The emergence of DNA in the RNA world: an in silico simulation study of genetic takeoverReport as inadecuate




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BMC Evolutionary Biology

, 15:272

First Online: 07 December 2015Received: 10 August 2015Accepted: 20 November 2015DOI: 10.1186-s12862-015-0548-1

Cite this article as: Ma, W., Yu, C., Zhang, W. et al. BMC Evol Biol 2015 15: 272. doi:10.1186-s12862-015-0548-1

Abstract

BackgroundIt is now popularly accepted that there was an -RNA world- in early evolution of life. This idea has a direct consequence that later on there should have been a takeover of genetic material – RNA by DNA. However, since genetic material carries genetic information, the -source code- of all living activities, it is actually reasonable to question the plausibility of such a -revolutionary- transition. Due to our inability to model relevant -primitive living systems- in reality, it is as yet impossible to explore the plausibility and mechanisms of the -genetic takeover- by experiments.

ResultsHere we investigated this issue by computer simulation using a Monte-Carlo method. It shows that an RNA-by-DNA genetic takeover may be triggered by the emergence of a nucleotide reductase ribozyme with a moderate activity in a pure RNA system. The transition is unstable and limited in scale i.e., cannot spread in the population, but can get strengthened and globalized if certain parameters are changed against RNA i.e., in favor of DNA. In relation to the subsequent evolution, an advanced system with a larger genome, which uses DNA as genetic material and RNA as functional material, is modeled – the system cannot sustain if the nucleotide reductase ribozyme is -turned off- thus, DNA cannot be synthesized. Moreover, the advanced system cannot sustain if only DNA’s stability, template suitability or replication fidelity any of the three is turned down to the level of RNA’s.

ConclusionsGenetic takeover should be plausible. In the RNA world, such a takeover may have been triggered by the emergence of some ribozyme favoring the formation of deoxynucleotides. The transition may initially have been -weak-, but could have been reinforced by environmental changes unfavorable to RNA such as temperature or pH rise, and would have ultimately become irreversible accompanying the genome’s enlargement. Several virtues of DNA versus RNA – higher stability against hydrolysis, greater suitability as template and higher fidelity in replication, should have, each in its own way, all been significant for the genetic takeover in evolution. This study enhances our understandings of the relationship between information and material in the living world.

KeywordsOrigin of life Molecular evolution Computer modeling AbbreviationsAsrThe amphiphile synthetase ribozyme

NrrThe nucleotide reductase ribozyme

NsrThe nucleotide synthetase ribozyme

NsprThe nucleotide precursor synthetase ribozyme

ntNucleotide

RepThe replicase ribozyme

Electronic supplementary materialThe online version of this article doi:10.1186-s12862-015-0548-1 contains supplementary material, which is available to authorized users.

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Author: Wentao Ma - Chunwu Yu - Wentao Zhang - Sanmao Wu - Yu Feng

Source: https://link.springer.com/




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