Multi-agent approach to sequence structure simulation in the RNA World hypothesis.

Jaroslaw Synak,Agnieszka Rybarczyk,Jacek Blazewicz,Jean-Luc Eph Darlix

doi:10.1371/journal.pone.0238253

Jaroslaw Synak, Agnieszka Rybarczyk + Show 2 more

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https://doi.org/10.1371/journal.pone.0238253

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Abstract

The origins of life on Earth have been the subject of inquiry since the early days of philosophical thought and are still intensively investigated by the researchers around the world. One of the theories explaining the life emergence, that gained the most attention recently is the RNA World hypothesis, which assumes that life on Earth was sparked by replicating RNA chains. Since wet lab analysis is time-consuming, many mathematical and computational approaches have been proposed that try to explain the origins of life. Recently proposed one, based on the work by Takeuchi and Hogeweg, addresses the problem of interplay between RNA replicases and RNA parasitic species, which is crucial for understanding the first steps of prebiotic evolution. In this paper, the aforementioned model has been extended and modified by introducing RNA sequence (structure) information and mutation rate close to real one. It allowed to observe the simple evolution mechanisms, which could have led to the more complicated systems and eventually, to the formation of the first cells. The main goal of this study was to determine the conditions that allowed the spontaneous emergence and evolution of the prebiotic replicases equipped with simple functional domains within a large population. Here we show that polymerase ribozymes could have appeared randomly and then quickly started to copy themselves in order for the system to reach equilibrium. It has been shown that evolutionary selection works even in the simplest systems.

Highlights

According to the RNA World theory, early evolution of life involved RNA molecules both as genetic information carrier and catalyst [1]. Strong support for this hypothesis came from the discovery of the self-splicing RNAs [2], the RNase P [3] and small endonucleolytic ribozymes such as hairpin, hammerhead and HDV [4,5,6], which are capable of cleaving RNA molecules
Parasite and replicase populations have the ability to regulate each other and their mutual interaction can result in equilibrium
In order to build a model that is closer to reality, we used the information of the primary and secondary RNA structure, hydrolysis rate of the phosphodiester bonds and we have introduced the characteristic catalytic motif within RNA replicase

Summary

Introduction

According to the RNA World theory, early evolution of life involved RNA molecules both as genetic information carrier and catalyst (enzyme) [1]. Additional evidence for RNA world preceding modern life includes the informational and catalytic role of RNA in translation, splicing and gene expression [7]. These findings, along with ongoing RNA-oriented research suggest that the synthesis and replication of RNA were the critical processes in the transition from prebiotic chemistry to life.

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