Format

Send to

Choose Destination
Biol Open. 2018 Jul 23;7(7). pii: bio036103. doi: 10.1242/bio.036103.

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

Author information

1
Biophysics Graduate Group, University of California, San Francisco 94158, USA.
2
Bioinformatics Graduate Group, University of California, San Francisco 94158, USA.
3
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco 94158, USA.
4
Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA.
5
Department of Chemistry Undergraduate Program, University of California, Davis 95616, USA.
6
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA.
7
Department of Cellular and Molecular Pharmacology, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA.
8
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester 01655, USA.
9
Department of Biochemistry and Biophysics, University of California, San Francisco 94158, USA martin.kampmann@ucsf.edu jfraser@fraserlab.com.
10
Institute for Neurodegenerative Diseases, University of California, San Francisco 94158, USA.
11
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology (QBI), San Francisco 94158, USA martin.kampmann@ucsf.edu jfraser@fraserlab.com.

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:

Deep mutational scanning; Evolution; Ubiquitin

Supplemental Content

Full text links

Icon for HighWire Icon for PubMed Central
Loading ...
Support Center