Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting
Category
Published on
Type
journal-article
Author
David Mavor and Kyle Barlow and Samuel Thompson and Benjamin A Barad and Alain R Bonny and Clinton L Cario and Garrett Gaskins and Zairan Liu and Laura Deming and Seth D Axen and Elena Caceres and Weilin Chen and Adolfo Cuesta and Rachel E Gate and Evan M Green and Kaitlin R Hulce and Weiyue Ji and Lillian R Kenner and Bruk Mensa and Leanna S Morinishi and Steven M Moss and Marco Mravic and Ryan K Muir and Stefan Niekamp and Chimno I Nnadi and Eugene Palovcak and Erin M Poss and Tyler D Ross and Eugenia C Salcedo and Stephanie K See and Meena Subramaniam and Allison W Wong and Jennifer Li and Kurt S Thorn and Shane Ó Conchúir and Benjamin P Roscoe and Eric D Chow and Joseph L DeRisi and Tanja Kortemme and Daniel N Bolon and James S Fraser
Citation
Mavor, D. et al., 2016. Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. eLife, 5. Available at: http://dx.doi.org/10.7554/elife.15802.
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.
