Paper

Extending Chemical Perturbations Of The Ubiquitin Fitness Landscape In A Classroom Setting

Kortemme, Tanja, Tibble, Ryan W, Town, Jason P, Poss, Erin M, Hendel, Nathan L, Lewis, Greyson R, Wassarman, Douglas R, Chow, Eric D, Suresh, Pooja, Madhani, Hiten D, Kirkemo, Lisa L, Ugur, Fatima S, Barlow, Kyle, Maxwell, Alison M, Rettko, Nicholas J, Lou, Kevin, Nagy, Tamas L, Taylor Arhar, Chen, Weilin, Helsell, Cole V M, Birman, Yuliya, Kern, Nadja, Redding, Sy, Schwarz, Daniel M C, Bogdanoff, Derek, Fraser, James S, Kenner, Lillian R, Li, Jennifer, Asarnow, Daniel, Thomas, Paul V, Kampmann, Martin, Green, Evan M, Dickinson, Miles S, Meyers-Turnbull, Douglas, Tsai, Mary K, Tian, Ruilin, Dai, Shizhong A, Thorn, Kurt S, Mctigue, Peter F, Nelson, Charlotte A, Swaney, Danielle L, Ary, Beatrice E, Wolff, Alexander M, Morinishi, Leanna S, Shane Thomas O'conch ir, Marin, Wesley M, Rohweder, Peter J, Wu, Taia S, Oltion, Keely, Natale, Andrew M, Elledge, Susanna, Mavor, David, Brunetti, Rachel M, Kang, Emily, Bolon, Daniel N A, Tan, Sophia K, Bauer, David P, Pourmal, Sergei, Khoroshkin, Matvei S, Bergman, Ian D, Derisi, Joseph L, Reder, Gabriel K, Chio, Cynthia M, Britain, Derek, Bruk Mensa

2017

Overview

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 reveal novel mutational sensitivities of ubiquitin residues. We found sensitization of Lys63 in eight new conditions. In total, our experiments have uncovered a highly 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.

• Publisher: Cold Spring Harbor Laboratory Press
• Subject: Amino acid sequence / Conserved sequence / Evolution / Experiments / Laboratories / Landscape / Reproductive fitness / Scanning / Ubiquitin