A proteomic survey of widespread protein aggregation in yeast

Molecular BioSystems

Volumn 10, Issue 4, 2014, Pages 851-861

  O'Connell, Jeremy D ^a   Tsechansky, Mark ^b   Royall, Ariel ^a   Boutz, Daniel R ^a   Ellington, Andrew D ^a   Marcotte, Edward M ^a  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ADENOSINE TRIPHOSPHATASE; ARSENIC; CHAPERONE; GLUTAMATE AMMONIA LIGASE; GLUTAMINE SYNTHETASE I; GREEN FLUORESCENT PROTEIN; HEAT SHOCK PROTEIN 70; HEAT SHOCK PROTEIN 90; HSP82 PROTEIN, S CEREVISIAE; PHOSPHOGLYCERATE MUTASE; SACCHAROMYCES CEREVISIAE PROTEIN; SSA1 PROTEIN, S CEREVISIAE; SSA3 PROTEIN, S CEREVISIAE;

CHEMISTRY; ENDOPLASMIC RETICULUM ASSOCIATED DEGRADATION; ENZYMOLOGY; GENETICS; HEAT SHOCK RESPONSE; METABOLISM; PROTEIN FOLDING; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SOLUBILITY;

ADENOSINE TRIPHOSPHATASES; ARSENIC; ENDOPLASMIC RETICULUM-ASSOCIATED DEGRADATION; GLUTAMATE-AMMONIA LIGASE; GREEN FLUORESCENT PROTEINS; HEAT-SHOCK RESPONSE; HSP70 HEAT-SHOCK PROTEINS; HSP90 HEAT-SHOCK PROTEINS; MOLECULAR CHAPERONES; PHOSPHOGLYCERATE MUTASE; PROTEIN FOLDING; PROTEOMICS; SACCHAROMYCES CEREVISIAE; SACCHAROMYCES CEREVISIAE PROTEINS; SOLUBILITY;

EID: 84897680356     PISSN: 1742206X     EISSN: 17422051     Source Type: Journal    
DOI: 10.1039/c3mb70508k     Document Type: Article

References (38)

1. R. Narayanaswamy M. Levy M. Tsechansky G. M. Stovall J. D. O'Connell J. Mirrielees A. D. Ellington E. M. Marcotte Widespread reorganization of metabolic enzymes into reversible assemblies upon nutrient starvation Proc. Natl. Acad. Sci. U. S. A. 2009 106 25 10147 10152
2. C. Noree B. K. Sato R. M. Broyer J. E. Wilhelm Identification of novel filament-forming proteins in Saccharomyces cerevisiae and drosophila melanogaster J. Cell Biol. 2010 190 4 541 551
3. K. Bagola T. Sommer Protein quality control: on IPODs and other JUNQ Curr. Biol. 2008 18 21 R1019 R1021
4. M. Ingerson-Mahar A. Briegel J. N. Werner G. J. Jensen Z. Gitai The metabolic enzyme CTP synthase forms cytoskeletal filaments Nat. Cell Biol. 2010 12 8 739 746
5. J.-L. Liu Intracellular compartmentation of CTP synthase in Drosophila J. Genet. Genomics 2010 37 5 281 296
6. K. Chen J. Zhang O. Y. Tastan Z. A. Deussen M. Y.-Y. Siswick J.-L. Liu Glutamine analogs promote cytoophidium assembly in human and Drosophila cells J. Genet. Genomics 2011 38 9 391 402
7. J. D. O'Connell A. Zhao A. D. Ellington E. M. Marcotte Dynamic Reorganization of Metabolic Enzymes into Intracellular Bodies Annu. Rev. Cell Dev. Biol. 2012 28 89 111
8. D. Kaganovich R. Kopito J. Frydman Misfolded proteins partition between two distinct quality control compartments Nature 2008 454 7208 1088 1095
9. B. Meusser C. Hirsch E. Jarosch T. Sommer ERAD: the long road to destruction Nat. Cell Biol. 2005 7 8 766 772
10. J. A. Johnston C. L. Ward R. R. Kopito Aggresomes: a cellular response to misfolded proteins J. Cell Biol. 1998 143 7 1883 1898
11. L. Goldschmidt P. K. Teng R. Riek D. Eisenberg Identifying the amylome, proteins capable of forming amyloid-like fibrils Proc. Natl. Acad. Sci. U. S. A. 2010 107 8 3487 3492
12. M. Brengues D. Teixeira R. Parker Movement of eukaryotic mRNAs between polysomes and cytoplasmic processing bodies Science 2005 310 5747 486 489
13. I. Sagot B. Pinson B. Salin B. Daignan-Fornier Actin bodies in yeast quiescent cells: an immediately available actin reserve? Mol. Biol. Cell 2006 17 11 4645 4655
14. J. V. Gray G. A. Petsko G. C. Johnston D. Ringe R. A. Singer M. Werner-Washburne 'Sleeping beauty': quiescence in Saccharomyces cerevisiae Microbiol. Mol. Biol. Rev. 2004 68 2 187 206
15. Y. O. Chernoff Stress and prions: lessons from the yeast model FEBS Lett. 2007 581 19 3695 3701
16. D. Beyersmann A. Hartwig Carcinogenic metal compounds: recent insight into molecular and cellular mechanisms Arch. Toxicol. 2008 82 8 493 512
17. T. Jacobson C. Navarrete S. K. Sharma T. C. Sideri S. Ibstedt S. Priya C. M. Grant P. Christen P. Goloubinoff M. J. Tamás Arsenite interferes with protein folding and triggers formation of protein aggregates in yeast J. Cell Sci. 2012 125 Pt 21 5073 5083
18. A.-C. Gavin P. Aloy P. Grandi R. Krause M. Boesche M. Marzioch C. Rau L. J. Jensen S. Bastuck B. Dümpelfeld A. Edelmann M.-A. Heurtier V. Hoffman C. Hoefert K. Klein M. Hudak A.-M. Michon M. Schelder M. Schirle M. Remor T. Rudi S. Hooper A. Bauer T. Bouwmeester G. Casari G. Drewes G. Neubauer J. M. Rick B. Kuster P. Bork R. B. Russell G. Superti-Furga Proteome survey reveals modularity of the yeast cell machinery Nature 2006 440 7084 631 636
19. A. P. Gasch P. T. Spellman C. M. Kao O. Carmel-Harel M. B. Eisen G. Storz D. Botstein P. O. Brown Genomic expression programs in the response of yeast cells to environmental changes Mol. Biol. Cell 2000 11 12 4241 4257
20. W.-K. Huh J. V. Falvo L. C. Gerke A. S. Carroll R. W. Howson J. S. Weissman E. K. O'Shea Global analysis of protein localization in budding yeast Nature 2003 425 6959 686 691
21. S. An R. Kumar E. D. Sheets S. J. Benkovic Reversible compartmentalization of de novo purine biosynthetic complexes in living cells Science 2008 320 5872 103 106
22. A. Zhao M. Tsechansky J. Swaminathan L. Cook A. D. Ellington E. M. Marcotte Transiently transfected purine biosynthetic enzymes form stress bodies PLoS One 2013 8 2 e56203
23. A.-M. Fernandez-Escamilla F. Rousseau J. Schymkowitz L. Serrano Prediction of sequence-dependent and mutational effects on the aggregation of peptides and proteins Nat. Biotechnol. 2004 22 10 1302 1306
24. D. Landgraf B. Okumus P. Chien T. A. Baker J. Paulsson Segregation of molecules at cell division reveals native protein localization Nat. Methods 2012 9 5 480 482
25. K. A. Geiler-Samerotte M. F. Dion B. A. Budnik S. M. Wang D. L. Hartl D. A. Drummond Misfolded proteins impose a dosage-dependent fitness cost and trigger a cytosolic unfolded protein response in yeast Proc. Natl. Acad. Sci. U. S. A. 2011 108 2 680 685
26. R. Williams mRNAs sit out the stress in EGP bodies J. Cell Biol. 2007 179 1 2
27. E. van Dijk N. Cougot S. Meyer S. Babajko E. Wahle B. Séraphin Human Dcp2: a catalytically active mRNA decapping enzyme located in specific cytoplasmic structures EMBO J. 2002 21 24 6915 6924
28. J. M. Shively F. Ball D. H. Brown R. E. Saunders Functional organelles in prokaryotes: polyhedral inclusions (carboxysomes) of thiobacillus neapolitanus Science 1973 182 4112 584 586
29. R. H. Doi A. Kosugi Cellulosomes: plant-cell-wall-degrading enzyme complexes Nat. Rev. Microbiol. 2004 2 7 541 551
30. M. S. Patel L. G. Korotchkina Regulation of the pyruvate dehydrogenase complex Biochem. Soc. Trans. 2006 34 Pt 2 217 222
31. M. Kato T. W. Han S. Xie K. Shi X. Du L. C. Wu H. Mirzaei E. J. Goldsmith J. Longgood J. Pei N. V. Grishin D. E. Frantz J. W. Schneider S. Chen L. Li M. R. Sawaya D. Eisenberg R. Tycko S. L. McKnight Cell-free formation of rna granules: low complexity sequence domains form dynamic fibers within hydrogels Cell 2012 149 4 753 767
32. S. J. Orr D. R. Boutz R. Wang C. Chronis N. C. Lea T. Thayaparan E. Hamilton H. Milewicz E. Blanc G. J. Mufti E. M. Marcotte N. S. B. Thomas Proteomic and protein interaction network analysis of human T lymphocytes during cell-cycle entry Mol. Syst. Biol. 2012 8 573
33. T. Kwon H. Choi C. Vogel A. I. Nesvizhskii E. M. Marcotte MSblender: A probabilistic approach for integrating peptide identifications from multiple database search engines J. Proteome Res. 2011 10 7 2949 2958
34. B. J. Diament W. S. Noble Faster SEQUEST searching for peptide identification from tandem mass spectra J. Proteome Res. 2011 10 9 3871 3879
35. S. Kim N. Mischerikow N. Bandeira J. D. Navarro L. Wich S. Mohammed A. J. R. Heck P. A. Pevzner The generating function of CID, ETD, and CID/ETD pairs of tandem mass spectra: applications to database search Mol. Cell. Proteomics 2010 9 12 2840 2852
36. S. Tanner H. Shu A. Frank L.-C. Wang E. Zandi M. Mumby P. A. Pevzner V. Bafna InsPecT: identification of posttranslationally modified peptides from tandem mass spectra Anal. Chem. 2005 77 14 4626 4629
37. P. Lu C. Vogel R. Wang X. Yao E. M. Marcotte Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation Nat. Biotechnol. 2007 25 1 117 124
38. A. P. French S. Mills R. Swarup M. J. Bennett T. P. Pridmore Colocalization of fluorescent markers in confocal microscope images of plant cells Nat. Protoc. 2008 3 4 619 628