A population-based experimental model for protein evolution: effects of mutation rate and selection stringency on evolutionary outcomes

Aaron M LeconteDavid R Liu


Protein evolution is a critical component of organismal evolution and a valuable method for the generation of useful molecules in the laboratory. Few studies, however, have experimentally characterized how fundamental parameters influence protein evolution outcomes over long evolutionary trajectories or multiple replicates. In this work, we applied phage-assisted continuous evolution (PACE) as an experimental platform to study evolving protein populations over hundreds of rounds of evolution. We varied evolutionary conditions as T7 RNA polymerase evolved to recognize the T3 promoter DNA sequence and characterized how specific combinations of both mutation rate and selection stringency reproducibly result in different evolutionary outcomes. We observed significant and dramatic increases in the activity of the evolved RNA polymerase variants on the desired target promoter after selection for 96 h, confirming positive selection occurred under all conditions. We used high-throughput sequencing to quantitatively define convergent genetic solutions, including mutational "signatures" and nonsignature mutations that map to specific regions of protein sequence. These findings illuminate key determinants of evolutionary outcomes, inform ...Continue Reading


May 16, 2013·Proceedings of the National Academy of Sciences of the United States of America·Bryan C DickinsonDavid R Liu
Feb 4, 2014·Nature Chemical Biology·Jacob C CarlsonDavid R Liu
Aug 29, 2013·Biotechnology and Bioengineering·Thomas GajCarlos F Barbas
Oct 8, 2015·Nature Communications·Ahmed H Badran, David R Liu
Jul 6, 2014·Current Opinion in Microbiology·Robert J CitorikTimothy K Lu
Dec 3, 2014·Current Opinion in Chemical Biology·Ahmed H Badran, David R Liu
Sep 3, 2014·PloS One·Jeremy R ThompsonKeith L Perry
Sep 12, 2014·PLoS Computational Biology·Krishnendu ChatterjeeMartin A Nowak
Feb 14, 2017·Nature Chemical Biology·Jinyue PuBryan C Dickinson
Feb 7, 2018·Nucleic Acids Research·Christopher Cozens, Vitor B Pinheiro
Oct 17, 2017·Nature Chemical Biology·David I BrysonDavid R Liu
Sep 23, 2017·Nature Reviews. Drug Discovery·Andrew M DavisEric Valeur
Oct 4, 2013·The Journal of Biological Chemistry·Zhaleh N Amini, Ulrich F Müller
Jul 24, 2019·Nature Biotechnology·Benjamin W ThuronyiDavid R Liu
Jun 26, 2020·Frontiers in Genetics·Xuan XiaoWang-Ren Qiu


Aug 15, 1991·Proceedings of the National Academy of Sciences of the United States of America·J W Drake
Jan 1, 1989·Advances in Biophysics·Y Husimi
Dec 19, 1970·Nature·W C Summers, R B Siegel
Jul 1, 1983·Annals of Human Genetics·M Nei, R K Chesser
Jan 10, 1980·Nature·A J Twigg, D Sherratt
Jun 21, 1994·Proceedings of the National Academy of Sciences of the United States of America·R R Breaker, Gerald F Joyce
Apr 15, 1993·Proceedings of the National Academy of Sciences of the United States of America·C A RaskinWilliam T McAllister
Apr 25, 1997·Science·M C Wright, Gerald F Joyce
Dec 22, 1999·Science·G M Cheetham, Thomas A Steitz
Mar 29, 2001·Proceedings of the National Academy of Sciences of the United States of America·F J GhadessyP Holliger
Jun 25, 2002·Journal of Molecular Biology·Xiaojun WangBrian K Shoichet
Nov 8, 2002·Nature·Tahir H TahirovShigeyuki Yokoyama
Jan 23, 2003·Proceedings of the National Academy of Sciences of the United States of America·Tim F CooperRichard E Lenski
Feb 6, 2003·Drug Discovery Today·Alain P VasserotJeffry D Watkins
May 31, 2003·Nature Reviews. Genetics·Santiago F Elena, Richard E Lenski
Aug 10, 2004·Nature Biotechnology·Jijumon Chelliserrykattil, Andrew D Ellington
Feb 19, 2005·Chembiochem : a European Journal of Chemical Biology·Reuben CarrNicholas J Turner
Jun 9, 2005·Journal of Molecular Biology·D Allan DrummondFrances H Arnold
Oct 22, 2005·Science·Mark LunzerAntony M Dean
Apr 4, 2006·Proceedings of the National Academy of Sciences of the United States of America·Jesse D BloomFrances H Arnold
Apr 8, 2006·Science·Daniel M WeinreichDaniel L Hartl
Jan 26, 2007·Nature·Frank J PoelwijkSander J Tans
Mar 14, 2007·Evolution; International Journal of Organic Evolution·Santiago F ElenaRichard E Lenski
Aug 19, 2007·Nature Reviews. Genetics·Antony M Dean, Joseph W Thornton
Feb 7, 2008·Heredity·Santiago F ElenaR Sanjuán
May 23, 2008·Journal of Molecular Biology·Shimon BershteinDan S Tawfik
Jun 25, 2008·Annual Review of Biophysics·Christian JäckelDonald Hilvert
Aug 9, 2008·Molecular Biology and Evolution·Shimon Bershtein, Dan S Tawfik
Jan 10, 2009·Science·Tracey A Lincoln, Gerald F Joyce
Apr 14, 2009·Nature Methods·Daniel G GibsonHamilton O Smith
Jun 16, 2009·Nature Chemical Biology·Susan M HancockStephen G Withers
Jul 22, 2009·Nature Chemical Biology·Nicholas J Turner
Aug 19, 2009·Nature Reviews. Genetics·Kent E Holsinger, Bruce S Weir
Sep 22, 2009·Current Opinion in Structural Biology·Nobuhiko Tokuriki, Dan S Tawfik
Oct 9, 2009·Current Opinion in Structural Biology·Thomas A Steitz
Nov 26, 2009·Nature Reviews. Molecular Cell Biology·Philip A Romero, Frances H Arnold
Jul 28, 2010·Biotechnology Advances·Jyoti PandeAshok K Grover
Jan 11, 2011·Nature Chemical Biology·Rinkoo D GuptaDan S Tawfik
Mar 17, 2011·PLoS Genetics·Merijn L M SalverdaJ Arjan G M de Visser
Mar 19, 2011·Science·Robert J WoodsRichard E Lenski
Apr 12, 2011·Nature·Kevin M EsveltDavid R Liu

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