Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance.

Autor:	Mavor D; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Barlow KA; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Asarnow D; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Birman Y; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Britain D; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Chen W; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Green EM; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Kenner LR; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Mensa B; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Morinishi LS; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Nelson CA; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Poss EM; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Suresh P; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Tian R; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Arhar T; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Ary BE; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Bauer DP; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Bergman ID; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Brunetti RM; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Chio CM; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Dai SA; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Dickinson MS; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Elledge SK; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Helsell CVM; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Hendel NL; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Kang E; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Kern N; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Khoroshkin MS; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Kirkemo LL; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Lewis GR; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Lou K; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Marin WM; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Maxwell AM; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., McTigue PF; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Myers-Turnbull D; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Nagy TL; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Natale AM; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Oltion K; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Pourmal S; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Reder GK; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Rettko NJ; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Rohweder PJ; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Schwarz DMC; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Tan SK; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Thomas PV; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Tibble RW; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Town JP; Bioinformatics Graduate Group, University of California, San Francisco 94158, USA., Tsai MK; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Ugur FS; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Wassarman DR; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Wolff AM; Biophysics Graduate Group, University of California, San Francisco 94158, USA., Wu TS; Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA., Bogdanoff D; Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA., Li J; Department of Chemistry Undergraduate Program, University of California, Davis 95616, USA., Thorn KS; Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA., O'Conchúir S; Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA., Swaney DL; Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA., Chow ED; Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA., Madhani HD; Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA., Redding S; Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA., Bolon DN; Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA., Kortemme T; Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA., DeRisi JL; Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA., Kampmann M; Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA martin.kampmann@ucsf.edu jfraser@fraserlab.com.; Institute for Neurodegenerative Diseases, University of California, San Francisco 94158, USA., Fraser JS; Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA martin.kampmann@ucsf.edu jfraser@fraserlab.com.
Jazyk:	angličtina
Zdroj:	Biology open [Biol Open] 2018 Jul 23; Vol. 7 (7). Date of Electronic Publication: 2018 Jul 23.
DOI:	10.1242/bio.036103
Abstrakt:	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 timescales. 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, CaCl 2 , Cerulenin, Cobalt Acetate, Menadione, Nickel Chloride, p-Fluorophenylalanine, Rapamycin, Tamoxifen, and Tunicamycin) reveal novel mutational sensitivities of ubiquitin residues. Collectively, our experiments have identified eight new sensitizing conditions for Lys63 and 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. Competing Interests: Competing interestsThe authors declare no competing or financial interests. (© 2018. Published by The Company of Biologists Ltd.)
Databáze:	MEDLINE
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