Literature DB >> 22727399

Evolutionary dynamics of RNA-like replicator systems: A bioinformatic approach to the origin of life.

Nobuto Takeuchi1, Paulien Hogeweg.   

Abstract

We review computational studies on prebiotic evolution, focusing on informatic processes in RNA-like replicator systems. In particular, we consider the following processes: the maintenance of information by replicators with and without interactions, the acquisition of information by replicators having a complex genotype-phenotype map, the generation of information by replicators having a complex genotype-phenotype-interaction map, and the storage of information by replicators serving as dedicated templates. Focusing on these informatic aspects, we review studies on quasi-species, error threshold, RNA-folding genotype-phenotype map, hypercycle, multilevel selection (including spatial self-organization, classical group selection, and compartmentalization), and the origin of DNA-like replicators. In conclusion, we pose a future question for theoretical studies on the origin of life. Published by Elsevier B.V.

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Year:  2012        PMID: 22727399      PMCID: PMC3466355          DOI: 10.1016/j.plrev.2012.06.001

Source DB:  PubMed          Journal:  Phys Life Rev        ISSN: 1571-0645            Impact factor:   11.025


  82 in total

1.  Neutral evolution of mutational robustness.

Authors:  E van Nimwegen; J P Crutchfield; M Huynen
Journal:  Proc Natl Acad Sci U S A       Date:  1999-08-17       Impact factor: 11.205

2.  Survival of replicators with parabolic growth tendency and exponential decay.

Authors:  I Scheuring; E Szathmáry
Journal:  J Theor Biol       Date:  2001-09-07       Impact factor: 2.691

3.  On a kinetic origin of heredity: minority control in a replicating system with mutually catalytic molecules.

Authors:  Kunihiko Kaneko; Tetsuya Yomo
Journal:  J Theor Biol       Date:  2002-02-21       Impact factor: 2.691

4.  Colicin diversity: a result of eco-evolutionary dynamics.

Authors:  L Pagie; P Hogeweg
Journal:  J Theor Biol       Date:  1999-01-21       Impact factor: 2.691

5.  The role of complex formation and deleterious mutations for the stability of RNA-like replicator systems.

Authors:  Nobuto Takeuchi; Paulien Hogeweg
Journal:  J Mol Evol       Date:  2007-10-23       Impact factor: 2.395

Review 6.  On the origin of RNA splicing and introns.

Authors:  P A Sharp
Journal:  Cell       Date:  1985-09       Impact factor: 41.582

7.  Ribozyme-catalyzed transcription of an active ribozyme.

Authors:  Aniela Wochner; James Attwater; Alan Coulson; Philipp Holliger
Journal:  Science       Date:  2011-04-08       Impact factor: 47.728

8.  Group selection of early replicators and the origin of life.

Authors:  E Szathmáry; L Demeter
Journal:  J Theor Biol       Date:  1987-10-21       Impact factor: 2.691

9.  The hypercycle. A principle of natural self-organization. Part A: Emergence of the hypercycle.

Authors:  M Eigen; P Schuster
Journal:  Naturwissenschaften       Date:  1977-11

10.  Multilevel selection in models of prebiotic evolution II: a direct comparison of compartmentalization and spatial self-organization.

Authors:  Nobuto Takeuchi; Paulien Hogeweg
Journal:  PLoS Comput Biol       Date:  2009-10-16       Impact factor: 4.475

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  42 in total

1.  Stable coevolutionary regimes for genetic parasites and their hosts: you must differ to coevolve.

Authors:  Faina Berezovskaya; Georgy P Karev; Mikhail I Katsnelson; Yuri I Wolf; Eugene V Koonin
Journal:  Biol Direct       Date:  2018-12-14       Impact factor: 4.540

2.  Emergence of coding and its specificity as a physico-informatic problem.

Authors:  Peter R Wills; Kay Nieselt; John S McCaskill
Journal:  Orig Life Evol Biosph       Date:  2015-06       Impact factor: 1.950

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

Review 4.  The LUCA and its complex virome.

Authors:  Mart Krupovic; Valerian V Dolja; Eugene V Koonin
Journal:  Nat Rev Microbiol       Date:  2020-07-14       Impact factor: 60.633

Review 5.  Virus world as an evolutionary network of viruses and capsidless selfish elements.

Authors:  Eugene V Koonin; Valerian V Dolja
Journal:  Microbiol Mol Biol Rev       Date:  2014-06       Impact factor: 11.056

Review 6.  Conceptualizing the origin of life in terms of evolution.

Authors:  N Takeuchi; P Hogeweg; K Kaneko
Journal:  Philos Trans A Math Phys Eng Sci       Date:  2017-12-28       Impact factor: 4.226

Review 7.  Global Organization and Proposed Megataxonomy of the Virus World.

Authors:  Eugene V Koonin; Valerian V Dolja; Mart Krupovic; Arvind Varsani; Yuri I Wolf; Natalya Yutin; F Murilo Zerbini; Jens H Kuhn
Journal:  Microbiol Mol Biol Rev       Date:  2020-03-04       Impact factor: 11.056

8.  Are viruses alive? The replicator paradigm sheds decisive light on an old but misguided question.

Authors:  Eugene V Koonin; Petro Starokadomskyy
Journal:  Stud Hist Philos Biol Biomed Sci       Date:  2016-03-07

Review 9.  Insuperable problems of the genetic code initially emerging in an RNA world.

Authors:  Peter R Wills; Charles W Carter
Journal:  Biosystems       Date:  2017-09-10       Impact factor: 1.973

10.  The role of energy in the emergence of biology from chemistry.

Authors:  Daria V Dibrova; Michail Y Chudetsky; Michael Y Galperin; Eugene V Koonin; Armen Y Mulkidjanian
Journal:  Orig Life Evol Biosph       Date:  2012-10       Impact factor: 1.950

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