Metabolically Coupled Replicator Systems: Overview of an RNA-world model concept of prebiotic evolution on mineral surfaces

The Evolution of Microbial Facilitation: Sociogenesis, Symbiogenesis, and Transition in Individuality

Metabolic cooperation is widespread, and it seems to be a ubiquitous and easily evolvable interaction in the microbial domain. Mutual metabolic cooperation, like syntrophy, is thought to have a crucial role in stabilizing interactions and communities, for example biofilms. Furthermore, cooperation is expected to feed back positively to the community under higher-level selection. In certain cases, cooperation can lead to a transition in individuality, when freely reproducing, unrelated entities (genes, microbes, etc.) irreversibly integrate to form a new evolutionary unit. The textbook example is endosymbiosis, prevalent among eukaryotes but virtually lacking among prokaryotes. Concerning the ubiquity of syntrophic microbial communities, it is intriguing why evolution has not lead to more transitions in individuality in the microbial domain. We set out to distinguish syntrophy-specific aspects of major transitions, to investigate why a transition in individuality within a syntrophic pair or community is so rare. We review the field of metabolic communities to identify potential evolutionary trajectories that may lead to a transition. Community properties, like joint metabolic capacity, functional profile, guild composition, assembly and interaction patterns are important concepts that may not only persist stably but according to thought-provoking theories, may provide the heritable information at a higher level of selection. We explore these ideas, relating to concepts of multilevel selection and of informational replication, to assess their relevance in the debate whether microbial communities may inherit community-level information or not.

Catalytic promiscuity in the RNA World may have aided the evolution of prebiotic metabolism

The Metabolically Coupled Replicator System (MCRS) model of early chemical evolution offers a plausible and efficient mechanism for the self-assembly and the maintenance of prebiotic RNA replicator communities, the likely predecessors of all life forms on Earth. The MCRS can keep different replicator species together due to their mandatory metabolic cooperation and limited mobility on mineral surfaces, catalysing reaction steps of a coherent reaction network that produces their own monomers from externally supplied compounds. The complexity of the MCRS chemical engine can be increased by assuming that each replicator species may catalyse more than a single reaction of metabolism, with different catalytic activities of the same RNA sequence being in a trade-off relation: one catalytic activity of a promiscuous ribozyme can increase only at the expense of the others on the same RNA strand. Using extensive spatially explicit computer simulations we have studied the possibility and the conditions of evolving ribozyme promiscuity in an initial community of single-activity replicators attached to a 2D surface, assuming an additional trade-off between replicability and catalytic activity. We conclude that our promiscuous replicators evolve under weak catalytic trade-off, relatively strong activity/replicability trade-off and low surface mobility of the replicators and the metabolites they produce, whereas catalytic specialists benefit from very strong catalytic trade-off, weak activity/replicability trade-off and high mobility. We argue that the combination of conditions for evolving promiscuity are more probable to occur for surface-bound RNA replicators, suggesting that catalytic promiscuity may have been a significant factor in the diversification of prebiotic metabolic reaction networks.

Complex biochemical machineries responsible for maintaining the correct ratio of enzymes and genes were highly unlikely to exist at the wake of life. Individual genes must have been subject to competition for resources of replication leading to the competitive exclusion between them, and thus to the loss of genetic information. A feasible scenario that avoids competitive exclusion requires the assumption of mandatory cooperation between the enzymes.

A potentially dynamically important but mostly neglected feature of RNA enzymes (ribozymes) is their capacity to catalyse more than a single reaction. Here, we analyse the possibility that this “promiscous” nature of prebiotic ribozymes could have helped the maintenance of early replicator communities cooperating in running a simple metabolism. To do so, we have implemented a spatially explicit computer model simulating the dynamics of replicating entities on a mineral surface–an extension of the Metabolically Coupled Replicator System including the possibility of multiple catalytic activities within the same replicator. Our results suggest that under realistic assumptions of replicator and metabolite mobility and feasible trade-off relations between different catalytic activities of the same RNA replicator molecule, catalytic promiscuity may have indeed helped booting up life through supporting the assembly of minimal metabolisms.

Cell Communications among Microorganisms, Plants, and Animals: Origin, Evolution, and Interplays

Cellular communications play pivotal roles in multi-cellular species, but they do so also in uni-cellular species. Moreover, cells communicate with each other not only within the same individual, but also with cells in other individuals belonging to the same or other species. These communications occur between two unicellular species, two multicellular species, or between unicellular and multicellular species. The molecular mechanisms involved exhibit diversity and specificity, but they share common basic features, which allow common pathways of communication between different species, often phylogenetically very distant. These interactions are possible by the high degree of conservation of the basic molecular mechanisms of interaction of many ligand-receptor pairs in evolutionary remote species. These inter-species cellular communications played crucial roles during Evolution and must have been positively selected, particularly when collectively beneficial in hostile environments. It is likely that communications between cells did not arise after their emergence, but were part of the very nature of the first cells. Synchronization of populations of non-living protocells through chemical communications may have been a mandatory step towards their emergence as populations of living cells and explain the large commonality of cell communication mechanisms among microorganisms, plants, and animals.

From self-replication to replicator systems en route to de novo life

The process by which chemistry can give rise to biology remains one of the biggest mysteries in contemporary science. The de novo synthesis and origin of life both require the functional integration of three key characteristics - replication, metabolism and compartmentalization - into a system that is maintained out of equilibrium and is capable of open-ended Darwinian evolution. This Review takes systems of self-replicating molecules as starting points and describes the steps necessary to integrate additional characteristics of life. We analyse how far experimental self-replicators have come in terms of Darwinian evolution. We also cover models of replicator communities that attempt to solve Eigen's paradox, whereby accurate replication needs complex machinery yet obtaining such complex self-replicators through evolution requires accurate replication. Successful models rely on a collective metabolism and a way of (transient) compartmentalization, suggesting that the invention and integration of these two characteristics is driven by evolution. Despite our growing knowledge, there remain numerous key challenges that may be addressed by a combined theoretical and experimental approach.

Emergence of light-driven protometabolism on recruitment of a photocatalytic cofactor by a self-replicator

Establishing how life can emerge from inanimate matter is among the grand challenges of contemporary science. Chemical systems that capture life's essential characteristics-replication, metabolism and compartmentalization-offer a route to understanding this momentous process. The synthesis of life, whether based on canonical biomolecules or fully synthetic molecules, requires the functional integration of these three characteristics. Here we show how a system of fully synthetic self-replicating molecules, on recruiting a cofactor, acquires the ability to transform thiols in its environment into disulfide precursors from which the molecules can replicate. The binding of replicator and cofactor enhances the activity of the latter in oxidizing thiols into disulfides through photoredox catalysis and thereby accelerates replication by increasing the availability of the disulfide precursors. This positive feedback marks the emergence of light-driven protometabolism in a system that bears no resemblance to canonical biochemistry and constitutes a major step towards the highly challenging aim of creating a new and completely synthetic form of life.

The Future of Origin of Life Research: Bridging Decades-Old Divisions

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories-e.g. bottom-up and top-down, RNA world vs. metabolism-first-have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research.

Dynamics and stability in prebiotic information integration: an RNA World model from first principles

The robust coevolution of catalytically active, metabolically cooperating prebiotic RNA replicators were investigated using an RNA World model of the origin of life based on physically and chemically plausible first principles. The Metabolically Coupled Replicator System assumes RNA replicators to supply metabolically essential catalytic activities indispensable to produce nucleotide monomers for their own template replication. Using external chemicals as the resource and the necessary ribozyme activities, Watson-Crick type replication produces complementary strands burdened by high-rate point mutations (insertions, deletions, substitutions). Metabolic ribozyme activities, replicabilities and decay rates are assigned to certain sequence and/or folding (thermodynamical) properties of single-stranded RNA molecules. Short and loosely folded sequences are given replication advantage, longer and tightly folded ones are better metabolic ribozymes and more resistant to hydrolytic decay. We show that the surface-bound MCRS evolves stable and metabolically functional communities of replicators of almost equal lengths, replicabilities and ribozyme activities. Being highly resistant to the invasion of parasitic (non-functional) replicators, it is also stable in the evolutionary sense. The template replication mechanism selects for catalytic “promiscuity”: the two (complementary) strands of the same evolved replicator will often carry more than a single catalytically active motif, thus maximizing functionality in a minimum of genetic information.

Detecting life signatures with RNA sequence similarity measures

The RNA World is currently the most plausible hypothesis for explaining the origins of life on Earth. The supporting body of evidence is growing and it comes from multiple areas, including astrobiology, chemistry, biology, mathematics, and, in particular, from computer simulations. Such methods frequently assume the existence of a hypothetical species on Earth, around three billion years ago, with a base sequence probably dissimilar from any in known genomes. However, it is often hard to verify whether or not a hypothetical sequence has the characteristics of biological sequences, and is thus likely to be functional. The primary objective of the presented research was to verify the possibility of building a computational 'life probe' for determining whether a given genetic sequence is biological, and assessing the sensitivity of such probes to the signatures of life present in known biological sequences. We have proposed decision algorithms based on the normalized compression distance (NCD) and Levenshtein distance (LD). We have validated the proposed method in the context of the RNA World hypothesis using short genetic sequences shorter than the error threshold value (i.e., 100 nucleotides). We have demonstrated that both measures can be successfully used to construct life probes that are significantly better than a random decision procedure, while varying from each other when it comes to detailed characteristics. We also observed that fragments of sequences related to replication have better discriminatory power than sequences having other molecular functions. In a broader context, this shows that the signatures of life in short RNA samples can be effectively detected using relatively simple means.

Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve

Background

Genetic parasites are ubiquitous satellites of cellular life forms most of which host a variety of mobile genetic elements including transposons, plasmids and viruses. Theoretical considerations and computer simulations suggest that emergence of genetic parasites is intrinsic to evolving replicator systems.

Results

Using methods of bifurcation analysis, we investigated the stability of simple models of replicator-parasite coevolution in a well-mixed environment. We first analyze what appears to be the simplest imaginable system of this type, one in which the parasite evolves during the replication of the host genome through a minimal mutation that renders the genome of the emerging parasite incapable of producing the replicase but able to recognize and recruit it for its own replication. This model has only trivial or “semi-trivial”, parasite-free equilibria: an inefficient parasite is outcompeted by the host and dies off, whereas an efficient one pushes the host out of existence, leading to the collapse of the entire system. We show that stable host-parasite coevolution (a non-trivial equilibrium) is possible in a modified model where the parasite is qualitatively distinct from the host replicator in that the replication of the parasite depends solely on the availability of the host but not on the carrying capacity of the environment.

Conclusions

We analytically determine the conditions for stable coevolution of genetic parasites and their hosts coevolution in simple mathematical models. It is shown that the evolutionary dynamics of a parasite that initially evolves from the host through the loss of the ability to replicate autonomously must substantially differ from that of the host, for a stable host-parasite coevolution regime to be established.

Electronic supplementary material

The online version of this article (10.1186/s13062-018-0230-9) contains supplementary material, which is available to authorized users.

Moderate sex between protocells can balance between a decrease in assortment load and an increase in parasite spread

Sexual reproduction is widespread in nature despite the different kinds of cost that it entails. We do not know exactly when the first sexual process took place and especially why it was beneficial at first. It is clearer why sex is advantageous for the prokaryotes and eukaryotes but the benefit of sex for protocells with individually replicating ribozymes is not yet fully understood. In this context sex is the simple horizontal gene transfer among two protocells that undergo transient fusion. Many authors argue that horizontal gene transfer (HGT) was very common in the early stage of evolution. However, HGT is a risky mechanism considering both the disruption of optimal compositions and the spread of parasites among protocells. In order to test the effects of HGT on the fitness of a protocell population, we explored by numerical simulations those conditions under which fusion might have been beneficial. We investigated multiple conceivable types of fusion in the stochastic corrector model framework and we considered the spread of parasites in every case. Protocells contain up to five species of unlinked, essential ribozymes; if a protocell has the same amount of each, it reaches maximum fitness. Fusion is dangerous not only due to the spread of parasites but also because it can ruin the cells with balanced ribozyme composition. We show that fusion can restore the ribozyme composition of the protocells under certain circumstances (high gene count, intermediate split size and low rate of fusion) and thus it can decrease the effect of the genetic load. Fusion could have been a useful early mechanism in contributing to the reliable coexistence of the different ribozymes before the spread of the chromosomes.

Mathematical modeling reveals spontaneous emergence of self-replication in chemical reaction systems

Explaining the origin of life requires us to elucidate how self-replication arises. To be specific, how can a self-replicating entity develop spontaneously from a chemical reaction system in which no reaction is self-replicating? Previously proposed mathematical models either supply an explicit framework for a minimal living system or consider only catalyzed reactions, and thus fail to provide a comprehensive theory. Here, we set up a general mathematical model for chemical reaction systems that properly accounts for energetics, kinetics, and the conservation law. We found that 1) some systems are collectively catalytic, a mode whereby reactants are transformed into end products with the assistance of intermediates (as in the citric acid cycle), whereas some others are self-replicating, that is, different parts replicate each other and the system self-replicates as a whole (as in the formose reaction, in which sugar is replicated from formaldehyde); 2) side reactions do not always inhibit such systems; 3) randomly chosen chemical universes (namely random artificial chemistries) often contain one or more such systems; 4) it is possible to construct a self-replicating system in which the entropy of some parts spontaneously decreases, in a manner similar to that discussed by Schrödinger; and 5) complex self-replicating molecules can emerge spontaneously and relatively easily from simple chemical reaction systems through a sequence of transitions. Together, these results start to explain the origins of prebiotic evolution.

Models of Replicator Proliferation Involving Differential Replicator Subunit Stability

Several models for the origin of life involve molecules that are capable of self-replication, such as self-replicating polymers composed of RNA or DNA or amino acids. Here we consider a hypothetical replicator (AB) composed of two subunits, A and B. Programs written in Python and C programming languages were used to model AB replicator abundance as a function of cycles of replication (iterations), under specified hypothetical conditions. Two non-exclusive models describe how a reduced stability for B relative to A can have an advantage for replicator activity and/or evolution by generating free A subunits. In model 1, free A subunits associate with AB replicators to create AAB replicators with greater activity. In simulations, reduced stability of B was beneficial when the replication activity of AAB was greater than two times the replication activity of AB. In model 2, the free A subunit is inactive for some number of iterations before it re-creates the B subunit. A re-creates the B subunit with an equal chance of creating B or B', where B' is a mutant that increases AB' replicator activity relative to AB. In simulations, at moderate number of iterations (< 15), a shorter survival time for B is beneficial when the stability of B is greater than the inactive time of A. The results are consistent with the hypothesis that reduced stability for a replicator subunit can be advantageous under appropriate conditions.

Exploring the emergence of complexity using synthetic replicators

A significant number of synthetic systems capable of replicating themselves or entities that are complementary to themselves have appeared in the last 30 years. Building on an understanding of the operation of synthetic replicators in isolation, this field has progressed to examples where catalytic relationships between replicators within the same network and the extant reaction conditions play a role in driving phenomena at the level of the whole system. Systems chemistry has played a pivotal role in the attempts to understand the origin of biological complexity by exploiting the power of synthetic chemistry, in conjunction with the molecular recognition toolkit pioneered by the field of supramolecular chemistry, thereby permitting the bottom-up engineering of increasingly complex reaction networks from simple building blocks. This review describes the advances facilitated by the systems chemistry approach in relating the expression of complex and emergent behaviour in networks of replicators with the connectivity and catalytic relationships inherent within them. These systems, examined within well-stirred batch reactors, represent conceptual and practical frameworks that can then be translated to conditions that permit replicating systems to overcome the fundamental limits imposed on selection processes in networks operating under closed conditions. This shift away from traditional spatially homogeneous reactors towards dynamic and non-equilibrium conditions, such as those provided by reaction-diffusion reaction formats, constitutes a key change that mimics environments within cellular systems, which possess obvious compartmentalisation and inhomogeneity.

Ecology and Evolution in the RNA World Dynamics and Stability of Prebiotic Replicator Systems

As of today, the most credible scientific paradigm pertaining to the origin of life on Earth is undoubtedly the RNA World scenario. It is built on the assumption that catalytically active replicators (most probably RNA-like macromolecules) may have been responsible for booting up life almost four billion years ago. The many different incarnations of nucleotide sequence (string) replicator models proposed recently are all attempts to explain on this basis how the genetic information transfer and the functional diversity of prebiotic replicator systems may have emerged, persisted and evolved into the first living cell. We have postulated three necessary conditions for an RNA World model system to be a dynamically feasible representation of prebiotic chemical evolution: (1) it must maintain and transfer a sufficient diversity of information reliably and indefinitely, (2) it must be ecologically stable and (3) it must be evolutionarily stable. In this review, we discuss the best-known prebiotic scenarios and the corresponding models of string-replicator dynamics and assess them against these criteria. We suggest that the most popular of prebiotic replicator systems, the hypercycle, is probably the worst performer in almost all of these respects, whereas a few other model concepts (parabolic replicator, open chaotic flows, stochastic corrector, metabolically coupled replicator system) are promising candidates for development into coherent models that may become experimentally accessible in the future.

Evolutionary Conflict Leads to Innovation: Symmetry Breaking in a Spatial Model of RNA-Like Replicators

Molecules that replicate in trans are vulnerable to evolutionary extinction because they decrease the catalysis of replication to become more available as a template for replication. This problem can be alleviated with higher-level selection that clusters molecules of the same phenotype, favouring those groups that contain more catalysis. Here, we study a simple replicator model with implicit higher-level selection through space. We ask whether the functionality of such system can be enhanced when molecules reproduce through complementary replication, representing RNA-like replicators. For high diffusion, symmetry breaking between complementary strands occurs: one strand becomes a specialised catalyst and the other a specialised template. In ensemble, such replicators can modulate their catalytic activity depending on their environment, thereby mitigating the conflict between levels of selection. In addition, these replicators are more evolvable, facilitating survival in extreme conditions (i.e., for higher diffusion rates). Our model highlights that evolution with implicit higher-level selection—i.e., as a result of local interactions and spatial patterning—is very flexible. For different diffusion rates, different solutions to the selective conflict arise. Our results support an RNA World by showing that complementary replicators may have various ways to evolve more complexity.

Toy trains, loaded dice and the origin of life: dimerization on mineral surfaces under periodic drive with Gaussian inputs

In a major extension of previous work, we model the putative hydrothermal rock pore setting for the origin of life on Earth as a series of coupled continuous flow units (the toy train). Perfusing through this train are reactants that set up thermochemical and pH oscillations, and an activated nucleotide that produces monomer and dimer monophosphates. The dynamical equations that model this system are thermally self-consistent. In an innovative step that breaks some new ground, we build stochasticity of the inputs into the model. The computational results infer various constraints and conditions on, and insights into, chemical evolution and the origin of life and its physical setting: long, interconnected porous structures with longitudinal non-uniformity would have been favourable, and the ubiquitous pH dependences of biology may have been established in the prebiotic era. We demonstrate the important role of Gaussian fluctuations of the inputs in driving polymerization, evolution and diversification. In particular, we find that the probability distribution of the resulting output fluctuations is left-skewed and right-weighted (the loaded dice), which could favour chemical evolution towards a living RNA world. We tentatively name this distribution 'Goldilocks'. These results also vindicate the general approach of constructing and running a simple model to learn important new information about a complex system.

An Experimental Framework for Generating Evolvable Chemical Systems in the Laboratory

Most experimental work on the origin of life has focused on either characterizing the chemical synthesis of particular biochemicals and their precursors or on designing simple chemical systems that manifest life-like properties such as self-propagation or adaptive evolution. Here we propose a new class of experiments, analogous to artificial ecosystem selection, where we select for spontaneously forming self-propagating chemical assemblages in the lab and then seek evidence of a response to that selection as a key indicator that life-like chemical systems have arisen. Since surfaces and surface metabolism likely played an important role in the origin of life, a key experimental challenge is to find conditions that foster nucleation and spread of chemical consortia on surfaces. We propose high-throughput screening of a diverse set of conditions in order to identify combinations of "food," energy sources, and mineral surfaces that foster the emergence of surface-associated chemical consortia that are capable of adaptive evolution. Identification of such systems would greatly advance our understanding of the emergence of self-propagating entities and the onset of adaptive evolution during the origin of life.

Co-operation between Polymerases and Nucleotide Synthetases in the RNA World

It is believed that life passed through an RNA World stage in which replication was sustained by catalytic RNAs (ribozymes). The two most obvious types of ribozymes are a polymerase, which uses a neighbouring strand as a template to make a complementary sequence to the template, and a nucleotide synthetase, which synthesizes monomers for use by the polymerase. When a chemical source of monomers is available, the polymerase can survive on its own. When the chemical supply of monomers is too low, nucleotide production by the synthetase is essential and the two ribozymes can only survive when they are together. Here we consider a computational model to investigate conditions under which coexistence and cooperation of these two types of ribozymes is possible. The model considers six types of strands: the two functional sequences, the complementary strands to these sequences (which are required as templates), and non-functional mutants of the two sequences (which act as parasites). Strands are distributed on a two-dimensional lattice. Polymerases replicate strands on neighbouring sites and synthetases produce monomers that diffuse in the local neighbourhood. We show that coexistence of unlinked polymerases and synthetases is possible in this spatial model under conditions in which neither sequence could survive alone; hence, there is a selective force for increasing complexity. Coexistence is dependent on the relative lengths of the two functional strands, the strand diffusion rate, the monomer diffusion rate, and the rate of deleterious mutations. The sensitivity of this two-ribozyme system suggests that evolution of a system of many types of ribozymes would be difficult in a purely spatial model with unlinked genes. We therefore speculate that linkage of genes onto mini-chromosomes and encapsulation of strands in protocells would have been important fairly early in the history of life as a means of enabling more complex systems to evolve.

Trans-acting polymerases are cooperative, because they copy neighbouring strands, and do not copy themselves directly. Inaccurate replication creates parasitic strands that act as templates but not ribozymes. It is known that in spatially distributed models with slow strand diffusion, clusters of cooperating polymerases arise that can survive in the presence of parasites provided that the error rate is less than a maximum limit (the error threshold). In the RNA World, we envisage multiple types of ribozymes working together. We would like to understand how a multi-ribozyme system could evolve from a system with a single type of polymerase ribozyme. As a first step in increasing complexity, we consider a two-ribozyme system in which there is one polymerase and one nucleotide synthetase that produces monomers for use by the polymerase. We are particularly interested to find conditions in which the chemical supply of monomers is too low for the polymerase to survive alone, but the additional monomers created by the synthetase allow the two-ribozyme system to survive where the single-ribozyme system could not. There is then a selective force for increasing the complexity of the system. Here we show that spatial clustering is sufficient to allow cooperation and survival of systems of unlinked ribozymes with different functions. Clusters form in which synthetases form fringes around the polymerases. Survival of the two-ribozyme system depends on several factors. The strand diffusion rate must be slow enough for cooperative clusters to emerge. The replication rate of the polymerase must be comparable to that of the synthetase. The diffusion rate of the monomers must be neither too slow nor too fast. The model considers the most difficult case for cooperation–unlinked genes with no compartments. The sensitivity of the two-ribozyme system that we study here suggests that evolution of a spatial system with multiple unlinked ribozymes would become increasingly more difficult as the number of components increased, and suggests that linkage and protocells would need to evolve relatively early in the history of life.

Dynamics of prebiotic RNA reproduction illuminated by chemical game theory

Many origins-of-life scenarios depict a situation in which there are common and potentially scarce resources needed by molecules that compete for survival and reproduction. The dynamics of RNA assembly in a complex mixture of sequences is a frequency-dependent process and mimics such scenarios. By synthesizing Azoarcus ribozyme genotypes that differ in their single-nucleotide interactions with other genotypes, we can create molecules that interact among each other to reproduce. Pairwise interplays between RNAs involve both cooperation and selfishness, quantifiable in a 2 × 2 payoff matrix. We show that a simple model of differential equations based on chemical kinetics accurately predicts the outcomes of these molecular competitions using simple rate inputs into these matrices. In some cases, we find that mixtures of different RNAs reproduce much better than each RNA type alone, reflecting a molecular form of reciprocal cooperation. We also demonstrate that three RNA genotypes can stably coexist in a rock-paper-scissors analog. Our experiments suggest a new type of evolutionary game dynamics, called prelife game dynamics or chemical game dynamics. These operate without template-directed replication, illustrating how small networks of RNAs could have developed and evolved in an RNA world.

Phenotype/genotype sequence complementarity and prebiotic replicator coexistence in the metabolically coupled replicator system

Background

RNA or RNA-like polymers are the most likely candidates for having played the lead roles on the stage of the origin of life. RNA is known to feature two of the three essential functions of living entities (metabolism, heredity and membrane): it is capable of unlimited heredity and it has a proven capacity for catalysing very different chemical reactions which may form simple metabolic networks. The Metabolically Coupled Replicator System is a class of simulation models built on these two functions to show that an RNA World scenario for the origin of life is ecologically feasible, provided that it is played on mineral surfaces. The fact that RNA templates and their copies are of complementary base sequences has an obvious dynamical relevance: complementary strains may have very different structures and, consequently, functions – one may specialize for increasing enzymatic activity while the other takes the role of the gene of the enzyme.

Results

Incorporating the functional divergence of template and copy into the Metabolically Coupled Replicator System model framework we show that sequence complementarity 1) does not ruin the coexistence of a set of metabolically cooperating replicators; 2) the replicator system remains resistant to, but also tolerant with its parasites; 3) opens the way to the evolutionary differentiation of phenotype and genotype through a primitive version of phenotype amplification.

Conclusions

The functional asymmetry of complementary RNA strains results in a shift of phenotype/genotype (enzyme/gene) proportions in MCRS, favouring a slight genotype dominance. This asymmetry is expected to reverse due to the evolved trade-off of high “gene” replicability and high catalytic activity of the corresponding “enzyme” in expense of its replicability. This trade-off is the first evolutionary step towards the “division of labour” among enzymes and genes, which has concluded in the extreme form of phenotype amplification characteristic of our recent DNA-RNA-protein World.

Electronic supplementary material

The online version of this article (doi:10.1186/s12862-014-0234-8) contains supplementary material, which is available to authorized users.