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Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting

David Mavor, View ORCID ProfileKyle A. Barlow, Daniel Asarnow, Yuliya Birman, Derek Britain, Weilin Chen, Evan M. Green, Lillian R. Kenner, Bruk Mensa, Leanna S. Morinishi, Charlotte Nelson, Erin M. Poss, Pooja Suresh, Ruilin Tian, Taylor Arhar, Beatrice Ary, David Bauer, Ian Bergman, Rachel Brunetti, Cynthia Chio, Shizhong Dai, Miles Dickinson, Susanna Elledge, Cole Helsell, Nathan Hendel, Emily Kang, Nadja Kern, Matvei Khoroshkin, Lisa Kirkemo, Greyson Lewis, Kevin Lou, Wesley Marin, Alison Maxwell, Peter McTigue, Douglas Myers-Turnbull, Tamas Nagy, Andrew Natale, Keely Oltion, Sergei Pourmal, Gabriel Reder, Nicholas Rettko, Peter Rohweder, Daniel Schwarz, Sophia Tan, Paul Thomas, Ryan Tibble, Jason Town, Kaitlyn Tsai, Fatima Ugur, Douglas R. Wassarmann, Alexander Wolff, Taia Wu, Derrick Bogdanoff, Jennifer Li, Kurt S. Thorn, Shane O’Conchúir, Danielle L. Swaney, Eric D. Chow, View ORCID ProfileHiten Madhani, Sy Redding, Daniel N. Bolon, Tanja Kortemme, Joseph L. DeRisi, View ORCID ProfileMartin Kampmann, View ORCID ProfileJames S. Fraser
doi: https://doi.org/10.1101/139352
David Mavor
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Kyle A. Barlow
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Daniel Asarnow
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Yuliya Birman
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Derek Britain
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Weilin Chen
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Evan M. Green
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Lillian R. Kenner
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Bruk Mensa
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Leanna S. Morinishi
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Charlotte Nelson
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Erin M. Poss
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Pooja Suresh
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Ruilin Tian
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Taylor Arhar
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Beatrice Ary
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David Bauer
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Ian Bergman
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Rachel Brunetti
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Cynthia Chio
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Shizhong Dai
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Miles Dickinson
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Susanna Elledge
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Cole Helsell
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Nathan Hendel
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Emily Kang
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Nadja Kern
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Matvei Khoroshkin
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Lisa Kirkemo
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Greyson Lewis
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Kevin Lou
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Wesley Marin
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Alison Maxwell
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Peter McTigue
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Douglas Myers-Turnbull
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Tamas Nagy
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Andrew Natale
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Daniel Schwarz
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Sophia Tan
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Jason Town
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Kaitlyn Tsai
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Fatima Ugur
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Douglas R. Wassarmann
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Jennifer Li
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Kurt S. Thorn
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Shane O’Conchúir
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Danielle L. Swaney
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Eric D. Chow
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Hiten Madhani
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Sy Redding
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Daniel N. Bolon
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Tanja Kortemme
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Joseph L. DeRisi
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Martin Kampmann
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  • For correspondence: martin.kampmann@ucsf.edu jfraser@fraserlab.com
James S. Fraser
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  • For correspondence: martin.kampmann@ucsf.edu jfraser@fraserlab.com
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Abstract

Although the primary protein sequence of ubiquitin (Ub) is extremely stable over evolutionary time, it is highly tolerant to mutation during selection experiments performed in the laboratory. We have proposed that this discrepancy results from the difference between fitness under laboratory culture conditions and the selective pressures in changing environments over evolutionary time scales. Building on our previous work (Mavor et al 2016), we used deep mutational scanning to determine how twelve new chemicals (3-Amino-1,2,4-triazole, 5-fluorocytosine, Amphotericin B, CaCl2, Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. We found sensitization of Lys63 in eight new conditions. In total, our experiments have uncovered a sensitizing condition for every position in Ub except Ser57 and Gln62. By determining the Ubiquitin fitness landscape under different chemical constraints, our work helps to resolve the inconsistencies between deep mutational scanning experiments and sequence conservation over evolutionary timescales.

Builds on Mavor D, Barlow KA, Thompson S, Barad BA, Bonny AR, Cario CL, Gaskins G, Liu Z, Deming L, Axen SD, Caceres E, Chen W, Cuesta A, Gate R, Green EM, Hulce KR, Ji W, Kenner LR, Mensa B, Morinishi LS, Moss SM, Mravic M, Muir RK, Niekamp S, Nnadi CI, Palovcak E, Poss EM, Ross TD, Salcedo E, See S, Subramaniam M, Wong AW, Li J, Thorn KS, Conchúir SÓ, Roscoe BP, Chow ED, DeRisi JL, Kortemme T, Bolon DN, Fraser JS. Determination of Ubiquitin Fitness Landscapes Under Different Chemical Stresses in a Classroom Setting. eLife. 2016.

Impact Statement We organized a project-based course that used deep mutational scanning in multiple chemical conditions to resolve the inconsistencies between tolerance to mutations in laboratory conditions and sequence conservation over evolutionary timescales.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted May 17, 2017.
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Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting
David Mavor, Kyle A. Barlow, Daniel Asarnow, Yuliya Birman, Derek Britain, Weilin Chen, Evan M. Green, Lillian R. Kenner, Bruk Mensa, Leanna S. Morinishi, Charlotte Nelson, Erin M. Poss, Pooja Suresh, Ruilin Tian, Taylor Arhar, Beatrice Ary, David Bauer, Ian Bergman, Rachel Brunetti, Cynthia Chio, Shizhong Dai, Miles Dickinson, Susanna Elledge, Cole Helsell, Nathan Hendel, Emily Kang, Nadja Kern, Matvei Khoroshkin, Lisa Kirkemo, Greyson Lewis, Kevin Lou, Wesley Marin, Alison Maxwell, Peter McTigue, Douglas Myers-Turnbull, Tamas Nagy, Andrew Natale, Keely Oltion, Sergei Pourmal, Gabriel Reder, Nicholas Rettko, Peter Rohweder, Daniel Schwarz, Sophia Tan, Paul Thomas, Ryan Tibble, Jason Town, Kaitlyn Tsai, Fatima Ugur, Douglas R. Wassarmann, Alexander Wolff, Taia Wu, Derrick Bogdanoff, Jennifer Li, Kurt S. Thorn, Shane O’Conchúir, Danielle L. Swaney, Eric D. Chow, Hiten Madhani, Sy Redding, Daniel N. Bolon, Tanja Kortemme, Joseph L. DeRisi, Martin Kampmann, James S. Fraser
bioRxiv 139352; doi: https://doi.org/10.1101/139352
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Research Advance: Extending chemical perturbations of the Ubiquitin fitness landscape in a classroom setting
David Mavor, Kyle A. Barlow, Daniel Asarnow, Yuliya Birman, Derek Britain, Weilin Chen, Evan M. Green, Lillian R. Kenner, Bruk Mensa, Leanna S. Morinishi, Charlotte Nelson, Erin M. Poss, Pooja Suresh, Ruilin Tian, Taylor Arhar, Beatrice Ary, David Bauer, Ian Bergman, Rachel Brunetti, Cynthia Chio, Shizhong Dai, Miles Dickinson, Susanna Elledge, Cole Helsell, Nathan Hendel, Emily Kang, Nadja Kern, Matvei Khoroshkin, Lisa Kirkemo, Greyson Lewis, Kevin Lou, Wesley Marin, Alison Maxwell, Peter McTigue, Douglas Myers-Turnbull, Tamas Nagy, Andrew Natale, Keely Oltion, Sergei Pourmal, Gabriel Reder, Nicholas Rettko, Peter Rohweder, Daniel Schwarz, Sophia Tan, Paul Thomas, Ryan Tibble, Jason Town, Kaitlyn Tsai, Fatima Ugur, Douglas R. Wassarmann, Alexander Wolff, Taia Wu, Derrick Bogdanoff, Jennifer Li, Kurt S. Thorn, Shane O’Conchúir, Danielle L. Swaney, Eric D. Chow, Hiten Madhani, Sy Redding, Daniel N. Bolon, Tanja Kortemme, Joseph L. DeRisi, Martin Kampmann, James S. Fraser
bioRxiv 139352; doi: https://doi.org/10.1101/139352

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