied membrane-affinity motifs. Such binding sequences are partially defined. Phospholipid-bound RNAs require divalents like Mg2+ and/or Ca2+, preferring more ordered bilayers: gel, ripple, or rafted membranes, in that order. RNAs also bind and stabilize bent or sharply deformed bilayers. RNA binding without divalents extends to negatively charged membranes formed from simpler anionic phospholipids and to plausibly prebiotic fatty acid bilayers. RNA-membranes frequently retain RNA solution functions: base pairing, passive transport of tryptophan, specific affinity for arginine side chains, and ribozymic ligase catalysis. Membrane-bound RNAs with several biochemical functions, linked by specific base-pairing, are readily constructed. Given these data, genetic roles seem feasible. RNA activities often require few nucleotides, easily joined in a small RNA. Base-paired groups of such RNAs can also be purposeful, joining related functions. Complex functions can therefore require only replication of short RNAs. RNA-membranes potentially segregate accurately during cell division and quickly evolve through new base pairings. Accordingly, ancient RNA-membranes could act as a protogenome, supporting encoded RNA expression, inheritance, and evolution before the DNA genome: for example, supporting organized biochemistry, coded translation, and a Standard Genetic Code.

Ribosomes: from conserved origin to functional/medical mobility and heterogeneity

Ribosomes, the molecular machines that translate the genetic code from mRNA into proteins in all living cells, are highly structurally conserved across all domains of life and hence are believed to have evolved from a structurally unified pocket. Initially perceived as uniform cellular factories for protein synthesis, currently, ribosomes have emerged as more complex entities. Structural, medical and biochemical studies, including ours, have revealed significant variability in their compositions across tissues, species, functions and developmental stages, highlighting their multifunctional potential. Moreover, the diversity of ribosomes, their components and their associated biological factors challenge the traditional perception of uniform interactions under various conditions, including stress, and expose their mobility and heterogeneity. Evidence for their functional diversity can be seen even in modifications of ribosomal genes, where minor changes may play critical roles under stress or may lead to diseases called ribosomopathies, including Diamond-Blackfan anaemia, some types of cancer and Alzheimer's disease. Thus, through in-depth structural explorations, we improve the understanding of the mechanisms regulating protein biosynthesis in response to various environmental stressors. These findings should potentially reshape the perceptions of the various ribosomal roles.This article is part of the discussion meeting issue 'Ribosome diversity and its impact on protein synthesis, development and disease'.

Origin of the RNA World in Cold Hadean Geothermal Fields Enriched in Zinc and Potassium: Abiogenesis as a Positive Fallout from the Moon-Forming Impact?

The ubiquitous, evolutionarily oldest RNAs and proteins exclusively use rather rare zinc as transition metal cofactor and potassium as alkali metal cofactor, which implies their abundance in the habitats of the first organisms. Intriguingly, lunar rocks contain a hundred times less zinc and ten times less potassium than the Earth's crust; the Moon is also depleted in other moderately volatile elements (MVEs). Current theories of impact formation of the Moon attribute this depletion to the MVEs still being in a gaseous state when the hot post-impact disk contracted and separated from the nascent Moon. The MVEs then fell out onto juvenile Earth's protocrust; zinc, as the most volatile metal, precipitated last, just after potassium. According to our calculations, the top layer of the protocrust must have contained up to 1019 kg of metallic zinc, a powerful reductant. The venting of hot geothermal fluids through this MVE-fallout layer, rich in metallic zinc and radioactive potassium, both capable of reducing carbon dioxide and dinitrogen, must have yielded a plethora of organic molecules released with the geothermal vapor. In the pools of vapor condensate, the RNA-like molecules may have emerged through a pre-Darwinian selection for low-volatile, associative, mineral-affine, radiation-resistant, nitrogen-rich, and polymerizable molecules.

Chemical Evolution of Life on Earth

Background/Objectives: The origin of genes and genetics is the story of the coevolution of translation systems and the genetic code. Remarkably, the history of the origin of life on Earth was inscribed and preserved in the sequences of tRNAs. Methods: Sequence logos demonstrate the patterning of pre-life tRNA sequences. Results: The pre-life type I and type II tRNA sequences are known to the last nucleotide with only a few ambiguities. Type I and type II tRNAs evolved from ligation of three 31 nt minihelices of highly patterned and known sequence followed by closely related 9 nt internal deletion(s) within ligated acceptor stems. The D loop 17 nt core was a truncated UAGCC repeat. The anticodon and T 17 nt stem-loop-stems are homologous sequences with 5 nt stems and 7 nt U-turn loops that were selected in pre-life to resist ribozyme nucleases and to present a 3 nt anticodon with a single wobble position. The 7 nt T loop in tRNA was selected to interact with the D loop at the "elbow". The 5'-acceptor stem was based on a 7 nt truncated GCG repeat. The 3'-acceptor stem was based on a complementary 7 nt CGC repeat. In pre-life, ACCA-Gly was a primitive adapter molecule ligated to many RNAs, including tRNAs, to synthesize polyglycine. Conclusions: Analysis of sequence logos of tRNAs from an ancient Archaeon substantiates how the pre-life to life transition occurred on Earth. Polyglycine is posited to have aggregated complex molecular assemblies, including minihelices, tRNAs, cooperating molecules, and protocells, leading to the first life on Earth.

Biomathematical enzyme kinetics model of prebiotic autocatalytic RNA networks: degenerating parasite-specific hyperparasite catalysts confer parasite resistance and herald the birth of molecular immunity

Catalysis and specifically autocatalysis are the quintessential building blocks of life. Yet, although autocatalytic networks are necessary, they are not sufficient for the emergence of life-like properties, such as replication and adaptation. The ultimate and potentially fatal threat faced by molecular replicators is parasitism; if the polymerase error rate exceeds a critical threshold, even the fittest molecular species will disappear. Here we have developed an autocatalytic RNA early life mathematical network model based on enzyme kinetics, specifically the steady-state approximation. We confirm previous models showing that these second-order autocatalytic cycles are sustainable, provided there is a sufficient nucleotide pool. However, molecular parasites become untenable unless they sequentially degenerate to hyperparasites (i.e. parasites of parasites). Parasite resistance-a parasite-specific host response decreasing parasite fitness-is acquired gradually, and eventually involves an increased binding affinity of hyperparasites for parasites. Our model is supported at three levels; firstly, ribozyme polymerases display Michaelis-Menten saturation kinetics and comply with the steady-state approximation. Secondly, ribozyme polymerases are capable of sustainable auto-amplification and of surmounting the fatal error threshold. Thirdly, with growing sequence divergence of host and parasite catalysts, the probability of self-binding is expected to increase and the trend towards cross-reactivity to diminish. Our model predicts that primordial host-RNA populations evolved via an arms race towards a host-parasite-hyperparasite catalyst trio that conferred parasite resistance within an RNA replicator niche. While molecular parasites have traditionally been viewed as a nuisance, our model argues for their integration into the host habitat rather than their separation. It adds another mechanism-with biochemical precision-by which parasitism can be tamed and offers an attractive explanation for the universal coexistence of catalyst trios within prokaryotes and the virosphere, heralding the birth of a primitive molecular immunity.

Overcoming nucleotide bias in the nonenzymatic copying of RNA templates

The RNA World hypothesis posits that RNA was the molecule of both heredity and function during the emergence of life. This hypothesis implies that RNA templates can be copied, and ultimately replicated, without the catalytic aid of evolved enzymes. A major problem with nonenzymatic template-directed polymerization has been the very poor copying of sequences containing rA and rU. Here, we overcome that problem by using a prebiotically plausible mixture of RNA mononucleotides and random-sequence oligonucleotides, all activated by methyl isocyanide chemistry, that direct the uniform copying of arbitrary-sequence templates, including those harboring rA and rU. We further show that the use of this mixture in copying reactions suppresses copying errors while also generating a more uniform distribution of mismatches than observed for simpler systems. We find that oligonucleotide competition for template binding sites, oligonucleotide ligation and the template binding properties of reactant intermediates work together to reduce product sequence bias and errors. Finally, we show that iterative cycling of templated polymerization and activation chemistry improves the yields of random-sequence products. These results for random-sequence template copying are a significant advance in the pursuit of nonenzymatic RNA replication.

RNA World with Inhibitors

During the evolution of the RNA World, compartments, which were fragments of space surrounded by a primitive lipid membrane, had to have emerged. These led eventually to the formation of modern cellular membranes. Inside these compartments, another process had to take place-switching from RNA to DNA as a primary storage of genetic information. The latter part needed a handful of enzymes for the DNA to be able to perform its function. A natural question arises, i.e., how the concentration of all vital molecules could have been kept in check without modern cellular mechanisms. The authors propose a theory on how it could have worked during early stages, using only short RNA molecules, which could have emerged spontaneously. The hypothesis was analysed mathematically and tested against different scenarios by using computer simulations.

Quasispecies theory and emerging viruses: challenges and applications

Quasispecies theory revolutionized our understanding of viral evolution by describing viruses as dynamic populations of genetically diverse variants constantly adapting. This article explores the theory's role in virus-host interactions, including immune evasion, drug resistance, and viral emergence. We review the original model, recent advances, and key virus dynamics needing incorporation into quasispecies theory. We introduce the ultracube concept as a more realistic multidimensional sequence space to investigate virus evolutionary dynamics.

On the aqueous origins of the condensation polymers of life

Water is essential for life as we know it, but it has paradoxically been considered inimical to the emergence of life. Proteins and nucleic acids have sustained evolution and life for billions of years, but both are condensation polymers, suggesting that their formation requires the elimination of water. This presents intrinsic challenges at the origins of life, including how condensation polymer synthesis can overcome the thermodynamic pressure of hydrolysis in water and how nucleophiles can kinetically outcompete water to yield condensation products. The answers to these questions lie in balancing thermodynamic activation and kinetic stability. For peptides, an effective strategy is to directly harness the energy trapped in prebiotic molecules, such as nitriles, and avoid the formation of fully hydrolysed monomers. In this Review, we discuss how chemical energy can be built into precursors, retained, and released selectively for polymer synthesis. Looking to the future, the outstanding goals include how nucleic acids can be synthesized, avoiding the formation of fully hydrolysed monomers and what caused information to flow from nucleic acids to proteins.

Viroid and viroid-like elements in plants and plant-associated microbiota: a new layer of biodiversity for plant holobionts

The functional relevance of plant-associated microorganisms is theoretically framed within the holobiont concept. The role of viruses in plant holobionts is being recognized both for their direct effects when hosted in plants (cryptic plant viruses) and for their indirect effects when infecting microorganisms associated with plants in tripartite interactions (e.g. mycoviruses and bacteriophages). We argue that viroids, the smallest infectious agents typically infecting only plant hosts, must also be included in plant holobiont studies. The same applies to the recently discovered large number of viroid-like elements infecting hosts of other life kingdoms that are closely associated with plants. Here we also describe in depth the diversity of such viroid-like elements and their initial functional characterization in plant-associated fungi.

Cross-chiral exponential amplification of an RNA enzyme

An RNA ligase ribozyme that catalyzes the joining of RNA molecules of the opposite chiral handedness was optimized for the ability to synthesize its own enantiomer from two component fragments. The mirror-image D- and L-ligases operate in concert to provide a system for cross-chiral replication, whereby they catalyze each other's synthesis and undergo mutual amplification at constant temperature, with apparent exponential growth and a doubling time of about 1 h. Neither the D- nor the L-RNA components alone can achieve autocatalytic self-replication. Cross-chiral exponential amplification can be continued indefinitely through a serial-transfer process that provides an ongoing supply of the component D- and L-substrates. Unlike the familiar paradigm of semiconservative nucleic acid replication that relies on Watson-Crick pairing between complementary strands, cross-chiral replication relies on tertiary interactions between structured nucleic acids "across the mirror." There are few examples, outside of biology, of autocatalytic self-replication systems that undergo exponential amplification and there are no prior examples, in either biological or chemical systems, of cross-chiral replication enabling exponential amplification.

Pioneering role of RNA in the early evolution of life

The catalytic, regulatory and structural properties of RNA, combined with their extraordinary ubiquity in cellular processes, are consistent with the proposal that this molecule played a much more conspicuous role in heredity and metabolism during the early stages of biological evolution. This review explores the pivotal role of RNA in the earliest life forms and its relevance in modern biological systems. It examines current models that study the early evolution of life, providing insights into the primordial RNA world and its legacy in contemporary biology.

A Concept of Complementarity Between Complexity and Redundancy can Account for Kant's Biological Teleology and Unify Mechanistic and Finalistic Biology

Over 160 years after Darwin and 70 years after the discovery of DNA, two fundamental questions of biology remain unanswered: What differentiates the living from the nonliving? How can mechanistic and finalistic or holistic biology be unified? Niels Bohr introduced a concept of complementarity in quantum physics and based on the paradox of light as a simultaneous wave and particle, conjectured that a similar concept might exist in biology that would solve the paradox of life originating from the nonliving. Bohr proposed that two mutually exclusive-independent observations may be necessary to explain a phenomenon and provided support to Immanuel Kant's idea that the "purposive" behaviour of organisms could only be explained in teleological terms and that mechanical and teleological approaches were necessary and complementary to explain biology. We present a concept of complementarity whereby biochemical pathways or cellular channels for the flow of information are simultaneously complex and redundant and complexity and redundancy complement each other. The postulates of biological complementarity are that (1) it was an essential condition in the origin of life; (2) it provided physiological flexibility that allowed organisms to mount self-protection response and complexity to evolve in the face of deleterious mutations before the evolution of bi-parental sex; (3) it laid the foundation for the evolution of a choice of response when confronted with threat; and (4) it applies to all levels of biological organizations and, thus, can serve as a basis for the unification of mechanistic and holistic biology. It is proposed that teleology is simultaneously constitutive and heuristic: constitutive because organisms' "purposive" behaviours are adaptive and are grounded in mechanism (complexity and redundancy), and heuristic because with our finite cognition and our goal-oriented (humans alone are aware of "tomorrow") and anthropomorphic pre-disposition, teleology will remain useful as a guide to our making sense of the world, even how to ask a meaningful question.