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Garde R, Dea A, Herwig MF, Ali A, Pincus D. Feedback control of the heat shock response by spatiotemporal regulation of Hsp70. J Cell Biol 2024; 223:e202401082. [PMID: 39302312 PMCID: PMC11415305 DOI: 10.1083/jcb.202401082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/31/2024] [Accepted: 09/04/2024] [Indexed: 09/22/2024] Open
Abstract
Cells maintain homeostasis via dynamic regulation of stress response pathways. Stress pathways transiently induce response regulons via negative feedback loops, but the extent to which individual genes provide feedback has not been comprehensively measured for any pathway. Here, we disrupted the induction of each gene in the Saccharomyces cerevisiae heat shock response (HSR) and quantified cell growth and HSR dynamics following heat shock. The screen revealed a core feedback loop governing the expression of the chaperone Hsp70 reinforced by an auxiliary feedback loop controlling Hsp70 subcellular localization. Mathematical modeling and live imaging demonstrated that multiple HSR targets converge to promote Hsp70 nuclear localization via its release from cytosolic condensates. Following ethanol stress, a distinct set of factors similarly converged on Hsp70, suggesting that nonredundant subsets of the HSR regulon confer feedback under different conditions. Flexible spatiotemporal feedback loops may broadly organize stress response regulons and expand their adaptive capacity.
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Affiliation(s)
- Rania Garde
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Annisa Dea
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Madeline F. Herwig
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Asif Ali
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA
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2
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Ciccarelli M, Andréasson C. Protein Misfolding Releases Human HSF1 from HSP70 Latency Control. J Mol Biol 2024; 436:168740. [PMID: 39122169 DOI: 10.1016/j.jmb.2024.168740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/25/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Heat shock factor 1 (HSF1) responds to stress to mount the heat shock response (HSR), a conserved transcriptional program that allows cells to maintain proteostasis by upregulating heat shock proteins (HSPs). The homeostatic stress regulation of HSF1 plays a key role in human physiology and health but its mechanism has remained difficult to pinpoint. Recent work in the budding yeast model has implicated stress-inducible chaperones of the HSP70 family as direct negative regulators of HSF1 activity. Here, we have investigated the latency control and activation of human HSF1 by HSP70 and misfolded proteins. Purified oligomeric HSF1-HSP70 (HSPA1A) complexes exhibited basal DNA binding activity that was inhibited by increasing the levels of HSP70 and, importantly, misfolded proteins reverted the inhibitory effect. Using site-specific UV photo-crosslinking, we monitored HSP70-HSF1 complexes in HEK293T cells. While HSF1 was bound by the substrate binding domain of HSP70 in unstressed cells, activation of HSF1 by heat shock as well as by inducing the misfolding of newly synthesized proteins resulted in release of HSF1 from the chaperone. Taken our results together, we conclude that latent HSF1 populate dynamic complexes with HSP70, which are sensitive to increased levels of misfolded proteins that compete for binding to the HSP70 substrate binding domain. Thus, human HSF1 is activated by various stress conditions that all titrate available HSP70.
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Affiliation(s)
- Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden.
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3
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Ulfig A, Jakob U. Cellular oxidants and the proteostasis network: balance between activation and destruction. Trends Biochem Sci 2024; 49:761-774. [PMID: 39168791 DOI: 10.1016/j.tibs.2024.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 06/27/2024] [Accepted: 07/09/2024] [Indexed: 08/23/2024]
Abstract
Loss of protein homeostasis (proteostasis) is a common hallmark of aging and age-associated diseases. Considered as the guardian of proteostasis, the proteostasis network (PN) acts to preserve the functionality of proteins during their lifetime. However, its activity declines with age, leading to disease manifestation. While reactive oxygen species (ROS) were traditionally considered culprits in this process, recent research challenges this view. While harmful at high concentrations, moderate ROS levels protect the cell against age-mediated onset of proteotoxicity by activating molecular chaperones, stress response pathways, and autophagy. This review explores the nuanced roles of ROS in proteostasis and discusses the most recent findings regarding the redox regulation of the PN and its potential in extending healthspan and delaying age-related pathologies.
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Affiliation(s)
- Agnes Ulfig
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Ursula Jakob
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA; Biological Chemistry Department, University of Michigan Medical School, Ann Arbor, MI, USA.
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4
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Zhang WJ, Feng H, Zhang MM, Liu JS, Li LT, Chen HC, Liu ZF. Pseudorabies virus UL13 primes inflammatory response through downregulating heat shock factor 1. Virology 2024; 600:110214. [PMID: 39243656 DOI: 10.1016/j.virol.2024.110214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2024] [Revised: 08/11/2024] [Accepted: 08/29/2024] [Indexed: 09/09/2024]
Abstract
Pseudorabies virus is a swine alpha-herpesvirus. We demonstrated that alpha-herpesvirus infection downregulates HSF1, a master transcription factor in the heat shock response. The serine/threonine protein kinase activity of late viral protein UL13 is indispensable for HSF1 depletion and phosphorylation, and UL13 does not degrade HSF1 posttranslationally but inhibits the HSF1 mRNA level. Importantly, UL13 increased HSF1 activity even though it reduced HSF1 mRNA. Furthermore, viral replication markedly decreased in the HSF1 knockout cell line or in the presence of an HSF1-specific inhibitor. Interestingly, HSF1 knockout accelerated the activation of NF-κB and p38MAPK. The K96 loci of UL13 are important to induce high levels of IL-6, TNF-α, and IL-β cytokines while playing a crucial role in promoting mild interstitial pneumonia, liver necrosis, and severe inflammatory cell infiltration in the footpad. Thus, UL13 steers the heat shock response to promote viral replication and the inflammatory response. IMPORTANCE: PRV is a ubiquitous pathogen that infects a variety of mammals, such as pigs, ruminants, carnivores, and rodents as well as human beings, causing enormous economic losses in the swine industry. Here, we employed PRV as a model to determine the relationship between α-herpesvirus and the inflammatory response. Overall, our findings indicated that PRV infection inhibits the level of HSF1 mRNA via the serine/threonine protein kinase activity of UL13. Additionally, we discovered that HSF1 was involved in NF-κB activation upon PRV infection. PRV UL13 orchestrates the level of HSF1 mRNA, HSF1 protein phosphorylation, and priming of the inflammatory response. Our study reveals a novel mechanism employed by UL13 serine/threonine protein kinase activity to promote the inflammatory response, providing novel clues for therapy against alpha-herpesvirus infection.
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Affiliation(s)
- Wen-Jing Zhang
- National Key Laboratory of Agricultural Microbiology and Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Han Feng
- National Key Laboratory of Agricultural Microbiology and Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Mei-Mei Zhang
- National Key Laboratory of Agricultural Microbiology and Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Jing-Song Liu
- National Key Laboratory of Agricultural Microbiology and Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin-Tao Li
- National Key Laboratory of Agricultural Microbiology and Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Huan-Chun Chen
- National Key Laboratory of Agricultural Microbiology and Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China
| | - Zheng-Fei Liu
- National Key Laboratory of Agricultural Microbiology and Hongshan Laboratory, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, China.
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5
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Alasady MJ, Koeva M, Takagishi SR, Segal D, Amici DR, Smith RS, Ansel DJ, Lindquist S, Whitesell L, Bartom ET, Taipale M, Mendillo ML. An HSF1-JMJD6-HSP feedback circuit promotes cell adaptation to proteotoxic stress. Proc Natl Acad Sci U S A 2024; 121:e2313370121. [PMID: 38985769 PMCID: PMC11260097 DOI: 10.1073/pnas.2313370121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 05/10/2024] [Indexed: 07/12/2024] Open
Abstract
Heat Shock Factor 1 (HSF1) is best known as the master transcriptional regulator of the heat-shock response (HSR), a conserved adaptive mechanism critical for protein homeostasis (proteostasis). Combining a genome-wide RNAi library with an HSR reporter, we identified Jumonji domain-containing protein 6 (JMJD6) as an essential mediator of HSF1 activity. In follow-up studies, we found that JMJD6 is itself a noncanonical transcriptional target of HSF1 which acts as a critical regulator of proteostasis. In a positive feedback circuit, HSF1 binds and promotes JMJD6 expression, which in turn reduces heat shock protein 70 (HSP70) R469 monomethylation to disrupt HSP70-HSF1 repressive complexes resulting in enhanced HSF1 activation. Thus, JMJD6 is intricately wired into the proteostasis network where it plays a critical role in cellular adaptation to proteotoxic stress.
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Affiliation(s)
- Milad J. Alasady
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Martina Koeva
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Cambridge, MA02139
| | - Seesha R. Takagishi
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Dmitri Segal
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
| | - David R. Amici
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Roger S. Smith
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Daniel J. Ansel
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Susan Lindquist
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
- HHMI, Cambridge, MA02139
| | - Luke Whitesell
- Whitehead Institute for Biomedical Research, Cambridge, MA02142
- Massachusetts Institute of Technology, Cambridge, MA02142
| | - Elizabeth T. Bartom
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
| | - Mikko Taipale
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ONM5S 3E1, Canada
| | - Marc L. Mendillo
- Department of Biochemistry and Molecular Genetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Simpson Querrey Center for Epigenetics, Northwestern University Feinberg School of Medicine, Chicago, IL60611
- Robert H. Lurie Comprehensive Cancer Center, Northwestern University Feinberg School of Medicine, Chicago, IL60611
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6
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Ruger-Herreros C, Svoboda L, Mogk A, Bukau B. Role of J-domain Proteins in Yeast Physiology and Protein Quality Control. J Mol Biol 2024; 436:168484. [PMID: 38331212 DOI: 10.1016/j.jmb.2024.168484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/02/2024] [Accepted: 02/02/2024] [Indexed: 02/10/2024]
Abstract
The Hsp70 chaperone system is a central component of cellular protein quality control (PQC) by acting in a multitude of protein folding processes ranging from the folding of newly synthesized proteins to the disassembly and refolding of protein aggregates. This multifunctionality of Hsp70 is governed by J-domain proteins (JDPs), which act as indispensable co-chaperones that target specific substrates to Hsp70. The number of distinct JDPs present in a species always outnumbers Hsp70, documenting JDP function in functional diversification of Hsp70. In this review, we describe the physiological roles of JDPs in the Saccharomyces cerevisiae PQC system, with a focus on the abundant JDP generalists, Zuo1, Ydj1 and Sis1, which function in fundamental cellular processes. Ribosome-bound Zuo1 cooperates with the Hsp70 chaperones Ssb1/2 in folding and assembly of nascent polypeptides. Ydj1 and Sis1 cooperate with the Hsp70 members Ssa1 to Ssa4 to exert overlapping functions in protein folding and targeting of newly synthesized proteins to organelles including mitochondria and facilitating the degradation of aberrant proteins by E3 ligases. Furthermore, they act in protein disaggregation reactions, though Ydj1 and Sis1 differ in their modes of Hsp70 cooperation and substrate specificities. This results in functional specialization as seen in prion propagation and the underlying dominant role of Sis1 in targeting Hsp70 for shearing of prion amyloid fibrils.
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Affiliation(s)
- Carmen Ruger-Herreros
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Instituto de Biomedicina de Sevilla (IBiS), Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Avda. Manuel Siurot, s/n, E-41013 Sevilla, Spain
| | - Lucia Svoboda
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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7
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Dea A, Pincus D. The Heat Shock Response as a Condensate Cascade. J Mol Biol 2024; 436:168642. [PMID: 38848866 PMCID: PMC11214683 DOI: 10.1016/j.jmb.2024.168642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 05/31/2024] [Accepted: 06/03/2024] [Indexed: 06/09/2024]
Abstract
The heat shock response (HSR) is a gene regulatory program controlling expression of molecular chaperones implicated in aging, cancer, and neurodegenerative disease. Long presumed to be activated by toxic protein aggregates, recent work suggests a new functional paradigm for the HSR in yeast. Rather than toxic aggregates, adaptive biomolecular condensates comprised of orphan ribosomal proteins (oRP) and stress granule components have been shown to be physiological chaperone clients. By titrating away the chaperones Sis1 and Hsp70 from the transcription factor Hsf1, these condensates activate the HSR. Upon release from Hsp70, Hsf1 forms spatially distinct transcriptional condensates that drive high expression of HSR genes. In this manner, the negative feedback loop controlling HSR activity - in which Hsf1 induces Hsp70 expression and Hsp70 represses Hsf1 activity - is embedded in the biophysics of the system. By analogy to phosphorylation cascades that transmit information via the dynamic activity of kinases, we propose that the HSR is organized as a condensate cascade that transmits information via the localized activity of molecular chaperones.
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Affiliation(s)
- Annisa Dea
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, United States; Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, United States; Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, United States.
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8
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Rich A, Acar O, Carvunis AR. Massively integrated coexpression analysis reveals transcriptional regulation, evolution and cellular implications of the yeast noncanonical translatome. Genome Biol 2024; 25:183. [PMID: 38978079 PMCID: PMC11232214 DOI: 10.1186/s13059-024-03287-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 05/20/2024] [Indexed: 07/10/2024] Open
Abstract
BACKGROUND Recent studies uncovered pervasive transcription and translation of thousands of noncanonical open reading frames (nORFs) outside of annotated genes. The contribution of nORFs to cellular phenotypes is difficult to infer using conventional approaches because nORFs tend to be short, of recent de novo origins, and lowly expressed. Here we develop a dedicated coexpression analysis framework that accounts for low expression to investigate the transcriptional regulation, evolution, and potential cellular roles of nORFs in Saccharomyces cerevisiae. RESULTS Our results reveal that nORFs tend to be preferentially coexpressed with genes involved in cellular transport or homeostasis but rarely with genes involved in RNA processing. Mechanistically, we discover that young de novo nORFs located downstream of conserved genes tend to leverage their neighbors' promoters through transcription readthrough, resulting in high coexpression and high expression levels. Transcriptional piggybacking also influences the coexpression profiles of young de novo nORFs located upstream of genes, but to a lesser extent and without detectable impact on expression levels. Transcriptional piggybacking influences, but does not determine, the transcription profiles of de novo nORFs emerging nearby genes. About 40% of nORFs are not strongly coexpressed with any gene but are transcriptionally regulated nonetheless and tend to form entirely new transcription modules. We offer a web browser interface ( https://carvunislab.csb.pitt.edu/shiny/coexpression/ ) to efficiently query, visualize, and download our coexpression inferences. CONCLUSIONS Our results suggest that nORF transcription is highly regulated. Our coexpression dataset serves as an unprecedented resource for unraveling how nORFs integrate into cellular networks, contribute to cellular phenotypes, and evolve.
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Affiliation(s)
- April Rich
- Joint Carnegie Mellon University-University of Pittsburgh, University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM), University of Pittsburgh, Pittsburgh, PA, USA
| | - Omer Acar
- Joint Carnegie Mellon University-University of Pittsburgh, University of Pittsburgh Computational Biology PhD Program, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
- Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM), University of Pittsburgh, Pittsburgh, PA, USA
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
- Pittsburgh Center for Evolutionary Biology and Medicine (CEBaM), University of Pittsburgh, Pittsburgh, PA, USA.
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9
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Çamoğlu T, Yurttaş Z, Kına ÜY, Akkuş Süt P, Sahin F, Dursun E, Gezen-Ak D. Fibrillar Alpha-Synuclein Alters the Intracellular Chaperone Levels within Hours of Its Internalization. ACS OMEGA 2024; 9:17185-17194. [PMID: 38645348 PMCID: PMC11025075 DOI: 10.1021/acsomega.3c10036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Revised: 02/26/2024] [Accepted: 02/29/2024] [Indexed: 04/23/2024]
Abstract
Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder worldwide. According to the Braak hypothesis, the disease spreads along specific neuroanatomical pathways. Studies indicate that fibrillar alpha-synuclein (F-αSyn) can propagate from cell-to-cell by following intercellular connections, leading to the selective death of certain cell groups like substantia nigra dopaminergic neurons and advancing the pathology. Internalized F-αSyn can be eliminated by lysosomes, proteasomes, or chaperones before it replicates inside the cell. Research has shown that F-αSyn can somehow escape from endosomes, lysosomes, and proteasomes and replicate itself. However, the impact of chaperones on intracellular levels during the initial hours of their internalization remains unknown. The present study investigates the effect of F-αSyn on chaperone levels within the first 6 and 12 h after internalization. Our findings showed that within the first 6 h, Hsc70 and Hsp90 levels were increased, while within 12 h, F-αSyn leads to a decrease or suppression of numerous intracellular chaperone levels. Exploring the pathological effects of PD on cells will contribute to identifying more targets for therapeutic interventions.
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Affiliation(s)
- Tugay Çamoğlu
- Brain
and Neurodegenerative Disorders Research Laboratories, Department
of Neuroscience, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey
| | - Zuhal Yurttaş
- Brain
and Neurodegenerative Disorders Research Laboratories, Department
of Neuroscience, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey
| | - Ümit Yaşar Kına
- Beykoz
Institute of Life Sciences and Biotechnology, Bezmialem Vakif University, Istanbul 34093, Turkey
| | - Pınar Akkuş Süt
- Department
of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
| | - Fikrettin Sahin
- Department
of Genetics and Bioengineering, Faculty of Engineering, Yeditepe University, Istanbul 34755, Turkey
| | - Erdinç Dursun
- Brain
and Neurodegenerative Disorders Research Laboratories, Department
of Neuroscience, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey
| | - Duygu Gezen-Ak
- Brain
and Neurodegenerative Disorders Research Laboratories, Department
of Neuroscience, Institute of Neurological Sciences, Istanbul University-Cerrahpasa, Istanbul 34098, Turkey
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10
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Keyport Kik S, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Lin KM, Squires AH, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. Nat Commun 2024; 15:3127. [PMID: 38605014 PMCID: PMC11009240 DOI: 10.1038/s41467-024-47355-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2023] [Accepted: 03/27/2024] [Indexed: 04/13/2024] Open
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL, USA
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Caitlin Wong Hickernell
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
| | - Kyle M Lin
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL, USA
- Interdisciplinary Scientist Training Program, The University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | | | - Tobin R Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, USA.
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11
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Montrose K, Lac DT, Burnetti AJ, Tong K, Bozdag GO, Hukkanen M, Ratcliff WC, Saarikangas J. Proteostatic tuning underpins the evolution of novel multicellular traits. SCIENCE ADVANCES 2024; 10:eadn2706. [PMID: 38457507 PMCID: PMC10923498 DOI: 10.1126/sciadv.adn2706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 02/06/2024] [Indexed: 03/10/2024]
Abstract
The evolution of multicellularity paved the way for the origin of complex life on Earth, but little is known about the mechanistic basis of early multicellular evolution. Here, we examine the molecular basis of multicellular adaptation in the multicellularity long-term evolution experiment (MuLTEE). We demonstrate that cellular elongation, a key adaptation underpinning increased biophysical toughness and organismal size, is convergently driven by down-regulation of the chaperone Hsp90. Mechanistically, Hsp90-mediated morphogenesis operates by destabilizing the cyclin-dependent kinase Cdc28, resulting in delayed mitosis and prolonged polarized growth. Reinstatement of Hsp90 or Cdc28 expression resulted in shortened cells that formed smaller groups with reduced multicellular fitness. Together, our results show how ancient protein folding systems can be tuned to drive rapid evolution at a new level of biological individuality by revealing novel developmental phenotypes.
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Affiliation(s)
- Kristopher Montrose
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Dung T. Lac
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anthony J. Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS), Georgia Institute of Technology, Atlanta, GA, USA
| | - G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mikaela Hukkanen
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki, Helsinki, Finland
- Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
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12
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Mühlhofer M, Offensperger F, Reschke S, Wallmann G, Csaba G, Berchtold E, Riedl M, Blum H, Haslbeck M, Zimmer R, Buchner J. Deletion of the transcription factors Hsf1, Msn2 and Msn4 in yeast uncovers transcriptional reprogramming in response to proteotoxic stress. FEBS Lett 2024; 598:635-657. [PMID: 38366111 DOI: 10.1002/1873-3468.14821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
The response to proteotoxic stresses such as heat shock allows organisms to maintain protein homeostasis under changing environmental conditions. We asked what happens if an organism can no longer react to cytosolic proteotoxic stress. To test this, we deleted or depleted, either individually or in combination, the stress-responsive transcription factors Msn2, Msn4, and Hsf1 in Saccharomyces cerevisiae. Our study reveals a combination of survival strategies, which together protect essential proteins. Msn2 and 4 broadly reprogram transcription, triggering the response to oxidative stress, as well as biosynthesis of the protective sugar trehalose and glycolytic enzymes, while Hsf1 mainly induces the synthesis of molecular chaperones and reverses the transcriptional response upon prolonged mild heat stress (adaptation).
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Affiliation(s)
- Moritz Mühlhofer
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Felix Offensperger
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Sarah Reschke
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Georg Wallmann
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Gergely Csaba
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Evi Berchtold
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Maximilian Riedl
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Helmut Blum
- Laboratory for Functional Genome Analysis at the Gene Center, LMU München, München, Germany
| | - Martin Haslbeck
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
| | - Ralf Zimmer
- Institute of Bioinformatics, Department of Informatics, Ludwig-Maximilians-Universität München, München, Germany
| | - Johannes Buchner
- Center for Protein Assemblies, Department of Bioscience, Technische Universität München, Garching, Germany
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13
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Minoia M, Quintana-Cordero J, Jetzinger K, Kotan IE, Turnbull KJ, Ciccarelli M, Masser AE, Liebers D, Gouarin E, Czech M, Hauryliuk V, Bukau B, Kramer G, Andréasson C. Chp1 is a dedicated chaperone at the ribosome that safeguards eEF1A biogenesis. Nat Commun 2024; 15:1382. [PMID: 38360885 PMCID: PMC10869706 DOI: 10.1038/s41467-024-45645-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 01/29/2024] [Indexed: 02/17/2024] Open
Abstract
Cotranslational protein folding depends on general chaperones that engage highly diverse nascent chains at the ribosomes. Here we discover a dedicated ribosome-associated chaperone, Chp1, that rewires the cotranslational folding machinery to assist in the challenging biogenesis of abundantly expressed eukaryotic translation elongation factor 1A (eEF1A). Our results indicate that during eEF1A synthesis, Chp1 is recruited to the ribosome with the help of the nascent polypeptide-associated complex (NAC), where it safeguards eEF1A biogenesis. Aberrant eEF1A production in the absence of Chp1 triggers instant proteolysis, widespread protein aggregation, activation of Hsf1 stress transcription and compromises cellular fitness. The expression of pathogenic eEF1A2 variants linked to epileptic-dyskinetic encephalopathy is protected by Chp1. Thus, eEF1A is a difficult-to-fold protein that necessitates a biogenesis pathway starting with dedicated folding factor Chp1 at the ribosome to protect the eukaryotic cell from proteostasis collapse.
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Affiliation(s)
- Melania Minoia
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Jany Quintana-Cordero
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Katharina Jetzinger
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Ilgin Eser Kotan
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kathryn Jane Turnbull
- Department of Clinical Microbiology, Rigshospitalet, 2200, Copenhagen, Denmark
- Department of Molecular Biology, Laboratory for Molecular Infection Medicine Sweden, Umeå Centre for Microbial Research, Science for Life Laboratory, Umeå University, Umeå, Sweden
| | - Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Anna E Masser
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Dorina Liebers
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Eloïse Gouarin
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Marius Czech
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - Vasili Hauryliuk
- Science for Life Laboratory, Department of Experimental Medical Science, Lund University, Lund, Sweden
- University of Tartu, Institute of Technology, 50411, Tartu, Estonia
| | - Bernd Bukau
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of the University of Heidelberg (ZMBH), DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden.
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14
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Montrose K, Lac DT, Burnetti AJ, Tong K, Ozan Bozdag G, Hukkanen M, Ratcliff WC, Saarikangas J. Proteostatic tuning underpins the evolution of novel multicellular traits. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.05.31.543183. [PMID: 37333256 PMCID: PMC10274739 DOI: 10.1101/2023.05.31.543183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
The evolution of multicellularity paved the way for the origin of complex life on Earth, but little is known about the mechanistic basis of early multicellular evolution. Here, we examine the molecular basis of multicellular adaptation in the Multicellularity Long Term Evolution Experiment (MuLTEE). We demonstrate that cellular elongation, a key adaptation underpinning increased biophysical toughness and organismal size, is convergently driven by downregulation of the chaperone Hsp90. Mechanistically, Hsp90-mediated morphogenesis operates by destabilizing the cyclin-dependent kinase Cdc28, resulting in delayed mitosis and prolonged polarized growth. Reinstatement of Hsp90 or Cdc28 expression resulted in shortened cells that formed smaller groups with reduced multicellular fitness. Together, our results show how ancient protein folding systems can be tuned to drive rapid evolution at a new level of biological individuality by revealing novel developmental phenotypes.
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Affiliation(s)
- Kristopher Montrose
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
| | - Dung T. Lac
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Anthony J. Burnetti
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kai Tong
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences (QBioS)
| | - G. Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Mikaela Hukkanen
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
| | - William C. Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Juha Saarikangas
- Helsinki Institute of Life Science, HiLIFE, University of Helsinki
- Faculty of Biological and Environmental Sciences, University of Helsinki
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15
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Gorczyca M, Białas W, Nicaud JM, Celińska E. 'Mother(Nature) knows best' - hijacking nature-designed transcriptional programs for enhancing stress resistance and protein production in Yarrowia lipolytica; presentation of YaliFunTome database. Microb Cell Fact 2024; 23:26. [PMID: 38238843 PMCID: PMC10797999 DOI: 10.1186/s12934-023-02285-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 12/21/2023] [Indexed: 01/22/2024] Open
Abstract
BACKGROUND In the era of rationally designed synthetic biology, heterologous metabolites production, and other counter-nature engineering of cellular metabolism, we took a step back and recalled that 'Mother(-Nature) knows best'. While still aiming at synthetic, non-natural outcomes of generating an 'over-production phenotype' we dug into the pre-designed transcriptional programs evolved in our host organism-Yarrowia lipolytica, hoping that some of these fine-tuned orchestrated programs could be hijacked and used. Having an interest in the practical outcomes of the research, we targeted industrially-relevant functionalities-stress resistance and enhanced synthesis of proteins, and gauged them over extensive experimental design's completion. RESULTS Technically, the problem was addressed by screening a broad library of over 120 Y. lipolytica strains under 72 combinations of variables through a carefully pre-optimized high-throughput cultivation protocol, which enabled actual phenotype development. The abundance of the transcription program elicitors-transcription factors (TFs), was secured by their overexpression, while challenging the strains with the multitude of conditions was inflicted to impact their activation stratus. The data were subjected to mathematical modeling to increase their informativeness. The amount of the gathered data prompted us to present them in the form of a searchable catalog - the YaliFunTome database ( https://sparrow.up.poznan.pl/tsdatabase/ )-to facilitate the withdrawal of biological sense from numerical data. We succeeded in the identification of TFs that act as omni-boosters of protein synthesis, enhance resistance to limited oxygen availability, and improve protein synthesis capacity under inorganic nitrogen provision. CONCLUSIONS All potential users are invited to browse YaliFunTome in the search for homologous TFs and the TF-driven phenotypes of interest.
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Affiliation(s)
- Maria Gorczyca
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland
| | - Wojciech Białas
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, 78350, Jouy-en-Josas, France
| | - Ewelina Celińska
- Department of Biotechnology and Food Microbiology, Poznan University of Life Sciences, 60-637, Poznań, Poland.
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16
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Garde R, Dea A, Herwig MF, Pincus D. Feedback control of the heat shock response by spatiotemporal regulation of Hsp70. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.09.574867. [PMID: 38260373 PMCID: PMC10802473 DOI: 10.1101/2024.01.09.574867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Cells maintain homeostasis via dynamic regulation of stress response pathways. Stress pathways transiently induce response regulons via negative feedback loops, but the extent to which individual genes provide feedback has not been comprehensively measured for any pathway. Here, we disrupted induction of each gene in the Saccharomyces cerevisiae heat shock response (HSR) and quantified cell growth and HSR dynamics following heat shock. The screen revealed a core feedback loop governing expression of the chaperone Hsp70 reinforced by an auxiliary feedback loop controlling Hsp70 subcellular localization. Mathematical modeling and live imaging demonstrated that multiple HSR targets converge to promote Hsp70 nuclear localization via its release from cytosolic condensates. Following ethanol stress, a distinct set of factors similarly converged on Hsp70, suggesting that nonredundant subsets of the HSR regulon confer feedback under different conditions. Flexible spatiotemporal feedback loops may broadly organize stress response regulons and expand their adaptive capacity.
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Affiliation(s)
- Rania Garde
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL
| | - Annisa Dea
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - Madeline F. Herwig
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL
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17
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Ali A, Garde R, Schaffer OC, Bard JAM, Husain K, Kik SK, Davis KA, Luengo-Woods S, Igarashi MG, Drummond DA, Squires AH, Pincus D. Adaptive preservation of orphan ribosomal proteins in chaperone-dispersed condensates. Nat Cell Biol 2023; 25:1691-1703. [PMID: 37845327 PMCID: PMC10868727 DOI: 10.1038/s41556-023-01253-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 09/12/2023] [Indexed: 10/18/2023]
Abstract
Ribosome biogenesis is among the most resource-intensive cellular processes, with ribosomal proteins accounting for up to half of all newly synthesized proteins in eukaryotic cells. During stress, cells shut down ribosome biogenesis in part by halting rRNA synthesis, potentially leading to massive accumulation of aggregation-prone 'orphan' ribosomal proteins (oRPs). Here we show that, during heat shock in yeast and human cells, oRPs accumulate as reversible peri-nucleolar condensates recognized by the Hsp70 co-chaperone Sis1/DnaJB6. oRP condensates are liquid-like in cell-free lysate but solidify upon depletion of Sis1 or inhibition of Hsp70. When cells recover from heat shock, oRP condensates disperse in a Sis1- and Hsp70-dependent manner, and the oRP constituents are incorporated into functional ribosomes in the cytosol, enabling cells to efficiently resume growth. Preserving biomolecules in reversible condensates-like mRNAs in cytosolic stress granules and oRPs at the nucleolar periphery-may be a primary function of the Hsp70 chaperone system.
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Affiliation(s)
- Asif Ali
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.
| | - Rania Garde
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
| | - Olivia C Schaffer
- Pritzker School for Molecular Engineering, University of Chicago, Chicago, IL, USA
| | - Jared A M Bard
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Kabir Husain
- Department of Physics, University of Chicago, Chicago, IL, USA
| | - Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, IL, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
| | - Kathleen A Davis
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Sofia Luengo-Woods
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Maya G Igarashi
- Graduate Program in Biophysical Sciences, University of Chicago, Chicago, IL, USA
| | - D Allan Drummond
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA
- Department of Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA
| | - Allison H Squires
- Pritzker School for Molecular Engineering, University of Chicago, Chicago, IL, USA
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.
- Institute for Biophysical Dynamics, University of Chicago, Chicago, IL, USA.
- Center for Physics of Evolving Systems, University of Chicago, Chicago, IL, USA.
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18
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Ciccarelli M, Masser AE, Kaimal JM, Planells J, Andréasson C. Genetic inactivation of essential HSF1 reveals an isolated transcriptional stress response selectively induced by protein misfolding. Mol Biol Cell 2023; 34:ar101. [PMID: 37467033 PMCID: PMC10551698 DOI: 10.1091/mbc.e23-05-0153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 07/06/2023] [Accepted: 07/12/2023] [Indexed: 07/20/2023] Open
Abstract
Heat Shock Factor 1 (Hsf1) in yeast drives the basal transcription of key proteostasis factors and its activity is induced as part of the core heat shock response. Exploring Hsf1 specific functions has been challenging due to the essential nature of the HSF1 gene and the extensive overlap of target promoters with environmental stress response (ESR) transcription factors Msn2 and Msn4 (Msn2/4). In this study, we constructed a viable hsf1∆ strain by replacing the HSF1 open reading frame with genes that constitutively express Hsp40, Hsp70, and Hsp90 from Hsf1-independent promoters. Phenotypic analysis showed that the hsf1∆ strain grows slowly, is sensitive to heat as well as protein misfolding and accumulates protein aggregates. Transcriptome analysis revealed that the transcriptional response to protein misfolding induced by azetidine-2-carboxylic acid is fully dependent on Hsf1. In contrast, the hsf1∆ strain responded to heat shock through the ESR. Following HS, Hsf1 and Msn2/4 showed functional compensatory induction with stronger activation of the remaining stress pathway when the other branch was inactivated. Thus, we provide a long-overdue genetic test of the function of Hsf1 in yeast using the novel hsf1∆ construct. Our data highlight that the accumulation of misfolded proteins is uniquely sensed by Hsf1-Hsp70 chaperone titration inducing a highly selective transcriptional stress response.
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Affiliation(s)
- Michela Ciccarelli
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | - Anna E Masser
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | | | - Jordi Planells
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-10691 Stockholm, Sweden
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19
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Ghosh S, Vashisth K, Ghosh S, Han SS, Bhaskar R, Sinha JK. From sleep to cancer to neurodegenerative disease: the crucial role of Hsp70 in maintaining cellular homeostasis and potential therapeutic implications. J Biomol Struct Dyn 2023:1-12. [PMID: 37643058 DOI: 10.1080/07391102.2023.2252509] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Accepted: 08/20/2023] [Indexed: 08/31/2023]
Abstract
Sleep is a fundamental process essential for reparatory and restorative mechanisms in all organisms. Recent research has linked sleep to various pathological conditions, including cancer and neurodegeneration, which are associated with various molecular changes in different cellular environments. Despite the potential significance of various molecules, the HSPA1A or Hsp70 protein, which has possible connections with sleep and different neuropsychological and pathological disorders, has been explored the least. This paper explores the potential for manipulating and discovering drugs related to the Hsp70 protein to alleviate sleep problems and improve the prognosis for various other health issues. This paper discusses the critical role of Hsp70 in cancer, neurodegeneration, apoptosis, sleep, and its regulation at the structural level through allosteric mechanisms and different substrates. The significant impact of Hsp70's connection to various conditions suggests that existing sleep medicine could be used to improve such conditions, leading to improved outcomes, minimized research costs, and a new direction for current research. Overall, this paper highlights the potential of Hsp70 protein as a key therapeutic target for developing new drugs for the treatment of sleep disorders, cancer, neurodegeneration, and other related pathological conditions. Further research into the molecular mechanisms of Hsp70 regulation and its interactions with other cellular pathways is necessary to develop targeted treatments for these conditions.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Shampa Ghosh
- GloNeuro, Sector 107, Vishwakarma Road, Noida, India
- ICMR - National Institute of Nutrition, Tarnaka, Hyderabad, India
| | | | - Soumya Ghosh
- GloNeuro, Sector 107, Vishwakarma Road, Noida, India
| | - Sung Soo Han
- School of Chemical Engineering, Yeungnam University, Gyeonsang, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
| | - Rakesh Bhaskar
- School of Chemical Engineering, Yeungnam University, Gyeonsang, Republic of Korea
- Research Institute of Cell Culture, Yeungnam University, Gyeongsan, Republic of Korea
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20
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Fink EE, Nanavaty V, Lee BH, Ting AH. Heat shock induces alternative polyadenylation through dynamic DNA methylation-regulated chromatin looping. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.25.554792. [PMID: 37662379 PMCID: PMC10473739 DOI: 10.1101/2023.08.25.554792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Alternative cleavage and polyadenylation (APA) is a gene regulatory mechanism used by cells under stress to upregulate proteostasis-promoting transcripts, but how cells achieve this remains poorly understood. Previously, we elucidated a DNA methylation-regulated APA mechanism, in which gene body DNA methylation enhances distal poly(A) isoform expression by blocking CTCF binding and chromatin loop formation at APA control regions. We hypothesized that DNA methylation-regulated APA is one mechanism cells employ to induce proteostasis-promoting poly(A) isoforms. At the DNAJB6 co-chaperone gene locus, acute heat shock resulted in binding of stress response transcription factors HSF1, ATF6, and YY1 at the APA control region and an increase in the expression of the proximal poly(A) isoform known to prevent protein aggregation. Furthermore, TET1 was recruited to rapidly demethylate DNA, facilitating CTCF binding and chromatin loop formation, thereby reinforcing preferential proximal poly(A) isoform expression. As cells recovered, the transcription factors vacated the APA control region, and DNMT1 was recruited to remethylate the region. This process resolved chromatin looping and reset the poly(A) isoform expression pattern. Our findings unveil an epigenetic mechanism enabling cells to dynamically modulate poly(A) isoforms in response to stress while shedding light on the interplay between DNA methylation, transcription factors, and chromatin looping.
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21
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Kik SK, Christopher D, Glauninger H, Hickernell CW, Bard JAM, Ford M, Sosnick TR, Drummond DA. An adaptive biomolecular condensation response is conserved across environmentally divergent species. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.07.28.551061. [PMID: 37546789 PMCID: PMC10402146 DOI: 10.1101/2023.07.28.551061] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/08/2023]
Abstract
Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide an unprecedented view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.
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Affiliation(s)
- Samantha Keyport Kik
- Committee on Genetics, Genomics, and Systems Biology, The University of Chicago, Chicago, IL
| | - Dana Christopher
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | - Hendrik Glauninger
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | | | - Jared A. M. Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
| | | | - Tobin R. Sosnick
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Graduate Program in Biophysical Sciences, The University of Chicago, Chicago, IL
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL
- Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL
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22
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van Oosten-Hawle P. Exploiting inter-tissue stress signaling mechanisms to preserve organismal proteostasis during aging. Front Physiol 2023; 14:1228490. [PMID: 37469564 PMCID: PMC10352849 DOI: 10.3389/fphys.2023.1228490] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 06/26/2023] [Indexed: 07/21/2023] Open
Abstract
Aging results in a decline of cellular proteostasis capacity which culminates in the accumulation of phototoxic material, causing the onset of age-related maladies and ultimately cell death. Mechanisms that regulate proteostasis such as cellular stress response pathways sense disturbances in the proteome. They are activated to increase the expression of protein quality control components that counteract cellular damage. Utilizing invertebrate model organisms such as Caenorhabditis elegans, it has become increasingly evident that the regulation of proteostasis and the activation of cellular stress responses is not a cell autonomous process. In animals, stress responses are orchestrated by signals coming from other tissues, including the nervous system, the intestine and the germline that have a profound impact on determining the aging process. Genetic pathways discovered in C. elegans that facilitate cell nonautonomous regulation of stress responses are providing an exciting feeding ground for new interventions. In this review I will discuss cell nonautonomous proteostasis mechanisms and their impact on aging as well as ongoing research and clinical trials that can increase organismal proteostasis to lengthen health- and lifespan.
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23
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Vazquez‐Calvo C, Kohler V, Höög JL, Büttner S, Ott M. Newly imported proteins in mitochondria are particularly sensitive to aggregation. Acta Physiol (Oxf) 2023; 238:e13985. [PMID: 37171464 PMCID: PMC10909475 DOI: 10.1111/apha.13985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/20/2023] [Accepted: 05/09/2023] [Indexed: 05/13/2023]
Abstract
AIM A functional proteome is essential for life and maintained by protein quality control (PQC) systems in the cytosol and organelles. Protein aggregation is an indicator of a decline of PQC linked to aging and disease. Mitochondrial PQC is critical to maintain mitochondrial function and thus cellular fitness. How mitochondria handle aggregated proteins is not well understood. Here we tested how the metabolic status impacts on formation and clearance of aggregates within yeast mitochondria and assessed which proteins are particularly sensitive to denaturation. METHODS Confocal microscopy, electron microscopy, immunoblotting and genetics were applied to assess mitochondrial aggregate handling in response to heat shock and ethanol using the mitochondrial disaggregase Hsp78 as a marker for protein aggregates. RESULTS We show that aggregates formed upon heat or ethanol stress with different dynamics depending on the metabolic state. While fermenting cells displayed numerous small aggregates that coalesced into one large foci that was resistant to clearance, respiring cells showed less aggregates and cleared these aggregates more efficiently. Acute inhibition of mitochondrial translation had no effect, while preventing protein import into mitochondria by inhibition of cytosolic translation prevented aggregate formation. CONCLUSION Collectively, our data show that the metabolic state of the cells impacts the dynamics of aggregate formation and clearance, and that mainly newly imported and not yet assembled proteins are prone to form aggregates. Because mitochondrial functionality is crucial for cellular metabolism, these results highlight the importance of efficient protein biogenesis to maintain the mitochondrial proteome operational during metabolic adaptations and cellular stress.
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Affiliation(s)
- Carmela Vazquez‐Calvo
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Verena Kohler
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
- Institute of Molecular BiosciencesUniversity of GrazGrazAustria
| | - Johanna L. Höög
- Department of Chemistry and Molecular BiologyUniversity of GothenburgGothenburgSweden
| | - Sabrina Büttner
- Department of Molecular Biosciences, The Wenner‐Gren InstituteStockholm UniversityStockholmSweden
| | - Martin Ott
- Department of Biochemistry and BiophysicsStockholm UniversityStockholmSweden
- Department of Medical Biochemistry and Cell BiologyUniversity of GothenburgGothenburgSweden
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24
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Park D, Yu Y, Kim JH, Lee J, Park J, Hong K, Seo JK, Lim C, Min KT. Suboptimal Mitochondrial Activity Facilitates Nuclear Heat Shock Responses for Proteostasis and Genome Stability. Mol Cells 2023; 46:374-386. [PMID: 37077029 PMCID: PMC10258458 DOI: 10.14348/molcells.2023.2181] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/16/2023] [Accepted: 01/17/2023] [Indexed: 04/21/2023] Open
Abstract
Thermal stress induces dynamic changes in nuclear proteins and relevant physiology as a part of the heat shock response (HSR). However, how the nuclear HSR is fine-tuned for cellular homeostasis remains elusive. Here, we show that mitochondrial activity plays an important role in nuclear proteostasis and genome stability through two distinct HSR pathways. Mitochondrial ribosomal protein (MRP) depletion enhanced the nucleolar granule formation of HSP70 and ubiquitin during HSR while facilitating the recovery of damaged nuclear proteins and impaired nucleocytoplasmic transport. Treatment of the mitochondrial proton gradient uncoupler masked MRP-depletion effects, implicating oxidative phosphorylation in these nuclear HSRs. On the other hand, MRP depletion and a reactive oxygen species (ROS) scavenger non-additively decreased mitochondrial ROS generation during HSR, thereby protecting the nuclear genome from DNA damage. These results suggest that suboptimal mitochondrial activity sustains nuclear homeostasis under cellular stress, providing plausible evidence for optimal endosymbiotic evolution via mitochondria-to-nuclear communication.
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Affiliation(s)
- Dongkeun Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Youngim Yu
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Ji-hyung Kim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jongbin Lee
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jongmin Park
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Kido Hong
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Jeong-Kon Seo
- UNIST Central Research Facilities (UCRF), Ulsan National Institute of Science and Technology, Ulsan 44919, Korea
| | - Chunghun Lim
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
| | - Kyung-Tai Min
- Department of Biological Sciences, Ulsan National Institute of Science and Technology (UNIST), Ulsan 44919, Korea
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25
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Sutandy FXR, Gößner I, Tascher G, Münch C. A cytosolic surveillance mechanism activates the mitochondrial UPR. Nature 2023:10.1038/s41586-023-06142-0. [PMID: 37286597 DOI: 10.1038/s41586-023-06142-0] [Citation(s) in RCA: 43] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 04/27/2023] [Indexed: 06/09/2023]
Abstract
The mitochondrial unfolded protein response (UPRmt) is essential to safeguard mitochondria from proteotoxic damage by activating a dedicated transcriptional response in the nucleus to restore proteostasis1,2. Yet, it remains unclear how the information on mitochondria misfolding stress (MMS) is signalled to the nucleus as part of the human UPRmt (refs. 3,4). Here, we show that UPRmt signalling is driven by the release of two individual signals in the cytosol-mitochondrial reactive oxygen species (mtROS) and accumulation of mitochondrial protein precursors in the cytosol (c-mtProt). Combining proteomics and genetic approaches, we identified that MMS causes the release of mtROS into the cytosol. In parallel, MMS leads to mitochondrial protein import defects causing c-mtProt accumulation. Both signals integrate to activate the UPRmt; released mtROS oxidize the cytosolic HSP40 protein DNAJA1, which leads to enhanced recruitment of cytosolic HSP70 to c-mtProt. Consequently, HSP70 releases HSF1, which translocates to the nucleus and activates transcription of UPRmt genes. Together, we identify a highly controlled cytosolic surveillance mechanism that integrates independent mitochondrial stress signals to initiate the UPRmt. These observations reveal a link between mitochondrial and cytosolic proteostasis and provide molecular insight into UPRmt signalling in human cells.
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Affiliation(s)
- F X Reymond Sutandy
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Ines Gößner
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Georg Tascher
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany
| | - Christian Münch
- Institute of Biochemistry II, Faculty of Medicine, Goethe University Frankfurt, Frankfurt am Main, Germany.
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26
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Josefson R, Kumar N, Hao X, Liu B, Nyström T. The GET pathway is a major bottleneck for maintaining proteostasis in Saccharomyces cerevisiae. Sci Rep 2023; 13:9285. [PMID: 37286562 DOI: 10.1038/s41598-023-35666-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 05/18/2023] [Indexed: 06/09/2023] Open
Abstract
A hallmark of aging in a variety of organisms is a breakdown of proteostasis and an ensuing accumulation of protein aggregates and inclusions. However, it is not clear if the proteostasis network suffers from a uniform breakdown during aging or if some distinct components act as bottlenecks especially sensitive to functional decline. Here, we report on a genome-wide, unbiased, screen for single genes in young cells of budding yeast required to keep the proteome aggregate-free under non-stress conditions as a means to identify potential proteostasis bottlenecks. We found that the GET pathway, required for the insertion of tail-anchored (TA) membrane proteins in the endoplasmic reticulum, is such a bottleneck as single mutations in either GET3, GET2 or GET1 caused accumulation of cytosolic Hsp104- and mitochondria-associated aggregates in nearly all cells when growing at 30 °C (non-stress condition). Further, results generated by a second screen identifying proteins aggregating in GET mutants and analyzing the behavior of cytosolic reporters of misfolding, suggest that there is a general collapse in proteostasis in GET mutants that affects other proteins than TA proteins.
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Affiliation(s)
- Rebecca Josefson
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Navinder Kumar
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Xinxin Hao
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Beidong Liu
- Department of Chemistry and Molecular Biology, Faculty of Science, University of Gothenburg, Gothenburg, Sweden
| | - Thomas Nyström
- Department of Microbiology and Immunology, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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27
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Garde R, Singh A, Ali A, Pincus D. Transcriptional regulation of Sis1 promotes fitness but not feedback in the heat shock response. eLife 2023; 12:e79444. [PMID: 37158601 PMCID: PMC10191621 DOI: 10.7554/elife.79444] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Accepted: 04/26/2023] [Indexed: 05/10/2023] Open
Abstract
The heat shock response (HSR) controls expression of molecular chaperones to maintain protein homeostasis. Previously, we proposed a feedback loop model of the HSR in which heat-denatured proteins sequester the chaperone Hsp70 to activate the HSR, and subsequent induction of Hsp70 deactivates the HSR (Krakowiak et al., 2018; Zheng et al., 2016). However, recent work has implicated newly synthesized proteins (NSPs) - rather than unfolded mature proteins - and the Hsp70 co-chaperone Sis1 in HSR regulation, yet their contributions to HSR dynamics have not been determined. Here, we generate a new mathematical model that incorporates NSPs and Sis1 into the HSR activation mechanism, and we perform genetic decoupling and pulse-labeling experiments to demonstrate that Sis1 induction is dispensable for HSR deactivation. Rather than providing negative feedback to the HSR, transcriptional regulation of Sis1 by Hsf1 promotes fitness by coordinating stress granules and carbon metabolism. These results support an overall model in which NSPs signal the HSR by sequestering Sis1 and Hsp70, while induction of Hsp70 - but not Sis1 - attenuates the response.
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Affiliation(s)
- Rania Garde
- Department of Molecular Genetics and Cell Biology, University of ChicagoChicagoUnited States
- Committee on Genetics, Genomics, and Systems Biology, University of ChicagoChicagoUnited States
| | - Abhyudai Singh
- Department of Electrical and Computer Engineering, University of DelawareNewarkUnited States
- Department of Biomedical Engineering, University of DelawareNewarkUnited States
- Department of Mathematical Sciences, University of DelawareNewarkUnited States
- Center for Bioinformatics and Computational Biology, University of DelawareNewarkUnited States
| | - Asif Ali
- Department of Molecular Genetics and Cell Biology, University of ChicagoChicagoUnited States
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of ChicagoChicagoUnited States
- Center for Physics of Evolving Systems, University of ChicagoChicagoUnited States
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28
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HSP70 mediates a crosstalk between the estrogen and the heat shock response pathways. J Biol Chem 2023; 299:102872. [PMID: 36610605 PMCID: PMC9926311 DOI: 10.1016/j.jbc.2023.102872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 12/24/2022] [Accepted: 12/27/2022] [Indexed: 01/06/2023] Open
Abstract
Cells respond to multiple signals from the environment simultaneously, which often creates crosstalk between pathways affecting the capacity to adapt to the changing environment. Chaperones are an important component in the cellular integration of multiple responses to environmental signals, often implicated in negative feedback and inactivation mechanisms. These mechanisms include the stabilization of steroid hormone nuclear receptors in the cytoplasm in the absence of their ligand. Here, we show using immunofluorescence, chromatin immunoprecipitation, and nascent transcripts production that the heat shock protein 70 (HSP70) chaperone plays a central role in a new crosstalk mechanism between the steroid and heat shock response pathways. HSP70-dependent feedback mechanisms are required to inactivate the heat shock factor 1 (HSF1) after activation. Interestingly, a steroid stimulation leads to faster accumulation of HSF1 in inactive foci following heat shock. Our results further show that in the presence of estrogen, HSP70 accumulates at HSF1-regulated noncoding regions, leading to deactivation of HSF1 and the abrogation of the heat shock transcriptional response. Using an HSP70 inhibitor, we demonstrate that the crosstalk between both pathways is dependent on the chaperone activity. These results suggest that HSP70 availability is a key determinant in the transcriptional integration of multiple external signals. Overall, these results offer a better understanding of the crosstalk between the heat shock and steroid responses, which are salient in neurodegenerative disorders and cancers.
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29
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Jawed A, Ho CT, Grousl T, Shrivastava A, Ruppert T, Bukau B, Mogk A. Balanced activities of Hsp70 and the ubiquitin proteasome system underlie cellular protein homeostasis. Front Mol Biosci 2023; 9:1106477. [PMID: 36660429 PMCID: PMC9845930 DOI: 10.3389/fmolb.2022.1106477] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 12/15/2022] [Indexed: 01/05/2023] Open
Abstract
To counteract proteotoxic stress and cellular aging, protein quality control (PQC) systems rely on the refolding, degradation and sequestration of misfolded proteins. In Saccharomyces cerevisiae the Hsp70 chaperone system plays a central role in protein refolding, while degradation is predominantly executed by the ubiquitin proteasome system (UPS). The sequestrases Hsp42 and Btn2 deposit misfolded proteins in cytosolic and nuclear inclusions, thereby restricting the accessibility of misfolded proteins to Hsp70 and preventing the exhaustion of limited Hsp70 resources. Therefore, in yeast, sequestrase mutants show negative genetic interactions with double mutants lacking the Hsp70 co-chaperone Fes1 and the Hsp104 disaggregase (fes1Δ hsp104Δ, ΔΔ) and suffering from low Hsp70 capacity. Growth of ΔΔbtn2Δ mutants is highly temperature-sensitive and results in proteostasis breakdown at non-permissive temperatures. Here, we probed for the role of the ubiquitin proteasome system in maintaining protein homeostasis in ΔΔbtn2Δ cells, which are affected in two major protein quality control branches. We show that ΔΔbtn2Δ cells induce expression of diverse stress-related pathways including the ubiquitin proteasome system to counteract the proteostasis defects. Ubiquitin proteasome system dependent degradation of the stringent Hsp70 substrate firefly Luciferase in the mutant cells mirrors such compensatory activities of the protein quality control system. Surprisingly however, the enhanced ubiquitin proteasome system activity does not improve but aggravates the growth defects of ΔΔbtn2Δ cells. Reducing ubiquitin proteasome system activity in the mutant by lowering the levels of functional 26S proteasomes improved growth, increased refolding yield of the Luciferase reporter and attenuated global stress responses. Our findings indicate that an imbalance between Hsp70-dependent refolding, sequestration and ubiquitin proteasome system-mediated degradation activities strongly affects protein homeostasis of Hsp70 capacity mutants and contributes to their severe growth phenotypes.
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Affiliation(s)
- Areeb Jawed
- Center for Molecular Biology of Heidelberg University (ZMBH), University of Heidelberg, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Chi-Ting Ho
- Center for Molecular Biology of Heidelberg University (ZMBH), University of Heidelberg, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Tomas Grousl
- Center for Molecular Biology of Heidelberg University (ZMBH), University of Heidelberg, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Aseem Shrivastava
- Center for Molecular Biology of Heidelberg University (ZMBH), University of Heidelberg, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Thomas Ruppert
- Center for Molecular Biology of Heidelberg University (ZMBH), University of Heidelberg, Heidelberg, Germany
| | - Bernd Bukau
- Center for Molecular Biology of Heidelberg University (ZMBH), University of Heidelberg, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany,*Correspondence: Axel Mogk, ; Bernd Bukau,
| | - Axel Mogk
- Center for Molecular Biology of Heidelberg University (ZMBH), University of Heidelberg, Heidelberg, Germany,German Cancer Research Center (DKFZ), Heidelberg, Germany,*Correspondence: Axel Mogk, ; Bernd Bukau,
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30
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Tiwari S, Fauvet B, Assenza S, De Los Rios P, Goloubinoff P. A fluorescent multi-domain protein reveals the unfolding mechanism of Hsp70. Nat Chem Biol 2023; 19:198-205. [PMID: 36266349 PMCID: PMC9889267 DOI: 10.1038/s41589-022-01162-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 09/06/2022] [Indexed: 02/04/2023]
Abstract
Detailed understanding of the mechanism by which Hsp70 chaperones protect cells against protein aggregation is hampered by the lack of a comprehensive characterization of the aggregates, which are typically heterogeneous. Here we designed a reporter chaperone substrate, MLucV, composed of a stress-labile luciferase flanked by stress-resistant fluorescent domains, which upon denaturation formed a discrete population of small aggregates. Combining Förster resonance energy transfer and enzymatic activity measurements provided unprecedented details on the aggregated, unfolded, Hsp70-bound and native MLucV conformations. The Hsp70 mechanism first involved ATP-fueled disaggregation and unfolding of the stable pre-aggregated substrate, which stretched MLucV beyond simply unfolded conformations, followed by native refolding. The ATP-fueled unfolding and refolding action of Hsp70 on MLucV aggregates could accumulate native MLucV species under elevated denaturing temperatures highly adverse to the native state. These results unambiguously exclude binding and preventing of aggregation from the non-equilibrium mechanism by which Hsp70 converts stable aggregates into metastable native proteins.
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Affiliation(s)
- Satyam Tiwari
- grid.9851.50000 0001 2165 4204Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland ,grid.5333.60000000121839049Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland
| | - Bruno Fauvet
- grid.5333.60000000121839049Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland
| | - Salvatore Assenza
- grid.5515.40000000119578126Departamento de Física Teórica de la Materia Condensada, Universidad Autónoma de Madrid, Madrid, Spain ,grid.5515.40000000119578126Condensed Matter Physics Center (IFIMAC), Universidad Autónoma de Madrid, Madrid, Spain ,grid.5515.40000000119578126Instituto Nicolás Cabrera, Universidad Autónoma de Madrid, Madrid, Spain
| | - Paolo De Los Rios
- Institute of Physics, School of Basic Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland. .,Institute of Bioengineering, School of Life Sciences, École Polytechnique Fédérale de Lausanne - EPFL, Lausanne, Switzerland.
| | - Pierre Goloubinoff
- Department of Plant Molecular Biology, Faculty of Biology and Medicine, University of Lausanne, Lausanne, Switzerland. .,School of Plant Sciences and Food Security, Tel-Aviv University, Tel Aviv, Israel.
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31
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Liu AY, Minetti CA, Remeta DP, Breslauer KJ, Chen KY. HSF1, Aging, and Neurodegeneration. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2023; 1409:23-49. [PMID: 35995906 DOI: 10.1007/5584_2022_733] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Heat shock factor 1 (HSF1) is a master transcription regulator that mediates the induction of heat shock protein chaperones for quality control (QC) of the proteome and maintenance of proteostasis as a protective mechanism in response to stress. Research in this particular area has accelerated dramatically over the past three decades following successful isolation, cloning, and characterization of HSF1. The intricate multi-protein complexes and transcriptional activation orchestrated by HSF1 are fundamental processes within the cellular QC machinery. Our primary focus is on the regulation and function of HSF1 in aging and neurodegenerative diseases (ND) which represent physiological and pathological states of dysfunction in protein QC. This chapter presents an overview of HSF1 structural, functional, and energetic properties in healthy cells while addressing the deterioration of HSF1 function viz-à-viz age-dependent and neuron-specific vulnerability to ND. We discuss the structural domains of HSF1 with emphasis on the intrinsically disordered regions and note that disease proteins associated with ND are often structurally disordered and exquisitely sensitive to changes in cellular environment as may occur during aging. We propose a hypothesis that age-dependent changes of the intrinsically disordered proteome likely hold answers to understand many of the functional, structural, and organizational changes of proteins and signaling pathways in aging - dysfunction of HSF1 and accumulation of disease protein aggregates in ND included.Structured AbstractsIntroduction: Heat shock factor 1 (HSF1) is a master transcription regulator that mediates the induction of heat shock protein chaperones for quality control (QC) of the proteome as a cyto-protective mechanism in response to stress. There is cumulative evidence of age-related deterioration of this QC mechanism that contributes to disease vulnerability. OBJECTIVES Herein we discuss the regulation and function of HSF1 as they relate to the pathophysiological changes of protein quality control in aging and neurodegenerative diseases (ND). METHODS We present an overview of HSF1 structural, functional, and energetic properties in healthy cells while addressing the deterioration of HSF1 function vis-à-vis age-dependent and neuron-specific vulnerability to neurodegenerative diseases. RESULTS We examine the impact of intrinsically disordered regions on the function of HSF1 and note that proteins associated with neurodegeneration are natively unstructured and exquisitely sensitive to changes in cellular environment as may occur during aging. CONCLUSIONS We put forth a hypothesis that age-dependent changes of the intrinsically disordered proteome hold answers to understanding many of the functional, structural, and organizational changes of proteins - dysfunction of HSF1 in aging and appearance of disease protein aggregates in neurodegenerative diseases included.
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Affiliation(s)
- Alice Y Liu
- Department of Cell Biology and Neuroscience, Rutgers The State University of New Jersey, Piscataway, NJ, USA.
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.
| | - Conceição A Minetti
- Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, NJ, USA
| | - David P Remeta
- Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, NJ, USA
| | - Kenneth J Breslauer
- Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, NJ, USA
| | - Kuang Yu Chen
- Department of Chemistry and Chemical Biology, Rutgers The State University of New Jersey, Piscataway, NJ, USA
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Chowdhary S, Kainth AS, Paracha S, Gross DS, Pincus D. Inducible transcriptional condensates drive 3D genome reorganization in the heat shock response. Mol Cell 2022; 82:4386-4399.e7. [PMID: 36327976 PMCID: PMC9701134 DOI: 10.1016/j.molcel.2022.10.013] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 08/28/2022] [Accepted: 10/10/2022] [Indexed: 11/12/2022]
Abstract
Mammalian developmental and disease-associated genes concentrate large quantities of the transcriptional machinery by forming membrane-less compartments known as transcriptional condensates. However, it is unknown whether these structures are evolutionarily conserved or involved in 3D genome reorganization. Here, we identify inducible transcriptional condensates in the yeast heat shock response (HSR). HSR condensates are biophysically dynamic spatiotemporal clusters of the sequence-specific transcription factor heat shock factor 1 (Hsf1) with Mediator and RNA Pol II. Uniquely, HSR condensates drive the coalescence of multiple Hsf1 target genes, even those located on different chromosomes. Binding of the chaperone Hsp70 to a site on Hsf1 represses clustering, whereas an intrinsically disordered region on Hsf1 promotes condensate formation and intergenic interactions. Mutation of both Hsf1 determinants reprograms HSR condensates to become constitutively active without intergenic coalescence, which comes at a fitness cost. These results suggest that transcriptional condensates are ancient and flexible compartments of eukaryotic gene control.
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Affiliation(s)
- Surabhi Chowdhary
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - Amoldeep S Kainth
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA
| | - Sarah Paracha
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, LA 71130, USA.
| | - David Pincus
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL 60637, USA; Center for Physics of Evolving Systems, University of Chicago, Chicago, IL 60637, USA.
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Meduri R, Rubio LS, Mohajan S, Gross DS. Phase-separation antagonists potently inhibit transcription and broadly increase nucleosome density. J Biol Chem 2022; 298:102365. [PMID: 35963432 PMCID: PMC9486037 DOI: 10.1016/j.jbc.2022.102365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 07/25/2022] [Accepted: 07/26/2022] [Indexed: 11/24/2022] Open
Abstract
Biomolecular condensates are self-organized membraneless bodies involved in many critical cellular activities, including ribosome biogenesis, protein synthesis, and gene transcription. Aliphatic alcohols are commonly used to study biomolecular condensates, but their effects on transcription are unclear. Here, we explore the impact of the aliphatic dialcohol, 1,6-hexanediol (1,6-HD), on Pol II transcription and nucleosome occupancy in budding yeast. As expected, 1,6-HD, a reagent effective in disrupting biomolecular condensates, strongly suppressed the thermal stress-induced transcription of Heat Shock Factor 1-regulated genes that have previously been shown to physically interact and coalesce into intranuclear condensates. Surprisingly, the isomeric dialcohol, 2,5-HD, typically used as a negative control, abrogated Heat Shock Factor 1-target gene transcription under the same conditions. Each reagent also abolished the transcription of genes that do not detectably coalesce, including Msn2/Msn4-regulated heat-inducible genes and constitutively expressed housekeeping genes. Thus, at elevated temperature (39 °C), HDs potently inhibit the transcription of disparate genes and as demonstrated by chromatin immunoprecipitation do so by abolishing occupancy of RNA polymerase in chromatin. Concurrently, histone H3 density increased at least twofold within all gene coding and regulatory regions examined, including quiescent euchromatic loci, silent heterochromatic loci, and Pol III-transcribed loci. Our results offer a caveat for the use of HDs in studying the role of condensates in transcriptional control and provide evidence that exposure to these reagents elicits a widespread increase in nucleosome density and a concomitant loss of both Pol II and Pol III transcription.
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Affiliation(s)
- Rajyalakshmi Meduri
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| | - Linda S Rubio
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| | - Suman Mohajan
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA
| | - David S Gross
- Department of Biochemistry and Molecular Biology, Louisiana State University Health Sciences Center, Shreveport, Louisiana, USA.
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34
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Nitika, Zheng B, Ruan L, Kline JT, Omkar S, Sikora J, Texeira Torres M, Wang Y, Takakuwa JE, Huguet R, Klemm C, Segarra VA, Winters MJ, Pryciak PM, Thorpe PH, Tatebayashi K, Li R, Fornelli L, Truman AW. Comprehensive characterization of the Hsp70 interactome reveals novel client proteins and interactions mediated by posttranslational modifications. PLoS Biol 2022; 20:e3001839. [PMID: 36269765 PMCID: PMC9629621 DOI: 10.1371/journal.pbio.3001839] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/02/2022] [Accepted: 09/21/2022] [Indexed: 01/06/2023] Open
Abstract
Hsp70 interactions are critical for cellular viability and the response to stress. Previous attempts to characterize Hsp70 interactions have been limited by their transient nature and the inability of current technologies to distinguish direct versus bridged interactions. We report the novel use of cross-linking mass spectrometry (XL-MS) to comprehensively characterize the Saccharomyces cerevisiae (budding yeast) Hsp70 protein interactome. Using this approach, we have gained fundamental new insights into Hsp70 function, including definitive evidence of Hsp70 self-association as well as multipoint interaction with its client proteins. In addition to identifying a novel set of direct Hsp70 interactors that can be used to probe chaperone function in cells, we have also identified a suite of posttranslational modification (PTM)-associated Hsp70 interactions. The majority of these PTMs have not been previously reported and appear to be critical in the regulation of client protein function. These data indicate that one of the mechanisms by which PTMs contribute to protein function is by facilitating interaction with chaperones. Taken together, we propose that XL-MS analysis of chaperone complexes may be used as a unique way to identify biologically important PTMs on client proteins.
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Affiliation(s)
- Nitika
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Bo Zheng
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Linhao Ruan
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jake T. Kline
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Siddhi Omkar
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Jacek Sikora
- Department of Molecular Biosciences, Department of Chemistry, and the Feinberg School of Medicine, Northwestern University, Evanston, Illinois, United States America
| | - Mara Texeira Torres
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Yuhao Wang
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
| | - Jade E. Takakuwa
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
| | - Romain Huguet
- Thermo Scientific, San Jose, California, United States America
| | - Cinzia Klemm
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Verónica A. Segarra
- Departments of Biological Sciences and Chemistry, Goucher College, Baltimore, Maryland, United States America
| | - Matthew J. Winters
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter M. Pryciak
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, Massachusetts, United States America
| | - Peter H. Thorpe
- School of Biological and Chemical Sciences, Queen Mary University, London, United Kingdom
| | - Kazuo Tatebayashi
- Laboratory of Molecular Genetics, Frontier Research Unit, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Rong Li
- Center for Cell Dynamics and Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Biochemistry, Cellular and Molecular Biology (BCMB) Graduate Program, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States America
- Mechanobiology Institute and Department of Biological Sciences, National University of Singapore, Singapore
- Department of Chemical and Biomolecular Engineering, Whiting School of Engineering, Johns Hopkins University, Baltimore, Maryland, United States America
| | - Luca Fornelli
- Department of Biology, University of Oklahoma, Norman, Oklahoma, United States America
| | - Andrew W. Truman
- Department of Biological Sciences, The University of North Carolina at Charlotte, Charlotte, North Carolina, United States America
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35
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Cyran AM, Zhitkovich A. HIF1, HSF1, and NRF2: Oxidant-Responsive Trio Raising Cellular Defenses and Engaging Immune System. Chem Res Toxicol 2022; 35:1690-1700. [PMID: 35948068 PMCID: PMC9580020 DOI: 10.1021/acs.chemrestox.2c00131] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
![]()
Cellular homeostasis is continuously challenged by damage
from
reactive oxygen species (ROS) and numerous reactive electrophiles.
Human cells contain various protective systems that are upregulated
in response to protein damage by electrophilic or oxidative stress.
In addition to the NRF2-mediated antioxidant response, ROS and reactive
electrophiles also activate HSF1 and HIF1 that control heat shock
response and hypoxia response, respectively. Here, we review chemical
and biological mechanisms of activation of these three transcription
factors by ROS/reactive toxicants and the roles of their gene expression
programs in antioxidant protection. We also discuss how NRF2, HSF1,
and HIF1 responses establish multilayered cellular defenses consisting
of largely nonoverlapping programs, which mitigates limitations of
each response. Some innate immunity links in these stress responses
help eliminate damaged cells, whereas others suppress deleterious
inflammation in normal tissues but inhibit immunosurveillance of cancer
cells in tumors.
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Affiliation(s)
- Anna M Cyran
- Department of Pathology and Laboratory Medicine, Legorreta Cancer Center, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
| | - Anatoly Zhitkovich
- Department of Pathology and Laboratory Medicine, Legorreta Cancer Center, Brown University, 70 Ship Street, Providence, Rhode Island 02912, United States
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36
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Response and regulatory mechanisms of heat resistance in pathogenic fungi. Appl Microbiol Biotechnol 2022; 106:5415-5431. [PMID: 35941254 PMCID: PMC9360699 DOI: 10.1007/s00253-022-12119-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 08/01/2022] [Accepted: 08/02/2022] [Indexed: 12/03/2022]
Abstract
Abstract Both the increasing environmental temperature in nature and the defensive body temperature response to pathogenic fungi during mammalian infection cause heat stress during the fungal existence, reproduction, and pathogenic infection. To adapt and respond to the changing environment, fungi initiate a series of actions through a perfect thermal response system, conservative signaling pathways, corresponding transcriptional regulatory system, corresponding physiological and biochemical processes, and phenotypic changes. However, until now, accurate response and regulatory mechanisms have remained a challenge. Additionally, at present, the latest research progress on the heat resistance mechanism of pathogenic fungi has not been summarized. In this review, recent research investigating temperature sensing, transcriptional regulation, and physiological, biochemical, and morphological responses of fungi in response to heat stress is discussed. Moreover, the specificity thermal adaptation mechanism of pathogenic fungi in vivo is highlighted. These data will provide valuable knowledge to further understand the fungal heat adaptation and response mechanism, especially in pathogenic heat-resistant fungi. Key points • Mechanisms of fungal perception of heat pressure are reviewed. • The regulatory mechanism of fungal resistance to heat stress is discussed. • The thermal adaptation mechanism of pathogenic fungi in the human body is highlighted.
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37
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He W, Li X, Xue H, Yang Y, Mencius J, Bai L, Zhang J, Xu J, Wu B, Xue Y, Quan S. Insights into the client protein release mechanism of the ATP-independent chaperone Spy. Nat Commun 2022; 13:2818. [PMID: 35595811 PMCID: PMC9122904 DOI: 10.1038/s41467-022-30499-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Molecular chaperones play a central role in regulating protein homeostasis, and their active forms often contain intrinsically disordered regions (IDRs). However, how IDRs impact chaperone action remains poorly understood. Here, we discover that the disordered N terminus of the prototype chaperone Spy facilitates client release. With NMR spectroscopy and molecular dynamics simulations, we find that the N terminus can bind transiently to the client-binding cavity of Spy primarily through electrostatic interactions mediated by the N-terminal D26 residue. This intramolecular interaction results in a dynamic competition of the N terminus with the client for binding to Spy, which promotes client discharge. Our results reveal the mechanism by which Spy releases clients independent of energy input, thus enriching the current knowledge on how ATP-independent chaperones release their clients and highlighting the importance of synergy between IDRs and structural domains in regulating protein function.
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Affiliation(s)
- Wei He
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Xinming Li
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China
| | - Hongjuan Xue
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China
| | - Yuanyuan Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jun Mencius
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Ling Bai
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jiayin Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Jianhe Xu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China
| | - Bin Wu
- National Facility for Protein Science in Shanghai, ZhangJiang Lab, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai, 201210, China.
| | - Yi Xue
- School of Life Sciences, Tsinghua-Peking Joint Center for Life Sciences, Beijing Advanced Innovation Center for Structural Biology, Tsinghua University, 100084, Beijing, China.
| | - Shu Quan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai Collaborative Innovation Center for Biomanufacturing (SCICB), Shanghai, 200237, China. .,Shanghai Frontiers Science Center of Optogenetic Techniques for Cell Metabolism, East China University of Science and Technology, Shanghai, 200237, China.
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38
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Kose S, Imai K, Watanabe A, Nakai A, Suzuki Y, Imamoto N. Lack of Hikeshi activates HSF1 activity under normal conditions and disturbs the heat-shock response. Life Sci Alliance 2022; 5:5/9/e202101241. [PMID: 35580988 PMCID: PMC9113944 DOI: 10.26508/lsa.202101241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 04/27/2022] [Accepted: 04/27/2022] [Indexed: 01/09/2023] Open
Abstract
Hikeshi mediates the nuclear import of the molecular chaperone HSP70 under heat-shock (acute heat stress) conditions, which is crucial for recovery from cellular damage. The cytoplasmic function of HSP70 is well studied, but its nuclear roles, particularly under nonstressed conditions, remain obscure. Here, we show that Hikeshi regulates the nucleocytoplasmic distribution of HSP70 not only under heat-shock conditions but also under nonstressed conditions. Nuclear HSP70 affects the transcriptional activity of HSF1 and nuclear proteostasis under nonstressed conditions. Depletion of Hikeshi induces a reduction in nuclear HSP70 and up-regulation of the mRNA expression of genes regulated by HSF1 under nonstressed conditions. In addition, the heat-shock response is impaired in Hikeshi-knockout cells. Our results suggest that HSF1 transcriptional activity is tightly regulated by nuclear HSP70 because nuclear-localized Hsp70 effectively suppresses transcriptional activity in a dose-dependent manner. Furthermore, the cytotoxicity of nuclear pathologic polyglutamine proteins was increased by Hikeshi depletion. Thus, proper nucleocytoplasmic distribution of HSP70, mediated by Hikeshi, is required for nuclear proteostasis and adaptive response to heat shock.
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Affiliation(s)
- Shingo Kose
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan,Correspondence: ;
| | - Kenichiro Imai
- Cellular and Molecular Biotechnology Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Tokyo, Japan
| | - Ai Watanabe
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan
| | - Akira Nakai
- Department of Biochemistry and Molecular Biology, Yamaguchi University School of Medicine, Ube, Japan
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Naoko Imamoto
- Cellular Dynamics Laboratory, RIKEN Cluster for Pioneering Research, Wako, Japan,Correspondence: ;
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39
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Expression of Huntingtin and TDP-43 Derivatives in Fission Yeast Can Cause Both Beneficial and Toxic Effects. Int J Mol Sci 2022; 23:ijms23073950. [PMID: 35409310 PMCID: PMC8999813 DOI: 10.3390/ijms23073950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 03/29/2022] [Accepted: 03/30/2022] [Indexed: 11/16/2022] Open
Abstract
Many neurodegenerative disorders display protein aggregation as a hallmark, Huntingtin and TDP-43 aggregates being characteristic of Huntington disease and amyotrophic lateral sclerosis, respectively. However, whether these aggregates cause the diseases, are secondary by-products, or even have protective effects, is a matter of debate. Mutations in both human proteins can modulate the structure, number and type of aggregates, as well as their toxicity. To study the role of protein aggregates in cellular fitness, we have expressed in a highly tractable unicellular model different variants of Huntingtin and TDP-43. They each display specific patterns of aggregation and toxicity, even though in both cases proteins have to be very highly expressed to affect cell fitness. The aggregation properties of Huntingtin, but not of TDP-43, are affected by chaperones such as Hsp104 and the Hsp40 couple Mas5, suggesting that the TDP-43, but not Huntingtin, derivatives have intrinsic aggregation propensity. Importantly, expression of the aggregating form of Huntingtin causes a significant extension of fission yeast lifespan, probably as a consequence of kidnapping chaperones required for maintaining stress responses off. Our study demonstrates that in general these prion-like proteins do not cause toxicity under normal conditions, and in fact they can protect cells through indirect mechanisms which up-regulate cellular defense pathways.
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40
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Yoo H, Bard JA, Pilipenko E, Drummond DA. Chaperones directly and efficiently disperse stress-triggered biomolecular condensates. Mol Cell 2022; 82:741-755.e11. [PMID: 35148816 PMCID: PMC8857057 DOI: 10.1016/j.molcel.2022.01.005] [Citation(s) in RCA: 51] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 09/30/2021] [Accepted: 01/06/2022] [Indexed: 12/28/2022]
Abstract
Stresses such as heat shock trigger the formation of protein aggregates and the induction of a disaggregation system composed of molecular chaperones. Recent work reveals that several cases of apparent heat-induced aggregation, long thought to be the result of toxic misfolding, instead reflect evolved, adaptive biomolecular condensation, with chaperone activity contributing to condensate regulation. Here we show that the yeast disaggregation system directly disperses heat-induced biomolecular condensates of endogenous poly(A)-binding protein (Pab1) orders of magnitude more rapidly than aggregates of the most commonly used misfolded model substrate, firefly luciferase. Beyond its efficiency, heat-induced condensate dispersal differs from heat-induced aggregate dispersal in its molecular requirements and mechanistic behavior. Our work establishes a bona fide endogenous heat-induced substrate for long-studied heat shock proteins, isolates a specific example of chaperone regulation of condensates, and underscores needed expansion of the proteotoxic interpretation of the heat shock response to encompass adaptive, chaperone-mediated regulation.
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Affiliation(s)
- Haneul Yoo
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Jared A.M. Bard
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - Evgeny Pilipenko
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA
| | - D. Allan Drummond
- Department of Biochemistry and Molecular Biology, The University of Chicago, Chicago, IL, 60637, USA,Department of Medicine, Section of Genetic Medicine, The University of Chicago, Chicago, IL, 60637, USA,Lead Contact,Correspondence: (D.A.D.)
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41
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Martin TG, Delligatti CE, Muntu NA, Stachowski-Doll MJ, Kirk JA. Pharmacological inhibition of BAG3-HSP70 with the proposed cancer therapeutic JG-98 is toxic for cardiomyocytes. J Cell Biochem 2022; 123:128-141. [PMID: 34487557 PMCID: PMC10037808 DOI: 10.1002/jcb.30140] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 07/11/2021] [Accepted: 08/26/2021] [Indexed: 11/06/2022]
Abstract
The co-chaperone Bcl2-associated athanogene-3 (BAG3) maintains cellular protein quality control through the regulation of heat shock protein 70 (HSP70). Cancer cells manipulate BAG3-HSP70-regulated pathways for tumor initiation and proliferation, which has led to the development of promising small molecule therapies, such as JG-98, which inhibit the BAG3-HSP70 interaction and mitigate tumor growth. However, it is not known how these broad therapies impact cardiomyocytes, where the BAG3-HSP70 complex is a key regulator of protein turnover and contractility. Here, we show that JG-98 exposure is toxic in neonatal rat ventricular myocytes (NRVMs). Using immunofluorescence microscopy to assess cell death, we found that apoptosis increased in NRVMs treated with JG-98 doses as low as 10 nM. JG-98 treatment also reduced autophagy flux and altered expression of BAG3 and several binding partners involved in BAG3-dependent autophagy, including SYNPO2 and HSPB8. We next assessed protein half-life with disruption of the BAG3-HSP70 complex by treating with JG-98 in the presence of cycloheximide and found BAG3, HSPB5, and HSPB8 half-lives were reduced, indicating that complex formation with HSP70 is important for their stability. Next, we assessed sarcomere structure using super-resolution microscopy and found that disrupting the interaction with HSP70 leads to sarcomere structural disintegration. To determine whether the effects of JG-98 could be mitigated by pharmacological autophagy induction, we cotreated NRVMs with rapamycin, which partially reduced the extent of apoptosis and sarcomere disarray. Finally, we investigated whether the effects of JG-98 extended to skeletal myocytes using C2C12 myotubes and found again increased apoptosis and reduced autophagic flux. Together, our data suggest that nonspecific targeting of the BAG3-HSP70 complex to treat cancer may be detrimental for cardiac and skeletal myocytes.
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Affiliation(s)
| | | | | | | | - Jonathan A. Kirk
- Corresponding Author: Jonathan A. Kirk, Ph.D., Department of Cell and Molecular Physiology, Loyola University Chicago Stritch School of Medicine, Center for Translational Research, Room 522, 2160 S. First Ave., Maywood, IL 60153, Ph: 708-216-6348,
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42
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Kmiecik SW, Mayer MP. Molecular mechanisms of heat shock factor 1 regulation. Trends Biochem Sci 2021; 47:218-234. [PMID: 34810080 DOI: 10.1016/j.tibs.2021.10.004] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Revised: 10/08/2021] [Accepted: 10/22/2021] [Indexed: 02/06/2023]
Abstract
To thrive and to fulfill their functions, cells need to maintain proteome homeostasis even in the face of adverse environmental conditions or radical restructuring of the proteome during differentiation. At the center of the regulation of proteome homeostasis is an ancient transcriptional mechanism, the so-called heat shock response (HSR), orchestrated in all eukaryotic cells by heat shock transcription factor 1 (Hsf1). As Hsf1 is implicated in aging and several pathologies like cancer and neurodegenerative disorders, understanding the regulation of Hsf1 could open novel therapeutic opportunities. In this review, we discuss the regulation of Hsf1's transcriptional activity by multiple layers of control circuits involving Hsf1 synthesis and degradation, conformational rearrangements and post-translational modifications (PTMs), and molecular chaperones in negative feedback loops.
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Affiliation(s)
- Szymon W Kmiecik
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH-Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany.
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43
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Pinho BR, Almeida LM, Duchen MR, Oliveira JMA. Allosteric activation of Hsp70 reduces mutant huntingtin levels, the clustering of N-terminal fragments, and their nuclear accumulation. Life Sci 2021; 285:120009. [PMID: 34600937 DOI: 10.1016/j.lfs.2021.120009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 01/09/2023]
Abstract
AIMS Huntington's disease (HD) is caused by a mutant huntingtin protein that misfolds, yields toxic N-terminal fragments, aggregates, and disrupts proteostasis. The Hsp70 chaperone is a potential therapeutic target as it prevents proteotoxicity by favouring protein folding, disaggregation, or degradation. We tested the hypothesis that allosteric Hsp70 activation with a pharmacological mimetic of the Hsp70 co-chaperone Hip, YM-1, could modulate huntingtin proteostasis. MAIN METHODS We used HD cell models expressing either N-terminal or full-length huntingtin. Using single-cell analysis we studied huntingtin aggregation in different cellular compartments by fluorescence microscopy. Protein interaction was evaluated by immunoprecipitation, while protein levels were quantified by immunofluorescence and western-blot. KEY FINDINGS N-terminal huntingtin interacted with Hsp70 and increased its levels. Treatment with YM-1 reduced N-terminal huntingtin clustering and nuclear aggregation. Full-length mutant huntingtin also interacted with Hsp70, and treatment with YM-1 reduced huntingtin levels when combined with Hsp70 induction by heat shock. Mechanistically, YM-1 increases the Hsp70 affinity for substrates, promoting their proteasomal degradation. Consistently, YM-1 reduced the levels of ubiquitinated proteins. Interestingly, YM-1 accumulated in mitochondria, interfered with its Hsp70 isoform involved in protein import, and increased NRF1 levels, a regulator of proteasome genes. We thus suggest that YM-1 may trigger the coordination of mitochondrial and cytosolic proteostasis, enhancing protein degradation. SIGNIFICANCE Our findings show that the strategy of allosteric Hsp70 activation holds potential for HD. While drug efficacy may be limited to tissues with elevated Hsp70, combined therapies with Hsp70 elevating strategies could harness the full potential of allosteric Hsp70 activators for HD.
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Affiliation(s)
- Brígida R Pinho
- UCIBIO-REQUIMTE - Applied Molecular Biosciences Unit, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Portugal.
| | - Liliana M Almeida
- UCIBIO-REQUIMTE - Applied Molecular Biosciences Unit, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Portugal
| | - Michael R Duchen
- Department of Cell and Developmental Biology, University College London, London WC1E 6BT, UK; Consortium for Mitochondrial Research (CfMR), University College London, Gower Street, WC1E 6BT London, UK
| | - Jorge M A Oliveira
- UCIBIO-REQUIMTE - Applied Molecular Biosciences Unit, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Portugal; Associate Laboratory i4HB - Institute for Health and Bioeconomy, Department of Drug Sciences, Faculty of Pharmacy, University of Porto, Portugal; Consortium for Mitochondrial Research (CfMR), University College London, Gower Street, WC1E 6BT London, UK.
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44
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PepFect14 Signaling and Transfection. Methods Mol Biol 2021. [PMID: 34766293 DOI: 10.1007/978-1-0716-1752-6_15] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/23/2023]
Abstract
PepFect14 is a cell-penetrating peptide (CPP) derived from stearylated transportan-10 (strearil-TP10) with which it shares the stearic acid residue on C' terminus and the amino acid sequence except for lysines that in PepFect14 are substituted with ornithines. Being non-proteinogenic amino acids, ornithines make PepFect14 less sensitive to serum proteases and due to its positive charges the CPP can form complexes with negatively charged cargos, such as splice correcting oligonucleotides (SCOs), plasmid DNA (pDNA), and proteins. It has been reported that PepFect14/SCO complexes enter the cells mainly through endocytosis, in particular: macopinocitosys and caveolae-mediated endocytosis through the interaction with two receptors of the scavenger receptors class A family (SCARAs). PepFect14 and its complexes trigger the chaperone-mediated autophagy response involving the heat shock protein family (HSP70) whose inhibition leads to an increase of PepFect14 transfection efficacy. Exploiting the interaction between HSP70 and PepFect14 and their ability to form nanoparticle. HSP70 has been delivered in Bomirsky Hamster Melanoma cells (BHM) using PepFect14 of which a protocol is described at the end of this chapter.
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45
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Verma K, Verma M, Chaphalkar A, Chakraborty K. Recent advances in understanding the role of proteostasis. Fac Rev 2021; 10:72. [PMID: 34632458 PMCID: PMC8483240 DOI: 10.12703/r/10-72] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Maintenance of a functional proteome is achieved through the mechanism of proteostasis that involves precise coordination between molecular machineries assisting a protein from its conception to demise. Although each organelle within a cell has its own set of proteostasis machinery, inter-organellar communication and cell non-autonomous signaling bring forth the multidimensional nature of the proteostasis network. Exposure to extrinsic and intrinsic stressors can challenge the proteostasis network, leading to the accumulation of aberrant proteins or a decline in the proteostasis components, as seen during aging and in several diseases. Here, we summarize recent advances in understanding the role of proteostasis and its regulation in aging and disease, including monogenetic and infectious diseases. We highlight some of the emerging as well as unresolved questions in proteostasis that need to be addressed to overcome pathologies associated with damaged proteins and to promote healthy aging.
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Affiliation(s)
- Kanika Verma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Monika Verma
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Aseem Chaphalkar
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
| | - Kausik Chakraborty
- CSIR-Institute of Genomics and Integrative Biology, Mathura Road, Delhi, India
- Academy of Scientific and Innovative Research, CSIR-HRDC, Ghaziabad, Uttar Pradesh, India
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Pagliuso DC, Bodas DM, Pasquinelli AE. Recovery from heat shock requires the microRNA pathway in Caenorhabditis elegans. PLoS Genet 2021; 17:e1009734. [PMID: 34351906 PMCID: PMC8370650 DOI: 10.1371/journal.pgen.1009734] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 08/17/2021] [Accepted: 07/22/2021] [Indexed: 12/16/2022] Open
Abstract
The heat shock response (HSR) is a highly conserved cellular process that promotes survival during stress. A hallmark of the HSR is the rapid induction of heat shock proteins (HSPs), such as HSP-70, by transcriptional activation. Once the stress is alleviated, HSPs return to near basal levels through incompletely understood mechanisms. Here, we show that the microRNA pathway acts during heat shock recovery in Caenorhabditis elegans. Depletion of the miRNA Argonaute, Argonaute Like Gene 1 (ALG-1), after an episode of heat shock resulted in decreased survival and perdurance of high hsp-70 levels. We present evidence that regulation of hsp-70 is dependent on miR-85 and sequences in the hsp-70 3’UTR that contain target sites for this miRNA. Regulation of hsp-70 by the miRNA pathway was found to be particularly important during recovery from HS, as animals that lacked miR-85 or its target sites in the hsp-70 3’UTR overexpressed HSP-70 and exhibited reduced viability. In summary, our findings show that down-regulation of hsp-70 by miR-85 after HS promotes survival, highlighting a previously unappreciated role for the miRNA pathway during recovery from stress. In the natural world, organisms constantly face stressful conditions such as oxidative stress, pathogen infection, starvation and heat stress. While many studies have focused on the cellular response to stress, less is known about how gene expression re-sets after the stress has been ameliorated. Here, we show that the microRNA pathway plays a critical role during the recovery phase after an episode of heat shock in the nematode, Caenorhabditis elegans. Elevated temperatures induce high expression of heat shock proteins (HSPs), including HSP-70, that provide protection from the damaging effects of high heat. We found that restoration of basal levels of HSP-70 after heat shock depends on Argonaute Like Gene 1 and miR-85. Moreover, loss of miRNA-mediated repression of HSP-70 results in compromised survival following heat shock. Our study draws attention to the recovery phase of the heat shock response and highlights an important role for the microRNA pathway in re-establishing gene expression programs needed for organismal viability post stress.
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Affiliation(s)
- Delaney C. Pagliuso
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
| | - Devavrat M. Bodas
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Amy E. Pasquinelli
- Division of Biology, University of California, San Diego, La Jolla, California, United States of America
- * E-mail:
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Tye BW, Churchman LS. Hsf1 activation by proteotoxic stress requires concurrent protein synthesis. Mol Biol Cell 2021; 32:1800-1806. [PMID: 34191586 PMCID: PMC8684711 DOI: 10.1091/mbc.e21-01-0014] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Heat shock factor 1 (Hsf1) activation is responsible for increasing the abundance of protein-folding chaperones and degradation machinery in response to proteotoxic conditions that give rise to misfolded or aggregated proteins. Here we systematically explored the link between concurrent protein synthesis and proteotoxic stress in the budding yeast, Saccharomyces cerevisiae. Consistent with prior work, inhibiting protein synthesis before inducing proteotoxic stress prevents Hsf1 activation, which we demonstrated across a broad array of stresses and validate using orthogonal means of blocking protein synthesis. However, other stress-dependent transcription pathways remained activatable under conditions of translation inhibition. Titrating the protein denaturant ethanol to a higher concentration results in Hsf1 activation in the absence of translation, suggesting extreme protein-folding stress can induce proteotoxicity independent of protein synthesis. Furthermore, we demonstrate this connection under physiological conditions where protein synthesis occurs naturally at reduced rates. We find that disrupting the assembly or subcellular localization of newly synthesized proteins is sufficient to activate Hsf1. Thus, new proteins appear to be especially sensitive to proteotoxic conditions, and we propose that their aggregation may represent the bulk of the signal that activates Hsf1 in the wake of these insults.
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Affiliation(s)
- Blake W Tye
- Department of Genetics, Harvard Medical School, Boston, MA 02115.,Program in Chemical Biology, Harvard University, Cambridge, MA 02138
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Kohler V, Andréasson C. Hsp70-mediated quality control: should I stay or should I go? Biol Chem 2021; 401:1233-1248. [PMID: 32745066 DOI: 10.1515/hsz-2020-0187] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Accepted: 07/11/2020] [Indexed: 12/30/2022]
Abstract
Chaperones of the 70 kDa heat shock protein (Hsp70) superfamily are key components of the cellular proteostasis system. Together with its co-chaperones, Hsp70 forms proteostasis subsystems that antagonize protein damage during physiological and stress conditions. This function stems from highly regulated binding and release cycles of protein substrates, which results in a flow of unfolded, partially folded and misfolded species through the Hsp70 subsystem. Specific factors control how Hsp70 makes decisions regarding folding and degradation fates of the substrate proteins. In this review, we summarize how the flow of Hsp70 substrates is controlled in the cell with special emphasis on recent advances regarding substrate release mechanisms.
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Affiliation(s)
- Verena Kohler
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
| | - Claes Andréasson
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, S-106 91 Stockholm, Sweden
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49
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Impact of Hydrogen Peroxide on Protein Synthesis in Yeast. Antioxidants (Basel) 2021; 10:antiox10060952. [PMID: 34204720 PMCID: PMC8231629 DOI: 10.3390/antiox10060952] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 01/03/2023] Open
Abstract
Cells must be able to respond and adapt to different stress conditions to maintain normal function. A common response to stress is the global inhibition of protein synthesis. Protein synthesis is an expensive process consuming much of the cell's energy. Consequently, it must be tightly regulated to conserve resources. One of these stress conditions is oxidative stress, resulting from the accumulation of reactive oxygen species (ROS) mainly produced by the mitochondria but also by other intracellular sources. Cells utilize a variety of antioxidant systems to protect against ROS, directing signaling and adaptation responses at lower levels and/or detoxification as levels increase to preclude the accumulation of damage. In this review, we focus on the role of hydrogen peroxide, H2O2, as a signaling molecule regulating protein synthesis at different levels, including transcription and various parts of the translation process, e.g., initiation, elongation, termination and ribosome recycling.
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50
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Lang BJ, Guerrero ME, Prince TL, Okusha Y, Bonorino C, Calderwood SK. The functions and regulation of heat shock proteins; key orchestrators of proteostasis and the heat shock response. Arch Toxicol 2021; 95:1943-1970. [PMID: 34003342 DOI: 10.1007/s00204-021-03070-8] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 05/03/2021] [Indexed: 12/14/2022]
Abstract
Cells respond to protein-damaging (proteotoxic) stress by activation of the Heat Shock Response (HSR). The HSR provides cells with an enhanced ability to endure proteotoxic insults and plays a crucial role in determining subsequent cell death or survival. The HSR is, therefore, a critical factor that influences the toxicity of protein stress. While named for its vital role in the cellular response to heat stress, various components of the HSR system and the molecular chaperone network execute essential physiological functions as well as responses to other diverse toxic insults. The effector molecules of the HSR, the Heat Shock Factors (HSFs) and Heat Shock Proteins (HSPs), are also important regulatory targets in the progression of neurodegenerative diseases and cancers. Modulation of the HSR and/or its extended network have, therefore, become attractive treatment strategies for these diseases. Development of effective therapies will, however, require a detailed understanding of the HSR, important features of which continue to be uncovered and are yet to be completely understood. We review recently described and hallmark mechanistic principles of the HSR, the regulation and functions of HSPs, and contexts in which the HSR is activated and influences cell fate in response to various toxic conditions.
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Affiliation(s)
- Benjamin J Lang
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Martin E Guerrero
- Laboratory of Oncology, Institute of Medicine and Experimental Biology of Cuyo (IMBECU), National Scientific and Technical Research Council (CONICET), 5500, Mendoza, Argentina
| | - Thomas L Prince
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Yuka Okusha
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Cristina Bonorino
- Departamento de Ciências Básicas da Saúde, Universidade Federal de Ciências da Saúde de Porto Alegre, Porto Alegre, RS, Brasil.,Department of Surgery, School of Medicine, University of California, La Jolla, San Diego, CA, 92093, USA
| | - Stuart K Calderwood
- Department of Radiation Oncology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA.
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