eLife (Apr 2016)
Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting
- David Mavor,
- Kyle Barlow,
- Samuel Thompson,
- Benjamin A Barad,
- Alain R Bonny,
- Clinton L Cario,
- Garrett Gaskins,
- Zairan Liu,
- Laura Deming,
- Seth D Axen,
- Elena Caceres,
- Weilin Chen,
- Adolfo Cuesta,
- Rachel E Gate,
- Evan M Green,
- Kaitlin R Hulce,
- Weiyue Ji,
- Lillian R Kenner,
- Bruk Mensa,
- Leanna S Morinishi,
- Steven M Moss,
- Marco Mravic,
- Ryan K Muir,
- Stefan Niekamp,
- Chimno I Nnadi,
- Eugene Palovcak,
- Erin M Poss,
- Tyler D Ross,
- Eugenia C Salcedo,
- Stephanie K See,
- Meena Subramaniam,
- Allison W Wong,
- Jennifer Li,
- Kurt S Thorn,
- Shane Ó Conchúir,
- Benjamin P Roscoe,
- Eric D Chow,
- Joseph L DeRisi,
- Tanja Kortemme,
- Daniel N Bolon,
- James S Fraser
Affiliations
- David Mavor
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Kyle Barlow
- ORCiD
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Samuel Thompson
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Benjamin A Barad
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Alain R Bonny
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Clinton L Cario
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Garrett Gaskins
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Zairan Liu
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Laura Deming
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- Seth D Axen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Elena Caceres
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Weilin Chen
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Adolfo Cuesta
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Rachel E Gate
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Evan M Green
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Kaitlin R Hulce
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Weiyue Ji
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Lillian R Kenner
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Bruk Mensa
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Leanna S Morinishi
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Steven M Moss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Marco Mravic
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Ryan K Muir
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Stefan Niekamp
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Chimno I Nnadi
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Eugene Palovcak
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Erin M Poss
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Tyler D Ross
- Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States
- Eugenia C Salcedo
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Stephanie K See
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Meena Subramaniam
- Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States
- Allison W Wong
- Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States
- Jennifer Li
- UCSF Science and Health Education Partnership, University of California, San Francisco, San Francisco, United States
- Kurt S Thorn
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- Shane Ó Conchúir
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
- Benjamin P Roscoe
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
- Eric D Chow
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States; Center for Advanced Technology, University of California, San Francisco, San Francisco, United States
- Joseph L DeRisi
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States; Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States
- Tanja Kortemme
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
- Daniel N Bolon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States
- James S Fraser
- ORCiD
- Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States
- DOI
- https://doi.org/10.7554/eLife.15802
- Journal volume & issue
-
Vol. 5
Abstract
Ubiquitin is essential for eukaryotic life and varies in only 3 amino acid positions between yeast and humans. However, recent deep sequencing studies indicate that ubiquitin is highly tolerant to single mutations. We hypothesized that this tolerance would be reduced by chemically induced physiologic perturbations. To test this hypothesis, a class of first year UCSF graduate students employed deep mutational scanning to determine the fitness landscape of all possible single residue mutations in the presence of five different small molecule perturbations. These perturbations uncover 'shared sensitized positions' localized to areas around the hydrophobic patch and the C-terminus. In addition, we identified perturbation specific effects such as a sensitization of His68 in HU and a tolerance to mutation at Lys63 in DTT. Our data show how chemical stresses can reduce buffering effects in the ubiquitin proteasome system. Finally, this study demonstrates the potential of lab-based interdisciplinary graduate curriculum.
Keywords
