Journal Article

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

Kortemme, Tanja, Thorn, Kurt S, Barad, Benjamin A, Moss, Steven M, Poss, Erin M, Subramaniam, Meena, Wong, Allison W, Nnadi, Chimno I, Conchúir, Shane Ó, Morinishi, Leanna S, Bonny, Alain R, Hulce, Kaitlin R, Chow, Eric D, Thompson, Samuel, DeRisi, Joseph L, Barlow, Kyle, Cuesta, Adolfo, Caceres, Elena, Gate, Rachel E, Chen, Weilin, Mravic, Marco, Mavor, David, Muir, Ryan K, Fraser, James S, Salcedo, Eugenia C, Liu, Zairan, Deming, Laura, Bolon, Daniel N, Axen, Seth D, Kenner, Lillian R, Li, Jennifer, Roscoe, Benjamin P, Ross, Tyler D, Palovcak, Eugene, Cario, Clinton L, Green, Evan M, Niekamp, Stefan, Mensa, Bruk, Gaskins, Garrett, Ji, Weiyue, See, Stephanie K

2016

Overview

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. The ability of an organism to grow and reproduce, that is, it’s “fitness”, is determined by how its genes interact with the environment. Yeast is a model organism in which researchers can control the exact mutations present in the yeast’s genes (its genotype) and the conditions in which the yeast cells live (their environment). This allows researchers to measure how a yeast cell’s genotype and environment affect its fitness. Ubiquitin is a protein that many organisms depend on to manage cell stress by acting as a tag that targets other proteins for degradation. Essential proteins such as ubiquitin often remain unchanged by mutation over long periods of time. As a result, these proteins evolve very slowly. Like all proteins, ubiquitin is built from a chain of amino acid molecules linked together, and the ubiquitin proteins of yeast and humans are made of almost identical sequences of amino acids. Although ubiquitin has barely changed its sequence over evolution, previous studies have shown that – under normal growth conditions in the laboratory – most amino acids in ubiquitin can be mutated without any loss of cell fitness. This led Mavor et al. to hypothesize that treating the yeast cells with chemicals that cause cell stress might lead to amino acids in ubiquitin becoming more sensitive to mutation. To test this idea, a class of graduate students at the University of California, San Francisco grew yeast cells with different ubiquitin mutations together, and with different chemicals that induce cell stress, and measured their growth rates. Sequencing the ubiquitin gene in the thousands of tested yeast cells revealed that three of the chemicals cause a shared set of amino acids in ubiquitin to become more sensitive to mutation. This result suggests that these amino acids are important for the stress response, possibly by altering the ability of yeast cells to target certain proteins for degradation. Conversely, another chemical causes yeast to become more tolerant to changes in the ubiquitin sequence. The experiments also link changes in particular amino acids in ubiquitin to specific stress responses. Mavor et al. show that many of ubquitin’s amino acids are sensitive to mutation under different stress conditions, while others can be mutated to form different amino acids without effecting fitness. By testing the effects of other chemicals, future experiments could further characterize how the yeast’s genotype and environment interact.

• Publisher: eLife Science Publications, Ltd,eLife Sciences Publications Ltd,eLife Sciences Publications, Ltd
• Subject: Amino acids / Biochemistry / Biology / Biology - education / Biophysics / C-Terminus / Caffeine / Cell cycle / chemical biology / Chemicals / Computational and Systems Biology / deep mutational scanning / Defects / Deoxyribonucleic acid / Dithiothreitol / DNA / DNA Mutational Analysis / Enzymes / Genomics and Evolutionary Biology / Humans / Hydrophobicity / Mutant Proteins - genetics / Mutant Proteins - metabolism / Mutation / Physiological aspects / proteasome / Proteasome Endopeptidase Complex - genetics / Proteasome Endopeptidase Complex - metabolism / Proteasomes / Proteins / proteostasis / Reproductive fitness / Saccharomyces cerevisiae - enzymology / Saccharomyces cerevisiae - physiology / Stress, Physiological / Students / Ubiquitin / Ubiquitin - genetics / Ubiquitin - metabolism / Universities