Biology Open (Jul 2018)
Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance
- 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 A. Nelson,
- Erin M. Poss,
- Pooja Suresh,
- Ruilin Tian,
- Taylor Arhar,
- Beatrice E. Ary,
- David P. Bauer,
- Ian D. Bergman,
- Rachel M. Brunetti,
- Cynthia M. Chio,
- Shizhong A. Dai,
- Miles S. Dickinson,
- Susanna K. Elledge,
- Cole V. M. Helsell,
- Nathan L. Hendel,
- Emily Kang,
- Nadja Kern,
- Matvei S. Khoroshkin,
- Lisa L. Kirkemo,
- Greyson R. Lewis,
- Kevin Lou,
- Wesley M. Marin,
- Alison M. Maxwell,
- Peter F. McTigue,
- Douglas Myers-Turnbull,
- Tamas L. Nagy,
- Andrew M. Natale,
- Keely Oltion,
- Sergei Pourmal,
- Gabriel K. Reder,
- Nicholas J. Rettko,
- Peter J. Rohweder,
- Daniel M. C Schwarz,
- Sophia K. Tan,
- Paul V. Thomas,
- Ryan W. Tibble,
- Jason P. Town,
- Mary K. Tsai,
- Fatima S. Ugur,
- Douglas R. Wassarman,
- Alexander M. Wolff,
- Taia S. Wu,
- Derek Bogdanoff,
- Jennifer Li,
- Kurt S. Thorn,
- Shane O'Conchúir,
- Danielle L. Swaney,
- Eric D. Chow,
- Hiten D. Madhani,
- Sy Redding,
- Daniel N. Bolon,
- Tanja Kortemme,
- Joseph L. DeRisi,
- Martin Kampmann,
- James S. Fraser
Affiliations
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Kyle A. Barlow
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Daniel Asarnow
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Yuliya Birman
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Derek Britain
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Evan M. Green
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Lillian R. Kenner
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Leanna S. Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Charlotte A. Nelson
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Erin M. Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Pooja Suresh
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Ruilin Tian
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Taylor Arhar
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Beatrice E. Ary
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- David P. Bauer
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Ian D. Bergman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Rachel M. Brunetti
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Cynthia M. Chio
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Shizhong A. Dai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Miles S. Dickinson
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Susanna K. Elledge
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Cole V. M. Helsell
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Nathan L. Hendel
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Emily Kang
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Nadja Kern
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Matvei S. Khoroshkin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Lisa L. Kirkemo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Greyson R. Lewis
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Kevin Lou
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Wesley M. Marin
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Alison M. Maxwell
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Peter F. McTigue
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Douglas Myers-Turnbull
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Tamas L. Nagy
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Andrew M. Natale
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Keely Oltion
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Sergei Pourmal
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Gabriel K. Reder
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Nicholas J. Rettko
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Peter J. Rohweder
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Daniel M. C Schwarz
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Sophia K. Tan
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Paul V. Thomas
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Ryan W. Tibble
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Jason P. Town
- Bioinformatics Graduate Group, University of California, San Francisco 94158, USA
- Mary K. Tsai
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Fatima S. Ugur
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Douglas R. Wassarman
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Alexander M. Wolff
- Biophysics Graduate Group, University of California, San Francisco 94158, USA
- Taia S. Wu
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA
- Derek Bogdanoff
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
- Jennifer Li
- Department of Chemistry Undergraduate Program, University of California, Davis 95616, USA
- Kurt S. Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
- Shane O'Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
- Danielle L. Swaney
- Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
- Eric D. Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
- Hiten D. Madhani
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
- Sy Redding
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
- Daniel N. Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA
- Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
- Joseph L. DeRisi
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
- Martin Kampmann
- Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA
- James S. Fraser
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA
- DOI
- https://doi.org/10.1242/bio.036103
- Journal volume & issue
-
Vol. 7,
no. 7
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 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, CaCl2, 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.
Keywords
