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

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)

Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.

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.

No MeSH data available.


Related in: MedlinePlus

Fitnesses determined in DMSO are well correlated to the previously determined unperturbed fitnesses.A linear regression (R2 = 0.785) and Pearson’s correlation coefficient (CC = 0.886) were calculated between the fitness scores determined in DMSO and the previously published unperturbed dataset (Roscoe et al., 2013).DOI:http://dx.doi.org/10.7554/eLife.15802.007
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fig3s2: Fitnesses determined in DMSO are well correlated to the previously determined unperturbed fitnesses.A linear regression (R2 = 0.785) and Pearson’s correlation coefficient (CC = 0.886) were calculated between the fitness scores determined in DMSO and the previously published unperturbed dataset (Roscoe et al., 2013).DOI:http://dx.doi.org/10.7554/eLife.15802.007


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

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)

Fitnesses determined in DMSO are well correlated to the previously determined unperturbed fitnesses.A linear regression (R2 = 0.785) and Pearson’s correlation coefficient (CC = 0.886) were calculated between the fitness scores determined in DMSO and the previously published unperturbed dataset (Roscoe et al., 2013).DOI:http://dx.doi.org/10.7554/eLife.15802.007
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4862753&req=5

fig3s2: Fitnesses determined in DMSO are well correlated to the previously determined unperturbed fitnesses.A linear regression (R2 = 0.785) and Pearson’s correlation coefficient (CC = 0.886) were calculated between the fitness scores determined in DMSO and the previously published unperturbed dataset (Roscoe et al., 2013).DOI:http://dx.doi.org/10.7554/eLife.15802.007
Bottom Line: 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.

View Article: PubMed Central - PubMed

Affiliation: Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.

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.

No MeSH data available.


Related in: MedlinePlus