Literature DB >> 17014951

Monte Carlo simulation of early molecular evolution in the RNA World.

Wentao Ma1, Chunwu Yu, Wentao Zhang.   

Abstract

The origin of life remains a highly speculative field, mainly due to the shortage of our knowledge on prebiotic chemistry and basic understanding on the essence of life. In this context, computer simulation is expected to play an important role. For instance, the scenario concerning the genesis of the widely accepted RNA World remains blurry, though we have gathered some circumstantial evidence and fragmented knowledge on several supposed stages, including formation of polynucleotides from a prebiotic nucleotide pool, emergence of RNA replicases (RNA molecules catalyzing their own replication), and evolution of RNA replicases. It is highly valuable to simulate the stages as a continuous process to evaluate the plausibility of the supposition and study the rules involved. Here we construct a computer simulation on the process using Monte Carlo method. It demonstrates that primordial RNA replicases may appear and spread in a nucleotide pool provided they could recognize their own sequence and their complements as catalytic targets, and then may evolve to more efficient RNA replicases. Apart from its indication on the genesis of the RNA World, the vivid simulation of emergence of the "first replicative molecules" and their subsequent evolution is impressive and may help to get insight into "how could self-replication and Darwinian evolution, two key features of life, emerge in a non-life background?" thus improve our understanding of "what is life" when studying origins of life.

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Year:  2006        PMID: 17014951     DOI: 10.1016/j.biosystems.2006.06.005

Source DB:  PubMed          Journal:  Biosystems        ISSN: 0303-2647            Impact factor:   1.973


  10 in total

1.  Nucleotide synthetase ribozymes may have emerged first in the RNA world.

Authors:  Wentao Ma; Chunwu Yu; Wentao Zhang; Jiming Hu
Journal:  RNA       Date:  2007-09-18       Impact factor: 4.942

2.  Computational Models of Polymer Synthesis Driven by Dehydration/Rehydration Cycles: Repurination in Simulated Hydrothermal Fields.

Authors:  Mason Hargrave; Spencer K Thompson; David Deamer
Journal:  J Mol Evol       Date:  2018-09-15       Impact factor: 2.395

Review 3.  The RNA World: molecular cooperation at the origins of life.

Authors:  Paul G Higgs; Niles Lehman
Journal:  Nat Rev Genet       Date:  2014-11-11       Impact factor: 53.242

4.  Universal sequence replication, reversible polymerization and early functional biopolymers: a model for the initiation of prebiotic sequence evolution.

Authors:  Sara Imari Walker; Martha A Grover; Nicholas V Hud
Journal:  PLoS One       Date:  2012-04-06       Impact factor: 3.240

5.  Co-operation between Polymerases and Nucleotide Synthetases in the RNA World.

Authors:  Ye Eun Kim; Paul G Higgs
Journal:  PLoS Comput Biol       Date:  2016-11-07       Impact factor: 4.475

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

Authors:  Natalia Szostak; Jaroslaw Synak; Marcin Borowski; Szymon Wasik; Jacek Blazewicz
Journal:  PLoS One       Date:  2017-07-10       Impact factor: 3.240

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

Authors:  Sanmao Wu; Chunwu Yu; Wentao Zhang; Shaolin Yin; Yong Chen; Yu Feng; Wentao Ma
Journal:  PLoS One       Date:  2017-03-02       Impact factor: 3.240

8.  From molecular to cellular form: modeling the first major transition during the arising of life.

Authors:  Shaolin Yin; Yong Chen; Chunwu Yu; Wentao Ma
Journal:  BMC Evol Biol       Date:  2019-04-03       Impact factor: 3.260

9.  The origin of life is a spatially localized stochastic transition.

Authors:  Meng Wu; Paul G Higgs
Journal:  Biol Direct       Date:  2012-11-24       Impact factor: 4.540

10.  Circularity and self-cleavage as a strategy for the emergence of a chromosome in the RNA-based protocell.

Authors:  Wentao Ma; Chunwu Yu; Wentao Zhang
Journal:  Biol Direct       Date:  2013-08-23       Impact factor: 4.540

  10 in total

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