Directed evolution of a synthetic phylogeny of programmable Trp repressors

Nature Chemical Biology
Jared W EllefsonAndrew D Ellington

Abstract

As synthetic regulatory programs expand in sophistication, an ever increasing number of biological components with predictable phenotypes is required. Regulators are often 'part mined' from a diverse, but uncharacterized, array of genomic sequences, often leading to idiosyncratic behavior. Here, we generate an entire synthetic phylogeny from the canonical allosteric transcription factor TrpR. Iterative rounds of positive and negative compartmentalized partnered replication (CPR) led to the exponential amplification of variants that responded with high affinity and specificity to halogenated tryptophan analogs and novel operator sites. Fourteen repressor variants were evolved with unique regulatory profiles across five operators and three ligands. The logic of individual repressors can be modularly programmed by creating heterodimeric fusions, resulting in single proteins that display logic functions, such as 'NAND'. Despite the evolutionarily limited regulatory role of TrpR, vast functional spaces exist around this highly conserved protein scaffold and can be harnessed to create synthetic regulatory programs.

References

May 15, 1978·Journal of Molecular Biology·G N Bennett, C Yanofsky
May 1, 1976·Journal of Bacteriology·M D Manson, C Yanofsky
Feb 15, 1975·Journal of Molecular Biology·C L SquiresC Yanofsky
Apr 6, 1990·Biochimica Et Biophysica Acta·B F Luisi, P B Sigler
Dec 1, 1990·Journal of Medicinal Chemistry·P Z De CroosB L Currie
May 1, 1987·The Journal of Antibiotics·J A BushK Tomita
Oct 14, 1988·Science·S BassP Youderian
Feb 1, 1988·Proceedings of the National Academy of Sciences of the United States of America·J Carey
Jan 1, 1985·Proceedings of the National Academy of Sciences of the United States of America·R L Kelley, C Yanofsky
Oct 6, 1985·Nature·R W SchevitzP B Sigler
Jan 1, 1984·Annual Review of Biochemistry·C O Pabo, R T Sauer
Dec 1, 1980·Proceedings of the National Academy of Sciences of the United States of America·R P Gunsalus, C Yanofsky
Dec 21, 1981·Nucleic Acids Research·C YanofskyA M Wu
May 13, 1994·Journal of Molecular Biology·H ZhangO Jardetzky
May 25, 1994·Nucleic Acids Research·D N ArvidsonP Youderian
Jan 1, 1993·Annual Review of Microbiology·M A Schell
Apr 26, 1996·Journal of Molecular Biology·J YangJ Carey
Aug 5, 1998·Proceedings of the National Academy of Sciences of the United States of America·J G Lawrence, H Ochman
Feb 13, 2003·Nucleic Acids Research·M Madan Babu, Sarah A Teichmann
Jul 10, 2003·Current Opinion in Biotechnology·Eva M Top, Dirk Springael
Sep 11, 2003·Microbiology and Molecular Biology Reviews : MMBR·Gary XieRoy A Jensen
Jul 2, 2008·Nature Reviews. Genetics·Luis López-MauryJürg Bähler
Jul 9, 2008·Metabolic Engineering·Nikolaos AnesiadisRadhakrishnan Mahadevan
Dec 3, 2008·Microbiology·Sarah E Maddocks, Petra C F Oyston
Jul 1, 2009·Cell·Jeffrey J TaborAndrew D Ellington
Jan 21, 2010·Cell·Christina KielLuis Serrano
Apr 7, 2010·Annual Review of Biochemistry·Jeffrey A DietrichJay D Keasling
Apr 19, 2012·PLoS Computational Biology·Dmitry NevozhayGábor Balázsi
Oct 9, 2012·Nature·Tae Seok MoonChristopher A Voigt
Nov 5, 2013·Nature Biotechnology·Jared W EllefsonAndrew D Ellington
Dec 10, 2013·Nature Chemical Biology·Brynne C StantonChristopher A Voigt
Apr 18, 2014·Nature·Hesam N MotlaghVincent J Hilser
May 2, 2014·Nature Methods·Jennifer A N Brophy, Christopher A Voigt
Dec 3, 2014·Proceedings of the National Academy of Sciences of the United States of America·Srivatsan RamanGeorge M Church
Jul 15, 2015·Nucleic Acids Research·Jameson K RogersGeorge M Church
Sep 8, 2016·ACS Synthetic Biology·Andre C Maranhao, Andrew D Ellington
Oct 8, 2016·Organic & Biomolecular Chemistry·Binuraj R K MenonJason Micklefield

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Citations

Nov 28, 2018·Nature Chemical Biology·Adam J MeyerChristopher A Voigt
Feb 28, 2018·Nature Chemical Biology·Andreas K Brödel, Mark Isalan
Nov 30, 2019·Nucleic Acids Research·Tim SnoekJay D Keasling
Dec 21, 2019·Biotechnology Journal·Austin G RottinghausTae Seok Moon
Feb 6, 2020·Biotechnology and Bioengineering·Jenny LandbergAlex Toftgaard Nielsen
Jun 19, 2019·Nature Biotechnology·Anna J SimonAndrew D Ellington
Dec 5, 2019·Journal of Biological Engineering·Leopoldo F M MachadoNeil Dixon
Sep 9, 2020·Nature Communications·Thomas M GrosecloseCorey J Wilson
Oct 23, 2019·Biotechnology for Biofuels·Guadalupe Alvarez-Gonzalez, Neil Dixon
Jul 8, 2020·Nature Biotechnology·Jaeyoung K JungJulius B Lucks
Sep 1, 2018·Nucleic Acids Research·Brendan J Hussey, David R McMillen
Jul 28, 2018·FEMS Microbiology Letters·Seong Gyeong KimGyoo Yeol Jung
Nov 17, 2020·Frontiers in Bioengineering and Biotechnology·Samuel A BradleyMichael K Jensen
Mar 25, 2021·Nature Communications·Masahiro TominagaAkihiko Kondo
Sep 22, 2020·Trends in Microbiology·Giuliano T AnteloDaiana A Capdevila
Jul 6, 2021·Nucleic Acids Research·Vasily A ShenshinYannick Rondelez
Jul 24, 2021·Chemical Reviews·Yajie WangHuimin Zhao
Feb 6, 2020·ACS Synthetic Biology·Adokiye BerepikiNeil Dixon
Nov 14, 2021·Proceedings of the National Academy of Sciences of the United States of America·Thomas M GrosecloseCorey J Wilson

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Methods Mentioned

BETA
PCR
biosensors
protein folding
biosensor

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