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

Towards an RNA/Peptides World by the Direct RNA Template Mechanism: The Emergence of Membrane-Stabilizing Peptides in RNA-Based Protocells

How functional peptides may have arisen is a significant problem for the scenario of the RNA world. An attractive idea, the direct RNA template (DRT) hypothesis, proposes that RNA molecules can bind amino acids specifically and promote the synthesis of corresponding peptides, thereby starting the RNA/peptides world. To investigate the plausibility of this idea, we modeled the emergence of a "membrane-stabilizing peptide" in RNA-based protocells-such a peptide was suggested to have appeared early in the RNA world based on experimental evidence. The computer simulation demonstrated that the protocells containing the "RNA gene" encoding this peptide may spread in the system owing to the peptide's function. The RNA gene may either originate de novo in protocells or emerge in protocells already containing ribozymes-here we adopt a nucleotide synthetase ribozyme as an example. Furthermore, interestingly, we show that a "nucleotide synthetase peptide" encoded by RNA (also via the DRT mechanism) may substitute the nucleotide synthetase ribozyme in evolution, which may represent how "functional-takeover" in the RNA world could have occurred. Overall, we conclude that the transition from the RNA world towards an RNA/peptides world may well have been mediated by the DRT mechanism. Remarkably, the successful modeling on the emergence of membrane-stabilizing peptide in RNA-based protocells is per se significant, which may imply a "promising" way for peptides to enter the RNA world, especially considering the weak interaction between RNA and the membrane in chemistry.

Rolling Circles as a Means of Encoding Genes in the RNA World

The rolling circle mechanism found in viroids and some RNA viruses is a likely way that replication could have begun in the RNA World. Here, we consider simulations of populations of protocells, each containing multiple copies of rolling circle RNAs that can replicate non-enzymatically. The mechanism requires the presence of short self-cleaving ribozymes such as hammerheads, which can cleave and re-circularize RNA strands. A rolling circle must encode a hammerhead and the complement of a hammerhead, so that both plus and minus strands can cleave. Thus, the minimal functional length is twice the length of the hammerhead sequence. Selection for speed of replication will tend to reduce circles to this minimum length. However, if sequence errors occur when copying the hammerhead sequence, this prevents cleavage at one point, but still allows cleavage on the next passage around the rolling circle. Thus, there is a natural doubling mechanism that creates strands that are multiple times the length of the minimal sequence. This can provide space for the origin of new genes with beneficial functions. We show that if a beneficial gene appears in this new space, the longer sequence with the beneficial function can be selected, even though it replicates more slowly. This provides a route for the evolution of longer circles encoding multiple genes.

The Effect of Environment on the Evolution and Proliferation of Protocells of Increasing Complexity

The formation, growth, division and proliferation of protocells containing RNA strands is an important step in ensuring the viability of a mixed RNA-lipid world. Experiments and computer simulations indicate that RNA encapsulated inside protocells can favor the protocell, promoting its growth while protecting the system from being over-run by selfish RNA sequences. Recent work has also shown that the rolling-circle replication mechanism can be harnessed to ensure the rapid growth of RNA strands and the probabilistic emergence and proliferation of protocells with functionally diverse ribozymes. Despite these advances in our understanding of a primordial RNA-lipid world, key questions remain about the ideal environment for the formation of protocells and its role in regulating the proliferation of functionally complex protocells. The hot spring hypothesis suggests that mineral-rich regions near hot springs, subject to dry-wet cycles, provide an ideal environment for the origin of primitive protocells. We develop a computational model to study protocellular evolution in such environments that are distinguished by the occurrence of three distinct phases, a wet phase, followed by a gel phase, and subsequently by a dry phase. We determine the conditions under which protocells containing multiple types of ribozymes can evolve and proliferate in such regions. We find that diffusion in the gel phase can inhibit the proliferation of complex protocells with the extent of inhibition being most significant when a small fraction of protocells is eliminated during environmental cycling. Our work clarifies how the environment can shape the evolution and proliferation of complex protocells.

Evolutionary transition from a single RNA replicator to a multiple replicator network

In prebiotic evolution, self-replicating molecules are believed to have evolved into complex living systems by expanding their information and functions open-endedly. Theoretically, such evolutionary complexification could occur through successive appearance of novel replicators that interact with one another to form replication networks. Here we perform long-term evolution experiments of RNA that replicates using a self-encoded RNA replicase. The RNA diversifies into multiple coexisting host and parasite lineages, whose frequencies in the population initially fluctuate and gradually stabilize. The final population, comprising five RNA lineages, forms a replicator network with diverse interactions, including cooperation to help the replication of all other members. These results support the capability of molecular replicators to spontaneously develop complexity through Darwinian evolution, a critical step for the emergence of life.

Long-term experimental evolution shows that a single polymerase-encoding RNA replicator can evolve into a complex replicator network, shedding light on how a molecular replicator could have developed complexity before the emergence of life.

The automatic parameter-exploration with a machine-learning-like approach: Powering the evolutionary modeling on the origin of life

The origin of life involved complicated evolutionary processes. Computer modeling is a promising way to reveal relevant mechanisms. However, due to the limitation of our knowledge on prebiotic chemistry, it is usually difficult to justify parameter-setting for the modeling. Thus, typically, the studies were conducted in a reverse way: the parameter-space was explored to find those parameter values “supporting” a hypothetical scene (that is, leaving the parameter-justification a later job when sufficient knowledge is available). Exploring the parameter-space manually is an arduous job (especially when the modeling becomes complicated) and additionally, difficult to characterize as regular “Methods” in a paper. Here we show that a machine-learning-like approach may be adopted, automatically optimizing the parameters. With this efficient parameter-exploring approach, the evolutionary modeling on the origin of life would become much more powerful. In particular, based on this, it is expected that more near-reality (complex) models could be introduced, and thereby theoretical research would be more tightly associated with experimental investigation in this field–hopefully leading to significant steps forward in respect to our understanding on the origin of life.

People have long been interested in the evolutionary processes through which life on our planet could have arisen from a non-life background. However, it seems that experimental studies in this field are proceeding slowly, perhaps owing to the complication of such processes. In the meantime, computer modeling has shown its potential to disclose the evolutionary mechanisms involved. Now a major difficulty of the computer modeling work is to justify the parameter-setting–on account of our limited knowledge on prebiotic chemistry and environments. Thus, people tend to explore the parameter space to seek parameter values in favor of the hypothetic scene and leave the parameter-justification a later job when sufficient knowledge is available. To date, the parameter-exploration is usually conducted manually (in many cases by trial and error), thus arduous and unpredictable. Inspired by the algorithm of machine-learning, we designed an automatic approach of parameter-exploration. The results showed that the approach is quite effective–that is, “good” parameter-sets in favor of hypothetic scenes in the origin of life can be found automatically. It is expected that such a machine-learning-like method would greatly enhance the efficiency of our evolutionary modeling studies on the origin of life in future.

Primitive Compartmentalization for the Sustainable Replication of Genetic Molecules

Sustainable replication and evolution of genetic molecules such as RNA are likely requisites for the emergence of life; however, these processes are easily affected by the appearance of parasitic molecules that replicate by relying on the function of other molecules, while not contributing to their replication. A possible mechanism to repress parasite amplification is compartmentalization that segregates parasitic molecules and limits their access to functional genetic molecules. Although extent cells encapsulate genomes within lipid-based membranes, more primitive materials or simple geological processes could have provided compartmentalization on early Earth. In this review, we summarize the current understanding of the types and roles of primitive compartmentalization regarding sustainable replication of genetic molecules, especially from the perspective of the prevention of parasite replication. In addition, we also describe the ability of several environments to selectively accumulate longer genetic molecules, which could also have helped select functional genetic molecules rather than fast-replicating short parasitic molecules.

Emergence of ribozyme and tRNA-like structures from mineral-rich muddy pools on prebiotic earth

The RNA world hypothesis, although a viable one regarding the origin of life on earth, has so far failed to provide a compelling explanation for the synthesis of RNA enzymes from free nucleotides via abiotic processes. To tackle this long-standing problem, we develop a realistic model for the onset of the RNA world, using experimentally determined rates for polymerization reactions. We start with minimal assumptions about the initial state that only requires the presence of short oligomers or just free nucleotides and consider the effects of environmental cycling by dividing a day into a dry, semi-wet and wet phases that are distinguished by the nature of reactions they support. Long polymers, with maximum lengths sometimes exceeding 100 nucleotides, spontaneously emerge due to a combination of non-enzymatic, non-templated polymer extension and template-directed primer extension processes. The former helps in increasing the lengths of RNA strands, whereas the later helps in producing complementary copies of the strands. Strands also undergo hydrolysis in a structure-dependent manner that favour breaking of bonds connecting unpaired nucleotides. We identify the most favourable conditions needed for the emergence of ribozyme and tRNA-like structures and double stranded RNA molecules, classify all RNA strands on the basis of their secondary structures and determine their abundance in the population. Our results indicate that under suitable environmental conditions, non-enzymatic processes would have been sufficient to lead to the emergence of a variety of ribozyme-like molecules with complex secondary structures and potential catalytic functions.

The generality of transient compartmentalization and its associated error thresholds

Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the presence of mutations and noise in replication, as both can be detrimental the survival of compartments. Our study comprises situations where compartments contain uncoupled autocatalytic reactions feeding on a common resource, and systems based on RNA molecules copied by replicases, following a recent experimental study. Using the theory of branching processes, we show analytically that two regimes are possible. In the diffusion-limited regime, replication is asynchronous which leads to a large variability in the composition of compartments. In contrast, in a replication-limited regime, the growth is synchronous and thus the compositional variability is low. Typically, simple autocatalysts are in the former regime, while polymeric replicators can access the latter. For deterministic growth dynamics, we introduce mutations that turn functional replicators into parasites. We derive the phase boundary separating coexistence or parasite dominance as a function of relative growth, inoculation size and mutation rate. We show that transient compartmentalization allows coexistence beyond the classical error threshold, above which the parasite dominates. Our findings invite to revisit major prebiotic transitions, notably the transitions towards cooperation, complex polymers and cell division.

The origin of the central dogma through conflicting multilevel selection

The central dogma of molecular biology rests on two kinds of asymmetry between genomes and enzymes: informatic asymmetry, where information flows from genomes to enzymes but not from enzymes to genomes; and catalytic asymmetry, where enzymes provide chemical catalysis but genomes do not. How did these asymmetries originate? Here, we show that these asymmetries can spontaneously arise from conflict between selection at the molecular level and selection at the cellular level. We developed a model consisting of a population of protocells, each containing a population of replicating catalytic molecules. The molecules are assumed to face a trade-off between serving as catalysts and serving as templates. This trade-off causes conflicting multilevel selection: serving as catalysts is favoured by selection between protocells, whereas serving as templates is favoured by selection between molecules within protocells. This conflict induces informatic and catalytic symmetry breaking, whereby the molecules differentiate into genomes and enzymes, establishing the central dogma. We show mathematically that the symmetry breaking is caused by a positive feedback between Fisher’s reproductive values and the relative impact of selection at different levels. This feedback induces a division of labour between genomes and enzymes, provided variation at the molecular level is sufficiently large relative to variation at the cellular level, a condition that is expected to hinder the evolution of altruism. Taken together, our results suggest that the central dogma is a logical consequence of conflicting multilevel selection.

Can the RNA World Still Function without Cytidine?

Most scenarios for the origin of life assume that RNA played a key role in both catalysis and information storage. The A, U, G, and C nucleobases in modern RNA all participate in secondary structure formation and replication. However, the rapid deamination of C to U and the absence of C in meteorite samples suggest that prebiotic RNA may have been deficient in cytosine. Here, we assess the ability of RNA sequences formed from a three-letter AUG alphabet to perform both structural and genetic roles in comparison to sequences formed from the AUGC alphabet. Despite forming less thermodynamically stable helices, the AUG alphabet can find a broad range of structures and thus appears sufficient for catalysis in the RNA World. However, in the AUG case, longer sequences are required to form structures with an equivalent complexity. Replication in the AUG alphabet requires GU pairing. Sequence fidelity in the AUG alphabet is low whenever G’s are present in the sequence. We find that AUG sequences evolve to AU sequences if GU pairing is rare, and to RU sequences if GU pairing is common (R denotes A or G). It is not possible to conserve a G at a specific site in either case. These problems do not rule out the possibility of an RNA World based on AUG, but they show that it wouldbe significantly more difficult than with a four-base alphabet.

Survival of RNA Replicators is much Easier in Protocells than in Surface-Based, Spatial Systems

In RNA-World scenarios for the origin of life, replication is catalyzed by polymerase ribozymes. Replicating RNA systems are subject to invasion by non-functional parasitic strands. It is well-known that there are two ways to avoid the destruction of the system by parasites: spatial clustering in models with limited diffusion, or group selection in protocells. Here, we compare computational models of replication in spatial models and protocells as closely as possible in order to determine the relative importance of these mechanisms in the RNA World. For the survival of the polymerases, the replication rate must be greater than a minimum threshold value, k_min, and the mutation rate in replication must be less than a maximum value, M_max, which is known as the error threshold. For the protocell models, we find that k_min is substantially lower and M_max is substantially higher than for the equivalent spatial models; thus, the survival of polymerases is much easier in protocells than on surfaces. The results depend on the maximum number of strands permitted in one protocell or one lattice site in the spatial model, and on whether replication is limited by the supply of monomers or the population size of protocells. The substantial advantages that are seen in the protocell models relative to the spatial models are robust to changing these details. Thus, cooperative polymerases with limited accuracy would have found it much easier to operate inside lipid compartments, and this suggests that protocells may have been a very early step in the development of life. We consider cases where parasites have an equal replication rate to polymerases, and cases where parasites multiply twice as fast as polymerases. The advantage of protocell models over spatial models is increased when the parasites multiply faster.

Horizontal transfer between loose compartments stabilizes replication of fragmented ribozymes

The emergence of replicases that can replicate themselves is a central issue in the origin of life. Recent experiments suggest that such replicases can be realized if an RNA polymerase ribozyme is divided into fragments short enough to be replicable by the ribozyme and if these fragments self-assemble into a functional ribozyme. However, the continued self-replication of such replicases requires that the production of every essential fragment be balanced and sustained. Here, we use mathematical modeling to investigate whether and under what conditions fragmented replicases achieve continued self-replication. We first show that under a simple batch condition, the replicases fail to display continued self-replication owing to positive feedback inherent in these replicases. This positive feedback inevitably biases replication toward a subset of fragments, so that the replicases eventually fail to sustain the production of all essential fragments. We then show that this inherent instability can be resolved by small rates of random content exchange between loose compartments (i.e., horizontal transfer). In this case, the balanced production of all fragments is achieved through negative frequency-dependent selection operating in the population dynamics of compartments. The horizontal transfer also ensures the presence of all essential fragments in each compartment, sustaining self-replication. Taken together, our results underline compartmentalization and horizontal transfer in the origin of the first self-replicating replicases.

How evolution got started is a crucial question in the origin of life. One possibility is that RNA molecules gained the ability to catalyze self-replication. Researchers recently proposed how this possibility might have been realized: a long RNA catalyst was divided into short replicable fragments, and these fragments self-assembled into the original long catalyst. Ingenious though it is, we expose a hidden flaw in this proposal. An auto-catalytic system based on fragmented catalysts involves positive feedback, which necessarily biases replication toward specific fragments and eventually halts the replication of the whole system. However, we also propose an effective remedy to this flaw: compartmentalization and content exchange among compartments generate negative feedback, which tightly coordinates the replication of different fragments.

From molecular to cellular form: modeling the first major transition during the arising of life

BACKGROUND

It has long been suggested that Darwinian evolution may have started at the molecular level and subsequently proceeded to a level with membrane boundary, i.e., of protocells. The transformation has been referred to as "the first major transition leading to life". However, so far, we actually have little knowledge about the relevant evolutionary mechanisms - and even about the plausibility - of such a transition. Here, based upon the scenario of the RNA world, we performed a computer simulation study to address this issue.

RESULTS

First, it was shown that at the molecular level, after the spread of one ribozyme (RNA replicase), another ribozyme (nucleotide synthetase) may emerge naturally in the system, and the two ribozymes would cooperate to spread in the naked scene. Then, when empty vesicles absorb the two ribozymes via "cytophagy", the resulting protocells may spread in the system and substitute the naked ribozymes. As for the driven power of such a transition, it was demonstrated that the membrane boundary's roles to ensure the cooperation between the two ribozymes and to prevent invasion of parasites are important. Beyond that, remarkably, it was found that another two factors may also have been significant: a possibly higher mobility of the raw materials in the environment (free water) and the protocells' potential capability to move around actively. Finally, the permeability of the membrane to raw materials was shown to be a major problem regarding the disadvantage for the cellular form.

CONCLUSIONS

The transition from the molecular level to the cellular level may have occurred naturally in early history of evolution. The evolutionary mechanisms for this process were complex. Besides the membrane boundary's roles to guarantee the molecular cooperation and to resist parasites, the greater chance for the protocells to access raw materials - either due to the diffusion of raw materials outside or the protocells' active movement, should also be highlighted, which may have at least to an extent compensated the disadvantage regarding the membrane's blocking effect against raw materials. The present study represents an effort of systematical exploration on this significant transition during the arising of life.

Selection Dynamics in Transient Compartmentalization

Transient compartments have been recently shown to be able to maintain functional replicators in the context of prebiotic studies. Here, we show that a broad class of selection dynamics is able to achieve this goal. We identify two key parameters, the relative amplification of nonactive replicators (parasites) and the size of compartments. These parameters account for competition and diversity, and the results are relevant to similar multilevel selection problems, such as those found in virus-host ecology and trait group selection.

Conceptualizing the origin of life in terms of evolution

In this opinion piece, we discuss how to place evolution in the context of origin-of-life research. Our discussion starts with a popular definition: 'life is a self-sustained chemical system capable of undergoing Darwinian evolution'. According to this definition, the origin of life is the same as the origin of evolution: evolution is the 'end' of the origin of life. This perspective, however, has a limitation, in that the ability of evolution in and of itself is insufficient to explain the origin of life as we know it, as indicated by Spiegelman's and Lincoln and Joyce's experiments. This limitation provokes a crucial question: What conditions are required for replicating systems to evolve into life? From this perspective, the origin of life includes the emergence of life through evolution: evolution is a 'means' of the origin of life. After reviewing Eigen's pioneering work on this question, we mention our ongoing work suggesting that a key condition might be conflicting multi-level evolution. Taken together, there are thus two questions regarding the origin of life: how evolution gets started, and how evolution produces life. Evolution is, therefore, at the centre of the origin of life, where the two lines of enquiry must meet.This article is part of the themed issue 'Reconceptualizing the origins of life'.

Kin Selection in the RNA World

Various steps in the RNA world required cooperation. Why did life’s first inhabitants, from polymerases to synthetases, cooperate? We develop kin selection models of the RNA world to answer these questions. We develop a very simple model of RNA cooperation and then elaborate it to model three relevant issues in RNA biology: (1) whether cooperative RNAs receive the benefits of cooperation; (2) the scale of competition in RNA populations; and (3) explicit replicator diffusion and survival. We show: (1) that RNAs are likely to express partial cooperation; (2) that RNAs will need mechanisms for overcoming local competition; and (3) in a specific example of RNA cooperation, persistence after replication and offspring diffusion allow for cooperation to overcome competition. More generally, we show how kin selection can unify previously disparate answers to the question of RNA world cooperation.

What Does "the RNA World" Mean to "the Origin of Life"?

Corresponding to life’s two distinct aspects: Darwinian evolution and self-sustainment, the origin of life should also split into two issues: the origin of Darwinian evolution and the arising of self-sustainment. Because the “self-sustainment” we concern about life should be the self-sustainment of a relevant system that is “defined” by its genetic information, the self-sustainment could not have arisen before the origin of Darwinian evolution, which was just marked by the emergence of genetic information. The logic behind the idea of the RNA world is not as tenable as it has been believed. That is, genetic molecules and functional molecules, even though not being the same material, could have emerged together in the beginning and launched the evolution—provided that the genetic molecules can “simply” code the functional molecules. However, due to these or those reasons, alternative scenarios are generally much less convincing than the RNA world. In particular, when considering the accumulating experimental evidence that is supporting a de novo origin of the RNA world, it seems now quite reasonable to believe that such a world may have just stood at the very beginning of life on the Earth. Therewith, we acquire a concrete scenario for our attempts to appreciate those fundamental issues that are involved in the origin of life. In the light of those possible scenes included in this scenario, Darwinian evolution may have originated at the molecular level, realized upon a functional RNA. When two or more functional RNAs emerged, for their efficient cooperation, there should have been a selective pressure for the emergence of protocells. But it was not until the appearance of the “unitary-protocell”, which had all of its RNA genes linked into a chromosome, that Darwinian evolution made its full step towards the cellular level—no longer severely constrained by the low-grade evolution at the molecular level. Self-sustainment did not make sense before protocells emerged. The selection pressure that was favoring the exploration of more and more fundamental raw materials resulted in an evolutionary tendency of life to become more and more self-sustained. New functions for the entities to adapt to environments, including those that are involved in the self-sustainment per se, would bring new burdens to the self-sustainment—the advantage of these functions must overweigh the corresponding disadvantage.

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.

Origin and Evolution of RNA-Dependent RNA Polymerase

RNA-dependent RNA polymerases (RdRp) are very ancient enzymes and are essential for all viruses with RNA genomes. We reconstruct the origin and evolution of this polymerase since the initial stages of the origin of life. The origin of the RdRp was traced back from tRNA ancestors. At the origin of the RdRp the most ancient part of the protein is the cofactor-binding site that had the capacity of binding to simple molecules as magnesium, calcium, and ribonucleotides. Our results suggest that RdRp originated from junctions of proto-tRNAs that worked as the first genes at the emergence of the primitive translation system, where the RNA was the informational molecule. The initial domain, worked as a building block for the emergence of the fingers and thumb domains. From the ancestral RdRp, we could establish the evolutionary stages of viral evolution from a rooted ancestor to modern viruses. It was observed that the selective pressure under the RdRp was the organization and functioning of the genome, where RNA double-stranded and RNA single-stranded virus formed a separate group. We propose an evolutionary route to the polymerases and the results suggest an ancient scenario for the origin of RNA viruses.

Chemical Evolution and the Evolutionary Definition of Life

Darwinian evolution requires a mechanism for generation of diversity in a population, and selective differences between individuals that influence reproduction. In biology, diversity is generated by mutations and selective differences arise because of the encoded functions of the sequences (e.g., ribozymes or proteins). Here, I draw attention to a process that I will call chemical evolution, in which the diversity is generated by random chemical synthesis instead of (or in addition to) mutation, and selection acts on physicochemical properties, such as hydrolysis, photolysis, solubility, or surface binding. Chemical evolution applies to short oligonucleotides that can be generated by random polymerization, as well as by template-directed replication, and which may be too short to encode a specific function. Chemical evolution is an important stage on the pathway to life, between the stage of "just chemistry" and the stage of full biological evolution. A mathematical model is presented here that illustrates the differences between these three stages. Chemical evolution leads to much larger differences in molecular concentrations than can be achieved by selection without replication. However, chemical evolution is not open-ended, unlike biological evolution. The ability to undergo Darwinian evolution is often considered to be a defining feature of life. Here, I argue that chemical evolution, although Darwinian, does not quite constitute life, and that a good place to put the conceptual boundary between non-life and life is between chemical and biological evolution.