Literature DB >> 18568430

Evolution of new gene functions: simulation and analysis of the amplification model.

Mats E Pettersson1, Song Sun, Dan I Andersson, Otto G Berg.   

Abstract

Creation of new genes and functions is a central feature of evolution. Duplication of existing genes has long been assumed to be the source of new genes, but the precise mechanism has remained unclear. One suggestion is that new genes are created via temporary amplifications, which simultaneously increase both the selective advantage of weak, pre-existing secondary functions and the target for optimizing mutations. This paper examines the amplification model by formalizing it into a mathematical framework. This framework is used to perform stochastic (Monte Carlo) simulations. In addition, experimental data from Salmonella typhimurium LT2 are used to support the modelling, by providing estimates for parameter values. The results show that amplification of tandem repeats is likely to contribute to creation of new genes in nature.

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Year:  2008        PMID： 18568430     DOI： 10.1007/s10709-008-9289-z

Source DB:  PubMed          Journal:  Genetica        ISSN： 0016-6707            Impact factor:   1.082


  30 in total

1.  In vitro evolution of beta-glucuronidase into a beta-galactosidase proceeds through non-specific intermediates.

Authors:  I Matsumura; A D Ellington
Journal:  J Mol Biol       Date:  2001-01-12       Impact factor: 5.469

Review 2.  Preservation of duplicate genes by complementary, degenerative mutations.

Authors:  A Force; M Lynch; F B Pickett; A Amores; Y L Yan; J Postlethwait
Journal:  Genetics       Date:  1999-04       Impact factor: 4.562

3.  Population-genetic models of the fates of duplicate genes.

Authors:  Bruce Walsh
Journal:  Genetica       Date:  2003-07       Impact factor: 1.082

4.  The amplification model for adaptive mutation: simulations and analysis.

Authors:  Mats E Pettersson; Dan I Andersson; John R Roth; Otto G Berg
Journal:  Genetics       Date:  2004-10-16       Impact factor: 4.562

5.  An adaptive radiation model for the origin of new gene functions.

Authors:  M Pilar Francino
Journal:  Nat Genet       Date:  2005-06       Impact factor: 38.330

6.  Adaptive evolution of bacterial metabolic networks by horizontal gene transfer.

Authors:  Csaba Pál; Balázs Papp; Martin J Lercher
Journal:  Nat Genet       Date:  2005-11-20       Impact factor: 38.330

7.  Reducing the fitness cost of antibiotic resistance by amplification of initiator tRNA genes.

Authors:  Annika I Nilsson; Anna Zorzet; Anna Kanth; Sabina Dahlström; Otto G Berg; Dan I Andersson
Journal:  Proc Natl Acad Sci U S A       Date:  2006-04-24       Impact factor: 11.205

8.  Ohno's dilemma: evolution of new genes under continuous selection.

Authors:  Ulfar Bergthorsson; Dan I Andersson; John R Roth
Journal:  Proc Natl Acad Sci U S A       Date:  2007-10-17       Impact factor: 11.205

9.  The origin of mutants.

Authors:  J Cairns; J Overbaugh; S Miller
Journal:  Nature       Date:  1988-09-08       Impact factor: 49.962

10.  Amplification-mutagenesis: evidence that "directed" adaptive mutation and general hypermutability result from growth with a selected gene amplification.

Authors:  Heather Hendrickson; E Susan Slechta; Ulfar Bergthorsson; Dan I Andersson; John R Roth
Journal:  Proc Natl Acad Sci U S A       Date:  2002-02-05       Impact factor: 11.205
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  23 in total

1.  Contribution of gene amplification to evolution of increased antibiotic resistance in Salmonella typhimurium.

Authors:  Song Sun; Otto G Berg; John R Roth; Dan I Andersson
Journal:  Genetics       Date:  2009-05-27       Impact factor: 4.562

Review 2.  Bacterial gene amplification: implications for the evolution of antibiotic resistance.

Authors:  Linus Sandegren; Dan I Andersson
Journal:  Nat Rev Microbiol       Date:  2009-08       Impact factor: 60.633

3.  Genetic Plasticity and Ethylmalonyl Coenzyme A Pathway during Acetate Assimilation in Rhodospirillum rubrum S1H under Photoheterotrophic Conditions.

Authors:  Quentin De Meur; Adam Deutschbauer; Matthias Koch; Ruddy Wattiez; Baptiste Leroy
Journal:  Appl Environ Microbiol       Date:  2018-01-17       Impact factor: 4.792

4.  Evolving promiscuously.

Authors:  Dan I Andersson
Journal:  Proc Natl Acad Sci U S A       Date:  2011-01-11       Impact factor: 11.205

Review 5.  Evolution of new functions de novo and from preexisting genes.

Authors:  Dan I Andersson; Jon Jerlström-Hultqvist; Joakim Näsvall
Journal:  Cold Spring Harb Perspect Biol       Date:  2015-06-01       Impact factor: 10.005

Review 6.  Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition.

Authors:  Ben Ryall; Gustavo Eydallin; Thomas Ferenci
Journal:  Microbiol Mol Biol Rev       Date:  2012-09       Impact factor: 11.056

7.  Gene Duplication in Pseudomonas aeruginosa Improves Growth on Adenosine.

Authors:  Jean-Paul Toussaint; Anna Farrell-Sherman; Tamar Perla Feldman; Nicole E Smalley; Amy L Schaefer; E Peter Greenberg; Ajai A Dandekar
Journal:  J Bacteriol       Date:  2017-10-03       Impact factor: 3.490

8.  Gene amplification as a form of population-level gene expression regulation.

Authors:  I Tomanek; R Grah; M Lagator; A M C Andersson; J P Bollback; G Tkačik; C C Guet
Journal:  Nat Ecol Evol       Date:  2020-03-09       Impact factor: 15.460

9.  Real-time evolution of new genes by innovation, amplification, and divergence.

Authors:  Joakim Näsvall; Lei Sun; John R Roth; Dan I Andersson
Journal:  Science       Date:  2012-10-19       Impact factor: 47.728

Review 10.  Mechanisms and clinical relevance of bacterial heteroresistance.

Authors:  Dan I Andersson; Hervé Nicoloff; Karin Hjort
Journal:  Nat Rev Microbiol       Date:  2019-06-24       Impact factor: 60.633
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