In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity

  title={In silico simulations reveal that replicators with limited dispersal evolve towards higher efficiency and fidelity},
  author={P{\'e}ter Szab{\'o} and Istv{\'a}n Scheuring and Tam{\'a}s L Cz{\'a}r{\'a}n and E{\"o}rs Szathm{\'a}ry},
The emergence of functional replicases, acting quickly and with high accuracy, was crucial to the origin of life. Although where the first RNA molecules came from is still unknown, it is nevertheless assumed that catalytic RNA enzymes (ribozymes) with replicase function emerged at some early stage of evolution. The fidelity of copying is especially important because the mutation load limits the length of replicating templates that can be maintained by natural selection. An increase in template… 

The origin of replicators and reproducers

  • E. Szathmáry
  • Biology
    Philosophical Transactions of the Royal Society B: Biological Sciences
  • 2006
The stochastic corrector model shows how a bag of genes can survive, and what the role of chromosome formation and intragenic recombination could be, in an infrabiological system built of two coupled autocatalytic systems.

Local Neutral Networks Help Maintain Inaccurately Replicating Ribozymes

It is shown that the degree of neutrality, i.e. the frequency of nearest-neighbour (one-step) neutral mutants is a remarkably accurate proxy for the overall frequency of such mutants in an experimentally verifiable formula for the phenotypic error threshold.

Simulating the origins of life: The dual role of RNA replicases as an obstacle to evolution

This paper confirms that the coexistence of parasite RNAs and replicases is possible in a spatially extended system, and shows that the presence of trade-off that takes into the account an RNA folding process could still pose a serious obstacle to the evolution of replication.

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

The model highlights that evolution with implicit higher-level selection—i.e., as a result of local interactions and spatial patterning—is very flexible, and supports an RNA World by showing that complementary replicators may have various ways to evolve more complexity.

The Role of Complex Formation and Deleterious Mutations for the Stability of RNA-Like Replicator Systems

It is shown that the formation of traveling wave patterns plays a crucial role in the stability of the system against parasites, and that the effect of complex formation is not straightforward; whether complex formation stabilizes or destabilizes the spatial system is a complex function of other parameters.

The evolution of cooperation in simple molecular replicators

  • S. LevinS. West
  • Biology
    Proceedings of the Royal Society B: Biological Sciences
  • 2017
Key life-history features in the evolution of the genome are suggested and it is suggested that the same factors can favour cooperation across the entire tree of life.

Tag mechanism as a strategy for the RNA replicase to resist parasites in the RNA world

A computer simulation using a Monte-Carlo model is conducted to study the evolutionary dynamics surrounding the development of a tag-driven (polymerase-type) RNA replicase in the RNA world and concluded that with the tag mechanism the replic enzyme could resist the parasites and become prosperous.

Evolution of the Division of Labor between Genes and Enzymes in the RNA World

This work shows, by computer simulations of protocells harboring unlinked RNA replicators, that the origin of replicational asymmetry producing more ribozymes from a gene template than gene strands from a ribozyme template is feasible and robust.



Avoiding catch-22 by early evolution of stepwise increase in copying fidelity

A step-by-step solution to the paradoxical situation of the reconstruction of the evolutionary processes creating a sophisticated, enzymatically aided replication apparatus from a system of primitive self-replicating oligomers is suggested through studying both nonenzymatic or enzymatic replication.

Early evolution: prokaryotes, the new kids on the block.

It is argued here that the ribosome (together with the RNAs involved in its assembly) is so large that it must have had a prior function before protein synthesis, which can explain many steps in the origin of life while accounting for the observation that eukaryotes have retained more vestiges of the RNA world.

Surface-promoted replication and exponential amplification of DNA analogues

An iterative, stepwise procedure for chemical replication which permits an exponential increase in the concentration of oligonucleotide analogues, called SPREAD, which combines the advantages of solid-phase chemistry with chemical replication, and can be further developed for the non-enzymatic and enzymatic amplification of RNA, peptides and other templates.

Selection versus Coexistence of Parabolic Replicators Spreading on Surfaces

A simplified, semi-analytic treatment confirms that competing parabolic replicators that spread on mineral surfaces are amenable for Darwinian selection under a wide range of parameter values.

The Fidelity of Template-Directed Oligonucleotide Ligation and the Inevitability of Polymerase Function

A method for evaluating ligation fidelity in which ligation substrates are selected from random sequence libraries supports a model for origins in which there was selective pressure for template-directed oligon nucleotide ligation to be gradually supplanted by mononucleotide polymerization.

Enzymatic determinants of DNA polymerase accuracy. Theory of coliphage T4 polymerase mechanisms.

Visualizing DNA replication in a catalytically active Bacillus DNA polymerase crystal

High-resolution crystal structures of a thermostable bacterial (Bacillus stearothermophilus) DNA polymerase I large fragment with DNA primer templates bound productively at the polymerase active site are presented.

RNA-Catalyzed RNA Polymerization: Accurate and General RNA-Templated Primer Extension

An RNA molecule is described that catalyzes the type of polymerization needed for RNA replication, which uses nucleoside triphosphates and the coding information of an RNA template to extend an RNA primer by the successive addition of up to 14 nucleotides.