An interaction network predicted from public data as a discovery tool: Application to the Hsp90 molecular chaperone machine

PLoS ONE

Volumn 6, Issue 10, 2011, Pages

  Echeverría, Pablo C ^a   Bernthaler, Andreas ^b   Dupuis, Pierre ^a   Mayer, Bernd ^b   Picard, Didier ^a  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b Emergentec Biodevelopment GmbH   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

AHA1 PROTEIN; BINDING PROTEIN; CHAPERONE; HEAT SHOCK PROTEIN 90; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; COMPUTER PREDICTION; CONTROLLED STUDY; DATA MINING; FIBROBLAST; MOUSE; NONHUMAN; NUCLEAR LOCALIZATION SIGNAL; NUCLEOCYTOPLASMIC TRANSPORT; PROTEIN DATABASE; PROTEIN PROTEIN INTERACTION; ACTIVE TRANSPORT; ANIMAL; HUMAN; METABOLISM; PROTEIN BINDING; REPRODUCIBILITY;

ACTIVE TRANSPORT, CELL NUCLEUS; ANIMALS; DATABASES, PROTEIN; HSP90 HEAT-SHOCK PROTEINS; HUMANS; MICE; PROTEIN BINDING; PROTEIN INTERACTION MAPS; REPRODUCIBILITY OF RESULTS;

EID: 80053976720     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0026044     Document Type: Article

References (62)

1. Taipale M, Jarosz DF, Lindquist S, (2010) HSP90 at the hub of protein homeostasis: emerging mechanistic insights. Nat Rev Mol Cell Biol 11: 515-528.
2. Neckers L, Mollapour M, Tsutsumi S, (2009) The complex dance of the molecular chaperone Hsp90. Trends Biochem Sci 34: 223-226.
3. Trepel J, Mollapour M, Giaccone G, Neckers L, (2010) Targeting the dynamic HSP90 complex in cancer. Nat Rev Cancer 10: 537-549.
4. Wandinger SK, Richter K, Buchner J, (2008) The Hsp90 chaperone machinery. J Biol Chem 283: 18473-18477.
5. Nathan DF, Vos MH, Lindquist S, (1997) In vivo functions of the Saccharomyces cerevisiae Hsp90 chaperone. Proc Natl Acad Sci USA 94: 12949-12956.
6. Kim YS, Alarcon SV, Lee S, Lee MJ, Giaccone G, et al. (2009) Update on Hsp90 inhibitors in clinical trial. Curr Top Med Chem 9: 1479-1492.
7. Porter JR, Fritz CC, Depew KM, (2010) Discovery and development of Hsp90 inhibitors: a promising pathway for cancer therapy. Curr Opin Chem Biol 14: 412-420.
8. Albanèse V, Yam AY, Baughman J, Parnot C, Frydman J, (2006) Systems analyses reveal two chaperone networks with distinct functions in eukaryotic cells. Cell 124: 75-88.
9. Pavithra SR, Kumar R, Tatu U, (2007) Systems analysis of chaperone networks in the malarial parasite Plasmodium falciparum. PLoS Comput Biol 3: 1701-1715.
10. Palotai R, Szalay MS, Csermely P, (2008) Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases. IUBMB Life 60: 10-18.
11. Gong Y, Kakihara Y, Krogan N, Greenblatt J, Emili A, et al. (2009) An atlas of chaperone-protein interactions in Saccharomyces cerevisiae: implications to protein folding pathways in the cell. Mol Syst Biol 5: 275.
12. Zhao R, Davey M, Hsu YC, Kaplanek P, Tong A, et al. (2005) Navigating the chaperone network: integrative map of physical and genetic interactions mediated by the Hsp90 chaperone. Cell 120: 715-727.
13. Millson SH, Truman AW, King V, Prodromou C, Pearl LH, et al. (2005) A two-hybrid screen of the yeast proteome for hsp90 interactors uncovers a novel Hsp90 chaperone requirement in the activity of a stress-activated mitogen-activated protein kinase, Slt2p (Mpk1p). Eukaryot Cell 4: 849-860.
14. Falsone SF, Gesslbauer B, Tirk F, Piccinini AM, Kungl AJ, (2005) A proteomic snapshot of the human heat shock protein 90 interactome. FEBS Lett 579: 6350-6354.
15. McClellan AJ, Xia Y, Deutschbauer AM, Davis RW, Gerstein M, et al. (2007) Diverse cellular functions of the Hsp90 molecular chaperone uncovered using systems approaches. Cell 131: 121-135.
16. Te J, Jia L, Rogers J, Miller A, Hartson SD, (2007) Novel subunits of the mammalian Hsp90 signal transduction chaperone. J Proteome Res 6: 1963-1973.
17. Falsone SF, Gesslbauer B, Rek A, Kungl AJ, (2007) A proteomic approach towards the Hsp90-dependent ubiquitinylated proteome. Proteomics 7: 2375-2383.
18. Caldas-Lopes E, Cerchietti L, Ahn JH, Clement CC, Robles AI, et al. (2009) Hsp90 inhibitor PU-H71, a multimodal inhibitor of malignancy, induces complete responses in triple-negative breast cancer models. Proc Natl Acad Sci USA 106: 8368-8373.
19. Tsaytler PA, Krijgsveld J, Goerdayal SS, Rudiger S, Egmond MR, (2009) Novel Hsp90 partners discovered using complementary proteomic approaches. Cell Stress Chaperones 14: 629-638.
20. Gano JJ, Simon JA, (2010) A proteomic investigation of ligand-dependent HSP90 complexes reveals CHORDC1 as a novel ADP-dependent HSP90-interacting protein. Mol Cell Proteomics 9: 255-270.
21. Wang X, Heuvelman DM, Carroll JA, Dufield DR, Masferrer JL, (2010) Geldanamycin-induced PCNA degradation in isolated Hsp90 complex from cancer cells. Cancer Invest 28: 635-641.
22. Skarra DV, Goudreault M, Choi H, Mullin M, Nesvizhskii AI, et al. (2011) Label-free quantitative proteomics and SAINT analysis enable interactome mapping for the human Ser/Thr protein phosphatase 5. Proteomics 11: 1508-1516.
23. Hartson SD, Matts RL, (2011) Approaches for defining the Hsp90-dependent proteome. Biochim Biophys Acta in press.
24. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
25. Platzer A, Perco P, Lukas A, Mayer B, (2007) Characterization of protein-interaction networks in tumors. BMC Bioinformatics 8: 224.
26. Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, et al. (2009) ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics 25: 1091-1093.
27. Shaner NC, Campbell RE, Steinbach PA, Giepmans BN, Palmer AE, et al. (2004) Improved monomeric red, orange and yellow fluorescent proteins derived from Discosoma sp. red fluorescent protein. Nat Biotechnol 22: 1567-1572.
28. Lehne B, Schlitt T, (2009) Protein-protein interaction databases: keeping up with growing interactomes. Hum Genomics 3: 291-297.
29. De Las Rivas J, Fontanillo C, (2010) Protein-protein interactions essentials: key concepts to building and analyzing interactome networks. PLoS Comput Biol 6: e1000807.
30. Walhout AJ, Vidal M, (2001) Protein interaction maps for model organisms. Nat Rev Mol Cell Biol 2: 55-62.
31. He F, Zhang Y, Chen H, Zhang Z, Peng YL, (2008) The prediction of protein-protein interaction networks in rice blast fungus. BMC genomics 9: 519.
32. Shin CJ, Davis MJ, Ragan MA, (2009) Towards the mammalian interactome: Inference of a core mammalian interaction set in mouse. Proteomics 9: 5256-5266.
33. Wang TY, He F, Hu QW, Zhang Z, (2011) A predicted protein-protein interaction network of the filamentous fungus Neurospora crassa. Molecular bioSystems 7: 2278-2285.
34. Breitkreutz BJ, Stark C, Reguly T, Boucher L, Breitkreutz A, et al. (2008) The BioGRID Interaction Database: 2008 update. Nucleic Acids Res 36: D637-640.
35. Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, et al. (2004) IntAct: an open source molecular interaction database. Nucleic Acids Res 32: D452-455.
36. Mishra GR, Suresh M, Kumaran K, Kannabiran N, Suresh S, et al. (2006) Human protein reference database-2006 update. Nucleic Acids Res 34: D411-414.
37. Xenarios I, Rice DW, Salwinski L, Baron MK, Marcotte EM, et al. (2000) DIP: the database of interacting proteins. Nucleic Acids Res 28: 289-291.
38. Zanzoni A, Montecchi-Palazzi L, Quondam M, Ausiello G, Helmer-Citterich M, et al. (2002) MINT: a Molecular INTeraction database. FEBS Lett 513: 135-140.
39. Bader GD, Betel D, Hogue CW, (2003) BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res 31: 248-250.
40. Jain E, Bairoch A, Duvaud S, Phan I, Redaschi N, et al. (2009) Infrastructure for the life sciences: design and implementation of the UniProt website. BMC Bioinformatics 10: 136.
41. Huang da W, Sherman BT, Lempicki RA, (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat Protoc 4: 44-57.
42. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
43. Hruz T, Laule O, Szabo G, Wessendorp F, Bleuler S, et al. (2008) Genevestigator v3: a reference expression database for the meta-analysis of transcriptomes. Adv Bioinformatics 2008: 420747.
44. Maslov S, Sneppen K, (2002) Specificity and stability in topology of protein networks. Science 296: 910-913.
45. Zhu X, Gerstein M, Snyder M, (2007) Getting connected: analysis and principles of biological networks. Genes Dev 21: 1010-1024.
46. Barrat A, Barthelemy M, Pastor-Satorras R, Vespignani A, (2004) The architecture of complex weighted networks. Proc Natl Acad Sci USA 101: 3747-3752.
47. Seebacher J, Gavin AC, (2011) SnapShot: Protein-Protein Interaction Networks. Cell 144: 1000-1000.e1001.
48. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL, (2002) Hierarchical organization of modularity in metabolic networks. Science 297: 1551-1555.
49. Newman MEJ, (2003) The structure and function of complex networks. SIAM Review 45: 167-256.
50. Tsan MF, Gao B, (2009) Heat shock proteins and immune system. J Leukoc Biol 85: 905-910.
51. Echeverría PC, Picard D, (2010) Molecular chaperones, essential partners of steroid hormone receptors for activity and mobility. Biochim Biophys Acta 1803: 641-649.
52. DeZwaan DC, Freeman BC, (2010) HSP90 manages the ends. Trends Biochem Sci 35: 384-391.
53. Grad I, Cederroth CR, Walicki J, Grey C, Barluenga S, et al. (2010) The molecular chaperone Hsp90α is required for meiotic progression of spermatocytes beyond pachytene in the mouse. PLoS ONE 5: e15770.
54. Endo T, Yamano K, (2010) Transport of proteins across or into the mitochondrial outer membrane. Biochim Biophys Acta 1803: 706-714.
55. Kovacs-Bogdan E, Soll J, Bolter B, (2010) Protein import into chloroplasts: the Tic complex and its regulation. Biochim Biophys Acta 1803: 740-747.
56. Galigniana MD, Echeverría PC, Erlejman A, Piwien-Pilipuk G, (2010) Role of molecular chaperones and TPR-domain proteins in the cytoplasmic transport of steroid receptors and their passage through the nuclear pore. Nucleus 1: 299-308.
57. Freedman ND, Yamamoto KR, (2004) Importin 7 and importin α/importin β are nuclear import receptors for the glucocorticoid receptor. Mol Biol Cell 15: 2276-2286.
58. Echeverria PC, Mazaira G, Erlejman A, Gomez-Sanchez C, Piwien Pilipuk G, et al. (2009) Nuclear import of the glucocorticoid receptor-Hsp90 complex through the nuclear pore complex is mediated by its interaction with Nup62 and importin β. Mol Cell Biol 29: 4788-4797.
59. Pratt WB, Toft DO, (1997) Steroid receptor interactions with heat shock protein and immunophilin chaperones. Endocr Rev 18: 306-360.
60. Martin A, Ochagavia ME, Rabasa LC, Miranda J, Fernandez-de-Cossio J, et al. (2010) BisoGenet: a new tool for gene network building, visualization and analysis. BMC Bioinformatics 11: 91.
61. Hartl FU, Hayer-Hartl M, (2002) Molecular chaperones in the cytosol: from nascent chain to folded protein. Science 295: 1852-1858.
62. Richter K, Haslbeck M, Buchner J, (2010) The heat shock response: life on the verge of death. Mol Cell 40: 253-266.