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The Proteostasis Network

Our studies began with the molecular cloning of human heat shock genes, Hsp70 and Hsp90, and a series of studies to elucidate the cis-elements that regulate Hsp70 gene transcription by heat shock and during cell growth, identification of the family of heat shock transcription factors including HSF-1, establishing the roles of Hsp70 and Hdj-1 in the relation of HSF-1 activity and autoregulation of the heat shock response and demonstrating that HSF-1 localizes to nuclear stress granules (Wu et al., 1985; 1986; 1987; Wu and Morimoto, 1985; Hunt and Morimoto, 1985; Watowich et al., 1988; Mosser et al., 1988; 1990; Williams et al., 1989; Abravaya et al., 1991; Sarge et al., 1991; 1993; Sistonen et al., 1992; 1994; Nakai et al., 1995; 1997; Shi et al., 1995; 1998; Jolly et al., 1997; Cotto et al., 1997).  For a further discussion please go to the section on the HEAT SHOCK RESPONSE.

 

We next turned our attention to the biochemical properties of human molecular chaperones.  Brian Freeman expressed and purified all of the major human chaperones and co-chaperones (that were known at the time) and developed in vitro assays revealing the “holding” function of Hsp70, Hsp90 and certain co-chaperones such as p23 and Cyp40 independent of ATP, the ATP-dependent function of “folding” of unfolded clients to their native functional state, and  the identification of the C-terminal EEVD motif of Hsp70 and Hsp90 as a site of interaction with co-chaperones (Freeman et al., 1995; 1996).  Subsequent studies by Dave Bimston and Jae Song (in collaboration with John Reed’s lab at the Sanford Burnham) identified Bag1 as a co-chaperone of Hsp70, which was studied further by Jae Song as a regulatory network for Raf1 kinase and the regulation of DNA replication (Takeyama et al, 1997; Bimston et al., 1998; Song et al., 2001).

 

Efforts to elucidate the composition of the Proteostasis Network followed from biochemistry and genetics complemented by informatics.  With the development and characterization of the polyglutamine (polyQ) transgenic C. elegans lines by Sanjeev Satyal and Jim Morley (Satyal et al., 2000; Morley et al., 2002), Ellen Nollen and Susana Garcia initiated a genome-wide interference RNA screen that led to the functional identification of the Proteostasis Network (Nollen et al., 2004).  Ellen and Susana were able to take advantage of the age-dependent polyQ protein aggregation in the Q35-YFP line to identify genes essential to prevent protein aggregation.  This genetic screen provided the identification of RNA processing, the ribosome and protein synthesis, protein folding (chaperones), protein transport and degradation as the core components of the Proteostasis Network.  Susana performed a forward genetic screen using the polyQ35 animals and identified a mutation in the neurotransmitter, GABA, that increased polyQ aggregation in body wall muscle cells (Garcia et al., 2007).  This study was the first observation that organismal proteostasis was regulated by cell non-autonomous control in that GABA is expressed in neurons and the polyQ is expressed in body wall muscle cells.   Subsequently, Catarina Silva performed a polyQ35 genome-wide RNAi screen for suppressors of aggregation, and among the many genes identified, found the acetylcholine (Ach) receptor leading to the discovery that the balance of Ach and GABA regulated HSF-1 and muscle cell proteostasis (Silva et al., 2011; 2013).  For a further discussion turn to the section on ORGANISMAL PROTEOSTASIS.

 

Kai Orton performed the initial informatic analysis to identify the members of the human chaperome that was used by Marc Brehme to analyze the transcriptome of the human frontal cortex of individuals from 20-99 yrs of age (Brehme et al., 2014).  Associated with aging was a decline of all ATP-dependent chaperones of the Hsp70, Hsp90 and Hsp60 family and an increase in Hsp90 co-chaperones.  Further comparison with Alzheimer’s disease and Huntington’s disease transcriptome datasets identified a common set of genes that consistently declined in disease and aging.  This was further put to an experimental test of hypothesis by Dan Garza and colleagues at Proteostasis Therapeutics, Inc. and Cindy Voisine using human cells expressing mutant Huntington with an expanded polyQ and C. elegans expressing Abeta or expanded polyQ to determine which chaperones suppressed aggregation.  This led to the identification of the same set of 18 chaperone genes in C. elegans and humans including members of the Hsp70, Hsp90, CCT, J-domain and TPR-containing co-chaperones.

 

Together with Bill Balch, Andy Dillin and Jeff Kelly, we proposed the PROTEOSTASIS NETWORK as the organizing principle for the regulation of the expression, stability and function of the proteome (Balch et al., 2008; Powers et al., 2009). 

 

 

References

Åkerfelt, M., R.I. Morimoto, and L. Sistonen. Heat Shock Factors: Integrators of Cell Stress, Development, and Lifespan. Nature Reviews Molecular Cell Biology 11: 545-555 (2010).

 

Beere H, Wolf B, Mosser R, Klein K, Kuwano T, Morimoto R, Cohen G and Green D. Heat shock protein 70 (Hsp70) inhibits apoptosis by preventing recruitment of procaspase-9 to aggregated Apaf-1. Nature Cell Bio. 2; 469-475, (2000).

​Beam, M., M. C. Silva, and R.I. Morimoto.  Dynamic Imaging by Fluorescence Correlation Spectroscopy Identifies Diverse Populations of Polyglutamine Oligomers Formed In vivo. J. Biological Chemistry 287: 26136-45, PMID: 22669943 (2012).

 

Ben-Zvi-A., E.A. Miller, and R.I. Morimoto. The Collapse of Proteostasis Represents an Early Molecular Event in C. elegans Aging. Proc. Natl. Acad. Sci. USA.  106: 14914-14919 (2009).

 

Bimston D, Song J, Winchester D, Takayama S, Reed JC, Morimoto RI. BAG-1, a negative regulator of Hsp70 chaperone activity, uncouples nucleotide hydrolysis from substrate release. EMBO 17: 6871-6878, (1998).

​Brehme, M., C. Voisine, T. Rolland, S. Wachi, J. Soper, Y. Zhu, K. Orton, A. Villella, D. Garza, M. Vidal, H. Ge, and R.I. Morimoto. A Conserved Chaperome Sub-Network Safeguards Protein Homeostasis in Aging and Neurodegenerative Disease. Cell Reports 9: 1135–1150, DOI: 10.1016/j, PMID: 25437566 (2014).

 

Calamini, B., C. Silva, F. Madoux, D. M. Hutt, S. Khanna, M. Chalfant, P. Hodder, B. Tait, D. Garza, W. Balch, and R.I. Morimoto. Small Molecule Proteostasis Regulators for Protein Conformational Disease. Nature Chemical Biology 8(2): 185-96. DOI. 10.1038/nchembio.763 (2011).

 

Ciryam, P., R. Kundra, R. I. Morimoto, C. M. Dobson, and M. Vendruscolo. Supersaturation is a Driving Force for Protein Aggregation in Neurodegenerative Diseases. Trends in Pharmacological Sciences 36: 72-77, DOI:10.1016/ j.tips.2014.12.004, PMID: 25626813 (2015).

 

Ciryam, P., I. Lambert-Smith, D. M. Bean, D. N. Saunders, M. R. Wilson, R. I. Morimoto, S. G. Oliver, C. M. Dobson, M. Vendruscolo, G. Favrin, and J. J. Yerbury. Tissue-specific Patterns of Supersaturation are Associated with Co-Aggregation in ALS Inclusion Bodies. Proc. Natl. Acad. Sci. USA. 114(20): E3935–E3943 DOI:10.1073/pnas.1613854114 (2017).

 

Ciryam, P., G. G. Tartaglia, R. I. Morimoto, C. M. Dobson, and M. Vendruscolo. Neurodegenerative Diseases and Widespread Aggregation are Associated with Supersaturated Proteins. Cell Reports 5: 781-790, DOI: 10.1016, PMID: 24183671 (2013).

 

Freeman BC. Morimoto RI. The human cytosolic molecular chaperones hsp90, hsp70 (hsc70) and hdj-1 have distinct roles in recognition of a non-native protein and protein refolding. EMBO Journal. 15(12): 2969-79. (1996).

Freeman BC. Myers MP. Schumacher R. Morimoto RI. Identification of a regulatory motif in Hsp70 that affects ATPase activity, substrate binding and interaction with HDJ-1. EMBO Journal 14(10): 2281-92. (1995).

Freeman BC, Toft DO and Morimoto RI. Molecular chaperone machines: chaperone activites of the cyclophilin Cyp-40 and the steroid aporeceptor-associated protein p23. Science 274: 1718-20. (1996).

 

Gidalevitz, T., E.A. Kikis, and R.I. Morimoto. A Cellular Perspective on Conformational Disease:  The Role of Genetic Background and Proteostasis Networks. Current Opinions in Structural Biology 20: 23-32 (2010).

 

Gidalevitz, T., T. Krupinski, S.M. Garcia, and R.I. Morimoto. Toxicity of Mutant SOD1 is Directed by Protein Polymorphisms. PLoS Genetics 5(3): e1000399 (2009).

 

Gidalevitz, G., N. Wang, T. Deravaj, and R.I. Morimoto. Natural Genetic Variation Determines Susceptibility to Aggregation or Toxicity in a C. elegans model for Polyglutamine Disease. BMC Biology 11: 100, DOI: 10.1186, PMID: 24079614 (2013).

 

Guisbert, E., D. M. Czyz, K. Richter, P. D. McMullen, and R. I. Morimoto. Identification of a Tissue-Selective Heat Shock Response Regulatory Network. PLoS Genetics 9(4): DOI: 10.1371, PMID: 23637632 (2013).

 

Holmberg C.I., Hietakangas V., Mikhailov A., Rantanen J.O., Kallio M., Meinander A., Hellman J., Morrice N., MacKintosh C., Morimoto R.I., Eriksson J.E., Sistonen L. Phosphorylation of serine 230 promotes inducible transcriptional activity of heat shock factor 1. EMBO, 20(14): 3800-3810. (2001).

Kennedy, B.K., S.L. Berger, A. Brunet, J. Campisi, A.M. Cuervo, E.S. Epel, C. Franceschi, G.J. Lithgow, R.I. Morimoto, J.E. Pessin, T.A. Rando, A. Richardson, E.E. Schadt, T. Wyss-Coray, and F. Sierra. Geroscience: Linking Aging to Disease. Cell 159: 709-713, PMID: 25417146 (2014).

 

Kirstein, J., K. Arnsburg, A. Scior, A. Szlachcic, D. Lys Guilbride, R.I. Morimoto, B. Bukau. and N.B. Nillegoda. In vivo Properties of the Disaggregase Function of J-domain Proteins and Hsc70 in C. elegans Stress and Aging.  Aging Cell 16: 1414-1424, DOI: 10.1111/acel.12686 (2017).

 

Kirstein, J., D. Morito, T. Kakihana, M. Sugihara, A. Minnen, M.S. Hipp, C. Nussbaum-Krammer, F.U. Hartl, K. Nagata, and R.I. Morimoto.  Proteotoxic Stress and Ageing Triggers the Loss of Redox Homeostasis Across Cellular Compartments. EMBO Journal 34: 2334-2349, PMID:26228940 (2015).

 

Kirstein-Miles, J., A. Scior, E. Duerling, and R.I. Morimoto. The Nascent Polypeptide Associated Complex is a Key Regulator of Proteostasis. The EMBO Journal 32(10): 1451-1468, PMID: 23604074 DOI: 10.1038, PMID: 23604074 (2013).

 

Krammer, C., K.W. Park, L. Li, R. Melki, and R.I. Morimoto.  Spreading of a Prion Domain from Cell to Cell by Vesicular Transport in C. elegans.  PLoS Genetics 9(3): DOI: 10.1371, PMID: 23555277 (2013).

 

Kundra, R., P. Ciryam, R. I. Morimoto, C. M. Dobson, and M. Vendruscolo. Protein Homeostasis of a Metastable Subproteome Associated with Alzheimer’s Disease. Proc. Natl. Acad. Sci. USA. 114(28): E5703-E5711 DOI: 10.1073/pnas.1618417114 (2017).

 

Labbadia, J., R. Brielmann, M. Neto, Y.-F. Lin, C.M. Haynes, and R.I. Morimoto.  Mitochondrial Stress Restores the Heat Shock Response and Prevents Proteostasis Collapse During Aging. Cell Reports 21: 1481-1494, DOI.org/10.1016/ j.celrep.2017.10.038 (2017).

 

Labbadia, J. and R.I. Morimoto. Repression of the Heat Shock Response is a Programmed Event at the Onset of Reproduction. Molecular Cell 59: 639-650, DOI 10.1016/j. molcel.2015.06.027 PMID: 266212459 (2015).

  

Labbadia, J., and R.I. Morimoto. The Biology of Proteostasis in Aging and Disease. Annual Reviews of Biochemistry 84: 435-464, DOI: 10.1146/annurev-biochem-060614-033955, PMID: 25784053 (2015).

 

Li, J., L. Chauve, G. Phelps, R. Brielmann, and R.I. Morimoto. E2F Co-regulates an Essential HSF Developmental Program Distinct from the Heat Shock Response. Genes and Development 30: 2062-2075 PMID 27688402 (2016).

 

Li, J., J. Labbadia, and R.I. Morimoto. Rethinking the Roles of HSF-1 in Cell Stress, Development and Organismal Health. Trends in Cell Biology 12: DOI: org/10.1016/ j.tcb.2017.08.002 (2017).

 

Matsumoto, G., S. Kim, and R.I. Morimoto. Huntingtin and mutant SOD1 form aggregate structures with distinct molecular properties in human cells. J Biol Chem. 281: 4477-4485 (2006).

McMullen, P.D., E. Z. Aprison, P. B. Winter, L. A. N. Amaral, R. I. Morimoto, and I. Ruvinsky. Maco-level Modeling of the Response of C. elegans Reproduction to Chronic Heat Stress. PLoS Computational Biology 8(1): e1002338. DOI: 10.1371/journal.pcbi.1002338. PMID: 22291584 (2012).

 

Montgomery DL, Morimoto RI, Gierasch LM Mutations in the substrate binding domain of the Escherichia coli 70 kDa molecular chaperone, DnaK, which alter substrate affinity or interdomain coupling. J Mol Biol:286(3): 915-32, (1999).

Morimoto. Polyglutamine protein aggregates are dynamic. Nature Cell Biology, 4: 826-831 (2002).

​Morimoto, R.I. Cell Non-Autonomous Regulation of Proteostasis in Aging and Disease. Cold Spring Harbor Perspectives in Biology.  DOI: 10.1101/cshperspect.a034074 (2019).

 

Morley J.F., Brignull H.R., Weyers J.J., Morimoto R.I. The threshold for polyglutamine-expansion protein aggregation and cellular toxicity is dynamic and influenced by aging in Caenorhabditis elegans. Proc Natl Acad Sci U S A.99(16):10417-22 (2002).

Mosser DD, Morimoto RI. Molecular chaperones and the stress of oncogenesis. Oncogene, 23(16): 2907-18 (2004).

Nillegoda, N.B., J. Kirstein, A. Szlachcic, M. Berynskyy, A. Stank, F. Stenge4, K. Arnsburg, X. Gao, R. Aebersold, D.L. Guilbride, R.C. Wade, R.I. Morimoto, M.P. Mayer, and B. Bukau.  Crucial Hsp70 Co-chaperone Complex Unlocks Metazoan Protein Disaggregation. Nature 524: 247-251. DOI: 10.1038/nature14884, PMID:26245380 (2015).

 

Nollen EA, Morimoto RI. Chaperoning signaling pathways: molecular chaperones as stress-sensing ‘heat shock’ proteins. J Cell Sci. 115: 2809-16 (2002).

Nussbaum-Krammer, C., and R.I. Morimoto. Caenorhabditis elegans as a Model System for Cell Non-Autonomous Mechanisms in Protein Misfolding Diseases. Disease Models and Mechanisms 7: 31-39, DOI: 10.1242, PMID: 24396152 (2014).

Prahlad, V., T. Cornelius and R.I. Morimoto, . Regulation of the Cellular Heat Shock Response in Caenorhabditis elegans by Thermosensory Neurons. Science 320: 811-814 (2008).

Prahlad, V., and R.I. Morimoto. Integrating the Stress Response: Lessons for Neurodegenerative Diseases from C. elegans. Trends in Cell Biology 19: 52-61 (2009). PMID: 19112021 [PubMed – as supplied by publisher]

Prahlad, V. and R.I. Morimoto. Neuronal Circuitry Regulates the Response of C. elegans to Misfolded Proteins. Proc. Natl. Acad. Sci. U.S.A. 108: 14204-14209, PMID: 1106557108 (2011).

 

​Powers, E.T., R.I. Morimoto, A. Dillin, J.W. Kelly, and W.E. Balch. Biological and Chemical Approaches to Diseases of Proteostasis Deficiency. Annual Reviews of Biochemistry 78: 959-991 (2009).

 

Rampelt, H., J. Kirstein-Miles, S. Scholz, N. Nillegoda, R.I. Morimoto, B. Bukau.  Metazoan Hsp70 Machines use Hsp110 to Power Protein Disaggregation. The EMBO Journal 31(21): 4221-4235, PMID: 22990239 (2012).

 

Rieger TR, Morimoto RI, and V. Hatzimanikatis. Bistability explains threshold phenomena in protein aggregation both in vitro and in vivo. Biophys J. 90: 886-95 (2006).

Roth, D. M., D.M. Hutt, J. Tong, M. Bouchecareih, N. Wang, D. Garza, R.I. Morimoto, and W.E. Balch. Correcting Misfolding Disease by Managing the Maladaptive Stress Response. PLoS Biology 12: e1001998, PMID: 25406061 (2014).

 

​Sala, A.J., L.C.  Bott, R.M. Brielmann, and R.I. Morimoto. Embryo Integrity Regulates Maternal Proteostasis and Stress Resilience. Genes and Development 34: 678-687. DOI:10.1101/gad.335422.119, PMID: 32217667 (2020).

 

Sala, A.J., L.C. Bott, and R.I. Morimoto. Shaping Proteostasis at the Cellular, Tissue, and Organismal Level. Journal of Cell Biology 216: DOI: 10.1083/jcb.201612111 (2017).

 

Satyal SH, Schmidt E, Kitagawa K, Sondheimer N, Lindquist S, Kramer JM, Morimoto RI. Polyglutamine aggregates alter protein folding homeostasis in Caenorhabditis elegans. Proc Natl Acad Sci U S A 23;97(11):5750-5. (2000).

Shen X, Ellis RE, Lee K, Liu CY, Yang K, Solomon A, Yoshida H, Morimoto R, Kurnit DM, Mori K, Kaufman RJ. Complementary signaling pathways regulate the unfolded protein response and are required for C. elegans development. Cell 107:893-903 (2001).

Shibata, Y., and R.I. Morimoto. How the Nucleus Copes with Proteotoxic Stress. Current Biology 24: R463-474, DOI: 10.1016/j.cub.2014.03.033, PMID: 24845679 (2014).

 

Silva, M. C., M. D. Amaral, and R.I. Morimoto. Neuronal Reprogramming of Protein Homeostasis by Calcium-Dependent Regulation of the Heat Shock Response. PLoS Genetics 9(8): DOI: 10.1371, e1003711, PMID: 24009518 (2013).

 

Silva, M. C., S. Fox, H. Thakkar, M. J. Rivera Beam, M. D. Amaral, and R.I. Morimoto. A Genetic Screening Strategy Identifies Novel Global Regulators of the Proteostasis Network. PLoS Genetics 7(12): DOI:10.1371 (2011).

 

​Sinnige, T., A.  Yu, and R.I.  Morimoto. Challenging Proteostasis: Role of the Chaperone Network to Control Aggregation-Prone Proteins in Human Disease. In: HSF1 and Molecular Chaperones in Biology and Disease, eds. M. Mendillo, D. Pincus and R. Scher-Shouval. Springer Nature Series on Advances in Experimental Medicine and Biology 1243: 53-68. DOI: 10.1007/978-3-030-40204-4_4.PMID: 32297211 (2020).

 

Song, J, Takeda M and Morimoto RI. Hsp70-Bag1 complex mediates a physiological stress signaling pathway that regulates Raf-1/ERK and cell growth. Nature Cell Biology 3: 276-282 (2001).

Takayama S. Bimston DN. Matsuzawa S. Freeman BC. Aime-Sempe C. Xie Z. Morimoto RI. Reed JC. BAG-1 modulates the chaperone activity of Hsp70/Hsc70. EMBO Journal 16(16): 4887-96. (1997).

Teixeira-Castro, A., M. Ailion, A. Jalles, H. R. Brignull, J.  L. Vilaça, N. Dias, P. Rodrigues, J. F. Oliveira, A. Neves-Carvalho, R. I. Morimoto, and P. Maciel. Neuron-Specific Proteotoxicity of Mutant Ataxin-3 in C. elegans: Rescue by the DAF-16 and HSF1 Pathways. Human Molecular Genetics 20(15): 2996-3009. PMID:21546381 (2011).

 

Thress K, Song J, Morimoto RI, Kornbluth S. Reversible inhibition of Hsp70 chaperone function by Scythe and Reaper. EMBO J 1:1033-1041 (2001).

van Oosten-Hawle, P., and R.I. Morimoto. Organismal Control of Proteostasis by Cell Non-Autonomous Regulation and Transcellular Stress Signaling. Genes and Development 28: 1533-1543, DOI: 10.1101/gad.241125.114, PMID: 25030693 (2014).

 

van Oosten-Hawle, P., R. Porter, and R. I. Morimoto. Regulation of Organismal Proteostasis by Transcellular Chaperone Signaling. Cell 153: 1366-1378. DOI:10.1016. PMID: 23746847 (2013).

 

Voisine, C., J. Pedersen, R.I. Morimoto.  Chaperone Networks: Tipping the Balance in Protein Misfolding Disease. Neurobiology of Disease 40: 10-20. (2010).

 

​Walther, D.M., P. Kasturi, M. Zheng, S. Pinkert, G. Vecchi, P. Ciryam, R.I. Morimoto, C.M. Dobson, M. Vendruscolo, M. Mann and F.-U. Hartl. Widespread Proteome Remodeling and Aggregation in Aging C. elegans. Cell 161(4): 919-932, DOI: 10.1016/j.cell.2015.03.032, PMID: 25957690 (2015).

Westerheide, S.D., J. Anckar, S.M. Stevens, Jr., L. Sistonen, and R.I. Morimoto. Stress-Inducible Regulation of Heat Shock Factor 1 by the Deacetylase SIRT1. Science 20: 1063-1066. (2009).

Yu, A., S.G. Fox, A. Cavallini, C. Kerridge, M. J. O’Neill, J. Wolak, S. Bose, and R. I. Morimoto. Tau Protein Aggregates Inhibit the Protein-Folding and Vesicular Trafficking Arms of the Cellular Proteostasis Network. J. Biological Chemistry 294(19): 7917-7930. DOI:10.1074/jbc.RA119.007527 (2019).

 

Yu, A., Y. Shibata, B. Shah, B. Calamini, D. Lo, and R.I. Morimoto.  Protein Aggregation Inhibits Clathrin-Mediated Endocytosis by Chaperone Competition. Proc. Natl. Acad. Sci. USA 111: E1481-1490. DOI: 10.1073/pnas.1321811111, PMID: 24706768 (2014).