Determination of ubiquitin fitness landscapes under different chemical stresses in a classroom setting.
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.
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
David
D
Mavor
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Kyle
0000-0002-9787-0066
K
Barlow
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Samuel
S
Thompson
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Benjamin A
BA
Barad
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Alain R
AR
Bonny
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Clinton L
CL
Cario
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Garrett
G
Gaskins
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Zairan
Z
Liu
Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.
Laura
L
Deming
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Seth D
SD
Axen
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Elena
E
Caceres
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Weilin
W
Chen
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Adolfo
A
Cuesta
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Rachel E
RE
Gate
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Evan M
EM
Green
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Kaitlin R
KR
Hulce
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Weiyue
W
Ji
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Lillian R
LR
Kenner
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Bruk
B
Mensa
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Leanna S
LS
Morinishi
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Steven M
SM
Moss
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Marco
M
Mravic
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Ryan K
RK
Muir
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Stefan
S
Niekamp
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Chimno I
CI
Nnadi
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Eugene
E
Palovcak
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Erin M
EM
Poss
Biophysics Graduate Group, University of California, San Francisco, San Francisco, United States.
Tyler D
TD
Ross
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Eugenia C
EC
Salcedo
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Stephanie K
SK
See
Bioinformatics Graduate Group, University of California, San Francisco, San Francisco, United States.
Meena
M
Subramaniam
Chemistry and Chemical Biology Graduate Program, University of California, San Francisco, San Francisco, United States.
Allison W
AW
Wong
UCSF Science and Health Education Partnership, University of California, San Francisco, San Francisco, United States.
Jennifer
J
Li
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.
Kurt S
KS
Thorn
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States.
Shane Ó
SÓ
Conchúir
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.
Benjamin P
BP
Roscoe
Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.|Center for Advanced Technology, University of California, San Francisco, San Francisco, United States.
Eric D
ED
Chow
Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States.|Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, United States.
Joseph L
JL
DeRisi
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States.
Tanja
T
Kortemme
Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, United States.
Daniel N
DN
Bolon
Department of Bioengineering and Therapeutic Sciences, California Institute for Quantitative Biology, University of California, San Francisco, San Francisco, United States.
James S
0000-0002-5080-2859
JS
Fraser
D001695:Biology / Q000193:education; D004252:DNA Mutational Analysis; D006801:Humans; D050505:Mutant Proteins / Q000235:genetics* / Q000378:metabolism*; D046988:Proteasome Endopeptidase Complex / Q000235:genetics / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000201:enzymology* / Q000502:physiology; D013312:Stress, Physiological; D013334:Students; D025801:Ubiquitin / Q000235:genetics* / Q000378:metabolism*; D014495:Universities
D050505:Mutant Proteins; D025801:Ubiquitin; D046988:Proteasome Endopeptidase Complex
S. cerevisiae; biophysics; chemical biology; computational biology; deep mutational scanning; evolutionary biology; genomics; proteasome; proteostasis; systems biology; ubiquitin