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


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.

Submission Details

ID: CdSscVh64

Submitter: Connie Wang

Submission Date: Dec. 14, 2016, 4:19 p.m.

Version: 1

Publication Details
Mavor D;Barlow K;Thompson S;Barad BA;Bonny AR;Cario CL;Gaskins G;Liu Z;Deming L;Axen SD;Caceres E;Chen W;Cuesta A;Gate RE;Green EM;Hulce KR;Ji W;Kenner LR;Mensa B;Morinishi LS;Moss SM;Mravic M;Muir RK;Niekamp S;Nnadi CI;Palovcak E;Poss EM;Ross TD;Salcedo EC;See SK;Subramaniam M;Wong AW;Li J;Thorn KS;Conchúir SÓ;Roscoe BP;Chow ED;DeRisi JL;Kortemme T;Bolon DN;Fraser JS,Elife (2016) Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting. PMID:27111525
Additional Information

Structure view and single mutant data analysis

Study data

No weblogo for data of varying length.
Colors: D E R H K S T N Q A V I L M F Y W C G P
 

Data Distribution

Studies with similar sequences (approximate matches)

Correlation with other assays (exact sequence matches)