Proteomic data from human cell cultures refine mechanisms of chaperone-mediated protein homeostasis

Andrija Finka1, Pierre Goloubinoff1
1Department of Plant Molecular Biology, University of Lausanne, 1015 Lausanne, Switzerland

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Albanese, 2010, A ribosome-anchored chaperone network that facilitates eukaryotic ribosome biogenesis, J Cell Biol, 189, 69, 10.1083/jcb.201001054

Albe, 1990, Cellular concentrations of enzymes and their substrates, J Theor Biol, 143, 163, 10.1016/S0022-5193(05)80266-8

Azem, 1995, The protein-folding activity of chaperonins correlates with the symmetric GroEL(14)(GroES(7))(2) heterooligomer, Proc Natl Acad Sci USA, 92, 12021, 10.1073/pnas.92.26.12021

Ben-Zvi, 2004, Active solubilization and refolding of stable protein aggregates by cooperative unfolding action of individual Hsp70 chaperones, J Biol Chem, 279, 37298, 10.1074/jbc.M405627200

Blacque, 2006, Bardet–Biedl syndrome: an emerging pathomechanism of intracellular transport, Cell Mol Life Sci, 63, 2145, 10.1007/s00018-006-6180-x

Cassina, 2009, The tightly regulated and compartmentalised import, sorting and folding of mitochondrial proteins, Open Biol J, 2, 200, 10.2174/1874196700902010200

Cong, 2010, 4.0-Angstrom resolution cryo-EM structure of the mammalian chaperonin TRiC/CCT reveals its unique subunit arrangement, Proc Natl Acad Sci USA, 107, 4967, 10.1073/pnas.0913774107

Cooper, 2000

Coppinger, 2012, A chaperone trap contributes to the onset of cystic fibrosis, PLoS One, 7, e37682, 10.1371/journal.pone.0037682

Csermely, 1993, ATP induces a conformational change of the 90-kDa heat shock protein (Hsp90), J Biol Chem, 268, 1901, 10.1016/S0021-9258(18)53939-9

De los Rios, 2006, Hsp70 chaperones accelerate protein translocation and the unfolding of stable protein aggregates by entropic pulling, Proc Natl Acad Sci U S A, 103, 6166, 10.1073/pnas.0510496103

Dekker, 2008, The interaction network of the chaperonin CCT, EMBO J, 27, 1827, 10.1038/emboj.2008.108

Dekker, 2012, On the evolutionary origin of the chaperonins, Proteins, 79, 1172, 10.1002/prot.22952

Diamant, 1995, Effect of free and ATP-bound magnesium and manganese ions on the atpase activity of chaperonin GroEL(14), Biochem-Us, 34, 273, 10.1021/bi00001a033

Diamant, 2000, Size-dependent disaggregation of stable protein aggregates by the DnaK chaperone machinery, J Biol Chem, 275, 21107, 10.1074/jbc.M001293200

Diamant, 1998, Temperature-controlled activity of DnaK-DnaJ-GrpE chaperones: protein-folding arrest and recovery during and after heat shock depends on the substrate protein and the GrpE concentration, Biochem-US, 37, 9688, 10.1021/bi980338u

Dittmar, 1997, Folding of the glucocorticoid receptor by the heat shock protein (hsp) 90-based chaperone machinery—the role of p23 is to stabilize receptor-hsp90 heterocomplexes formed by hsp90-p60-hsp70, J Biol Chem, 272, 21213, 10.1074/jbc.272.34.21213

Duncan, 1983, Identification and quantitation of levels of protein synthesis initiation factors in crude HeLa cell lysates by two-dimensional polyacrylamide gel electrophoresis, J Biol Chem, 258, 7228, 10.1016/S0021-9258(18)32356-1

Echeverria, 2011, An interaction network predicted from public data as a discovery tool: application to the Hsp90 molecular chaperone machine, PLoS One, 6, e26044, 10.1371/journal.pone.0026044

Eisenberg, 2007, Multiple roles of auxilin and Hsc70 in clathrin-mediated endocytosis, Traffic, 8, 640, 10.1111/j.1600-0854.2007.00568.x

Ellis, 2001, Macromolecular crowding: obvious but underappreciated, Trends Biochem Sci, 26, 597, 10.1016/S0968-0004(01)01938-7

Erlinger, 1982, Decrease in protein-content and cell volume of cultured dog kidney epithelial cells during growth—importance for transport measurements, Vitro Cell Dev B, 18, 196

Eymery, 2009, A transcriptomic analysis of human centromeric and pericentric sequences in normal and tumor cells, Nucleic Acids Res, 37, 6340, 10.1093/nar/gkp639

Fiaux, 2010, Structural analysis of the ribosome-associated complex (RAC) reveals an unusual Hsp70/Hsp40 interaction, J Biol Chem, 285, 3227, 10.1074/jbc.M109.075804

Fink, 1999, Chaperone-mediated protein folding, Physiol Rev, 79, 425, 10.1152/physrev.1999.79.2.425

Finka, 2011, Meta-analysis of heat- and chemically upregulated chaperone genes in plant and human cells, Cell Stress Chaperones, 16, 15, 10.1007/s12192-010-0216-8

Geiger, 2012, Mann M (2012) Comparative proteomic analysis of eleven common cell lines reveals ubiquitous but varying expression of most proteins, Mol Cell Proteomics, 11, 10.1074/mcp.M111.014050

Genest, 2011, Heat shock protein 90 from Escherichia coli collaborates with the DnaK chaperone system in client protein remodeling, Proc Natl Acad Sci U S A, 108, 8206, 10.1073/pnas.1104703108

Goloubinoff, 1989, Reconstitution of active dimeric ribulose bisphosphate carboxylase from an unfolded state depends on 2 chaperonin proteins and Mg-Atp, Nature, 342, 884, 10.1038/342884a0

Goloubinoff, 2007, The mechanism of Hsp70 chaperones: (entropic) pulling the models together, Trends Biochem Sci, 32, 372, 10.1016/j.tibs.2007.06.008

Goloubinoff, 1989, GroE heat-shock proteins promote assembly of foreign prokaryotic ribulose bisphosphate carboxylase oligomers in Escherichia coli, Nature, 337, 44, 10.1038/337044a0

Gragerov, 1992, Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia coli, Proc Natl Acad Sci U S A, 89, 10341, 10.1073/pnas.89.21.10341

Gross, 1996, Function and regulation of the heat shock proteins

Hemmingsen, 1988, Homologous plant and bacterial proteins chaperone oligomeric protein assembly, Nature, 333, 330, 10.1038/333330a0

Hetz, 2012, The unfolded protein response: controlling cell fate decisions under ER stress and beyond, Nat Rev Mol Cell Bio, 13, 89, 10.1038/nrm3270

Hinault, 2006, Chaperones and proteases—cellular fold-controlling factors of proteins in neurodegenerative diseases and aging, J Mol Neurosci, 30, 249, 10.1385/JMN:30:3:249

Hinault, 2011, Molecular chaperones and associated cellular clearance mechanisms against toxic protein conformers in Parkinson's disease, Neurodegener Dis, 8, 397, 10.1159/000324514

Jin, 2007, Identification of novel proteins associated with both alpha-synuclein and DJ-1, Mol Cell Proteomics, 6, 845, 10.1074/mcp.M600182-MCP200

Kalia LV, Kalia SK, Chau H, Lozano AM, Hyman BT, McLean PJ (2011) Ubiquitinylation of alpha-synuclein by carboxyl terminus Hsp70-interacting protein (CHIP) is regulated by Bcl-2-associated athanogene 5 (BAG5). PLoS One 6(2). doi:10.1371/journal.pone.0014695

Kampinga, 2009, Guidelines for the nomenclature of the human heat shock proteins, Cell Stress Chaperones, 14, 105, 10.1007/s12192-008-0068-7

Karagoz, 2011, N-terminal domain of human Hsp90 triggers binding to the cochaperone p23, Proc Natl Acad Sci U S A, 108, 580, 10.1073/pnas.1011867108

Kikis, 2010, Protein homeostasis in models of aging and age-related conformational disease, Adv Exp Med Biol, 694, 138, 10.1007/978-1-4419-7002-2_11

Kline, 2010, Protein quantitation using isotope-assisted mass spectrometry, Annu Rev Biophys, 39, 291, 10.1146/annurev.biophys.093008.131339

Koplin, 2010, A dual function for chaperones SSB-RAC and the NAC nascent polypeptide-associated complex on ribosomes, J Cell Biol, 189, 57, 10.1083/jcb.200910074

Lew, 1995, Generation of normal human red-cell volume, hemoglobin content, and membrane area distributions by birth or regulation, Blood, 86, 334, 10.1182/blood.V86.1.334.bloodjournal861334

Lewis, 1992, T-Complex polypeptide-1 is a subunit of a heteromeric particle in the eukaryotic cytosol, Nature, 358, 249, 10.1038/358249a0

Lin, 2008, GroEL stimulates protein folding through forced unfolding, Nat Struct Mol Biol, 15, 303, 10.1038/nsmb.1394

Llorca, 2001, The ‘sequential allosteric ring’ mechanism in the eukaryotic chaperonin-assisted folding of actin and tubulin, EMBO J, 20, 4065, 10.1093/emboj/20.15.4065

Llorca, 1999, Eukaryotic type II chaperonin CCT interacts with actin through specific subunits, Nature, 402, 693, 10.1038/45294

Lodish, 2000

Luciani, 2001, Changes in cell volume and internal sodium concentration in HeLa cells during exponential growth and following ionidamine treatment, Eur J Cell Biol, 80, 187, 10.1078/0171-9335-00102

Lundin, 2010, Quality control of cytoskeletal proteins and human disease, Trends Biochem Sci, 35, 288, 10.1016/j.tibs.2009.12.007

Lurje, 2009, EGFR signaling and drug discovery, Oncology-Basel, 77, 400, 10.1159/000279388

Marzec, 2012, GRP94: An Hsp90-like protein specialized for protein folding and quality control in the endoplasmic reticulum, BBA Mol Cell Res, 1823, 774

Melville, 2003, The Hsp70 and TRiC/CCT chaperone systems cooperate in vivo to assemble the von Hippel–Lindau tumor suppressor complex, Mol Cell Biol, 23, 3141, 10.1128/MCB.23.9.3141-3151.2003

Morimoto, 2008, Proteotoxic stress and inducible chaperone networks in neurodegenerative disease and aging, Gene Dev, 22, 1427, 10.1101/gad.1657108

Muller P, Ruckova E, Halada P, Coates PJ, Hrstka R, Lane DP, Vojtesek B (2012) C-terminal phosphorylation of Hsp70 and Hsp90 regulates alternate binding to co-chaperones CHIP and HOP to determine cellular protein folding/degradation balances. Oncogene 1-10. doi:http://www.nature.com/onc/journal/vaop/ncurrent/suppinfo/onc2012314s1.html

Nagaraj, 2011, Deep proteome and transcriptome mapping of a human cancer cell line, Mol Syst Biol, 7, 548, 10.1038/msb.2011.81

Nakamoto, 2007, The small heat shock proteins and their clients, Cell Mol Life Sci, 64, 294, 10.1007/s00018-006-6321-2

Neupert, 1981, How proteins are transported into mitochondria, Trends Biochem Sci, 6, 1, 10.1016/0968-0004(81)90002-5

Pierpaoli, 1997, The power stroke of the DnaK/DnaJ/GrpE molecular chaperone system, J Mol Biol, 269, 757, 10.1006/jmbi.1997.1072

Polier, 2008, Structural basis for the cooperation of Hsp70 and Hsp110 chaperones in protein folding, Cell, 133, 1068, 10.1016/j.cell.2008.05.022

Pollard, 1984, Citation classic—actin and myosin and cell-movement, Life Sci, 30, 13

Posakony, 1977, Mitochondrial growth and division during the cell cycle in HeLa cells, J Cell Biol, 74, 468, 10.1083/jcb.74.2.468

Prodromou, 2012, The ‘active life’ of Hsp90 complexes, BBA Mol Cell Res, 1823, 614

Rampelt H, Kirstein-Miles J, Nillegoda NB, Chi K, Scholz SR, Morimoto RI, Bukau B (2012) Metazoan Hsp70 machines use Hsp110 to power protein disaggregation. EMBO J 31 (21):4221-4235. doi:http://www.nature.com/emboj/journal/v31/n21/suppinfo/emboj2012264a_S1.html

Rampelt, 2011, Nucleotide exchange factors for Hsp70 chaperones, 83

Rapoport, 2007, Transport of proteins in and out of the endoplasmic reticulum, FASEB J, 21, A207, 10.1096/fasebj.21.5.A207-c

Riggs, 2003, The Hsp90-binding peptidylprolyl isomerase FKBP52 potentiates glucocorticoid signaling in vivo, EMBO J, 22, 1158, 10.1093/emboj/cdg108

Rutherford, 1998, Hsp90 as a capacitor for morphological evolution, Nature, 396, 336, 10.1038/24550

Salaklang, 2008, Superparamagnetic nanoparticles as a powerful systems biology characterization tool in the physiological context, Angew Chem Int Edit, 47, 7857, 10.1002/anie.200800357

Schmidt A, Beck M, Malmstrom J, Lam H, Claassen M, Campbell D, Aebersold R (2011) Absolute quantification of microbial proteomes at different states by directed mass spectrometry. Molecular Systems Biology 7: 510. doi:http://www.nature.com/msb/journal/v7/n1/suppinfo/msb201137_S1.html

Schuermann, 2008, Structure of the Hsp110:Hsc70 nucleotide exchange machine, Mol Cell, 31, 232, 10.1016/j.molcel.2008.05.006

Schwanhausser, 2011, Global quantification of mammalian gene expression control, Nature, 473, 337, 10.1038/nature10098

Sharma K, Vabulas RM, Macek B, Pinkert S, Cox J, Mann M, Hartl FU (2012) Quantitative proteomics reveals that Hsp90 inhibition preferentially targets kinases and the DNA damage response. Mol Cell Proteomics 11(3). doi:10.1074/mcp.M111.014654

Sharma, 2010, The kinetic parameters and energy cost of the Hsp70 chaperone as a polypeptide unfoldase, Nat Chem Biol, 6, 914, 10.1038/nchembio.455

Sharma, 2011, Probing the different chaperone activities of the bacterial Hsp70–Hsp40 system using a thermolabile luciferase substrate, Proteins Struct Funct Bioinform, 79, 1991, 10.1002/prot.23024

Shorter J (2011) The mammalian disaggregase machinery: Hsp110 synergizes with Hsp70 and Hsp40 to catalyze protein disaggregation and reactivation in a cell-free system. PLoS One 6(10). doi:10.1371/journal.pone.0026319

Siegenthaler, 2006, Tuning of DnaK chaperone action by nonnative protein sensor DnaJ and thermosensor GrpE, J Biol Chem, 281, 34448, 10.1074/jbc.M606382200

Siegers, 1999, Compartmentation of protein folding in vivo: sequestration of non-native polypeptide by the chaperonin–GimC system, EMBO J, 18, 75, 10.1093/emboj/18.1.75

Sousa, 2006, Keep the traffic moving: mechanism of the Hsp70 motor, Traffic, 7, 1596, 10.1111/j.1600-0854.2006.00497.x

Tissieres, 1974, Protein synthesis in salivary glands of Drosophila melanogaster—relation to chromosome puffs, J Mol Biol, 84, 389, 10.1016/0022-2836(74)90447-1

Torok, 1996, Fluorescence detection of symmetric GroEL(14)(GroES(7))(2) heterooligomers involved in protein release during the chaperonin cycle, J Biol Chem, 271, 16180, 10.1074/jbc.271.27.16180

Van de Water L, 3rd, Olmsted JB, 1980, The quantitation of tubulin in neuroblastoma cells by radioimmunoassay, J Biol Chem, 255, 10744, 10.1016/S0021-9258(19)70370-6

van der Vaart, 2004, The unfolding action of GroEL on a protein substrate, Biophys J, 87, 562, 10.1529/biophysj.103.037333

Veinger, 1998, The small heat-shock protein IbpB from Escherichia coli stabilizes stress-denatured proteins for subsequent refolding by a multichaperone network, J Biol Chem, 273, 11032, 10.1074/jbc.273.18.11032

Volpe, 1970, Quantitative studies on cell proteins in suspension cultures, Eur J Biochem, 12, 195, 10.1111/j.1432-1033.1970.tb00837.x

Wang, 2003, Total body protein: a new cellular level mass and distribution prediction model, Am J Clin Nutr, 78, 979, 10.1093/ajcn/78.5.979

Weiss, 2007, Enhanced heat shock protein 70 expression alters proteasomal degradation of I kappa B kinase in experimental acute respiratory distress syndrome, Crit Care Med, 35, 2128, 10.1097/01.CCM.0000278915.78030.74

Wistow, 1988, Lens crystallins—the evolution and expression of proteins for a highly specialized tissue, Annu Rev Biochem, 57, 479, 10.1146/annurev.bi.57.070188.002403

Wolf, 1977, Nuclear metabolism of ribosomal RNA in growing, methionine-limited, and ethionine-treated HeLa cells, Biochem-Us, 16, 2783, 10.1021/bi00631a031

Yebenes, 2011, Chaperonins: two rings for folding, Trends Biochem Sci, 36, 424, 10.1016/j.tibs.2011.05.003

Yeyati, 2007, Hsp90 selectively modulates phenotype in vertebrate development, PLoS Genet, 3, 431, 10.1371/journal.pgen.0030043

Young, 2003, Molecular chaperones Hsp90 and Hsp70 deliver preproteins to the mitochondrial import receptor Tom70, Cell, 112, 41, 10.1016/S0092-8674(02)01250-3

Zuehlke, 2010, Hsp90 and co-chaperones twist the functions of diverse client proteins, Biopolym, 93, 211, 10.1002/bip.21292