Emergence and diversification of a host-parasite RNA ecosystem through Darwinian evolution

Abstract

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.

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

“…First, the irregularly changing host and parasitic RNA concentrations in the early stage turned into a relatively regular oscillation in the late stage. Second, parasitic RNAs with different lengths (~ 220 nt, ~1100 nt, and ~500 nt) newly appeared only in the early stage, as reported previously 29 , and ~500 nt parasitic RNAs dominated the population throughout the late stage, although a small amount of ~220 nt RNAs was detected transiently (at rounds 136-140, 147-151, 178-181, and 207-210). These results suggested that the mode of evolution changed in the late stage.…”

“…S1). We conducted 120 rounds of the transfer cycle (rounds 1-120) in the previous studies 28,29 and additional 120 rounds (rounds 121-240) in this study.…”

“…To understand the evolutionary dynamics, we analyzed host and parasitic RNA sequences throughout the long-term replication experiment. For rounds 1-115, we used the data obtained previously 29 . For rounds 116-240, we recovered RNA mixtures at 18 points and subjected host and ~500 nt parasitic RNAs to PacBio sequencing.…”

“…During replication, mutations are introduced, and occasional recombination deletes replicase-encoded regions to generate a parasitic RNA that replicates by exploiting the self-replicating "host" RNA. The RNAs can undergo Darwinian evolution in a serial transfer experiment, and a previous attempt (120 rounds, 600 h) demonstrated the successive appearance of new host and parasitic RNA lineages showing defense and counter-defense properties 28,29 . However, these lineages dominated the population in turn and only transiently, possibly due to a short evolutionary timescale.…”

Survival of Self-Replicating Molecules under Transient Compartmentalization with Natural Selection

“…By studying the sequence information of the replicase and its parasites, they suggested that parasites can take an active part in the evolution of their host and not just in their own. Different sub-populations of parasites can appear, forming an ecosystem [22], which accelerates evolution. Future studies are needed to quantify these co-evolutionary mechanisms, and perhaps our model could help in that task.…”