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Science 323 (5922): 1693-1697

Copyright © 2009 by the American Association for the Advancement of Science

Comprehensive Characterization of Genes Required for Protein Folding in the Endoplasmic Reticulum

Martin C. Jonikas,1,2,3,4 Sean R. Collins,1,3,4 Vladimir Denic,1,3,4* Eugene Oh,1,3,4 Erin M. Quan,1,3,4 Volker Schmid,5 Jimena Weibezahn,1,3,4 Blanche Schwappach,5 Peter Walter,2,3 Jonathan S. Weissman,1,3,4{dagger} Maya Schuldiner1,3,4{ddagger}

Abstract: Protein folding in the endoplasmic reticulum is a complex process whose malfunction is implicated in disease and aging. By using the cell's endogenous sensor (the unfolded protein response), we identified several hundred yeast genes with roles in endoplasmic reticulum folding and systematically characterized their functional interdependencies by measuring unfolded protein response levels in double mutants. This strategy revealed multiple conserved factors critical for endoplasmic reticulum folding, including an intimate dependence on the later secretory pathway, a previously uncharacterized six-protein transmembrane complex, and a co-chaperone complex that delivers tail-anchored proteins to their membrane insertion machinery. The use of a quantitative reporter in a comprehensive screen followed by systematic analysis of genetic dependencies should be broadly applicable to functional dissection of complex cellular processes from yeast to human.

1 Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, CA 94143, USA.
2 Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94143, USA.
3 Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94143, USA.
4 California Institute for Quantitative Biomedical Research, San Francisco, CA 94143, USA.
5 Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, UK.

* Present address: Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA.

{ddagger} Present address: Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.

{dagger} To whom correspondence should be addressed. E-mail: weissman{at}

Automated identification of pathways from quantitative genetic interaction data.
A. Battle, M. C. Jonikas, P. Walter, J. S. Weissman, and D. Koller (2014)
Mol Syst Biol 6, 379
   Abstract »    Full Text »    PDF »
Quality control: ER-associated degradation: Protein quality control and beyond.
A. Ruggiano, O. Foresti, and P. Carvalho (2014)
J. Cell Biol. 204, 869-879
   Abstract »    Full Text »    PDF »
The Natural Diyne-Furan Fatty Acid EV-086 Is an Inhibitor of Fungal Delta-9 Fatty Acid Desaturation with Efficacy in a Model of Skin Dermatophytosis.
P. Knechtle, M. Diefenbacher, K. B. V. Greve, F. Brianza, C. Folly, H. Heider, M. A. Lone, L. Long, J.-P. Meyer, P. Roussel, et al. (2014)
Antimicrob. Agents Chemother. 58, 455-466
   Abstract »    Full Text »    PDF »
The LC3 interactome at a glance.
P. Wild, D. G. McEwan, and I. Dikic (2014)
J. Cell Sci. 127, 3-9
   Abstract »    Full Text »    PDF »
Golgi enlargement in Arf-depleted yeast cells is due to altered dynamics of cisternal maturation.
M. Bhave, E. Papanikou, P. Iyer, K. Pandya, B. K. Jain, A. Ganguly, C. Sharma, K. Pawar, J. Austin II, K. J. Day, et al. (2014)
J. Cell Sci. 127, 250-257
   Abstract »    Full Text »    PDF »
Sequential Cytoprotective Responses to Sigma1 Ligand-Induced Endoplasmic Reticulum Stress.
J. M. Schrock, C. M. Spino, C. G. Longen, S. M. Stabler, J. C. Marino, G. W. Pasternak, and F. J. Kim (2013)
Mol. Pharmacol. 84, 751-762
   Abstract »    Full Text »    PDF »
Identifying proteins controlling key disease signaling pathways.
A. Gitter and Z. Bar-Joseph (2013)
Bioinformatics 29, i227-i236
   Abstract »    Full Text »    PDF »
Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells.
M. Kampmann, M. C. Bassik, and J. S. Weissman (2013)
PNAS 110, E2317-E2326
   Abstract »    Full Text »    PDF »
A stalled retrotranslocation complex reveals physical linkage between substrate recognition and proteasomal degradation during ER-associated degradation.
K. Nakatsukasa, J. L. Brodsky, and T. Kamura (2013)
Mol. Biol. Cell 24, 1765-1775
   Abstract »    Full Text »    PDF »
Futile Protein Folding Cycles in the ER Are Terminated by the Unfolded Protein O-Mannosylation Pathway.
C. Xu, S. Wang, G. Thibault, and D. T. W. Ng (2013)
Science 340, 978-981
   Abstract »    Full Text »    PDF »
Precise timing of ATPase activation drives targeting of tail-anchored proteins.
M. E. Rome, M. Rao, W. M. Clemons, and S.-o. Shan (2013)
PNAS 110, 7666-7671
   Abstract »    Full Text »    PDF »
N-terminal acetylation of the yeast Derlin Der1 is essential for Hrd1 ubiquitin-ligase activity toward luminal ER substrates.
D. Zattas, D. J. Adle, E. M. Rubenstein, and M. Hochstrasser (2013)
Mol. Biol. Cell 24, 890-900
   Abstract »    Full Text »    PDF »
ERdj3 regulates BiP occupancy in living cells.
F. Guo and E. L. Snapp (2013)
J. Cell Sci. 126, 1429-1439
   Abstract »    Full Text »    PDF »
Biosynthesis of ionotropic acetylcholine receptors requires the evolutionarily conserved ER membrane complex.
M. Richard, T. Boulin, V. J. P. Robert, J. E. Richmond, and J.-L. Bessereau (2013)
PNAS 110, E1055-E1063
   Abstract »    Full Text »    PDF »
Tail-anchored PEX26 targets peroxisomes via a PEX19-dependent and TRC40-independent class I pathway.
Y. Yagita, T. Hiromasa, and Y. Fujiki (2013)
J. Cell Biol. 200, 651-666
   Abstract »    Full Text »    PDF »
The Contribution of Systematic Approaches to Characterizing the Proteins and Functions of the Endoplasmic Reticulum.
M. Schuldiner and J. S. Weissman (2013)
Cold Spring Harb Perspect Biol 5, a013284
   Abstract »    Full Text »    PDF »
Ataxin-2 interacts with FUS and intermediate-length polyglutamine expansions enhance FUS-related pathology in amyotrophic lateral sclerosis.
M. A. Farg, K. Y. Soo, S. T. Warraich, V. Sundaramoorthy, I. P. Blair, and J. D. Atkin (2013)
Hum. Mol. Genet. 22, 717-728
   Abstract »    Full Text »    PDF »
Secretory Protein Biogenesis and Traffic in the Early Secretory Pathway.
C. K. Barlowe and E. A. Miller (2013)
Genetics 193, 383-410
   Abstract »    Full Text »    PDF »
Get3 is a holdase chaperone and moves to deposition sites for aggregated proteins when membrane targeting is blocked.
K. Powis, B. Schrul, H. Tienson, I. Gostimskaya, M. Breker, S. High, M. Schuldiner, U. Jakob, and B. Schwappach (2013)
J. Cell Sci. 126, 473-483
   Abstract »    Full Text »    PDF »
Cell Biology of the Endoplasmic Reticulum and the Golgi Apparatus through Proteomics.
J. Smirle, C. E. Au, M. Jain, K. Dejgaard, T. Nilsson, and J. Bergeron (2013)
Cold Spring Harb Perspect Biol 5, a015073
   Abstract »    Full Text »    PDF »
Regulation of Chaperone Effects on a Yeast Prion by Cochaperone Sgt2.
D. A. Kiktev, J. C. Patterson, S. Muller, B. Bariar, T. Pan, and Y. O. Chernoff (2012)
Mol. Cell. Biol. 32, 4960-4970
   Abstract »    Full Text »    PDF »
Genetic Analysis of Mps3 SUN Domain Mutants in Saccharomyces cerevisiae Reveals an Interaction with the SUN-Like Protein Slp1.
J. M. Friederichs, J. M. Gardner, C. J. Smoyer, C. R. Whetstine, M. Gogol, B. D. Slaughter, and S. L. Jaspersen (2012)
g3 2, 1703-1718
   Abstract »    Full Text »    PDF »
Role of the AAA protease Yme1 in folding of proteins in the intermembrane space of mitochondria.
B. Schreiner, H. Westerburg, I. Forne, A. Imhof, W. Neupert, and D. Mokranjac (2012)
Mol. Biol. Cell 23, 4335-4346
   Abstract »    Full Text »    PDF »
The Endosomal Protein-Sorting Receptor Sortilin Has a Role in Trafficking {alpha}-1 Antitrypsin.
C. L. Gelling, I. W. Dawes, D. H. Perlmutter, E. A. Fisher, and J. L. Brodsky (2012)
Genetics 192, 889-903
   Abstract »    Full Text »    PDF »
Ergosterol content specifies targeting of tail-anchored proteins to mitochondrial outer membranes.
K. Krumpe, I. Frumkin, Y. Herzig, N. Rimon, C. Ozbalci, B. Brugger, D. Rapaport, and M. Schuldiner (2012)
Mol. Biol. Cell 23, 3927-3935
   Abstract »    Full Text »    PDF »
Glycosylphosphatidylinositol anchors regulate glycosphingolipid levels.
U. Loizides-Mangold, F. P. A. David, V. J. Nesatyy, T. Kinoshita, and H. Riezman (2012)
J. Lipid Res. 53, 1522-1534
   Abstract »    Full Text »    PDF »
Activation of the unfolded protein response pathway causes ceramide accumulation in yeast and INS-1E insulinoma cells.
S. Epstein, C. L. Kirkpatrick, G. A. Castillon, M. Muniz, I. Riezman, F. P. A. David, C. B. Wollheim, and H. Riezman (2012)
J. Lipid Res. 53, 412-420
   Abstract »    Full Text »    PDF »
Interaction Surface and Topology of Get3-Get4-Get5 Protein Complex, Involved in Targeting Tail-anchored Proteins to Endoplasmic Reticulum.
Y.-W. Chang, T.-W. Lin, Y.-C. Li, Y.-S. Huang, Y.-J. Sun, and C.-D. Hsiao (2012)
J. Biol. Chem. 287, 4783-4789
   Abstract »    Full Text »    PDF »
Proteomes of hard and soft near-isogenic wheat lines reveal that kernel hardness is related to the amplification of a stress response during endosperm development.
V. S. Lesage, M. Merlino, C. Chambon, B. Bouchet, D. Marion, and G. Branlard (2012)
J. Exp. Bot. 63, 1001-1011
   Abstract »    Full Text »    PDF »
The unfolded protein response supports cellular robustness as a broad-spectrum compensatory pathway.
G. Thibault, N. Ismail, and D. T. W. Ng (2011)
PNAS 108, 20597-20602
   Abstract »    Full Text »    PDF »
Imaging of Plasmodium Liver Stages to Drive Next-Generation Antimalarial Drug Discovery.
S. Meister, D. M. Plouffe, K. L. Kuhen, G. M. C. Bonamy, T. Wu, S. W. Barnes, S. E. Bopp, R. Borboa, A. T. Bright, J. Che, et al. (2011)
Science 334, 1372-1377
   Abstract »    Full Text »    PDF »
Getting the whole picture: combining throughput with content in microscopy.
N. Rimon and M. Schuldiner (2011)
J. Cell Sci. 124, 3743-3751
   Abstract »    Full Text »    PDF »
Membrane aberrancy and unfolded proteins activate the endoplasmic reticulum stress sensor Ire1 in different ways.
T. Promlek, Y. Ishiwata-Kimata, M. Shido, M. Sakuramoto, K. Kohno, and Y. Kimata (2011)
Mol. Biol. Cell 22, 3520-3532
   Abstract »    Full Text »    PDF »
POD1 Regulates Pollen Tube Guidance in Response to Micropylar Female Signaling and Acts in Early Embryo Patterning in Arabidopsis.
H.-J. Li, Y. Xue, D.-J. Jia, T. Wang, D.-Q. hi, J. Liu, F. Cui, Q. Xie, D. Ye, and W.-C. Yang (2011)
PLANT CELL 23, 3288-3302
   Abstract »    Full Text »    PDF »
Neuronal circuitry regulates the response of Caenorhabditis elegans to misfolded proteins.
V. Prahlad and R. I. Morimoto (2011)
PNAS 108, 14204-14209
   Abstract »    Full Text »    PDF »
Phosphatidate Phosphatase Activity Plays Key Role in Protection against Fatty Acid-induced Toxicity in Yeast.
S. Fakas, Y. Qiu, J. L. Dixon, G.-S. Han, K. V. Ruggles, J. Garbarino, S. L. Sturley, and G. M. Carman (2011)
J. Biol. Chem. 286, 29074-29085
   Abstract »    Full Text »    PDF »
The yeast p24 complex regulates GPI-anchored protein transport and quality control by monitoring anchor remodeling.
G. A. Castillon, A. Aguilera-Romero, J. Manzano-Lopez, S. Epstein, K. Kajiwara, K. Funato, R. Watanabe, H. Riezman, and M. Muniz (2011)
Mol. Biol. Cell 22, 2924-2936
   Abstract »    Full Text »    PDF »
Lipid Droplet Formation Is Dispensable for Endoplasmic Reticulum-associated Degradation.
J. A. Olzmann and R. R. Kopito (2011)
J. Biol. Chem. 286, 27872-27874
   Abstract »    Full Text »    PDF »
Drosophila RNAi screening in a postgenomic world.
C. Bakal (2011)
Briefings in Functional Genomics
   Abstract »    Full Text »    PDF »
WRB is the receptor for TRC40/Asna1-mediated insertion of tail-anchored proteins into the ER membrane.
F. Vilardi, H. Lorenz, and B. Dobberstein (2011)
J. Cell Sci. 124, 1301-1307
   Abstract »    Full Text »    PDF »
Exploring transcription regulation through cell-to-cell variability.
R. Rinott, A. Jaimovich, and N. Friedman (2011)
PNAS 108, 6329-6334
   Abstract »    Full Text »    PDF »
Loss of Subcellular Lipid Transport Due to ARV1 Deficiency Disrupts Organelle Homeostasis and Activates the Unfolded Protein Response.
C. F. Shechtman, A. L. Henneberry, T. A. Seimon, A. H. Tinkelenberg, L. J. Wilcox, E. Lee, M. Fazlollahi, A. B. Munkacsi, H. J. Bussemaker, I. Tabas, et al. (2011)
J. Biol. Chem. 286, 11951-11959
   Abstract »    Full Text »    PDF »
Modular analysis of the probabilistic genetic interaction network.
L. Hou, L. Wang, M. Qian, D. Li, C. Tang, Y. Zhu, M. Deng, and F. Li (2011)
Bioinformatics 27, 853-859
   Abstract »    Full Text »    PDF »
J Domain Co-chaperone Specificity Defines the Role of BiP during Protein Translocation.
S. S. Vembar, M. C. Jonikas, L. M. Hendershot, J. S. Weissman, and J. L. Brodsky (2010)
J. Biol. Chem. 285, 22484-22494
   Abstract »    Full Text »    PDF »
Structural characterization of the Get4/Get5 complex and its interaction with Get3.
J. W. Chartron, C. J. M. Suloway, M. Zaslaver, and W. M. Clemons Jr. (2010)
PNAS 107, 12127-12132
   Abstract »    Full Text »    PDF »
Bat3 promotes the membrane integration of tail-anchored proteins.
P. Leznicki, A. Clancy, B. Schwappach, and S. High (2010)
J. Cell Sci. 123, 2170-2178
   Abstract »    Full Text »    PDF »
Regulation of basal cellular physiology by the homeostatic unfolded protein response.
D. T. Rutkowski and R. S. Hegde (2010)
J. Cell Biol. 189, 783-794
   Abstract »    Full Text »    PDF »
Osteopotentia regulates osteoblast maturation, bone formation, and skeletal integrity in mice.
M. L. Sohaskey, Y. Jiang, J. J. Zhao, A. Mohr, F. Roemer, and R. M. Harland (2010)
J. Cell Biol. 189, 511-525
   Abstract »    Full Text »    PDF »
Asna1/TRC40-mediated membrane insertion of tail-anchored proteins.
V. Favaloro, F. Vilardi, R. Schlecht, M. P. Mayer, and B. Dobberstein (2010)
J. Cell Sci. 123, 1522-1530
   Abstract »    Full Text »    PDF »
Crystal Structure of Get4-Get5 Complex and Its Interactions with Sgt2, Get3, and Ydj1.
Y.-W. Chang, Y.-C. Chuang, Y.-C. Ho, M.-Y. Cheng, Y.-J. Sun, C.-D. Hsiao, and C. Wang (2010)
J. Biol. Chem. 285, 9962-9970
   Abstract »    Full Text »    PDF »
The Genetic Landscape of a Cell.
M. Costanzo, A. Baryshnikova, J. Bellay, Y. Kim, E. D. Spear, C. S. Sevier, H. Ding, J. L.Y. Koh, K. Toufighi, S. Mostafavi, et al. (2010)
Science 327, 425-431
   Abstract »    Full Text »    PDF »
PtdIns4P recognition by Vps74/GOLPH3 links PtdIns 4-kinase signaling to retrograde Golgi trafficking.
C. S. Wood, K. R. Schmitz, N. J. Bessman, T. G. Setty, K. M. Ferguson, and C. G. Burd (2009)
J. Cell Biol. 187, 967-975
   Abstract »    Full Text »    PDF »
Structural insights into tail-anchored protein binding and membrane insertion by Get3.
G. Bozkurt, G. Stjepanovic, F. Vilardi, S. Amlacher, K. Wild, G. Bange, V. Favaloro, K. Rippe, E. Hurt, B. Dobberstein, et al. (2009)
PNAS 106, 21131-21136
   Abstract »    Full Text »    PDF »
Neurodegenerative diseases: Lessons from genome-wide screens in small model organisms.
T. J. van Ham, R. Breitling, M. A. Swertz, and E. A. A. Nollen (2009)
EMBO Mol Med. 1, 360-370
   Abstract »    Full Text »    PDF »
Protein quality control--linking the unfolded protein response to disease: Conference on 'From Unfolded Proteins in the Endoplasmic Reticulum to Disease'.
D. M. Cyr and D. N. Hebert (2009)
EMBO Rep. 10, 1206-1210
   Full Text »    PDF »
Biogenesis of tail-anchored proteins: the beginning for the end?.
C. Rabu, V. Schmid, B. Schwappach, and S. High (2009)
J. Cell Sci. 122, 3605-3612
   Abstract »    Full Text »    PDF »
Model for eukaryotic tail-anchored protein binding based on the structure of Get3.
C. J. M. Suloway, J. W. Chartron, M. Zaslaver, and W. M. Clemons Jr. (2009)
PNAS 106, 14849-14854
   Abstract »    Full Text »    PDF »
Genomewide Analysis Reveals Novel Pathways Affecting Endoplasmic Reticulum Homeostasis, Protein Modification and Quality Control.
A. Copic, M. Dorrington, S. Pagant, J. Barry, M. C. S. Lee, I. Singh, J. L. Hartman IV, and E. A. Miller (2009)
Genetics 182, 757-769
   Abstract »    Full Text »    PDF »

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