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Elife. 2016 Apr 25;5. pii: e15802. doi: 10.7554/eLife.15802.

Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.

Author information

1
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
2
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
3
Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.
4
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
5
UCSF Science and Health Education Partnership, University of California, San Francisco, San Francisco, United States.
6
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.
7
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States.
8
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.
9
Center for Advanced Technology, University of California, San Francisco, San Francisco, United States.

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:

S. cerevisiae; biophysics; chemical biology; computational biology; deep mutational scanning; evolutionary biology; genomics; proteasome; proteostasis; systems biology; ubiquitin

PMID:
27111525
PMCID:
PMC4862753
DOI:
10.7554/eLife.15802
[Indexed for MEDLINE]
Free PMC Article

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