Energy-dependent fitness: a quantitative model for the evolution of yeast transcription factor binding sites.

Proceedings of the National Academy of Sciences of the United States of America
Ville MustonenMichael Lässig

Abstract

We present a genomewide cross-species analysis of regulation for broad-acting transcription factors in yeast. Our model for binding site evolution is founded on biophysics: the binding energy between transcription factor and site is a quantitative phenotype of regulatory function, and selection is given by a fitness landscape that depends on this phenotype. The model quantifies conservation, as well as loss and gain, of functional binding sites in a coherent way. Its predictions are supported by direct cross-species comparison between four yeast species. We find ubiquitous compensatory mutations within functional sites, such that the energy phenotype and the function of a site evolve in a significantly more constrained way than does its sequence. We also find evidence for substantial evolution of regulatory function involving point mutations as well as sequence insertions and deletions within binding sites. Genes lose their regulatory link to a given transcription factor at a rate similar to the neutral point mutation rate, from which we infer a moderate average fitness advantage of functional over nonfunctional sites. In a wider context, this study provides an example of inference of selection acting on a quantitative molecula...Continue Reading

References

Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Feb 12, 1971·Nature·M Kimura, T Ohta
Jan 1, 1995·Molecular Biology and Evolution·J KarotamJ G Oakeshott
Jan 1, 1997·Journal of Molecular Evolution·W M Fitch
Jan 1, 1997·Journal of Molecular Evolution·T Ohta
Aug 15, 1997·Journal of Molecular Biology·D S FieldsG D Stormo
May 15, 1998·Trends in Biochemical Sciences·G D Stormo, D S Fields
Jul 10, 1998·Molecular Biology and Evolution·A L Halpern, W J Bruno
Feb 2, 2000·Journal of Molecular Evolution·H Tachida
Oct 2, 2002·Journal of Molecular Evolution·Ulrich Gerland, Terence Hwa
Oct 26, 2002·Science·Tong Ihn LeeRichard A Young
Jun 5, 2003·Molecular Biology and Evolution·Gregory A WrayLaura A Romano
Jun 26, 2003·Nucleic Acids Research·Ramu ChennaJulie D Thompson
Aug 30, 2003·BMC Evolutionary Biology·Alan M MosesMichael B Eisen
Jan 1, 1961·Cold Spring Harbor Symposia on Quantitative Biology·J MONOD, F JACOB
Feb 26, 2004·Proceedings of the National Academy of Sciences of the United States of America·C T Brown, C G Callan
May 8, 2004·Nature Reviews. Genetics·Wyeth W Wasserman, Albin Sandelin
Sep 3, 2004·Nature·Christopher T HarbisonRichard A Young
Oct 30, 2004·BMC Evolutionary Biology·Johannes BergMichael Lässig
Mar 11, 2005·PLoS Biology·Michael Z LudwigMartin Kreitman
Jul 8, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ari Löytynoja, Nick Goldman
Jul 30, 2005·Evolution; International Journal of Organic Evolution·Daniel M WeinreichLin Chao
Oct 21, 2005·Proceedings of the National Academy of Sciences of the United States of America·Ville Mustonen, Michael Lässig
Mar 9, 2006·BMC Bioinformatics·Kenzie D MacIsaacErnest Fraenkel
Apr 8, 2006·Science·Daniel M WeinreichDaniel L Hartl
Nov 30, 2006·Nucleic Acids Research·Mikhail PachkovErik van Nimwegen
Jan 2, 2007·Proceedings of the National Academy of Sciences of the United States of America·Justin B KinneyCurtis G Callan
Jan 16, 2007·Science·Sebastian J Maerkl, Stephen R Quake
Feb 9, 2007·Proceedings of the National Academy of Sciences of the United States of America·Ville Mustonen, Michael Lässig
May 29, 2007·PLoS Computational Biology·Scott W Doniger, Justin C Fay
Aug 11, 2007·Science·Anthony R BornemanMichael Snyder
Nov 14, 2007·PLoS Computational Biology·Saurabh Sinha, Xin He
Dec 6, 2007·BMC Bioinformatics·Stephen Winters-Hilt, Sam Merat

❮ Previous
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Citations

Oct 21, 2009·Proceedings of the National Academy of Sciences of the United States of America·Sebastian J Maerkl, Stephen R Quake
Feb 11, 2010·Proceedings of the National Academy of Sciences of the United States of America·Ville Mustonen, Michael Lässig
May 26, 2011·Proceedings of the National Academy of Sciences of the United States of America·C Scott Wylie, Eugene I Shakhnovich
Jun 21, 2013·Proceedings of the National Academy of Sciences of the United States of America·Donate Weghorn, Michael Lässig
Jan 5, 2011·Molecular Biology and Evolution·Asher D Cutter, Alan M Moses
Nov 15, 2011·Molecular Biology and Evolution·Xin HeSaurabh Sinha
Apr 20, 2012·Journal of the Royal Society, Interface·Philip J Gerrish, Paul D Sniegowski
Aug 16, 2013·Proceedings. Biological Sciences·Alexander J Stewart, Joshua B Plotkin
Mar 3, 2010·Genome Research·Michael M Hoffman, Ewan Birney
Jun 29, 2010·BMC Bioinformatics·Matias PiipariTim Jp Hubbard
Oct 9, 2012·BMC Evolutionary Biology·Olga V TsoyMikhail S Gelfand
Dec 10, 2009·PLoS Computational Biology·Yue ZhaoGary D Stormo
Oct 15, 2011·PLoS Computational Biology·Armita Nourmohammad, Michael Lässig
Jan 10, 2009·PLoS Genetics·Jaebum KimSaurabh Sinha
Mar 30, 2012·PLoS Genetics·Matthew T MauranoJohn A Stamatoyannopoulos
Sep 9, 2011·Genetics·Robert K Arthur, Ilya Ruvinsky
Aug 14, 2012·Genetics·Alexander J StewartJoshua B Plotkin
Oct 15, 2013·Molecular Biology and Evolution·Adrian W R Serohijos, Eugene I Shakhnovich
Jun 11, 2014·Nature Reviews. Genetics·J Arjan G M de Visser, Joachim Krug
Jun 3, 2014·BMC Systems Biology·Joshua L Payne, Andreas Wagner
Dec 24, 2014·Proceedings of the National Academy of Sciences of the United States of America·Michael Lynch, Kyle Hagner
Jul 28, 2012·Theoretical Population Biology·Michael ManhartAlexandre V Morozov
Sep 8, 2010·Trends in Genetics : TIG·Alan M Moses, Christian R Landry
Feb 24, 2009·Trends in Genetics : TIG·Ville Mustonen, Michael Lässig
Jun 20, 2014·Proceedings of the National Academy of Sciences of the United States of America·Yuval ElhanatiAleksandra M Walczak
Mar 20, 2013·Molecular Ecology·Asher D CutterAlivia Dey
May 6, 2015·Journal of Theoretical Biology·Bhavin S Khatri, Richard A Goldstein
Dec 3, 2013·Current Opinion in Genetics & Development·Armita NourmohammadMichael Lässig
Jul 2, 2014·Current Opinion in Structural Biology·Dmitry N IvankovFyodor A Kondrashov
Sep 15, 2014·Current Opinion in Genetics & Development·Adam Siepel, Leonardo Arbiza
Nov 7, 2015·PLoS Genetics·Murat TuğrulGašper Tkačik
Aug 12, 2010·PLoS Computational Biology·Masaki E Tsuda, Masakado Kawata
Aug 7, 2007·PLoS Genetics·Monica M HorvathDouglas A Bell
May 29, 2007·PLoS Computational Biology·Scott W Doniger, Justin C Fay
Apr 22, 2015·Meta Gene·Yoshiyuki Suzuki
Jul 11, 2014·PLoS Computational Biology·Allan HaldaneAlexandre V Morozov
May 8, 2018·Proceedings of the National Academy of Sciences of the United States of America·Nathan M BelliveauRob Phillips

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