In prebiotic evolution, molecular self-replicators are considered to develop into diverse, complex living organisms. The appearance of parasitic replicators is believed inevitable in this process. However, the role of parasitic replicators in prebiotic evolution remains elusive. Here, we demonstrated experimental coevolution of RNA self-replicators (host RNAs) and emerging parasitic replicators (parasitic RNAs) using an RNA-protein replication system we developed. During a long-term replication experiment, a clonal population of the host RNA turned into an evolving host-parasite ecosystem through the continuous emergence of new types of host and parasitic RNAs produced by replication errors. The host and parasitic RNAs diversified into at least two and three different lineages, respectively, and they exhibited evolutionary arms-race dynamics. The parasitic RNA accumulated unique mutations, thus adding a new genetic variation to the whole replicator ensemble. These results provide the first experimental evidence that the coevolutionary interplay between host-parasite molecules plays a key role in generating diversity and complexity in prebiotic molecular evolution.

A crucial problem for primitive replicators before the origin of life is the appearance of parasitic or selfish replicators, which destabilize molecular cooperation and prevent the development of complexity. To date, theoretical and experimental studies have indicated that spatial structures, such as cell-like compartments, support sustainable replication of primitive replicators even in the presence of parasites. However, it is still a mystery how these host and parasitic replicators can evolve when they undergo long-term co-replication. Here, we investigated the coevolutionary process between an artificial RNA replicator (host RNA) and spontaneously appearing parasitic replicator (parasitic RNA) in artificial cell-like compartments. We performed a long-term replication experiment and found that the population dynamics of the host and parasitic RNAs gradually changed and novel types of hosts and parasites continued to appear. Competitive replication assays confirmed that parasite-resistant evolution of the host RNA and counter-adaptive evolution of the parasitic RNA occurred one after another. These results demonstrated that evolutionary arms races occur in this simple molecular system and generate a continuously-evolving molecular ecosystem. This coevolutionary process between host and parasitic molecules might play an important role in the open-ended evolution and development of complexity for primitive self-replication systems. ResultsRNA replication system. The RNA replication system used in this study consists of two types of singlestranded RNAs (host and parasitic RNAs) and a reconstituted translation system of E. coli [31] (Fig.1A). A distinctive feature between the host and parasitic RNAs is the capability of providing an RNA replicase (Qβ replicase). The host RNA provides the catalytic β-subunit of the replicase via translation, which forms active Fig.1 | Host and parasitic RNA replication system. (A) Replication scheme of the host and parasitic RNAs. The host RNA encodes Qβ replicase subunit, while the parasitic RNA does not. Both RNAs are replicated by the translated Qβ replicase in the reconstituted translation system of E. coli. (B) Replication-dilution cycle for a long-term replication experiment. The host RNA is encapsulated in water-in-oil droplets with approximately 2 μm diameter. The parasitic RNA spontaneously appears. (1) The droplets are incubated at 37 °C for 5 h for translation and replication. (2) 80 % of droplets are removed and (3) diluted with new droplets containing the translation system (i.e., 5-fold dilution). (4) Diluted dropletsare vigorously mixed to induce random fusion and division among the droplets. We repeated this cycle for 120 rounds.Reaction volume was 1 mL with 1% aqueous phase, corresponding to approximately 10 8 droplets.

RNA‐based genomes are used to synthesize artificial cells that harbor genome replication systems. Previously, continuous replication of an artificial genomic RNA that encoded an RNA replicase was demonstrated. The next important challenge is to expand such genomes by increasing the number of encoded genes. However, technical difficulties are encountered during such expansions because the introduction of new genes disrupts the secondary structure of RNA and makes RNA nonreplicable through replicase. Herein, a fusion method that enables the construction of a longer RNA from two replicable RNAs, while retaining replication capability, is proposed. Two replicable RNAs that encode different genes at various positions are fused, and a new parameter, the unreplicable index, which negatively correlates with the replication ability of the fused RNAs better than that of the previous parameter, is determined. The unreplicable index represents the expected value of the number of G or C nucleotides that are unpaired in both the template and complementary strands. It is also observed that some of the constructed fused RNAs replicate efficiently by using the internally translated replicase. The method proposed herein could contribute to the development of an expanded RNA genome that can be used for the purpose of artificial cell synthesis.

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