UMMS Affiliation
Department of Biochemistry and Molecular Pharmacology
Publication Date
2018-07-23
Document Type
Article
Disciplines
Amino Acids, Peptides, and Proteins | Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Ecology and Evolutionary Biology | Genetic Phenomena
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
Rights and Permissions
Copyright © 2018. Published by The Company of Biologists Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0), which permits unrestricted use, distribution and reproduction in any medium provided that the original work is properly attributed.
DOI of Published Version
10.1242/bio.036103
Source
Biol Open. 2018 Jul 23;7(7). pii: 7/7/bio036103. doi: 10.1242/bio.036103. Link to article on publisher's site
Journal/Book/Conference Title
Biology open
Related Resources
PubMed ID
30037883
Repository Citation
Mavor, David; Bolon, Daniel N.; Kampmann, Martin; and Fraser, James S., "Extending chemical perturbations of the ubiquitin fitness landscape in a classroom setting reveals new constraints on sequence tolerance" (2018). Open Access Articles. 3549.
https://escholarship.umassmed.edu/oapubs/3549
Creative Commons License
This work is licensed under a Creative Commons Attribution 3.0 License.
Included in
Amino Acids, Peptides, and Proteins Commons, Biochemistry, Biophysics, and Structural Biology Commons, Bioinformatics Commons, Ecology and Evolutionary Biology Commons, Genetic Phenomena Commons
Comments
Full author list omitted for brevity. For the full list of authors, see article.