851
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Conformation transitions of the polypeptide-binding pocket support an active substrate release from Hsp70s. Nat Commun 2017; 8:1201. [PMID: 29084938 PMCID: PMC5662698 DOI: 10.1038/s41467-017-01310-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/07/2017] [Indexed: 12/21/2022] Open
Abstract
Cellular protein homeostasis depends on heat shock proteins 70 kDa (Hsp70s), a class of ubiquitous and highly conserved molecular chaperone. Key to the chaperone activity is an ATP-induced allosteric regulation of polypeptide substrate binding and release. To illuminate the molecular mechanism of this allosteric coupling, here we present a novel crystal structure of an intact human BiP, an essential Hsp70 in ER, in an ATP-bound state. Strikingly, the polypeptide-binding pocket is completely closed, seemingly excluding any substrate binding. Our FRET, biochemical and EPR analysis suggests that this fully closed conformation is the major conformation for the ATP-bound state in solution, providing evidence for an active release of bound polypeptide substrates following ATP binding. The Hsp40 co-chaperone converts this fully closed conformation to an open conformation to initiate productive substrate binding. Taken together, this study provided a mechanistic understanding of the dynamic nature of the polypeptide-binding pocket in the Hsp70 chaperone cycle. Hsp70s are highly conserved molecular chaperones that play multiple essential roles in maintaining cellular protein homeostasis. Here, the authors provide structural evidence for active substrate release by Hsp70s upon ATP binding and provide insight into the molecular mechanism of ATP-driven Hsp70 chaperone activity.
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852
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Broadening the functionality of a J-protein/Hsp70 molecular chaperone system. PLoS Genet 2017; 13:e1007084. [PMID: 29084221 PMCID: PMC5679652 DOI: 10.1371/journal.pgen.1007084] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 11/09/2017] [Accepted: 10/18/2017] [Indexed: 12/21/2022] Open
Abstract
By binding to a multitude of polypeptide substrates, Hsp70-based molecular chaperone systems perform a range of cellular functions. All J-protein co-chaperones play the essential role, via action of their J-domains, of stimulating the ATPase activity of Hsp70, thereby stabilizing its interaction with substrate. In addition, J-proteins drive the functional diversity of Hsp70 chaperone systems through action of regions outside their J-domains. Targeting to specific locations within a cellular compartment and binding of specific substrates for delivery to Hsp70 have been identified as modes of J-protein specialization. To better understand J-protein specialization, we concentrated on Saccharomyces cerevisiae SIS1, which encodes an essential J-protein of the cytosol/nucleus. We selected suppressors that allowed cells lacking SIS1 to form colonies. Substitutions changing single residues in Ydj1, a J-protein, which, like Sis1, partners with Hsp70 Ssa1, were isolated. These gain-of-function substitutions were located at the end of the J-domain, suggesting that suppression was connected to interaction with its partner Hsp70, rather than substrate binding or subcellular localization. Reasoning that, if YDJ1 suppressors affect Ssa1 function, substitutions in Hsp70 itself might also be able to overcome the cellular requirement for Sis1, we carried out a selection for SSA1 suppressor mutations. Suppressing substitutions were isolated that altered sites in Ssa1 affecting the cycle of substrate interaction. Together, our results point to a third, additional means by which J-proteins can drive Hsp70's ability to function in a wide range of cellular processes-modulating the Hsp70-substrate interaction cycle.
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853
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Ma FH, An Y, Wang J, Song Y, Liu Y, Shi L. Synthetic Nanochaperones Facilitate Refolding of Denatured Proteins. ACS NANO 2017; 11:10549-10557. [PMID: 28968070 DOI: 10.1021/acsnano.7b05947] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The folding process of a protein is inherently error-prone, owing to the large number of possible conformations that a protein chain can adopt. Partially folded or misfolded proteins typically expose hydrophobic surfaces and tend to form dysfunctional protein aggregates. Therefore, materials that can stabilize unfolded proteins and then efficiently assist them refolding to its bioactive form are of significant interest. Inspired by natural chaperonins, we have synthesized a series of polymeric nanochaperones that can facilitate the refolding of denatured proteins with a high recovery efficiency (up to 97%). Such nanochaperones possess phase-separated structure with hydrophobic microdomains on the surface. This structure allows nanochaperones to stabilize denatured proteins by binding them to the hydrophobic microdomains. We have also investigated the mechanism by which nanochaperones assist the protein refolding and established the design principles of nanochaperones in order to achieve effective recovery of a certain protein from their denatured forms. With a carefully designed composition of the microdomains according to the surface properties of the client proteins, the binding affinity between the hydrophobic microdomain and the denatured protein molecules can be tuned precisely, which enables the self-sorting of the polypeptides and the refolding of the proteins into their bioactive states. This work provides a feasible and effective strategy to recover inclusion bodies to their bioactive forms, which has potential to reduce the cost of the manufacture of recombinant proteins significantly.
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Affiliation(s)
- Fei-He Ma
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Yingli An
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Jianzu Wang
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Yiqing Song
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Yang Liu
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University , Tianjin 300071, China
| | - Linqi Shi
- Key Laboratory of Functional Polymer Materials of Ministry of Education, State Key Laboratory of Medicinal Chemical Biology and Institute of Polymer Chemistry, College of Chemistry, Nankai University , Tianjin 300071, China
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854
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Yau RG, Doerner K, Castellanos ER, Haakonsen DL, Werner A, Wang N, Yang XW, Martinez-Martin N, Matsumoto ML, Dixit VM, Rape M. Assembly and Function of Heterotypic Ubiquitin Chains in Cell-Cycle and Protein Quality Control. Cell 2017; 171:918-933.e20. [PMID: 29033132 DOI: 10.1016/j.cell.2017.09.040] [Citation(s) in RCA: 206] [Impact Index Per Article: 29.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Revised: 07/21/2017] [Accepted: 09/20/2017] [Indexed: 12/21/2022]
Abstract
Posttranslational modification with ubiquitin chains controls cell fate in all eukaryotes. Depending on the connectivity between subunits, different ubiquitin chain types trigger distinct outputs, as seen with K48- and K63-linked conjugates that drive protein degradation or complex assembly, respectively. Recent biochemical analyses also suggested roles for mixed or branched ubiquitin chains, yet without a method to monitor endogenous conjugates, the physiological significance of heterotypic polymers remained poorly understood. Here, we engineered a bispecific antibody to detect K11/K48-linked chains and identified mitotic regulators, misfolded nascent polypeptides, and pathological Huntingtin variants as their endogenous substrates. We show that K11/K48-linked chains are synthesized and processed by essential ubiquitin ligases and effectors that are mutated across neurodegenerative diseases; accordingly, these conjugates promote rapid proteasomal clearance of aggregation-prone proteins. By revealing key roles of K11/K48-linked chains in cell-cycle and quality control, we establish heterotypic ubiquitin conjugates as important carriers of biological information.
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Affiliation(s)
- Richard G Yau
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Kerstin Doerner
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Erick R Castellanos
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA
| | - Diane L Haakonsen
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, Berkeley, CA, USA
| | - Achim Werner
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA
| | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - X William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience & Human Behavior, University of California, Los Angeles, Los Angeles, CA, USA; Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLA, University of California, Los Angeles, Los Angeles, CA, USA
| | - Nadia Martinez-Martin
- Department of Microchemistry, Proteomics, and Lipidomics, Genentech Inc., South San Francisco, CA, USA
| | - Marissa L Matsumoto
- Department of Structural Biology, Genentech Inc., South San Francisco, CA, USA.
| | - Vishva M Dixit
- Department of Physiological Chemistry, Genentech Inc., South San Francisco, CA, USA.
| | - Michael Rape
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, Berkeley, CA, USA.
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855
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Karagöz GE, Acosta-Alvear D, Nguyen HT, Lee CP, Chu F, Walter P. An unfolded protein-induced conformational switch activates mammalian IRE1. eLife 2017; 6:30700. [PMID: 28971800 PMCID: PMC5699868 DOI: 10.7554/elife.30700] [Citation(s) in RCA: 138] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 10/02/2017] [Indexed: 12/17/2022] Open
Abstract
The unfolded protein response (UPR) adjusts the cell’s protein folding capacity in the endoplasmic reticulum (ER) according to need. IRE1 is the most conserved UPR sensor in eukaryotic cells. It has remained controversial, however, whether mammalian and yeast IRE1 use a common mechanism for ER stress sensing. Here, we show that similar to yeast, human IRE1α’s ER-lumenal domain (hIRE1α LD) binds peptides with a characteristic amino acid bias. Peptides and unfolded proteins bind to hIRE1α LD’s MHC-like groove and induce allosteric changes that lead to its oligomerization. Mutation of a hydrophobic patch at the oligomerization interface decoupled peptide binding to hIRE1α LD from its oligomerization, yet retained peptide-induced allosteric coupling within the domain. Importantly, impairing oligomerization of hIRE1α LD abolished IRE1’s activity in living cells. Our results provide evidence for a unifying mechanism of IRE1 activation that relies on unfolded protein binding-induced oligomerization. Proteins are long string-like molecules that fold into specific three-dimensional shapes. Most proteins that a cell uses to communicate with its environment are folded within a part of the cell called the endoplasmic reticulum. Dedicated sensor proteins in this cellular compartment track this process to make sure that it continues to meet the cell’s demand for protein folding. If it cannot meet the demand, unfolded or poorly folded proteins build up, which stresses the cell. IRE1 is a sensor protein that detects stress in the endoplasmic reticulum. It is found in a range of organisms from yeast to humans, where it spans the membrane that encloses the endoplasmic reticulum. When unfolded proteins accumulate, IRE1 proteins come together and form so-called oligomers. The IRE1 oligomers then become active and send signals outside of the endoplasmic reticulum. These signals adjust the cell’s protein-folding capacity according to its needs at that time. The yeast version of IRE1 directly recognizes unfolded proteins in the endoplasmic reticulum. Yet, its human counterpart was found to have a different three-dimensional structure, which suggested that it might use a different mechanism to detect the stress. Now, Karagöz et al. show that, as in yeast, the sensor part of human IRE1 does indeed bind to unfolded proteins directly. This binding causes this part of the protein to engage other copies of IRE1 and form the oligomers. To understand this interaction in more detail, Karagöz et al. used a technique called nuclear magnetic resonance spectroscopy to monitor changes in the shape of proteins. These observations revealed that binding to an unfolded protein causes other parts of IRE1 protein to change shape. In turn, these shape changes act as a switch that causes the oligomers to form. Stopping the sensor domains from forming oligomers inactivated the IRE1 protein in mammalian cells; this rendered IRE1 unresponsive to stress within the endoplasmic reticulum. The regulation of IRE1 affects many health disorders, including diabetes, cancer and neurodegenerative diseases. By showing that unfolded proteins switch IRE1 into its active, oligomeric state, these findings might lead to new approaches to manipulate IRE1’s activity with small molecules to help to treat these diseases.
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Affiliation(s)
- G Elif Karagöz
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Diego Acosta-Alvear
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Hieu T Nguyen
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Crystal P Lee
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
| | - Feixia Chu
- Department of Molecular, Cellular, and Biomedical Sciences, University of New Hampshire, Durham, United States
| | - Peter Walter
- Department of Biochemistry and Biophysics, Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
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856
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Slp1-Emp65: A Guardian Factor that Protects Folding Polypeptides from Promiscuous Degradation. Cell 2017; 171:346-357.e12. [DOI: 10.1016/j.cell.2017.08.036] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Revised: 07/06/2017] [Accepted: 08/21/2017] [Indexed: 02/05/2023]
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857
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Marín M, Fernández-Calero T, Ehrlich R. Protein folding and tRNA biology. Biophys Rev 2017; 9:573-588. [PMID: 28944442 PMCID: PMC5662057 DOI: 10.1007/s12551-017-0322-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2017] [Accepted: 08/28/2017] [Indexed: 12/14/2022] Open
Abstract
Polypeptides can fold into tertiary structures while they are synthesized by the ribosome. In addition to the amino acid sequence, protein folding is determined by several factors within the cell. Among others, the folding pathway of a nascent polypeptide can be affected by transient interactions with other proteins, ligands, or the ribosome, as well as by the translocation through membrane pores. Particularly, the translation machinery and the population of tRNA under different physiological or adaptive responses can dramatically affect protein folding. This review summarizes the scientific evidence describing the role of translation kinetics and tRNA populations on protein folding and addresses current efforts to better understand tRNA biology. It is organized into three main parts, which are focused on: (i) protein folding in the cellular context; (ii) tRNA biology and the complexity of the tRNA population; and (iii) available methods and technical challenges in the characterization of tRNA pools. In this manner, this work illustrates the ways by which functional properties of proteins may be modulated by cellular tRNA populations.
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Affiliation(s)
- Mónica Marín
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
| | - Tamara Fernández-Calero
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Bioinformatics Unit, Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
| | - Ricardo Ehrlich
- Biochemistry-Molecular Biology Section, Cellular and Molecular Biology Department, Faculty of Sciences, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay
- Institut Pasteur Montevideo, Mataojo 2020, 11400 Montevideo, Uruguay
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858
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Protein aggregation: From background to inhibition strategies. Int J Biol Macromol 2017; 103:208-219. [DOI: 10.1016/j.ijbiomac.2017.05.048] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 05/11/2017] [Accepted: 05/12/2017] [Indexed: 01/01/2023]
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859
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Pokrzywa W, Lorenz R, Hoppe T. Chaperone-directed ubiquitylation maintains proteostasis at the expense of longevity. WORM 2017; 6:e1371403. [PMID: 28959501 PMCID: PMC5612283 DOI: 10.1080/21624054.2017.1371403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 08/18/2017] [Indexed: 11/24/2022]
Abstract
The integrity of the cellular proteome is supported by quality control networks, which govern protein synthesis, folding, and degradation. It is generally accepted that an age-related decline in protein homeostasis (proteostasis) contributes to protein aggregation diseases. However, the mechanistic principles underlying proteostasis imbalance and the impact on life expectancy are not well understood. We recently demonstrated that this interrelation is affected by chaperone-directed ubiquitylation, shifting the amount of the conserved DAF-2/insulin receptor both in Caenorhabditis elegans and Drosophila melanogaster. The ubiquitin ligase CHIP either targets the membrane bound insulin receptor or misfolded proteins for degradation, which depends on the cellular proteostasis status. Increased proteotoxicity triggers chaperone-assisted redirection of CHIP toward protein aggregates, limiting its capacity to degrade the insulin receptor and prevent premature aging. In light of these findings, we discuss a new concept for understanding the impact of proteome imbalance on longevity risk.
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Affiliation(s)
- Wojciech Pokrzywa
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany.,International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Robin Lorenz
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Cologne, Germany
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860
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Abstract
Proteins fold under mechanical forces in a number of biological processes, ranging from muscle contraction to co-translational folding. As force hinders the folding transition, chaperones must play a role in this scenario, although their influence on protein folding under force has not been directly monitored yet. Here, we introduce single-molecule magnetic tweezers to study the folding dynamics of protein L in presence of the prototypical molecular chaperone trigger factor over the range of physiological forces (4–10 pN). Our results show that trigger factor increases prominently the probability of folding against force and accelerates the refolding kinetics. Moreover, we find that trigger factor catalyzes the folding reaction in a force-dependent manner; as the force increases, higher concentrations of trigger factor are needed to rescue folding. We propose that chaperones such as trigger factor can work as foldases under force, a mechanism which could be of relevance for several physiological processes. Proteins fold under mechanical force during co-translational folding at the ribosome. Here, the authors use single molecule magnetic tweezers to study the influence of chaperones on protein folding and show that the ribosomal chaperone trigger factor acts as a mechanical foldase by promoting protein folding under force.
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861
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Sekhar A, Nagesh J, Rosenzweig R, Kay LE. Conformational heterogeneity in the Hsp70 chaperone-substrate ensemble identified from analysis of NMR-detected titration data. Protein Sci 2017; 26:2207-2220. [PMID: 28833766 DOI: 10.1002/pro.3276] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 08/17/2017] [Indexed: 01/06/2023]
Abstract
The Hsp70 chaperone system plays a critical role in cellular homeostasis by binding to client protein molecules. We have recently shown by methyl-TROSY NMR methods that the Escherichia coli Hsp70, DnaK, can form multiple bound complexes with a small client protein, hTRF1. In an effort to characterize the interactions further we report here the results of an NMR-based titration study of hTRF1 and DnaK, where both molecular components are monitored simultaneously, leading to a binding model. A central finding is the formation of a previously undetected 3:1 hTRF1-DnaK complex, suggesting that under heat shock conditions, DnaK might be able to protect cytosolic proteins whose net concentrations would exceed that of the chaperone. Moreover, these results provide new insight into the heterogeneous ensemble of complexes formed by DnaK chaperones and further emphasize the unique role of NMR spectroscopy in obtaining information about individual events in a complex binding scheme by exploiting a large number of probes that report uniquely on distinct binding processes.
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Affiliation(s)
- Ashok Sekhar
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada
| | - Jayashree Nagesh
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Ontario, M5S 3H6, Canada
| | - Rina Rosenzweig
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, 76100, Israel
| | - Lewis E Kay
- Departments of Molecular Genetics, Biochemistry and Chemistry, University of Toronto, Toronto, Ontario, M5S 1A8, Canada.,Program in Molecular Medicine, 555 University Avenue, Hospital for Sick Children, Toronto, Ontario, M5G 1X8, Canada
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862
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San Gil R, Ooi L, Yerbury JJ, Ecroyd H. The heat shock response in neurons and astroglia and its role in neurodegenerative diseases. Mol Neurodegener 2017; 12:65. [PMID: 28923065 PMCID: PMC5604514 DOI: 10.1186/s13024-017-0208-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2017] [Accepted: 09/01/2017] [Indexed: 12/13/2022] Open
Abstract
Protein inclusions are a predominant molecular pathology found in numerous neurodegenerative diseases, including amyotrophic lateral sclerosis and Huntington's disease. Protein inclusions form in discrete areas of the brain characteristic to the type of neurodegenerative disease, and coincide with the death of neurons in that region (e.g. spinal cord motor neurons in amyotrophic lateral sclerosis). This suggests that the process of protein misfolding leading to inclusion formation is neurotoxic, and that cell-autonomous and non-cell autonomous mechanisms that maintain protein homeostasis (proteostasis) can, at times, be insufficient to prevent protein inclusion formation in the central nervous system. The heat shock response is a pro-survival pathway induced under conditions of cellular stress that acts to maintain proteostasis through the up-regulation of heat shock proteins, a superfamily of molecular chaperones, other co-chaperones and mitotic regulators. The kinetics and magnitude of the heat shock response varies in a stress- and cell-type dependent manner. It remains to be determined if and/or how the heat shock response is activated in the different cell-types that comprise the central nervous system (e.g. neurons and astroglia) in response to protein misfolding events that precede cellular dysfunctions in neurodegenerative diseases. This is particularly relevant considering emerging evidence demonstrating the non-cell autonomous nature of amyotrophic lateral sclerosis and Huntington's disease (and other neurodegenerative diseases) and the destructive role of astroglia in disease progression. This review highlights the complexity of heat shock response activation and addresses whether neurons and glia sense and respond to protein misfolding and aggregation associated with neurodegenerative diseases, in particular Huntington's disease and amyotrophic lateral sclerosis, by inducing a pro-survival heat shock response.
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Affiliation(s)
- Rebecca San Gil
- Illawarra Health and Medical Research Institute and School of Biological Sciences, University of Wollongong, Northfields Ave, Wollongong, 2522 Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute and School of Biological Sciences, University of Wollongong, Northfields Ave, Wollongong, 2522 Australia
| | - Justin J. Yerbury
- Illawarra Health and Medical Research Institute and School of Biological Sciences, University of Wollongong, Northfields Ave, Wollongong, 2522 Australia
| | - Heath Ecroyd
- Illawarra Health and Medical Research Institute and School of Biological Sciences, University of Wollongong, Northfields Ave, Wollongong, 2522 Australia
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863
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Overlapping and Specific Functions of the Hsp104 N Domain Define Its Role in Protein Disaggregation. Sci Rep 2017; 7:11184. [PMID: 28894176 PMCID: PMC5593927 DOI: 10.1038/s41598-017-11474-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/21/2017] [Indexed: 11/08/2022] Open
Abstract
Hsp104 is a ring-forming protein disaggregase that rescues stress-damaged proteins from an aggregated state. To facilitate protein disaggregation, Hsp104 cooperates with Hsp70 and Hsp40 chaperones (Hsp70/40) to form a bi-chaperone system. How Hsp104 recognizes its substrates, particularly the importance of the N domain, remains poorly understood and multiple, seemingly conflicting mechanisms have been proposed. Although the N domain is dispensable for protein disaggregation, it is sensitive to point mutations that abolish the function of the bacterial Hsp104 homolog in vitro, and is essential for curing yeast prions by Hsp104 overexpression in vivo. Here, we present the crystal structure of an N-terminal fragment of Saccharomyces cerevisiae Hsp104 with the N domain of one molecule bound to the C-terminal helix of the neighboring D1 domain. Consistent with mimicking substrate interaction, mutating the putative substrate-binding site in a constitutively active Hsp104 variant impairs the recovery of functional protein from aggregates. We find that the observed substrate-binding defect can be rescued by Hsp70/40 chaperones, providing a molecular explanation as to why the N domain is dispensable for protein disaggregation when Hsp70/40 is present, yet essential for the dissolution of Hsp104-specific substrates, such as yeast prions, which likely depends on a direct N domain interaction.
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864
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Dominguez CE, Cunningham D, Chandler DS. SMN regulation in SMA and in response to stress: new paradigms and therapeutic possibilities. Hum Genet 2017; 136:1173-1191. [PMID: 28852871 PMCID: PMC6201753 DOI: 10.1007/s00439-017-1835-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022]
Abstract
Low levels of the survival of motor neuron (SMN) protein cause the neurodegenerative disease spinal muscular atrophy (SMA). SMA is a pediatric disease characterized by spinal motor neuron degeneration. SMA exhibits several levels of severity ranging from early antenatal fatality to only mild muscular weakness, and disease prognosis is related directly to the amount of functional SMN protein that a patient is able to express. Current therapies are being developed to increase the production of functional SMN protein; however, understanding the effect that natural stresses have on the production and function of SMN is of critical importance to ensuring that these therapies will have the greatest possible effect for patients. Research has shown that SMN, both on the mRNA and protein level, is highly affected by cellular stress. In this review we will summarize the research that highlights the roles of SMN in the disease process and the response of SMN to various environmental stresses.
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Affiliation(s)
- Catherine E Dominguez
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - David Cunningham
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
| | - Dawn S Chandler
- Molecular, Cellular and Developmental Biology Graduate Program and The Center for RNA Biology, The Ohio State University, Columbus, OH, USA.
- Center for Childhood Cancer and Blood Diseases, The Research Institute at Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA.
- Department of Pediatrics, The Ohio State University College of Medicine, Columbus, OH, USA.
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865
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Ambadipudi S, Biernat J, Riedel D, Mandelkow E, Zweckstetter M. Liquid-liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau. Nat Commun 2017; 8:275. [PMID: 28819146 PMCID: PMC5561136 DOI: 10.1038/s41467-017-00480-0] [Citation(s) in RCA: 471] [Impact Index Per Article: 67.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/30/2017] [Indexed: 02/08/2023] Open
Abstract
The protein Tau aggregates into tangles in the brain of patients with Alzheimer’s disease. In solution, however, Tau is intrinsically disordered, highly soluble, and binds to microtubules. It is still unclear what initiates the conversion from an innocuous phase of high solubility and functionality to solid-like neurotoxic deposits. Here, we show that the microtubule-binding repeats of Tau, which are lysine-rich, undergo liquid–liquid phase separation in solution. Liquid–liquid demixing causes molecular crowding of amyloid-promoting elements of Tau and drives electrostatic coacervation. Furthermore, we demonstrate that three-repeat and four-repeat isoforms of Tau differ in their ability for demixing. Alternative splicing of Tau can thus regulate the formation of Tau-containing membrane-less compartments. In addition, phosphorylation of Tau repeats promotes liquid–liquid phase separation at cellular protein conditions. The combined data propose a mechanism in which liquid droplets formed by the positively charged microtubule-binding domain of Tau undergo coacervation with negatively charged molecules to promote amyloid formation. Tau forms aggregates in the brains of Alzheimer patients. Here, the authors identify conditions, where the microtubule-binding repeats of Tau undergo a phosphorylation-dependent liquid–liquid phase separation, leading to molecular crowding in the formed Tau liquid droplets and characterize them by NMR and other biophysical methods.
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Affiliation(s)
- Susmitha Ambadipudi
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Jacek Biernat
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Dietmar Riedel
- Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077, Göttingen, Germany
| | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,CAESAR Research Center, Bonn, and MPI for Metabolism Research, Hamburg Outstation, 22607, Hamburg, Germany
| | - Markus Zweckstetter
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), von-Siebold-Str. 3a, 37075, Göttingen, Germany. .,Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077, Göttingen, Germany. .,Department of Neurology, University Medical Center Göttingen, University of Göttingen, Waldweg 33, 37073, Göttingen, Germany.
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866
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Cato L, Neeb A, Sharp A, Buzón V, Ficarro SB, Yang L, Muhle-Goll C, Kuznik NC, Riisnaes R, Nava Rodrigues D, Armant O, Gourain V, Adelmant G, Ntim EA, Westerling T, Dolling D, Rescigno P, Figueiredo I, Fauser F, Wu J, Rottenberg JT, Shatkina L, Ester C, Luy B, Puchta H, Troppmair J, Jung N, Bräse S, Strähle U, Marto JA, Nienhaus GU, Al-Lazikani B, Salvatella X, de Bono JS, Cato ACB, Brown M. Development of Bag-1L as a therapeutic target in androgen receptor-dependent prostate cancer. eLife 2017; 6:e27159. [PMID: 28826504 PMCID: PMC5629025 DOI: 10.7554/elife.27159] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 08/07/2017] [Indexed: 12/12/2022] Open
Abstract
Targeting the activation function-1 (AF-1) domain located in the N-terminus of the androgen receptor (AR) is an attractive therapeutic alternative to the current approaches to inhibit AR action in prostate cancer (PCa). Here we show that the AR AF-1 is bound by the cochaperone Bag-1L. Mutations in the AR interaction domain or loss of Bag-1L abrogate AR signaling and reduce PCa growth. Clinically, Bag-1L protein levels increase with progression to castration-resistant PCa (CRPC) and high levels of Bag-1L in primary PCa associate with a reduced clinical benefit from abiraterone when these tumors progress. Intriguingly, residues in Bag-1L important for its interaction with the AR AF-1 are within a potentially druggable pocket, implicating Bag-1L as a potential therapeutic target in PCa.
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867
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868
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Boone DK, Weisz HA, Bi M, Falduto MT, Torres KEO, Willey HE, Volsko CM, Kumar AM, Micci MA, Dewitt DS, Prough DS, Hellmich HL. Evidence linking microRNA suppression of essential prosurvival genes with hippocampal cell death after traumatic brain injury. Sci Rep 2017; 7:6645. [PMID: 28751711 PMCID: PMC5532254 DOI: 10.1038/s41598-017-06341-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 06/13/2017] [Indexed: 01/09/2023] Open
Abstract
The underlying molecular mechanisms of how dysregulated microRNAs (miRNAs) cause neurodegeneration after traumatic brain injury (TBI) remain elusive. Here we analyzed the biological roles of approximately 600 genes - we previously found these dysregulated in dying and surviving rat hippocampal neurons - that are targeted by ten TBI-altered miRNAs. Bioinformatic analysis suggests that neurodegeneration results from a global miRNA-mediated suppression of genes essential for maintaining proteostasis; many are hub genes - involved in RNA processing, cytoskeletal metabolism, intracellular trafficking, cell cycle progression, repair/maintenance, bioenergetics and cell-cell signaling - whose disrupted expression is linked to human disease. Notably, dysregulation of these essential genes would significantly impair synaptic function and functional brain connectivity. In surviving neurons, upregulated miRNA target genes are co-regulated members of prosurvival pathways associated with cellular regeneration, neural plasticity, and development. This study captures the diversity of miRNA-regulated genes that may be essential for cell repair and survival responses after TBI.
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Affiliation(s)
- Deborah Kennedy Boone
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Harris A Weisz
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Min Bi
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | | | - Hannah E Willey
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Christina M Volsko
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Anjali M Kumar
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Maria-Adelaide Micci
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Douglas S Dewitt
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Donald S Prough
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Helen L Hellmich
- Department of Anesthesiology, University of Texas Medical Branch, Galveston, Texas, USA.
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869
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Proteostasis of Huntingtin in Health and Disease. Int J Mol Sci 2017; 18:ijms18071568. [PMID: 28753941 PMCID: PMC5536056 DOI: 10.3390/ijms18071568] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 07/15/2017] [Accepted: 07/18/2017] [Indexed: 12/28/2022] Open
Abstract
Huntington's disease (HD) is a fatal neurodegenerative disorder characterized by motor dysfunction, cognitive deficits and psychosis. HD is caused by mutations in the Huntingtin (HTT) gene, resulting in the expansion of polyglutamine (polyQ) repeats in the HTT protein. Mutant HTT is prone to aggregation, and the accumulation of polyQ-expanded fibrils as well as intermediate oligomers formed during the aggregation process contribute to neurodegeneration. Distinct protein homeostasis (proteostasis) nodes such as chaperone-mediated folding and proteolytic systems regulate the aggregation and degradation of HTT. Moreover, polyQ-expanded HTT fibrils and oligomers can lead to a global collapse in neuronal proteostasis, a process that contributes to neurodegeneration. The ability to maintain proteostasis of HTT declines during the aging process. Conversely, mechanisms that preserve proteostasis delay the onset of HD. Here we will review the link between proteostasis, aging and HD-related changes.
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870
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Horowitz S, Koldewey P, Stull F, Bardwell JC. Folding while bound to chaperones. Curr Opin Struct Biol 2017; 48:1-5. [PMID: 28734135 DOI: 10.1016/j.sbi.2017.06.009] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/23/2017] [Accepted: 06/28/2017] [Indexed: 01/08/2023]
Abstract
Chaperones are important in preventing protein aggregation and aiding protein folding. How chaperones aid protein folding remains a key question in understanding their mechanism. The possibility of proteins folding while bound to chaperones was reintroduced recently with the chaperone Spy, many years after the phenomenon was first reported with the chaperones GroEL and SecB. In this review, we discuss the salient features of folding while bound in the cases for which it has been observed and speculate about its biological importance and possible occurrence in other chaperones.
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Affiliation(s)
- Scott Horowitz
- Department of Chemistry & Biochemistry and the Knoebel Institute for Healthy Aging, University of Denver, 2155 E. Wesley Avenue, Denver, CO 80208, USA.
| | - Philipp Koldewey
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
| | - Frederick Stull
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA
| | - James Ca Bardwell
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, University of Michigan, 830 N. University, Ann Arbor, MI 48109, USA.
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871
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Rosenzweig R, Sekhar A, Nagesh J, Kay LE. Promiscuous binding by Hsp70 results in conformational heterogeneity and fuzzy chaperone-substrate ensembles. eLife 2017; 6. [PMID: 28708484 PMCID: PMC5511010 DOI: 10.7554/elife.28030] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 06/28/2017] [Indexed: 01/05/2023] Open
Abstract
The Hsp70 chaperone system is integrated into a myriad of biochemical processes that are critical for cellular proteostasis. Although detailed pictures of Hsp70 bound with peptides have emerged, correspondingly detailed structural information on complexes with folding-competent substrates remains lacking. Here we report a methyl-TROSY based solution NMR study showing that the Escherichia coli version of Hsp70, DnaK, binds to as many as four distinct sites on a small 53-residue client protein, hTRF1. A fraction of hTRF1 chains are also bound to two DnaK molecules simultaneously, resulting in a mixture of DnaK-substrate sub-ensembles that are structurally heterogeneous. The interactions of Hsp70 with a client protein at different sites results in a fuzzy chaperone-substrate ensemble and suggests a mechanism for Hsp70 function whereby the structural heterogeneity of released substrate molecules enables them to circumvent kinetic traps in their conformational free energy landscape and fold efficiently to the native state. DOI:http://dx.doi.org/10.7554/eLife.28030.001
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Affiliation(s)
- Rina Rosenzweig
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel
| | - Ashok Sekhar
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada
| | - Jayashree Nagesh
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, Toronto, Canada
| | - Lewis E Kay
- Department of Molecular Genetics, The University of Toronto, Toronto, Canada.,Department of Biochemistry, The University of Toronto, Toronto, Canada.,Department of Chemistry, University of Toronto, Toronto, Canada.,Hospital for Sick Children, Program in Molecular Structure and Function, Toronto, Canada
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872
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Abstract
The incidence and prevalence of cardiac diseases, which are the main cause of death worldwide, are likely to increase because of population ageing. Prevailing theories about the mechanisms of ageing feature the gradual derailment of cellular protein homeostasis (proteostasis) and loss of protein quality control as central factors. In the heart, loss of protein patency, owing to flaws in genetically-determined design or because of environmentally-induced 'wear and tear', can overwhelm protein quality control, thereby triggering derailment of proteostasis and contributing to cardiac ageing. Failure of protein quality control involves impairment of chaperones, ubiquitin-proteosomal systems, autophagy, and loss of sarcomeric and cytoskeletal proteins, all of which relate to induction of cardiomyocyte senescence. Targeting protein quality control to maintain cardiac proteostasis offers a novel therapeutic strategy to promote cardiac health and combat cardiac disease. Currently marketed drugs are available to explore this concept in the clinical setting.
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Affiliation(s)
- Robert H Henning
- Department of Clinical Pharmacy and Pharmacology, University Medical Centre Groningen, University of Groningen, Hanzeplein 1, 9713 GZ Groningen, The Netherlands
| | - Bianca J J M Brundel
- Department of Physiology, Amsterdam Cardiovascular Sciences, VU University Medical Center, De Boelelaan 1117, 1081 HZ Amsterdam, The Netherlands
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873
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Flagmeier P, De S, Wirthensohn DC, Lee SF, Vincke C, Muyldermans S, Knowles TPJ, Gandhi S, Dobson CM, Klenerman D. Ultrasensitive Measurement of Ca 2+
Influx into Lipid Vesicles Induced by Protein Aggregates. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700966] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Patrick Flagmeier
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Suman De
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - David C. Wirthensohn
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Steven F. Lee
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology; Vrije Universiteit Brussel; Brussels Belgium
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology; Vrije Universiteit Brussel; Brussels Belgium
| | - Tuomas P. J. Knowles
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - Sonia Gandhi
- Department of Molecular Neuroscience; Institute of Neurology; University College London; Queen Square London WC1N 3BG UK
| | - Christopher M. Dobson
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
| | - David Klenerman
- Department of Chemistry; University of Cambridge; Lensfield Road Cambridge CB2 1EW UK
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874
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Rusmini P, Cristofani R, Galbiati M, Cicardi ME, Meroni M, Ferrari V, Vezzoli G, Tedesco B, Messi E, Piccolella M, Carra S, Crippa V, Poletti A. The Role of the Heat Shock Protein B8 (HSPB8) in Motoneuron Diseases. Front Mol Neurosci 2017; 10:176. [PMID: 28680390 PMCID: PMC5478700 DOI: 10.3389/fnmol.2017.00176] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 05/18/2017] [Indexed: 12/13/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and spinal and bulbar muscular atrophy (SBMA) are two motoneuron diseases (MNDs) characterized by aberrant protein behavior in affected cells. In familial ALS (fALS) and in SBMA specific gene mutations lead to the production of neurotoxic proteins or peptides prone to misfold, which then accumulate in form of aggregates. Notably, some of these proteins accumulate into aggregates also in sporadic ALS (sALS) even if not mutated. To prevent proteotoxic stresses detrimental to cells, misfolded and/or aggregated proteins must be rapidly removed by the protein quality control (PQC) system. The small heat shock protein B8 (HSPB8) is a chaperone induced by harmful events, like proteasome inhibition. HSPB8 is expressed both in motoneuron and muscle cells, which are both targets of misfolded protein toxicity in MNDs. In ALS mice models, in presence of the mutant proteins, HSPB8 is upregulated both in spinal cord and muscle. HSPB8 interacts with the HSP70 co-chaperone BAG3 and enhances the degradation of misfolded proteins linked to sALS, or causative of fALS and of SBMA. HSPB8 acts by facilitating autophagy, thereby preventing misfolded protein accumulation in affected cells. BAG3 and BAG1 compete for HSP70-bound clients and target them for disposal to the autophagy or proteasome, respectively. Enhancing the selective targeting of misfolded proteins by HSPB8-BAG3-HSP70 to autophagy may also decrease their delivery to the proteasome by the BAG1-HSP70 complex, thereby limiting possible proteasome overwhelming. Thus, approaches aimed at potentiating HSPB8-BAG3 may contribute to the maintenance of proteostasis and may delay MNDs progression.
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Affiliation(s)
- Paola Rusmini
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Riccardo Cristofani
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Mariarita Galbiati
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Maria E Cicardi
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Marco Meroni
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Veronica Ferrari
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Giulia Vezzoli
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Barbara Tedesco
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Elio Messi
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Margherita Piccolella
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy
| | - Serena Carra
- Dipartimento di Scienze Biomediche, Metaboliche e Neuroscienze, Università di Modena e Reggio EmiliaModena, Italy
| | - Valeria Crippa
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy.,C. Mondino National Neurological InstitutePavia, Italy
| | - Angelo Poletti
- Dipartimento di Scienze Farmacologiche e Biomolecolari (DiSFeB), Centro di Eccellenza sulle Malattie Neurodegenerative, Università degli Studi di MilanoMilano, Italy.,Centro Interuniversitario sulle Malattie Neurodegenerative, Università degli Studi di Firenze, Roma Tor VergataMilano, Italy
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875
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Affiliation(s)
- F. Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
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876
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Abstract
A healthy proteome is essential for cell survival. Protein misfolding is linked to a rapidly expanding list of human diseases, ranging from neurodegenerative diseases to aging and cancer. Many of these diseases are characterized by the accumulation of misfolded proteins in intra- and extracellular inclusions, such as amyloid plaques. The clear link between protein misfolding and disease highlights the need to better understand the elaborate machinery that manages proteome homeostasis, or proteostasis, in the cell. Proteostasis depends on a network of molecular chaperones and clearance pathways involved in the recognition, refolding, and/or clearance of aberrant proteins. Recent studies reveal that an integral part of the cellular management of misfolded proteins is their spatial sequestration into several defined compartments. Here, we review the properties, function, and formation of these compartments. Spatial sequestration plays a central role in protein quality control and cellular fitness and represents a critical link to the pathogenesis of protein aggregation-linked diseases.
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Affiliation(s)
| | - Rahul S Samant
- Department of Biology, Stanford University, Stanford, California 94305; , ,
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California 94305; , ,
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877
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Chiti F, Dobson CM. Protein Misfolding, Amyloid Formation, and Human Disease: A Summary of Progress Over the Last Decade. Annu Rev Biochem 2017; 86:27-68. [DOI: 10.1146/annurev-biochem-061516-045115] [Citation(s) in RCA: 1668] [Impact Index Per Article: 238.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Peptides and proteins have been found to possess an inherent tendency to convert from their native functional states into intractable amyloid aggregates. This phenomenon is associated with a range of increasingly common human disorders, including Alzheimer and Parkinson diseases, type II diabetes, and a number of systemic amyloidoses. In this review, we describe this field of science with particular reference to the advances that have been made over the last decade in our understanding of its fundamental nature and consequences. We list the proteins that are known to be deposited as amyloid or other types of aggregates in human tissues and the disorders with which they are associated, as well as the proteins that exploit the amyloid motif to play specific functional roles in humans. In addition, we summarize the genetic factors that have provided insight into the mechanisms of disease onset. We describe recent advances in our knowledge of the structures of amyloid fibrils and their oligomeric precursors and of the mechanisms by which they are formed and proliferate to generate cellular dysfunction. We show evidence that a complex proteostasis network actively combats protein aggregation and that such an efficient system can fail in some circumstances and give rise to disease. Finally, we anticipate the development of novel therapeutic strategies with which to prevent or treat these highly debilitating and currently incurable conditions.
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Affiliation(s)
- Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences “Mario Serio,” Section of Biochemistry, Università di Firenze, 50134 Firenze, Italy
| | - Christopher M. Dobson
- Department of Chemistry, Centre for Misfolding Diseases, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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878
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Elia F, Cantini F, Chiti F, Dobson CM, Bemporad F. Direct Conversion of an Enzyme from Native-like to Amyloid-like Aggregates within Inclusion Bodies. Biophys J 2017; 112:2540-2551. [PMID: 28636911 PMCID: PMC5479110 DOI: 10.1016/j.bpj.2017.05.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 05/02/2017] [Accepted: 05/08/2017] [Indexed: 01/29/2023] Open
Abstract
The acylphosphatase from Sulfolobus solfataricus (Sso AcP) is a globular protein able to aggregate in vitro from a native-like conformational ensemble without the need for a transition across the major unfolding energy barrier. This process leads to the formation of assemblies in which the protein retains its native-like structure, which subsequently convert into amyloid-like aggregates. Here, we investigate the mechanism by which Sso AcP aggregates in vivo to form bacterial inclusion bodies after expression in E. coli. Shortly after the initiation of expression, Sso AcP is incorporated into inclusion bodies as a native-like protein, still exhibiting small but significant enzymatic activity. Additional experiments revealed that this overall process of aggregation is enhanced by the presence of the unfolded N-terminal region of the sequence and by destabilization of the globular segment of the protein. At later times, the Sso AcP molecules in the inclusion bodies lose their native-like properties and convert into β-sheet-rich amyloid-like structures, as indicated by their ability to bind thioflavin T and Congo red. These results show that the aggregation behavior of this protein is similar in vivo to that observed in vitro, and that, at least for a predominant part of the protein population, the transition from a native to an amyloid-like structure occurs within the aggregate state.
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Affiliation(s)
- Francesco Elia
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | - Francesca Cantini
- Centro Risonanze Magnetiche (CERM) and Department of Chemistry, University of Florence, Sesto Fiorentino, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy
| | | | - Francesco Bemporad
- Department of Experimental and Clinical Biomedical Sciences "Mario Serio," University of Florence, Firenze, Italy.
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879
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Krainer G, Gracia P, Frotscher E, Hartmann A, Gröger P, Keller S, Schlierf M. Slow Interconversion in a Heterogeneous Unfolded-State Ensemble of Outer-Membrane Phospholipase A. Biophys J 2017. [PMID: 28629619 DOI: 10.1016/j.bpj.2017.05.037] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Structural and dynamic investigations of unfolded proteins are important for understanding protein-folding mechanisms as well as the interactions of unfolded polypeptide chains with other cell components. In the case of outer-membrane proteins (OMPs), unfolded-state properties are of particular physiological relevance, because these proteins remain unfolded for extended periods of time during their biogenesis and rely on interactions with binding partners to support proper folding. Using a combination of ensemble and single-molecule spectroscopy, we have scrutinized the unfolded state of outer-membrane phospholipase A (OmpLA) to provide a detailed view of its structural dynamics on timescales from nanoseconds to milliseconds. We find that even under strongly denaturing conditions and in the absence of residual secondary structure, OmpLA populates an ensemble of slowly (>100 ms) interconverting and conformationally heterogeneous unfolded states that lack the fast chain-reconfiguration motions expected for an unstructured, fully unfolded chain. The drastically slowed sampling of potentially folding-competent states, as compared with a random-coil polypeptide, may contribute to the slow in vitro folding kinetics observed for many OMPs. In vivo, however, slow intramolecular long-range dynamics might be advantageous for entropically favored binding of unfolded OMPs to chaperones and, by facilitating conformational selection after release from chaperones, for preserving binding-competent conformations before insertion into the outer membrane.
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Affiliation(s)
- Georg Krainer
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany; Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Pablo Gracia
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Erik Frotscher
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Andreas Hartmann
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Philip Gröger
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany
| | - Sandro Keller
- Molecular Biophysics, University of Kaiserslautern, Kaiserslautern, Germany.
| | - Michael Schlierf
- B CUBE - Center for Molecular Bioengineering, Technische Universität Dresden, Dresden, Germany.
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880
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Koldewey P, Horowitz S, Bardwell JCA. Chaperone-client interactions: Non-specificity engenders multifunctionality. J Biol Chem 2017; 292:12010-12017. [PMID: 28620048 DOI: 10.1074/jbc.r117.796862] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Here, we provide an overview of the different mechanisms whereby three different chaperones, Spy, Hsp70, and Hsp60, interact with folding proteins, and we discuss how these chaperones may guide the folding process. Available evidence suggests that even a single chaperone can use many mechanisms to aid in protein folding, most likely due to the need for most chaperones to bind clients promiscuously. Chaperone mechanism may be better understood by always considering it in the context of the client's folding pathway and biological function.
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Affiliation(s)
- Philipp Koldewey
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - Scott Horowitz
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109
| | - James C A Bardwell
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan 48109; Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109.
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881
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Gottschling DE, Nyström T. The Upsides and Downsides of Organelle Interconnectivity. Cell 2017; 169:24-34. [PMID: 28340346 DOI: 10.1016/j.cell.2017.02.030] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Revised: 02/13/2017] [Accepted: 02/21/2017] [Indexed: 12/31/2022]
Abstract
Interconnectivity and feedback control are hallmarks of biological systems. This includes communication between organelles, which allows them to function and adapt to changing cellular environments. While the specific mechanisms for all communications remain opaque, unraveling the wiring of organelle networks is critical to understand how biological systems are built and why they might collapse, as occurs in aging. A comprehensive understanding of all the routes involved in inter-organelle communication is still lacking, but important themes are beginning to emerge, primarily in budding yeast. These routes are reviewed here in the context of sub-system proteostasis and complex adaptive systems theory.
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Affiliation(s)
| | - Thomas Nyström
- Institute for Biomedicine, Sahlgrenska Academy, University of Gothenburg, 405 30 Gothenburg, Sweden.
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882
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Hwang J, Walczak CP, Shaler TA, Olzmann JA, Zhang L, Elias JE, Kopito RR. Characterization of protein complexes of the endoplasmic reticulum-associated degradation E3 ubiquitin ligase Hrd1. J Biol Chem 2017; 292:9104-9116. [PMID: 28411238 PMCID: PMC5454095 DOI: 10.1074/jbc.m117.785055] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2017] [Revised: 04/05/2017] [Indexed: 12/20/2022] Open
Abstract
Hrd1 is the core structural component of a large endoplasmic reticulum membrane-embedded protein complex that coordinates the destruction of folding-defective proteins in the early secretory pathway. Defining the composition, dynamics, and ultimately, the structure of the Hrd1 complex is a crucial step in understanding the molecular basis of glycoprotein quality control but has been hampered by the lack of suitable techniques to interrogate this complex under native conditions. In this study we used genome editing to generate clonal HEK293 (Hrd1.KI) cells harboring a homozygous insertion of a small tandem affinity tag knocked into the endogenous Hrd1 locus. We found that steady-state levels of tagged Hrd1 in these cells are indistinguishable from those of Hrd1 in unmodified cells and that the tagged variant is functional in supporting the degradation of well characterized luminal and membrane substrates. Analysis of detergent-solubilized Hrd1.KI cells indicates that the composition and stoichiometry of Hrd1 complexes are strongly influenced by Hrd1 expression levels. Analysis of affinity-captured Hrd1 complexes from these cells by size-exclusion chromatography, immunodepletion, and absolute quantification mass spectrometry identified two major high-molecular-mass complexes with distinct sets of interacting proteins and variable stoichiometries, suggesting a hitherto unrecognized heterogeneity in the functional units of Hrd1-mediated protein degradation.
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Affiliation(s)
| | | | | | | | - Lichao Zhang
- Chemical and Systems Biology, Stanford University, Stanford, California 94305 and
| | - Joshua E Elias
- Chemical and Systems Biology, Stanford University, Stanford, California 94305 and
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883
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Abstract
The carboxyl terminal of Hsp70-interacting protein (CHIP) is an E3 ubiquitin ligase that plays a pivotal role in the protein quality control system by shifting the balance of the folding-refolding machinery toward the degradative pathway. However, the precise mechanisms by which nonnative proteins are selected for degradation by CHIP either directly or indirectly via chaperone Hsp70 or Hsp90 are still not clear. In this review, we aim to provide a comprehensive model of the mechanism by which CHIP degrades its substrate in a chaperone-dependent or direct manner. In addition, through tight regulation of the protein level of its substrates, CHIP plays important roles in many physiological and pathological conditions, including cancers, neurological disorders, cardiac diseases, bone metabolism, immunity, and so on. Nonetheless, the precise mechanisms underlying the regulation of the immune system by CHIP are still poorly understood despite accumulating developments in our understanding of the regulatory roles of CHIP in both innate and adaptive immune responses. In this review, we also aim to provide a view of CHIP-mediated regulation of immune responses and the signaling pathways involved in the model described. Finally, we discuss the roles of CHIP in immune-related diseases.
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Affiliation(s)
- Shaohua Zhan
- a Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences , National Key Laboratory of Medical Molecular Biology & Department of Immunology , Dongcheng District , Beijing , China
| | - Tianxiao Wang
- b Key Laboratory of Carcinogenesis and Translational Research, Department of Head and Neck Surgery , Peking University Cancer Hospital & Institute , Beijing , China
| | - Wei Ge
- a Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences , National Key Laboratory of Medical Molecular Biology & Department of Immunology , Dongcheng District , Beijing , China
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884
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Javed A, Christodoulou J, Cabrita LD, Orlova EV. The ribosome and its role in protein folding: looking through a magnifying glass. Acta Crystallogr D Struct Biol 2017; 73:509-521. [PMID: 28580913 PMCID: PMC5458493 DOI: 10.1107/s2059798317007446] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 05/19/2017] [Indexed: 11/21/2022] Open
Abstract
Protein folding, a process that underpins cellular activity, begins co-translationally on the ribosome. During translation, a newly synthesized polypeptide chain enters the ribosomal exit tunnel and actively interacts with the ribosome elements - the r-proteins and rRNA that line the tunnel - prior to emerging into the cellular milieu. While understanding of the structure and function of the ribosome has advanced significantly, little is known about the process of folding of the emerging nascent chain (NC). Advances in cryo-electron microscopy are enabling visualization of NCs within the exit tunnel, allowing early glimpses of the interplay between the NC and the ribosome. Once it has emerged from the exit tunnel into the cytosol, the NC (still attached to its parent ribosome) can acquire a range of conformations, which can be characterized by NMR spectroscopy. Using experimental restraints within molecular-dynamics simulations, the ensemble of NC structures can be described. In order to delineate the process of co-translational protein folding, a hybrid structural biology approach is foreseeable, potentially offering a complete atomic description of protein folding as it occurs on the ribosome.
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Affiliation(s)
- Abid Javed
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - John Christodoulou
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - Lisa D. Cabrita
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
- Institute of Structural and Molecular Biology, University College London (UCL), Gower Street, London WC1E 6BT, England
| | - Elena V. Orlova
- Institute of Structural and Molecular Biology, Birkbeck College, Malet Street, London WC1E 7HX, England
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885
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Lucas X, Ciulli A. Recognition of substrate degrons by E3 ubiquitin ligases and modulation by small-molecule mimicry strategies. Curr Opin Struct Biol 2017; 44:101-110. [DOI: 10.1016/j.sbi.2016.12.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 12/12/2016] [Accepted: 12/16/2016] [Indexed: 12/11/2022]
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886
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Sorokina I, Mushegian A. Rotational restriction of nascent peptides as an essential element of co-translational protein folding: possible molecular players and structural consequences. Biol Direct 2017; 12:14. [PMID: 28569180 PMCID: PMC5452302 DOI: 10.1186/s13062-017-0186-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2017] [Accepted: 05/23/2017] [Indexed: 12/13/2022] Open
Abstract
Background A basic tenet of protein science is that all information about the spatial structure of proteins is present in their sequences. Nonetheless, many proteins fail to attain native structure upon experimental denaturation and refolding in vitro, raising the question of the specific role of cellular machinery in protein folding in vivo. Recently, we hypothesized that energy-dependent twisting of the protein backbone is an unappreciated essential factor guiding the protein folding process in vivo. Torque force may be applied by the ribosome co-translationally, and when accompanied by simultaneous restriction of the rotational mobility of the distal part of the growing chain, the resulting tension in the protein backbone would facilitate the formation of local secondary structure and direct the folding process. Results Our model of the early stages of protein folding in vivo postulates that the free motion of both terminal regions of the protein during its synthesis and maturation is restricted. The long-known but unexplained phenomenon of statistical overrepresentation of protein termini on the surfaces of the protein structures may be an indication of the backbone twist-based folding mechanism; sustained maintenance of a twist requires that both ends of the protein chain are anchored in space, and if the ends are released only after the majority of folding is complete, they are much more likely to remain on the surface of the molecule. We identified the molecular components that are likely to play a role in the twisting of the nascent protein chain and in the anchoring of its N-terminus. The twist may be induced at the C-terminus of the nascent polypeptide by the peptidyltransferase center of the ribosome. Several ribosome-associated proteins, including the trigger factor in bacteria and the nascent polypeptide-associated complex in archaea and eukaryotes, may restrict the rotational mobility of the N-proximal regions of the peptides. Conclusions Many experimental observations are consistent with the hypothesis of co-translational twisting of the protein backbone. Several molecular players in this hypothetical mechanism of protein folding can be suggested. In addition, the new view of protein folding in vivo opens the possibility of novel potential drug targets to combat human protein folding diseases. Reviewers This article was reviewed by Lakshminarayan Iyer and István Simon. Electronic supplementary material The online version of this article (doi:10.1186/s13062-017-0186-1) contains supplementary material, which is available to authorized users.
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887
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Capaz JC, Tunnah L, MacCormack TJ, Lamarre SG, Sykes AV, Driedzic WR. Hypoxic Induced Decrease in Oxygen Consumption in Cuttlefish ( Sepia officinalis) Is Associated with Minor Increases in Mantle Octopine but No Changes in Markers of Protein Turnover. Front Physiol 2017; 8:344. [PMID: 28603503 PMCID: PMC5445181 DOI: 10.3389/fphys.2017.00344] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2017] [Accepted: 05/11/2017] [Indexed: 12/25/2022] Open
Abstract
The common cuttlefish (Sepia officinalis), a dominant species in the north-east Atlantic ocean and Mediterranean Sea, is potentially subject to hypoxic conditions due to eutrophication of coastal waters and intensive aquaculture. Here we initiate studies on the biochemical response to an anticipated level of hypoxia. Cuttlefish challenged for 1 h at an oxygen level of 50% dissolved oxygen saturation showed a decrease in oxygen consumption of 37% associated with an 85% increase in ventilation rate. Octopine levels were increased to a small but significant level in mantle, whereas there was no change in gill or heart. There were no changes in mantle free glucose or glycogen levels. Similarly, the hypoxic period did not result in changes in HSP70 or polyubiquinated protein levels in mantle, gill, or heart. As such, it appears that although there was a decrease in metabolic rate there was only a minor increase in anaerobic metabolism as evidenced by octopine accumulation and no biochemical changes that are hallmarks of alterations in protein trafficking. Experiments with isolated preparations of mantle, gill, and heart revealed that pharmacological inhibition of protein synthesis could decrease oxygen consumption by 32 to 42% or Na+/K+ ATPase activity by 24 to 54% dependent upon tissue type. We propose that the decrease in whole animal oxygen consumption was potentially the result of controlled decreases in the energy demanding processes of both protein synthesis and Na+/K+ ATPase activity.
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Affiliation(s)
- Juan C Capaz
- Centro de Ciências do Mar do Algarve, Universidade do AlgarveFaro, Portugal
| | - Louise Tunnah
- Department of Chemistry and Biochemistry, Mount Allison UniversitySackville, NB, Canada
| | - Tyson J MacCormack
- Department of Chemistry and Biochemistry, Mount Allison UniversitySackville, NB, Canada
| | - Simon G Lamarre
- Département de Biologie, Université de MonctonMoncton, NB, Canada
| | - Antonio V Sykes
- Centro de Ciências do Mar do Algarve, Universidade do AlgarveFaro, Portugal
| | - William R Driedzic
- Department of Ocean Sciences, Memorial University of NewfoundlandSt. John's, NL, Canada
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888
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Mutual Interplay between the Human Cytomegalovirus Terminase Subunits pUL51, pUL56, and pUL89 Promotes Terminase Complex Formation. J Virol 2017; 91:JVI.02384-16. [PMID: 28356534 DOI: 10.1128/jvi.02384-16] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 03/17/2017] [Indexed: 01/05/2023] Open
Abstract
Human cytomegalovirus (HCMV) genome encapsidation requires several essential viral proteins, among them pUL56, pUL89, and the recently described pUL51, which constitute the viral terminase. To gain insight into terminase complex assembly, we investigated interactions between the individual subunits. For analysis in the viral context, HCMV bacterial artificial chromosomes carrying deletions in the open reading frames encoding the terminase proteins were used. These experiments were complemented by transient-transfection assays with plasmids expressing the terminase components. We found that if one terminase protein was missing, the levels of the other terminase proteins were markedly diminished, which could be overcome by proteasome inhibition or providing the missing subunit in trans These data imply that sequestration of the individual subunits within the terminase complex protects them from proteasomal turnover. The finding that efficient interactions among the terminase proteins occurred only when all three were present together is reminiscent of a folding-upon-binding principle leading to cooperative stability. Furthermore, whereas pUL56 was translocated into the nucleus on its own, correct nuclear localization of pUL51 and pUL89 again required all three terminase constituents. Altogether, these features point to a model of the HCMV terminase as a multiprotein complex in which the three players regulate each other concerning stability, subcellular localization, and assembly into the functional tripartite holoenzyme.IMPORTANCE HCMV is a major risk factor in immunocompromised individuals, and congenital CMV infection is the leading viral cause for long-term sequelae, including deafness and mental retardation. The current treatment of CMV disease is based on drugs sharing the same mechanism, namely, inhibiting viral DNA replication, and often results in adverse side effects and the appearance of resistant virus strains. Recently, the HCMV terminase has emerged as an auspicious target for novel antiviral drugs. A new drug candidate inhibiting the HCMV terminase, Letermovir, displayed excellent potency in clinical trials; however, its precise mode of action is not understood yet. Here, we describe the mutual dependence of the HCMV terminase constituents for their assembly into a functional terminase complex. Besides providing new basic insights into terminase formation, these results will be valuable when studying the mechanism of action for drugs targeting the HCMV terminase and developing additional substances interfering with viral genome encapsidation.
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889
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Magariños M, Pulido S, Aburto MR, de Iriarte Rodríguez R, Varela-Nieto I. Autophagy in the Vertebrate Inner Ear. Front Cell Dev Biol 2017; 5:56. [PMID: 28603711 PMCID: PMC5445191 DOI: 10.3389/fcell.2017.00056] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2017] [Accepted: 05/09/2017] [Indexed: 12/13/2022] Open
Abstract
Autophagy is a conserved catabolic process that results in the lysosomal degradation of cell components. During development, autophagy is associated with tissue and organ remodeling, and under physiological conditions it is tightly regulated as it plays a housekeeping role in removing misfolded proteins and damaged organelles. The vertebrate inner ear is a complex sensory organ responsible for the perception of sound and for balance. Cell survival, death and proliferation, as well as cell fate specification and differentiation, are processes that are strictly coordinated during the development of the inner ear in order to generate the more than a dozen specialized cell types that constitute this structure. Here, we review the existing evidence that implicates autophagy in the generation of the vertebrate inner ear. At early stages of chicken otic development, inhibiting autophagy impairs neurogenesis and causes aberrant otocyst morphogenesis. Autophagy provides energy for the clearing of dying cells and it favors neuronal differentiation. Moreover, autophagy is required for proper vestibular development in the mouse inner ear. The autophagy-related genes Becn1, Atg4g, Atg5, and Atg9, are expressed in the inner ear from late developmental stages to adulthood, and Atg4b mutants show impaired vestibular behavior associated to defects in otoconial biogenesis that are also common to Atg5 mutants. Autophagic flux appears to be age-regulated, augmenting from perinatal stages to young adulthood in mice. This up-regulation is concomitant with the functional maturation of the hearing receptor. Hence, autophagy can be considered an intracellular pathway fundamental for in vertebrate inner ear development and maturation.
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Affiliation(s)
- Marta Magariños
- Department of Endocrine and Nervous Systems Pathophysiology, Instituto de Investigaciones Biomédicas "Alberto Sols," CSIC-UAMMadrid, Spain.,CIBERER, Unit 761, Instituto de Salud Carlos IIIMadrid, Spain.,Departamento de Biología, Universidad Autónoma de MadridMadrid, Spain
| | - Sara Pulido
- Department of Endocrine and Nervous Systems Pathophysiology, Instituto de Investigaciones Biomédicas "Alberto Sols," CSIC-UAMMadrid, Spain.,CIBERER, Unit 761, Instituto de Salud Carlos IIIMadrid, Spain
| | - María R Aburto
- Department of Endocrine and Nervous Systems Pathophysiology, Instituto de Investigaciones Biomédicas "Alberto Sols," CSIC-UAMMadrid, Spain
| | - Rocío de Iriarte Rodríguez
- Department of Endocrine and Nervous Systems Pathophysiology, Instituto de Investigaciones Biomédicas "Alberto Sols," CSIC-UAMMadrid, Spain
| | - Isabel Varela-Nieto
- Department of Endocrine and Nervous Systems Pathophysiology, Instituto de Investigaciones Biomédicas "Alberto Sols," CSIC-UAMMadrid, Spain.,CIBERER, Unit 761, Instituto de Salud Carlos IIIMadrid, Spain.,Instituto de Investigación Hospital Universitario La Paz (IdiPAZ)Madrid, Spain
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890
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Using bicistronic constructs to evaluate the chaperone activities of heat shock proteins in cells. Sci Rep 2017; 7:2387. [PMID: 28539657 PMCID: PMC5443837 DOI: 10.1038/s41598-017-02459-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 04/12/2017] [Indexed: 01/03/2023] Open
Abstract
Heat shock proteins (Hsps) are molecular chaperones that prevent the aggregation of client proteins by facilitating their refolding, or trafficking them for degradation. The chaperone activities of Hsps are dependent on dynamic protein-protein interactions, including their oligomerisation into large multi-subunit complexes. Thus, tagging Hsps with fluorescent proteins can interfere with their chaperone activity. To overcome this limitation, we have exploited bicistronic constructs for the concurrent expression of a non-tagged Hsp and fluorescent reporter from a single mRNA in cells. We used the Hsp-encoding bicistronic constructs in a cell-based model of protein aggregation, using a destabilised (mutant) form of firefly luciferase (mFluc) that forms inclusion bodies in cells. Expression of Hsp40, Hsp70, or Hsp40 and Hsp70 in cells expressing mFluc decreased the formation of inclusion bodies by 25–46% compared to controls. Moreover, there was a concentration-dependent decrease in the proportion of cells with inclusions when Hsp70, or Hsp40 and Hsp70 were co-expressed with mFluc in cells. The Hsp-encoding bicistronic constructs enable transfection efficiencies and concentration-dependent effects of Hsp expression to be determined using fluorescence based techniques, without the need to tag the Hsp with a fluorescent protein.
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891
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Sopha P, Ren HY, Grove DE, Cyr DM. Endoplasmic reticulum stress-induced degradation of DNAJB12 stimulates BOK accumulation and primes cancer cells for apoptosis. J Biol Chem 2017; 292:11792-11803. [PMID: 28536268 DOI: 10.1074/jbc.m117.785113] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Revised: 05/19/2017] [Indexed: 12/18/2022] Open
Abstract
DNAJB12 (JB12) is an endoplasmic reticulum (ER)-associated Hsp40 family protein that recruits Hsp70 to the ER surface to coordinate the function of ER-associated and cytosolic chaperone systems in protein quality control. Hsp70 is stress-inducible, but paradoxically, we report here that JB12 was degraded by the proteasome during severe ER stress. Destabilized JB12 was degraded by ER-associated degradation complexes that contained HERP, Sel1L, and gp78. JB12 was the only ER-associated chaperone that was destabilized by reductive stress. JB12 knockdown by siRNA led to the induction of caspase processing but not the unfolded protein response. ER stress-induced apoptosis is regulated by the highly labile and ER-associated BCL-2 family member BOK, which is controlled at the level of protein stability by ER-associated degradation components. We found that JB12 was required in human hepatoma cell line 7 (Huh-7) liver cancer cells to maintain BOK at low levels, and BOK was detected in complexes with JB12 and gp78. Depletion of JB12 during reductive stress or by shRNA from Huh-7 cells was associated with accumulation of BOK and activation of Caspase 3, 7, and 9. The absence of JB12 sensitized Huh-7 to death caused by proteotoxic agents and the proapoptotic chemotherapeutic LCL-161. In summary, JB12 is a stress-sensitive Hsp40 whose degradation during severe ER stress provides a mechanism to promote BOK accumulation and induction of apoptosis.
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Affiliation(s)
- Pattarawut Sopha
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599; Program of Applied Biological Sciences, Chulabhorn Graduate Institute, 54 Kamphaeng Phet 6, Talat Bang Khen, Lak Si, Bangkok 10210, Thailand.
| | - Hong Yu Ren
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Diane E Grove
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599
| | - Douglas M Cyr
- Department of Cell Biology and Physiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599.
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892
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Upadhyay A, Joshi V, Amanullah A, Mishra R, Arora N, Prasad A, Mishra A. E3 Ubiquitin Ligases Neurobiological Mechanisms: Development to Degeneration. Front Mol Neurosci 2017; 10:151. [PMID: 28579943 PMCID: PMC5437216 DOI: 10.3389/fnmol.2017.00151] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2017] [Accepted: 05/04/2017] [Indexed: 01/08/2023] Open
Abstract
Cells regularly synthesize new proteins to replace old or damaged proteins. Deposition of various aberrant proteins in specific brain regions leads to neurodegeneration and aging. The cellular protein quality control system develop various defense mechanisms against the accumulation of misfolded and aggregated proteins. The mechanisms underlying the selective recognition of specific crucial protein or misfolded proteins are majorly governed by quality control E3 ubiquitin ligases mediated through ubiquitin-proteasome system. Few known E3 ubiquitin ligases have shown prominent neurodevelopmental functions, but their interactions with different developmental proteins play critical roles in neurodevelopmental disorders. Several questions are yet to be understood properly. How E3 ubiquitin ligases determine the specificity and regulate degradation of a particular substrate involved in neuronal proliferation and differentiation is certainly the one, which needs detailed investigations. Another important question is how neurodevelopmental E3 ubiquitin ligases specifically differentiate between their versatile range of substrates and timing of their functional modulations during different phases of development. The premise of this article is to understand how few E3 ubiquitin ligases sense major molecular events, which are crucial for human brain development from its early embryonic stages to throughout adolescence period. A better understanding of these few E3 ubiquitin ligases and their interactions with other potential proteins will provide invaluable insight into disease mechanisms to approach toward therapeutic interventions.
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Affiliation(s)
- Arun Upadhyay
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Vibhuti Joshi
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Ayeman Amanullah
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Ribhav Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
| | - Naina Arora
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Amit Prasad
- School of Basic Sciences, Indian Institute of Technology MandiMandi, India
| | - Amit Mishra
- Cellular and Molecular Neurobiology Unit, Indian Institute of Technology JodhpurJodhpur, India
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893
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Flagmeier P, De S, Wirthensohn DC, Lee SF, Vincke C, Muyldermans S, Knowles TPJ, Gandhi S, Dobson CM, Klenerman D. Ultrasensitive Measurement of Ca 2+ Influx into Lipid Vesicles Induced by Protein Aggregates. Angew Chem Int Ed Engl 2017; 56:7750-7754. [PMID: 28474754 PMCID: PMC5615231 DOI: 10.1002/anie.201700966] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/23/2017] [Indexed: 12/15/2022]
Abstract
To quantify and characterize the potentially toxic protein aggregates associated with neurodegenerative diseases, a high‐throughput assay based on measuring the extent of aggregate‐induced Ca2+ entry into individual lipid vesicles has been developed. This approach was implemented by tethering vesicles containing a Ca2+ sensitive fluorescent dye to a passivated surface and measuring changes in the fluorescence as a result of membrane disruption using total internal reflection microscopy. Picomolar concentrations of Aβ42 oligomers could be observed to induce Ca2+ influx, which could be inhibited by the addition of a naturally occurring chaperone and a nanobody designed to bind to the Aβ peptide. We show that the assay can be used to study aggregates from other proteins, such as α‐synuclein, and to probe the effects of complex biofluids, such as cerebrospinal fluid, and thus has wide applicability.
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Affiliation(s)
- Patrick Flagmeier
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Suman De
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David C Wirthensohn
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Steven F Lee
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Cécile Vincke
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Serge Muyldermans
- Laboratory of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Brussels, Belgium
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - Sonia Gandhi
- Department of Molecular Neuroscience, Institute of Neurology, University College London, Queen Square, London, WC1N 3BG, UK
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge, CB2 1EW, UK
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894
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Aivazidis S, Coughlan CM, Rauniyar AK, Jiang H, Liggett LA, Maclean KN, Roede JR. The burden of trisomy 21 disrupts the proteostasis network in Down syndrome. PLoS One 2017; 12:e0176307. [PMID: 28430800 PMCID: PMC5400264 DOI: 10.1371/journal.pone.0176307] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2017] [Accepted: 04/07/2017] [Indexed: 12/27/2022] Open
Abstract
Down syndrome (DS) is a genetic disorder caused by trisomy of chromosome 21. Abnormalities in chromosome number have the potential to lead to disruption of the proteostasis network (PN) and accumulation of misfolded proteins. DS individuals suffer from several comorbidities, and we hypothesized that disruption of proteostasis could contribute to the observed pathology and decreased cell viability in DS. Our results confirm the presence of a disrupted PN in DS, as several of its elements, including the unfolded protein response, chaperone system, and proteasomal degradation exhibited significant alterations compared to euploid controls in both cell and mouse models. Additionally, when cell models were treated with compounds that promote disrupted proteostasis, we observed diminished levels of cell viability in DS compared to controls. Collectively our findings provide a cellular-level characterization of PN dysfunction in DS and an improved understanding of the potential pathogenic mechanisms contributing to disrupted cellular physiology in DS. Lastly, this study highlights the future potential of designing therapeutic strategies that mitigate protein quality control dysfunction.
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Affiliation(s)
- Stefanos Aivazidis
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, United States of America
| | - Christina M. Coughlan
- Department of Neurology, University of Colorado School of Medicine, Aurora, CO, United States of America
- The Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States of America
| | - Abhishek K. Rauniyar
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, United States of America
| | - Hua Jiang
- The Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States of America
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - L. Alexander Liggett
- The Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States of America
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - Kenneth N. Maclean
- The Linda Crnic Institute for Down Syndrome, University of Colorado, Aurora, CO, United States of America
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO, United States of America
| | - James R. Roede
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado, Aurora, CO, United States of America
- * E-mail:
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895
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Lai AL, Clerico EM, Blackburn ME, Patel NA, Robinson CV, Borbat PP, Freed JH, Gierasch LM. Key features of an Hsp70 chaperone allosteric landscape revealed by ion-mobility native mass spectrometry and double electron-electron resonance. J Biol Chem 2017; 292:8773-8785. [PMID: 28428246 PMCID: PMC5448104 DOI: 10.1074/jbc.m116.770404] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2016] [Revised: 04/12/2017] [Indexed: 11/06/2022] Open
Abstract
Proteins are dynamic entities that populate conformational ensembles, and most functions of proteins depend on their dynamic character. Allostery, in particular, relies on ligand-modulated shifts in these conformational ensembles. Hsp70s are allosteric molecular chaperones with conformational landscapes that involve large rearrangements of their two domains (viz. the nucleotide-binding domain and substrate-binding domain) in response to adenine nucleotides and substrates. However, it remains unclear how the Hsp70 conformational ensemble is populated at each point of the allosteric cycle and how ligands control these populations. We have mapped the conformational species present under different ligand-binding conditions throughout the allosteric cycle of the Escherichia coli Hsp70 DnaK by two complementary methods, ion-mobility mass spectrometry and double electron-electron resonance. Our results obtained under biologically relevant ligand-bound conditions confirm the current picture derived from NMR and crystallographic data of domain docking upon ATP binding and undocking in response to ADP and substrate. Additionally, we find that the helical lid of DnaK is a highly dynamic unit of the structure in all ligand-bound states. Importantly, we demonstrate that DnaK populates a partially docked state in the presence of ATP and substrate and that this state represents an energy minimum on the DnaK allosteric landscape. Because Hsp70s are emerging as potential drug targets for many diseases, fully mapping an allosteric landscape of a molecular chaperone like DnaK will facilitate the development of small molecules that modulate Hsp70 function via allosteric mechanisms.
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Affiliation(s)
- Alex L Lai
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-2703
| | | | - Mandy E Blackburn
- the School of Environmental, Physical, and Applied Sciences, University of Central Missouri, Warrensburg, Missouri 64093, and
| | - Nisha A Patel
- the Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Carol V Robinson
- the Physical and Theoretical Chemistry Laboratory, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Peter P Borbat
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-2703
| | - Jack H Freed
- From the Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-2703
| | - Lila M Gierasch
- the Departments of Biochemistry and Molecular Biology and .,Chemistry, University of Massachusetts, Amherst, Massachusetts 01003
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896
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Sampuda KM, Riley M, Boyd L. Stress induced nuclear granules form in response to accumulation of misfolded proteins in Caenorhabditis elegans. BMC Cell Biol 2017; 18:18. [PMID: 28424053 PMCID: PMC5395811 DOI: 10.1186/s12860-017-0136-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/07/2017] [Indexed: 01/30/2023] Open
Abstract
Background Environmental stress can affect the viability or fecundity of an organism. Environmental stressors may affect the genome or the proteome and can cause cellular distress by contributing to protein damage or misfolding. This study examines the cellular response to environmental stress in the germline of the nematode, C. elegans. Results Salt stress, oxidative stress, and starvation, but not heat shock, induce the relocalization of ubiquitin, proteasome, and the TIAR-2 protein into distinct subnuclear regions referred to as stress induced nuclear granules (SINGs). The SINGs form within 1 h of stress initiation and do not require intertissue signaling. K48-linked polyubiquitin chains but not K63 chains are enriched in SINGs. Worms with a mutation in the conjugating enzyme, ubc-18, do not form SINGs. Additionally, knockdown of ubc-20 and ubc-22 reduces the level of SING formation as does knockdown of the ubiquitin ligase chn-1, a CHIP homolog. The nuclear import machinery is required for SING formation. Stressed embryos containing SINGs fail to hatch and cell division in these embryos is halted. The formation of SINGs can be prevented by pre-exposure to a brief period of heat shock before stress exposure. Heat shock inhibition of SINGs is dependent upon the HSF-1 transcription factor. Conclusions The heat shock results suggest that chaperone expression can prevent SING formation and that the accumulation of damaged or misfolded proteins is a necessary precursor to SING formation. Thus, SINGs may be part of a novel protein quality control system. The data suggest an interesting model where SINGs represent sites of localized protein degradation for nuclear or cytosolic proteins. Thus, the physiological impacts of environmental stress may begin at the cellular level with the formation of stress induced nuclear granules. Electronic supplementary material The online version of this article (doi:10.1186/s12860-017-0136-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Katherine M Sampuda
- Department of Biology, Middle Tennessee State University, 1301 E. Main Street, Murfreesboro, TN, 37132, USA
| | - Mason Riley
- Department of Biology, Middle Tennessee State University, 1301 E. Main Street, Murfreesboro, TN, 37132, USA
| | - Lynn Boyd
- Department of Biology, Middle Tennessee State University, 1301 E. Main Street, Murfreesboro, TN, 37132, USA.
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897
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Jha JK, Li M, Ghirlando R, Miller Jenkins LM, Wlodawer A, Chattoraj D. The DnaK Chaperone Uses Different Mechanisms To Promote and Inhibit Replication of Vibrio cholerae Chromosome 2. mBio 2017; 8:e00427-17. [PMID: 28420739 PMCID: PMC5395669 DOI: 10.1128/mbio.00427-17] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2017] [Accepted: 03/20/2017] [Indexed: 12/17/2022] Open
Abstract
Replication of Vibrio cholerae chromosome 2 (Chr2) depends on molecular chaperone DnaK to facilitate binding of the initiator (RctB) to the replication origin. The binding occurs at two kinds of site, 12-mers and 39-mers, which promote and inhibit replication, respectively. Here we show that DnaK employs different mechanisms to enhance the two kinds of binding. We found that mutations in rctB that reduce DnaK binding also reduce 12-mer binding and initiation. The initiation defect is suppressed by second-site mutations that increase 12-mer binding only marginally. Instead, they reduce replication inhibitory mechanisms: RctB dimerization and 39-mer binding. One suppressing change was in a dimerization domain which is folded similarly to the initiator of an iteron plasmid-the presumed progenitor of Chr2. In plasmids, DnaK promotes initiation by reducing dimerization. A different mutation was in the 39-mer binding domain of RctB and inactivated it, indicating an alternative suppression mechanism. Paradoxically, although DnaK increases 39-mer binding, the increase was also achieved by inactivating the DnaK binding site of RctB. This result suggests that the site inhibits the 39-mer binding domain (via autoinhibition) when prevented from binding DnaK. Taken together, our results reveal an important feature of the transition from plasmid to chromosome: the Chr2 initiator retains the plasmid-like dimerization domain and its control by chaperones but uses the chaperones in an unprecedented way to control the inhibitory 39-mer binding.IMPORTANCE The capacity of proteins to undergo remodeling provides opportunities to control their function. However, remodeling remains a poorly understood aspect of the structure-function paradigm due to its dynamic nature. Here we have studied remodeling of the initiator of replication of Vibrio cholerae Chr2 by the molecular chaperone, DnaK. We show that DnaK binds to a site on the Chr2 initiator (RctB) that promotes initiation by reducing the initiator's propensity to dimerize. Dimerization of the initiator of the putative plasmid progenitor of Chr2 is also reduced by DnaK, which promotes initiation. Paradoxically, the DnaK binding also promotes replication inhibition by reducing an autoinhibitory activity of RctB. In the plasmid-to-chromosome transition, it appears that the initiator has acquired an autoinhibitory activity and along with it a new chaperone activity that apparently helps to control replication inhibition independently of replication promotion.
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Affiliation(s)
- Jyoti K Jha
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, Maryland, USA
| | - Mi Li
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland, USA
- Basic Science Program, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Rodolfo Ghirlando
- Laboratory of Molecular Biology, NIDDK, NIH, Bethesda, Maryland, USA
| | | | - Alexander Wlodawer
- Macromolecular Crystallography Laboratory, NCI, Frederick, Maryland, USA
| | - Dhruba Chattoraj
- Laboratory of Biochemistry and Molecular Biology, CCR, NCI, NIH, Bethesda, Maryland, USA
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898
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Liu F, Qin Y, Yu S, Soares DC, Yang L, Weng J, Li C, Gao M, Lu Z, Hu X, Liu X, Jiang T, Liu JY, Shu X, Tang Z, Liu M. Pathogenic mutations in retinitis pigmentosa 2 predominantly result in loss of RP2 protein stability in humans and zebrafish. J Biol Chem 2017; 292:6225-6239. [PMID: 28209709 PMCID: PMC5391753 DOI: 10.1074/jbc.m116.760314] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 02/14/2017] [Indexed: 12/20/2022] Open
Abstract
Mutations in retinitis pigmentosa 2 (RP2) account for 10-20% of X-linked retinitis pigmentosa (RP) cases. The encoded RP2 protein is implicated in ciliary trafficking of myristoylated and prenylated proteins in photoreceptor cells. To date >70 mutations in RP2 have been identified. How these mutations disrupt the function of RP2 is not fully understood. Here we report a novel in-frame 12-bp deletion (c.357_368del, p.Pro120_Gly123del) in zebrafish rp2 The mutant zebrafish shows reduced rod phototransduction proteins and progressive retinal degeneration. Interestingly, the protein level of mutant Rp2 is almost undetectable, whereas its mRNA level is near normal, indicating a possible post-translational effect of the mutation. Consistent with this hypothesis, the equivalent 12-bp deletion in human RP2 markedly impairs RP2 protein stability and reduces its protein level. Furthermore, we found that a majority of the RP2 pathogenic mutations (including missense, single-residue deletion, and C-terminal truncation mutations) severely destabilize the RP2 protein. The destabilized RP2 mutant proteins are degraded via the proteasome pathway, resulting in dramatically decreased protein levels. The remaining non-destabilizing mutations T87I, R118H/R118G/R118L/R118C, E138G, and R211H/R211L are suggested to impair the interaction between RP2 and its protein partners (such as ARL3) or with as yet unknown partners. By utilizing a combination of in silico, in vitro, and in vivo approaches, our work comprehensively indicates that loss of RP2 protein structural stability is the predominating pathogenic consequence for most RP2 mutations. Our study also reveals a role of the C-terminal domain of RP2 in maintaining the overall protein stability.
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Affiliation(s)
- Fei Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Yayun Qin
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Shanshan Yu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Dinesh C Soares
- MRC Human Genetics Unit/Centre for Genomic and Experimental Medicine, MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, United Kingdom, and
| | - Lifang Yang
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jun Weng
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Chang Li
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Meng Gao
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Zhaojing Lu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xuebin Hu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xiliang Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Tao Jiang
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Jing Yu Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Xinhua Shu
- Department of Life Sciences, Glasgow Caledonian University, Glasgow G4 0BA, United Kingdom
| | - Zhaohui Tang
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| | - Mugen Liu
- From the Key Laboratory of Molecular Biophysics of Ministry of Education, Department of Genetics and Developmental Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China,
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899
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Sala AJ, Bott LC, Morimoto RI. Shaping proteostasis at the cellular, tissue, and organismal level. J Cell Biol 2017; 216:1231-1241. [PMID: 28400444 PMCID: PMC5412572 DOI: 10.1083/jcb.201612111] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/20/2017] [Accepted: 03/20/2017] [Indexed: 01/22/2023] Open
Abstract
The proteostasis network (PN) regulates protein synthesis, folding, transport, and degradation to maintain proteome integrity and limit the accumulation of protein aggregates, a hallmark of aging and degenerative diseases. In multicellular organisms, the PN is regulated at the cellular, tissue, and systemic level to ensure organismal health and longevity. Here we review these three layers of PN regulation and examine how they collectively maintain cellular homeostasis, achieve cell type-specific proteomes, and coordinate proteostasis across tissues. A precise understanding of these layers of control has important implications for organismal health and could offer new therapeutic approaches for neurodegenerative diseases and other chronic disorders related to PN dysfunction.
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Affiliation(s)
- Ambre J Sala
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208
| | - Laura C Bott
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208
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900
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Mannini B, Chiti F. Chaperones as Suppressors of Protein Misfolded Oligomer Toxicity. Front Mol Neurosci 2017; 10:98. [PMID: 28424588 PMCID: PMC5380756 DOI: 10.3389/fnmol.2017.00098] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 03/23/2017] [Indexed: 01/30/2023] Open
Abstract
Chaperones have long been recognized to play well defined functions such as to: (i) assist protein folding and promote formation and maintenance of multisubunit complexes; (ii) mediate protein degradation; (iii) inhibit protein aggregation; and (iv) promote disassembly of undesired aberrant protein aggregates. In addition to these well-established functions, it is increasingly clear that chaperones can also interact with aberrant protein aggregates, such as pre-fibrillar oligomers and fibrils, and inhibit their toxicity commonly associated with neurodegenerative diseases without promoting their disassembly. In particular, the evidence collected so far in different labs, exploiting different experimental approaches and using different chaperones and client aggregated proteins, indicates the existence of two distinct mechanisms of action mediated by the chaperones to neutralize the toxicity of aberrant proteins oligomers: (i) direct binding of the chaperones to the hydrophobic patches exposed on the oligomer/fibril surface, with resulting shielding or masking of the moieties responsible for the aberrant interactions with cellular targets; (ii) chaperone-mediated conversion of aberrant protein aggregates into large and more innocuous species, resulting in a decrease of their surface-to-volume ratio and diffusibility and in deposits more easily manageable by clearance mechanisms, such as autophagy. In this review article we will describe the in vitro and in vivo evidence supporting both mechanisms and how this results in a suppression of the detrimental effects caused by protein misfolded aggregates.
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Affiliation(s)
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of FlorenceFlorence, Italy
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