Darwinian properties and their trade-offs in autocatalytic RNA reaction networks

Abstract

33Evolution via template-based replication 1-4 was probably preceded by a more rudimentary form 34 of evolution based on networks of autocatalytic reactions [5][6][7][8] . However, reaction networks 35 possessing the Darwinian properties of variation (in composition, the catalysts present and their 36 relative amounts), differential reproduction (accumulation of products), and heredity 37 (persistence of composition), have so far not been identified. Here we show that networks of 38 catalytic RNAs can possess certain properties of Darwinian systems, that these properties are 39 controlled by network topology, and characterize important trade-offs between them. By 40 combining barcoded sequencing with droplet microfluidics, we screened ̴ 20,000 reactions 41 corresponding to more than 1,800 distinct networks of ribozymes that catalyse their own 42 formation from RNA fragments. We found that more highly connected networks tend to 43 reproduce more quickly (accumulate more ribozymes) and be more robust to perturbations, 44 indicating a trade-off between variation and reproduction. Variations are strongest when adding 45 upstream ribozymes with novel reaction specificities (innovations) which target weakly 46 connected networks. In turn, innovations increase connectivity, thus buffer against further 47 Main 59In the prebiotic world, the spontaneous appearance of an RNA polymerase ribozyme (a 60 replicase) with sufficient processivity to allow self-replication and enough fidelity to avoid an 61 error catastrophe 5,6 seems unlikely, given that known replicases are long (>165 nt) and 62 structurally complex 1-4 . However, theoretical studies suggest that earlier modes of evolution 63 could have been supported by autocatalytic sets, where reproduction results from networks of 64 more rudimentary catalysts [11][12][13] . Consistently, recent experiments indicate that RNA 65 polymerase ribozymes can assemble from catalytic networks of RNA oligomers 14 , suggesting 66 that replicases may have emerged as components of such networks. Nevertheless, sustaining 67 evolution in reaction networks is by no means trivial, as the Darwinian properties of variation, 68 heredity and selection are mediated by chemical compositions (the proportion of different 69 chemical species) rather than the copying of a sequence. Furthermore, the possibility to evolve 70 chemistries may be constained by trade-offs between these properties. For instance, robustness 71 to environmental perturbations and persistence of compositions are necessary for selection to 72 act, but must be balanced with variation to explore novel states. So far, none of these Darwinian 73properties, nor their interplay, have been experimentally studied at a large scale in a 74 prebiotically relevant system. 75We studied an experimental model of autocatalytic RNAs derived from the group I intron of 76 the Azoarcus bacterium 15 . Fragments (denoted WXY and Z) assemble into non-covalent 77 complexes that catalyze the formation of more efficient covalent ribozymes 16,17 (denoted 78...

Self-Reproduction and Darwinian Evolution in Autocatalytic Chemical Reaction Systems

“…In order to establish the role of network connectivity in controlling compositional variation, growth, and robustness, Ameta et al [ 160 ] constructed multiple diverse networks (an ensemble of >20,000 isolated network configurations) using combinations of the food set. Employing a high-throughput strategy by combining droplet-based microfluidics and barcoded-sequencing, they quantified the compositional landscape (relative proportion of ribozymes in a network) of the networks at an unprecedented resolution.…”

“…While both RNA-based systems can self-reproduce and exhibit variation (though limited, this can be achieved by recombination reactions in the case of the Azoarcus system), Darwinian evolution in such networks also requires the demonstration of compositional heredity and selection. Compositional heredity was attempted in a test network from the Azoarcus system but could not be faithfully demonstrated because, due to spontaneous (background) reactions, different compositions converge to a single state after two steps in a serial-transfer experiment [ 160 ].…”

“…Variation in an autocatalytic network can also occur due to the spontaneous (random) addition or removal of species from the network. Such a scenario has been explored experimentally using the Azoarcus system where a compositional landscape of thousands of networks has been used to understand tradeoffs between compositional variation (which requires low network connectivity) and robustness against addition or deletion of new species in network (which requires high network connectivity) [ 160 ].…”

“…This is particularly so, given that many of the experimental chemical systems cannot be subject to high-throughput analysis, limiting their scope for the exploration of multiple parameter regimes and protocols. Chemistries based on small molecules need mass-spectrometric methods, which typically have a lower throughput compared to sequencing methods employed [ 53 , 160 , 164 , 165 ] for nucleic acid-based self-reproducing systems. Furthermore, droplet-based microfluidics can be combined with next-generation sequencing, massively increasing the exploration of multiple parameters [ 160 ].…”

Origin of Species before Origin of Life: The Role of Speciation in Chemical Evolution

“…One such example, mentioned previously, is the emergence of distinct fatty vesicle species that grow or shrink based on incorporation of a catalytic seryl-histidine dipeptide [ 74 ]. Inside a primitive compartment, a complex network of replicative autocatalytic reactions could also potentially emerge [ 149 , 150 ] and would survive by being fed by a constant input of nutrients from the outside. In some cases, some molecules or systems of molecules would be favored, i.e., thermodynamically, kinetically, by possible self-replication, etc., and be replicated with an increasing accuracy and efficiency (whether due to being in a more favorable environment within the compartment interior, or due to specific characteristics of the compartment itself which promote such reactions).…”