1
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Guo Z, Chiesa G, Yin J, Sanford A, Meier S, Khalil AS, Cheng JX. Structural Mapping of Protein Aggregates in Live Cells Modeling Huntington's Disease. Angew Chem Int Ed Engl 2024:e202408163. [PMID: 38880765 DOI: 10.1002/anie.202408163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 06/18/2024]
Abstract
While protein aggregation is a hallmark of many neurodegenerative diseases, acquiring structural information on protein aggregates inside live cells remains challenging. Traditional microscopy does not provide structural information on protein systems. Routinely used fluorescent protein tags, such as Green Fluorescent Protein (GFP), might perturb native structures. Here, we report a counter-propagating mid-infrared photothermal imaging approach enabling mapping of secondary structure of protein aggregates in live cells modeling Huntington's disease. By comparing mid-infrared photothermal spectra of label-free and GFP-tagged huntingtin inclusions, we demonstrate that GFP fusions indeed perturb the secondary structure of aggregates. By implementing spectra with small spatial step for dissecting spectral features within sub-micrometer distances, we reveal that huntingtin inclusions partition into a β-sheet-rich core and a ɑ-helix-rich shell. We further demonstrate that this structural partition exists only in cells with the [RNQ+] prion state, while [rnq-] cells only carry smaller β-rich non-toxic aggregates. Collectively, our methodology has the potential to unveil detailed structural information on protein assemblies in live cells, enabling high-throughput structural screenings of macromolecular assemblies.
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Affiliation(s)
- Zhongyue Guo
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
| | - Giulio Chiesa
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Jiaze Yin
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
| | - Adam Sanford
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
| | - Stefan Meier
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
| | - Ahmad S Khalil
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Biological Design Center, Boston University, Boston, MA 02215, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02215, USA
| | - Ji-Xin Cheng
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA
- Photonics Center, Boston University, Boston, MA 02215, USA
- Department of Electrical and Computer Engineering, Boston University, Boston, MA 02215, USA
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2
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Aviner R, Lee TT, Masto VB, Li KH, Andino R, Frydman J. Polyglutamine-mediated ribotoxicity disrupts proteostasis and stress responses in Huntington's disease. Nat Cell Biol 2024; 26:892-902. [PMID: 38741019 DOI: 10.1038/s41556-024-01414-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Accepted: 04/01/2024] [Indexed: 05/16/2024]
Abstract
Huntington's disease (HD) is a neurodegenerative disorder caused by expansion of a CAG trinucleotide repeat in the Huntingtin (HTT) gene, encoding a homopolymeric polyglutamine (polyQ) tract. Although mutant HTT (mHTT) protein is known to aggregate, the links between aggregation and neurotoxicity remain unclear. Here we show that both translation and aggregation of wild-type HTT and mHTT are regulated by a stress-responsive upstream open reading frame and that polyQ expansions cause abortive translation termination and release of truncated, aggregation-prone mHTT fragments. Notably, we find that mHTT depletes translation elongation factor eIF5A in brains of symptomatic HD mice and cultured HD cells, leading to pervasive ribosome pausing and collisions. Loss of eIF5A disrupts homeostatic controls and impairs recovery from acute stress. Importantly, drugs that inhibit translation initiation reduce premature termination and mitigate this escalating cascade of ribotoxic stress and dysfunction in HD.
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Affiliation(s)
- Ranen Aviner
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
- Chan Zuckerberg Biohub San Francisco, San Francisco, CA, USA
| | - Ting-Ting Lee
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Vincent B Masto
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA
| | - Kathy H Li
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, USA
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, CA, USA
| | - Judith Frydman
- Department of Biology and Department of Genetics, Stanford University, Stanford, CA, USA.
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3
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Zhao DY, Bäuerlein FJB, Saha I, Hartl FU, Baumeister W, Wilfling F. Autophagy preferentially degrades non-fibrillar polyQ aggregates. Mol Cell 2024; 84:1980-1994.e8. [PMID: 38759629 DOI: 10.1016/j.molcel.2024.04.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 01/30/2024] [Accepted: 04/23/2024] [Indexed: 05/19/2024]
Abstract
Aggregation of proteins containing expanded polyglutamine (polyQ) repeats is the cytopathologic hallmark of a group of dominantly inherited neurodegenerative diseases, including Huntington's disease (HD). Huntingtin (Htt), the disease protein of HD, forms amyloid-like fibrils by liquid-to-solid phase transition. Macroautophagy has been proposed to clear polyQ aggregates, but the efficiency of aggrephagy is limited. Here, we used cryo-electron tomography to visualize the interactions of autophagosomes with polyQ aggregates in cultured cells in situ. We found that an amorphous aggregate phase exists next to the radially organized polyQ fibrils. Autophagosomes preferentially engulfed this amorphous material, mediated by interactions between the autophagy receptor p62/SQSTM1 and the non-fibrillar aggregate surface. In contrast, amyloid fibrils excluded p62 and evaded clearance, resulting in trapping of autophagic structures. These results suggest that the limited efficiency of autophagy in clearing polyQ aggregates is due to the inability of autophagosomes to interact productively with the non-deformable, fibrillar disease aggregates.
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Affiliation(s)
- Dorothy Y Zhao
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Felix J B Bäuerlein
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; University Medical Center Göttingen, Institute of Neuropathology, 37077 Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, 37077 Göttingen, Germany
| | - Itika Saha
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA
| | - F Ulrich Hartl
- Max Planck Institute of Biochemistry, Cellular Biochemistry, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
| | - Florian Wilfling
- Max Planck Institute of Biochemistry, Molecular Machines and Signaling, 82152 Martinsried, Germany; Max Planck Institute of Biochemistry, Molecular Structural Biology, 82152 Martinsried, Germany; Max Planck Institute of Biophysics, Mechanisms of Cellular Quality Control, 60438 Frankfurt, Germany; Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD 20815, USA.
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4
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Schneider KL, Hao X, Keuenhof KS, Berglund LL, Fischbach A, Ahmadpour D, Chawla S, Gómez P, Höög JL, Widlund PO, Nyström T. Elimination of virus-like particles reduces protein aggregation and extends replicative lifespan in Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2024; 121:e2313538121. [PMID: 38527193 PMCID: PMC10998562 DOI: 10.1073/pnas.2313538121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 02/04/2024] [Indexed: 03/27/2024] Open
Abstract
A major consequence of aging and stress, in yeast to humans, is an increased accumulation of protein aggregates at distinct sites within the cells. Using genetic screens, immunoelectron microscopy, and three-dimensional modeling in our efforts to elucidate the importance of aggregate annexation, we found that most aggregates in yeast accumulate near the surface of mitochondria. Further, we show that virus-like particles (VLPs), which are part of the retrotransposition cycle of Ty elements, are markedly enriched in these sites of protein aggregation. RNA interference-mediated silencing of Ty expression perturbed aggregate sequestration to mitochondria, reduced overall protein aggregation, mitigated toxicity of a Huntington's disease model, and expanded the replicative lifespan of yeast in a partially Hsp104-dependent manner. The results are in line with recent data demonstrating that VLPs might act as aging factors in mammals, including humans, and extend these findings by linking VLPs to a toxic accumulation of protein aggregates and raising the possibility that they might negatively influence neurological disease progression.
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Affiliation(s)
- K. L. Schneider
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - X. Hao
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - K. S. Keuenhof
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - L. L. Berglund
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - A. Fischbach
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - D. Ahmadpour
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - S. Chawla
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - P. Gómez
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - J. L. Höög
- Department for Chemistry and Molecular Biology, University of Gothenburg, Gothenburg41390, Sweden
| | - P. O. Widlund
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
| | - T. Nyström
- Department of Microbiology and Immunology, Institute for Biomedicine, Sahlgrenska Academy, Centre for Ageing and Health—AgeCap, University of Gothenburg, Gothenburg40530, Sweden
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5
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McCafferty CL, Klumpe S, Amaro RE, Kukulski W, Collinson L, Engel BD. Integrating cellular electron microscopy with multimodal data to explore biology across space and time. Cell 2024; 187:563-584. [PMID: 38306982 DOI: 10.1016/j.cell.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 01/03/2024] [Accepted: 01/03/2024] [Indexed: 02/04/2024]
Abstract
Biology spans a continuum of length and time scales. Individual experimental methods only glimpse discrete pieces of this spectrum but can be combined to construct a more holistic view. In this Review, we detail the latest advancements in volume electron microscopy (vEM) and cryo-electron tomography (cryo-ET), which together can visualize biological complexity across scales from the organization of cells in large tissues to the molecular details inside native cellular environments. In addition, we discuss emerging methodologies for integrating three-dimensional electron microscopy (3DEM) imaging with multimodal data, including fluorescence microscopy, mass spectrometry, single-particle analysis, and AI-based structure prediction. This multifaceted approach fills gaps in the biological continuum, providing functional context, spatial organization, molecular identity, and native interactions. We conclude with a perspective on incorporating diverse data into computational simulations that further bridge and extend length scales while integrating the dimension of time.
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Affiliation(s)
| | - Sven Klumpe
- Research Group CryoEM Technology, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Rommie E Amaro
- Department of Molecular Biology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Wanda Kukulski
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
| | - Lucy Collinson
- Electron Microscopy Science Technology Platform, Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Benjamin D Engel
- Biozentrum, University of Basel, Spitalstrasse 41, 4056 Basel, Switzerland.
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6
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Bai Y, Zhang S, Dong H, Liu Y, Liu C, Zhang X. Advanced Techniques for Detecting Protein Misfolding and Aggregation in Cellular Environments. Chem Rev 2023; 123:12254-12311. [PMID: 37874548 DOI: 10.1021/acs.chemrev.3c00494] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
Protein misfolding and aggregation, a key contributor to the progression of numerous neurodegenerative diseases, results in functional deficiencies and the creation of harmful intermediates. Detailed visualization of this misfolding process is of paramount importance for improving our understanding of disease mechanisms and for the development of potential therapeutic strategies. While in vitro studies using purified proteins have been instrumental in delivering significant insights into protein misfolding, the behavior of these proteins in the complex milieu of living cells often diverges significantly from such simplified environments. Biomedical imaging performed in cell provides cellular-level information with high physiological and pathological relevance, often surpassing the depth of information attainable through in vitro methods. This review highlights a variety of methodologies used to scrutinize protein misfolding within biological systems. This includes optical-based methods, strategies leaning on mass spectrometry, in-cell nuclear magnetic resonance, and cryo-electron microscopy. Recent advancements in these techniques have notably deepened our understanding of protein misfolding processes and the features of the resulting misfolded species within living cells. The progression in these fields promises to catalyze further breakthroughs in our comprehension of neurodegenerative disease mechanisms and potential therapeutic interventions.
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Affiliation(s)
- Yulong Bai
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Shengnan Zhang
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
| | - Hui Dong
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- University of the Chinese Academy of Sciences, 19 A Yuquan Road, Shijingshan District, Beijing 100049, China
| | - Yu Liu
- CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, Liaoning 116023, China
| | - Cong Liu
- Interdisciplinary Research Center on Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai 201210, China
- State Key Laboratory of Chemical Biology, Shanghai Institute of Organic Chemistry, University of Chinese Academy of Sciences, Shanghai 200032, China
| | - Xin Zhang
- Department of Chemistry, Research Center for Industries of the Future, Westlake University, 600 Dunyu Road, Hangzhou 310030, Zhejiang Province, China
- Westlake Laboratory of Life Sciences and Biomedicine, 18 Shilongshan Road, Hangzhou 310024, Zhejiang Province, China
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7
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Llamas E, Koyuncu S, Lee HJ, Wehrmann M, Gutierrez-Garcia R, Dunken N, Charura N, Torres-Montilla S, Schlimgen E, Mandel AM, Theile EB, Grossbach J, Wagle P, Lackmann JW, Schermer B, Benzing T, Beyer A, Pulido P, Rodriguez-Concepcion M, Zuccaro A, Vilchez D. In planta expression of human polyQ-expanded huntingtin fragment reveals mechanisms to prevent disease-related protein aggregation. NATURE AGING 2023; 3:1345-1357. [PMID: 37783816 PMCID: PMC10645592 DOI: 10.1038/s43587-023-00502-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 09/01/2023] [Indexed: 10/04/2023]
Abstract
In humans, aggregation of polyglutamine repeat (polyQ) proteins causes disorders such as Huntington's disease. Although plants express hundreds of polyQ-containing proteins, no pathologies arising from polyQ aggregation have been reported. To investigate this phenomenon, we expressed an aggregation-prone fragment of human huntingtin (HTT) with an expanded polyQ stretch (Q69) in Arabidopsis thaliana plants. In contrast to animal models, we find that Arabidopsis sp. suppresses Q69 aggregation through chloroplast proteostasis. Inhibition of chloroplast proteostasis diminishes the capacity of plants to prevent cytosolic Q69 aggregation. Moreover, endogenous polyQ-containing proteins also aggregate on chloroplast dysfunction. We find that Q69 interacts with the chloroplast stromal processing peptidase (SPP). Synthetic Arabidopsis SPP prevents polyQ-expanded HTT aggregation in human cells. Likewise, ectopic SPP expression in Caenorhabditis elegans reduces neuronal Q67 aggregation and subsequent neurotoxicity. Our findings suggest that synthetic plant proteins, such as SPP, hold therapeutic potential for polyQ disorders and other age-related diseases involving protein aggregation.
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Affiliation(s)
- Ernesto Llamas
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Seda Koyuncu
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Hyun Ju Lee
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Markus Wehrmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Ricardo Gutierrez-Garcia
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Nick Dunken
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - Nyasha Charura
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | | | - Elena Schlimgen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany
| | - Amrei M Mandel
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
| | - Erik Boelen Theile
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Jan Grossbach
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Prerana Wagle
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Jan-Wilm Lackmann
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
| | - Bernhard Schermer
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Thomas Benzing
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Department II of Internal Medicine, University Hospital Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Andreas Beyer
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany
- Institute for Genetics, University of Cologne, Cologne, Germany
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany
| | - Pablo Pulido
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Científicas, Madrid, Spain
| | | | - Alga Zuccaro
- Cluster of Excellence on Plant Sciences, Institute for Plant Sciences, University of Cologne, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases, University of Cologne, Cologne, Germany.
- Institute for Integrated Stress Response Signaling, Faculty of Medicine, University Hospital Cologne, Cologne, Germany.
- Institute for Genetics, University of Cologne, Cologne, Germany.
- Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany.
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8
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Zelenka T, Papamatheakis DA, Tzerpos P, Panagopoulos G, Tsolis KC, Papadakis VM, Mariatos Metaxas D, Papadogkonas G, Mores E, Kapsetaki M, Papamatheakis J, Stanek D, Spilianakis C. A novel SATB1 protein isoform with different biophysical properties. Front Cell Dev Biol 2023; 11:1242481. [PMID: 37635874 PMCID: PMC10457122 DOI: 10.3389/fcell.2023.1242481] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 07/21/2023] [Indexed: 08/29/2023] Open
Abstract
Intra-thymic T cell development is coordinated by the regulatory actions of SATB1 genome organizer. In this report, we show that SATB1 is involved in the regulation of transcription and splicing, both of which displayed deregulation in Satb1 knockout murine thymocytes. More importantly, we characterized a novel SATB1 protein isoform and described its distinct biophysical behavior, implicating potential functional differences compared to the commonly studied isoform. SATB1 utilized its prion-like domains to transition through liquid-like states to aggregated structures. This behavior was dependent on protein concentration as well as phosphorylation and interaction with nuclear RNA. Notably, the long SATB1 isoform was more prone to aggregate following phase separation. Thus, the tight regulation of SATB1 isoforms expression levels alongside with protein post-translational modifications, are imperative for SATB1's mode of action in T cell development. Our data indicate that deregulation of these processes may also be linked to disorders such as cancer.
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Affiliation(s)
- Tomas Zelenka
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Dionysios-Alexandros Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Petros Tzerpos
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | | | - Konstantinos C. Tsolis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Vassilis M. Papadakis
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | | | - George Papadogkonas
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Eleftherios Mores
- Department of Biology, University of Crete, Heraklion, Crete, Greece
| | - Manouela Kapsetaki
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - Joseph Papamatheakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
| | - David Stanek
- Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Charalampos Spilianakis
- Department of Biology, University of Crete, Heraklion, Crete, Greece
- Institute of Molecular Biology and Biotechnology—Foundation for Research and Technology Hellas, Heraklion, Crete, Greece
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9
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Folger A, Chen C, Kabbaj MH, Frey K, Wang Y. Neurodegenerative disease-associated inclusion bodies are cleared by selective autophagy in budding yeast. AUTOPHAGY REPORTS 2023; 2:2236407. [PMID: 37680383 PMCID: PMC10482306 DOI: 10.1080/27694127.2023.2236407] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Revised: 06/13/2023] [Accepted: 07/06/2023] [Indexed: 09/09/2023]
Abstract
Protein misfolding, aggregation, and accumulation cause neurodegenerative disorders. One such disorder, Huntington's disease, is caused by an increased number of glutamine-encoding trinucleotide repeats CAG in the first exon of the huntingtin (HTT) gene. Mutant proteins of Htt exon 1 with polyglutamine expansion are prone to aggregation and form pathological inclusion bodies in neurons. Extensive studies have shown that misfolded proteins are cleared by the ubiquitin-proteasome system or autophagy to alleviate their cytotoxicity. Misfolded proteins can form small soluble aggregates or large insoluble inclusion bodies. Previous works have elucidated the role of autophagy in the clearance of misfolded protein aggregates, but autophagic clearance of inclusion bodies remains poorly characterized. Here we use mutant Htt exon 1 with 103 polyglutamine (Htt103QP) as a model substrate to study the autophagic clearance of inclusion bodies in budding yeast. We found that the core autophagy-related proteins were required for Htt103QP inclusion body autophagy. Moreover, our evidence indicates that the autophagy of Htt103QP inclusion bodies is selective. Interestingly, Cue5/Tollip, a known autophagy receptor for aggrephagy, is dispensable for this inclusion body autophagy. From the known selective autophagy receptors in budding yeast, we identified three that are essential for inclusion body autophagy. Amyloid beta peptide (Aβ42) is a major component of amyloid plaques found in Alzheimer's disease brains. Interestingly, a similar selective autophagy pathway contributes to the clearance of Aβ42 inclusion bodies in budding yeast. Therefore, our results reveal a novel autophagic pathway specific for inclusion bodies associated with neurodegenerative diseases, which we have termed IBophagy.
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Affiliation(s)
- Austin Folger
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300
| | - Chuan Chen
- College of Biological Sciences, Hebei University, Baoding, China
| | - Marie-Helene Kabbaj
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300
| | - Karina Frey
- Department of Biological Sciences, Florida State University (undergraduate student)
| | - Yanchang Wang
- Department of Biomedical Sciences, College of Medicine, Florida State University, 1115 West Call Street, Tallahassee, FL 32306-4300
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10
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Zhang S, Pei G, Li B, Li P, Lin Y. Abnormal phase separation of biomacromolecules in human diseases. Acta Biochim Biophys Sin (Shanghai) 2023; 55:1133-1152. [PMID: 37475546 PMCID: PMC10423695 DOI: 10.3724/abbs.2023139] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 07/07/2023] [Indexed: 07/22/2023] Open
Abstract
Membrane-less organelles (MLOs) formed through liquid-liquid phase separation (LLPS) are associated with numerous important biological functions, but the abnormal phase separation will also dysregulate the physiological processes. Emerging evidence points to the importance of LLPS in human health and diseases. Nevertheless, despite recent advancements, our knowledge of the molecular relationship between LLPS and diseases is frequently incomplete. In this review, we outline our current understanding about how aberrant LLPS affects developmental disorders, tandem repeat disorders, cancers and viral infection. We also examine disease mechanisms driven by aberrant condensates, and highlight potential treatment approaches. This study seeks to expand our understanding of LLPS by providing a valuable new paradigm for understanding phase separation and human disorders, as well as to further translate our current knowledge regarding LLPS into therapeutic discoveries.
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Affiliation(s)
- Songhao Zhang
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Gaofeng Pei
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Boya Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
| | - Pilong Li
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- Frontier Research Center for Biological StructureTsinghua UniversityBeijing100084China
| | - Yi Lin
- State Key Laboratory of Membrane BiologyTsinghua University-Peking University Joint Centre for Life SciencesSchool of Life SciencesTsinghua UniversityBeijing100084China
- IDG/McGovern Institute for Brain Research at Tsinghua UniversityBeijing100084China
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11
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Bresgen N, Kovacs M, Lahnsteiner A, Felder TK, Rinnerthaler M. The Janus-Faced Role of Lipid Droplets in Aging: Insights from the Cellular Perspective. Biomolecules 2023; 13:912. [PMID: 37371492 DOI: 10.3390/biom13060912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Revised: 05/22/2023] [Accepted: 05/29/2023] [Indexed: 06/29/2023] Open
Abstract
It is widely accepted that nine hallmarks-including mitochondrial dysfunction, epigenetic alterations, and loss of proteostasis-exist that describe the cellular aging process. Adding to this, a well-described cell organelle in the metabolic context, namely, lipid droplets, also accumulates with increasing age, which can be regarded as a further aging-associated process. Independently of their essential role as fat stores, lipid droplets are also able to control cell integrity by mitigating lipotoxic and proteotoxic insults. As we will show in this review, numerous longevity interventions (such as mTOR inhibition) also lead to strong accumulation of lipid droplets in Saccharomyces cerevisiae, Caenorhabditis elegans, Drosophila melanogaster, and mammalian cells, just to name a few examples. In mammals, due to the variety of different cell types and tissues, the role of lipid droplets during the aging process is much more complex. Using selected diseases associated with aging, such as Alzheimer's disease, Parkinson's disease, type II diabetes, and cardiovascular disease, we show that lipid droplets are "Janus"-faced. In an early phase of the disease, lipid droplets mitigate the toxicity of lipid peroxidation and protein aggregates, but in a later phase of the disease, a strong accumulation of lipid droplets can cause problems for cells and tissues.
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Affiliation(s)
- Nikolaus Bresgen
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
| | - Melanie Kovacs
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
| | - Angelika Lahnsteiner
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
| | - Thomas Klaus Felder
- Department of Laboratory Medicine, Paracelsus Medical University, 5020 Salzburg, Austria
| | - Mark Rinnerthaler
- Department of Biosciences and Medical Biology, Paris-Lodron University Salzburg, 5020 Salzburg, Austria
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12
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Kamitsuka PJ, Ghanem MM, Ziar R, McDonald SE, Thomas MG, Kwakye GF. Defective Mitochondrial Dynamics and Protein Degradation Pathways Underlie Cadmium-Induced Neurotoxicity and Cell Death in Huntington's Disease Striatal Cells. Int J Mol Sci 2023; 24:ijms24087178. [PMID: 37108341 PMCID: PMC10139096 DOI: 10.3390/ijms24087178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2023] [Revised: 03/31/2023] [Accepted: 03/31/2023] [Indexed: 04/29/2023] Open
Abstract
Exposure to heavy metals, including cadmium (Cd), can induce neurotoxicity and cell death. Cd is abundant in the environment and accumulates in the striatum, the primary brain region selectively affected by Huntington's disease (HD). We have previously reported that mutant huntingtin protein (mHTT) combined with chronic Cd exposure induces oxidative stress and promotes metal dyshomeostasis, resulting in cell death in a striatal cell model of HD. To understand the effect of acute Cd exposure on mitochondrial health and protein degradation pathways, we hypothesized that expression of mHTT coupled with acute Cd exposure would cooperatively alter mitochondrial bioenergetics and protein degradation mechanisms in striatal STHdh cells to reveal novel pathways that augment Cd cytotoxicity and HD pathogenicity. We report that mHTT cells are significantly more susceptible to acute Cd-induced cell death as early as 6 h after 40 µM CdCl2 exposure compared with wild-type (WT). Confocal microscopy, biochemical assays, and immunoblotting analysis revealed that mHTT and acute Cd exposure synergistically impair mitochondrial bioenergetics by reducing mitochondrial potential and cellular ATP levels and down-regulating the essential pro-fusion proteins MFN1 and MFN2. These pathogenic effects triggered cell death. Furthermore, Cd exposure increases the expression of autophagic markers, such as p62, LC3, and ATG5, and reduces the activity of the ubiquitin-proteasome system to promote neurodegeneration in HD striatal cells. Overall, these results reveal a novel mechanism to further establish Cd as a pathogenic neuromodulator in striatal HD cells via Cd-triggered neurotoxicity and cell death mediated by an impairment in mitochondrial bioenergetics and autophagy with subsequent alteration in protein degradation pathways.
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Affiliation(s)
- Paul J Kamitsuka
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Marwan M Ghanem
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Rania Ziar
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Sarah E McDonald
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Morgan G Thomas
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
| | - Gunnar F Kwakye
- Neuroscience Department, Oberlin College, 119 Woodland Street, Oberlin, OH 44074, USA
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13
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Berger C, Premaraj N, Ravelli RBG, Knoops K, López-Iglesias C, Peters PJ. Cryo-electron tomography on focused ion beam lamellae transforms structural cell biology. Nat Methods 2023; 20:499-511. [PMID: 36914814 DOI: 10.1038/s41592-023-01783-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 01/20/2023] [Indexed: 03/16/2023]
Abstract
Cryogenic electron microscopy and data processing enable the determination of structures of isolated macromolecules to near-atomic resolution. However, these data do not provide structural information in the cellular environment where macromolecules perform their native functions, and vital molecular interactions can be lost during the isolation process. Cryogenic focused ion beam (FIB) fabrication generates thin lamellae of cellular samples and tissues, enabling structural studies on the near-native cellular interior and its surroundings by cryogenic electron tomography (cryo-ET). Cellular cryo-ET benefits from the technological developments in electron microscopes, detectors and data processing, and more in situ structures are being obtained and at increasingly higher resolution. In this Review, we discuss recent studies employing cryo-ET on FIB-generated lamellae and the technological developments in ultrarapid sample freezing, FIB fabrication of lamellae, tomography, data processing and correlative light and electron microscopy that have enabled these studies. Finally, we explore the future of cryo-ET in terms of both methods development and biological application.
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Affiliation(s)
- Casper Berger
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
- Structural Biology, The Rosalind Franklin Institute, Didcot, UK
| | - Navya Premaraj
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Raimond B G Ravelli
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Kèvin Knoops
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Carmen López-Iglesias
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands
| | - Peter J Peters
- Division of Nanoscopy, Maastricht MultiModal Molecular Imaging Institute, Maastricht University, Maastricht, the Netherlands.
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14
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Elena-Real CA, Sagar A, Urbanek A, Popovic M, Morató A, Estaña A, Fournet A, Doucet C, Lund XL, Shi ZD, Costa L, Thureau A, Allemand F, Swenson RE, Milhiet PE, Crehuet R, Barducci A, Cortés J, Sinnaeve D, Sibille N, Bernadó P. The structure of pathogenic huntingtin exon 1 defines the bases of its aggregation propensity. Nat Struct Mol Biol 2023; 30:309-320. [PMID: 36864173 DOI: 10.1038/s41594-023-00920-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/05/2023] [Indexed: 03/04/2023]
Abstract
Huntington's disease is a neurodegenerative disorder caused by a CAG expansion in the first exon of the HTT gene, resulting in an extended polyglutamine (poly-Q) tract in huntingtin (httex1). The structural changes occurring to the poly-Q when increasing its length remain poorly understood due to its intrinsic flexibility and the strong compositional bias. The systematic application of site-specific isotopic labeling has enabled residue-specific NMR investigations of the poly-Q tract of pathogenic httex1 variants with 46 and 66 consecutive glutamines. Integrative data analysis reveals that the poly-Q tract adopts long α-helical conformations propagated and stabilized by glutamine side chain to backbone hydrogen bonds. We show that α-helical stability is a stronger signature in defining aggregation kinetics and the structure of the resulting fibrils than the number of glutamines. Our observations provide a structural perspective of the pathogenicity of expanded httex1 and pave the way to a deeper understanding of poly-Q-related diseases.
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Affiliation(s)
- Carlos A Elena-Real
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Amin Sagar
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Annika Urbanek
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Matija Popovic
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Anna Morató
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Alejandro Estaña
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
- LAAS-CNRS, University of Toulouse, CNRS, Toulouse, France
| | - Aurélie Fournet
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Christine Doucet
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Xamuel L Lund
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
- Institute of Laue Langevin, Grenoble, France
| | - Zhen-Dan Shi
- The Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | - Luca Costa
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | | | - Frédéric Allemand
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Rolf E Swenson
- The Chemistry and Synthesis Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Rockville, MD, USA
| | | | - Ramon Crehuet
- Institute for Advanced Chemistry of Catalonia (IQAC), CSIC, Barcelona, Spain
| | - Alessandro Barducci
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Juan Cortés
- LAAS-CNRS, University of Toulouse, CNRS, Toulouse, France
| | - Davy Sinnaeve
- Univ. Lille, INSERM, CHU Lille, Institut Pasteur de Lille, U1167 - RID-AGE - Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- CNRS, EMR9002, Integrative Structural Biology, Lille, France
| | - Nathalie Sibille
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France
| | - Pau Bernadó
- Centre for Structural Biology, University of Montpellier, INSERM, CNRS, Montpellier, France.
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15
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Wu GH, Smith-Geater C, Galaz-Montoya JG, Gu Y, Gupte SR, Aviner R, Mitchell PG, Hsu J, Miramontes R, Wang KQ, Geller NR, Hou C, Danita C, Joubert LM, Schmid MF, Yeung S, Frydman J, Mobley W, Wu C, Thompson LM, Chiu W. CryoET reveals organelle phenotypes in huntington disease patient iPSC-derived and mouse primary neurons. Nat Commun 2023; 14:692. [PMID: 36754966 PMCID: PMC9908936 DOI: 10.1038/s41467-023-36096-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Accepted: 01/13/2023] [Indexed: 02/10/2023] Open
Abstract
Huntington's disease (HD) is caused by an expanded CAG repeat in the huntingtin gene, yielding a Huntingtin protein with an expanded polyglutamine tract. While experiments with patient-derived induced pluripotent stem cells (iPSCs) can help understand disease, defining pathological biomarkers remains challenging. Here, we used cryogenic electron tomography to visualize neurites in HD patient iPSC-derived neurons with varying CAG repeats, and primary cortical neurons from BACHD, deltaN17-BACHD, and wild-type mice. In HD models, we discovered sheet aggregates in double membrane-bound organelles, and mitochondria with distorted cristae and enlarged granules, likely mitochondrial RNA granules. We used artificial intelligence to quantify mitochondrial granules, and proteomics experiments reveal differential protein content in isolated HD mitochondria. Knockdown of Protein Inhibitor of Activated STAT1 ameliorated aberrant phenotypes in iPSC- and BACHD neurons. We show that integrated ultrastructural and proteomic approaches may uncover early HD phenotypes to accelerate diagnostics and the development of targeted therapeutics for HD.
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Affiliation(s)
- Gong-Her Wu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Charlene Smith-Geater
- Department of Psychiatry & Human Behavior University of California Irvine, Irvine, CA, 92697, USA
| | - Jesús G Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Yingli Gu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037-0662, USA
| | - Sanket R Gupte
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - Ranen Aviner
- Department of Biology, Stanford University, Stanford, CA, 94305, USA
| | - Patrick G Mitchell
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Joy Hsu
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA
| | - Ricardo Miramontes
- Department of Memory Impairment and Neurological Disorders, University of California Irvine, Irvine, CA, 92697, USA
| | - Keona Q Wang
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 96267, USA
| | - Nicolette R Geller
- Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 96267, USA
| | - Cathy Hou
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Cristina Danita
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA
| | - Lydia-Marie Joubert
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Michael F Schmid
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA
| | - Serena Yeung
- Department of Computer Science, Stanford University, Stanford, CA, 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA, 94305, USA
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University, Stanford, CA, 94305, USA
| | - William Mobley
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037-0662, USA
| | - Chengbiao Wu
- Department of Neurosciences, University of California San Diego, La Jolla, CA, 92037-0662, USA
| | - Leslie M Thompson
- Department of Psychiatry & Human Behavior University of California Irvine, Irvine, CA, 92697, USA. .,Department of Memory Impairment and Neurological Disorders, University of California Irvine, Irvine, CA, 92697, USA. .,Department of Neurobiology and Behavior, University of California Irvine, Irvine, CA, 96267, USA. .,Sue & Bill Gross Stem Cell Research Center, University of California Irvine, Irvine, CA, 96267, USA. .,Department of Biological Chemistry, University of California Irvine, Irvine, CA, 92617, USA.
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA, 94305, USA. .,Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Stanford University, Menlo Park, CA, 94025, USA. .,Department of Microbiology and Immunology, Stanford University, Stanford, CA, 94305, USA.
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16
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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17
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Krämer L, Dalheimer N, Räschle M, Storchová Z, Pielage J, Boos F, Herrmann JM. MitoStores: chaperone-controlled protein granules store mitochondrial precursors in the cytosol. EMBO J 2023; 42:e112309. [PMID: 36704946 PMCID: PMC10068336 DOI: 10.15252/embj.2022112309] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Revised: 01/05/2023] [Accepted: 01/12/2023] [Indexed: 01/28/2023] Open
Abstract
Hundreds of nucleus-encoded mitochondrial precursor proteins are synthesized in the cytosol and imported into mitochondria in a post-translational manner. However, the early processes associated with mitochondrial protein targeting remain poorly understood. Here, we show that in Saccharomyces cerevisiae, the cytosol has the capacity to transiently store mitochondrial matrix-destined precursors in dedicated deposits that we termed MitoStores. Competitive inhibition of mitochondrial protein import via clogging of import sites greatly enhances the formation of MitoStores, but they also form during physiological cell growth on nonfermentable carbon sources. MitoStores are enriched for a specific subset of nucleus-encoded mitochondrial proteins, in particular those containing N-terminal mitochondrial targeting sequences. Our results suggest that MitoStore formation suppresses the toxic potential of aberrantly accumulating mitochondrial precursor proteins and is controlled by the heat shock proteins Hsp42 and Hsp104. Thus, the cytosolic protein quality control system plays an active role during the early stages of mitochondrial protein targeting through the coordinated and localized sequestration of mitochondrial precursor proteins.
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Affiliation(s)
- Lena Krämer
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Niko Dalheimer
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Markus Räschle
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Zuzana Storchová
- Molecular Genetics, University of Kaiserslautern, Kaiserslautern, Germany
| | - Jan Pielage
- Zoology and Neurobiology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
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18
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Ferdosi S, Stukalov A, Hasan M, Tangeysh B, Brown TR, Wang T, Elgierari EM, Zhao X, Huang Y, Alavi A, Lee-McMullen B, Chu J, Figa M, Tao W, Wang J, Goldberg M, O'Brien ES, Xia H, Stolarczyk C, Weissleder R, Farias V, Batzoglou S, Siddiqui A, Farokhzad OC, Hornburg D. Enhanced Competition at the Nano-Bio Interface Enables Comprehensive Characterization of Protein Corona Dynamics and Deep Coverage of Proteomes. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2022; 34:e2206008. [PMID: 35986672 DOI: 10.1002/adma.202206008] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Revised: 08/11/2022] [Indexed: 06/15/2023]
Abstract
Introducing engineered nanoparticles (NPs) into a biofluid such as blood plasma leads to the formation of a selective and reproducible protein corona at the particle-protein interface, driven by the relationship between protein-NP affinity and protein abundance. This enables scalable systems that leverage protein-nano interactions to overcome current limitations of deep plasma proteomics in large cohorts. Here the importance of the protein to NP-surface ratio (P/NP) is demonstrated and protein corona formation dynamics are modeled, which determine the competition between proteins for binding. Tuning the P/NP ratio significantly modulates the protein corona composition, enhancing depth and precision of a fully automated NP-based deep proteomic workflow (Proteograph). By increasing the binding competition on engineered NPs, 1.2-1.7× more proteins with 1% false discovery rate are identified on the surface of each NP, and up to 3× more proteins compared to a standard plasma proteomics workflow. Moreover, the data suggest P/NP plays a significant role in determining the in vivo fate of nanomaterials in biomedical applications. Together, the study showcases the importance of P/NP as a key design element for biomaterials and nanomedicine in vivo and as a powerful tuning strategy for accurate, large-scale NP-based deep proteomic studies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Amir Alavi
- Seer, Inc., Redwood City, CA, 94065, USA
| | | | | | - Mike Figa
- Seer, Inc., Redwood City, CA, 94065, USA
| | - Wei Tao
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jian Wang
- Seer, Inc., Redwood City, CA, 94065, USA
| | | | | | | | | | - Ralph Weissleder
- Department of Systems Biology, Harvard Medical School, 200 Longwood Ave, Boston, MA, 02115, USA
- Center for Systems Biology, Massachusetts General Hospital, 185 Cambridge St, CPZN 5206, Boston, MA, 02114, USA
| | - Vivek Farias
- Sloan School and Operations Research Center, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | | | | | - Omid C Farokhzad
- Seer, Inc., Redwood City, CA, 94065, USA
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
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19
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Zhang L, Kang H, Perez-Aguilar JM, Zhou R. Possible Co-Evolution of Polyglutamine and Polyproline in Huntingtin Protein: Proline-Rich Domain as Transient Folding Chaperone. J Phys Chem Lett 2022; 13:6331-6341. [PMID: 35796410 DOI: 10.1021/acs.jpclett.2c01184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Huntington's disease is an inherited neurodegenerative disorder caused by the overduplication of CAG repeats in the Huntingtin gene. Recent findings revealed that among the orthologs, the expansion of CAG repeats (polyQ) in the Huntingtin gene occurs in tandem with the duplication of CCG repeats (polyP). However, the molecular mechanism of this possible co-evolution remains unknown. We examined the structures of Huntingtin exon 1 (HttEx1) from six species along with five designed mutants. We found that the polyP segments "chaperone" the rest of the HttEx1 by forming ad hoc polyP binding grooves. Such a process elongates the otherwise poorly solvated polyQ domain, while modulating its secondary structure propensity from β-strands to α-helices. This chaperoning effect is achieved mostly through transient hydrogen bond interactions between polyP and the rest of HttEx1, resulting in a striking golden ratio of ∼2:1 between the chain lengths of polyQ and polyP.
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Affiliation(s)
- Leili Zhang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Hongsuk Kang
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
| | - Jose Manuel Perez-Aguilar
- School of Chemical Sciences, Meritorious Autonomous University of Puebla (BUAP), University City, Puebla 72570, Mexico
| | - Ruhong Zhou
- Computational Biology Center, IBM Thomas J. Watson Research Center, Yorktown Heights, New York 10598, United States
- Institute of Quantitative Biology, College of Life Sciences, Zhejiang University, Hangzhou 310027, China
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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20
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Nazarov S, Chiki A, Boudeffa D, Lashuel HA. Structural Basis of Huntingtin Fibril Polymorphism Revealed by Cryogenic Electron Microscopy of Exon 1 HTT Fibrils. J Am Chem Soc 2022; 144:10723-10735. [PMID: 35679155 DOI: 10.1021/jacs.2c00509] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The lack of detailed insight into the structure of aggregates formed by the huntingtin protein (HTT) has hampered the efforts to develop therapeutics and diagnostics targeting pathology formation in the brain of patients with Huntington's disease. To address this knowledge gap, we investigated the structural properties of in vitro-generated fibrils from exon1 of the huntingtin protein by cryogenic electron microscopy and single-particle analyses. We show that wildtype and mutant exon1 of the huntingtin protein form nonhelical fibrils with a polyglutamine amyloid core composed of β-hairpins with unique characteristics that have not been previously observed with other amyloid filaments. The stacks of β-hairpins form long planar β-sheets (protofilaments) which combine inter- and intra-molecular interactions, with variable stacking angles and occasional out-of-register states of individual β-hairpins. These features and the propensity of protofilaments to undergo lateral association result in a high degree of fibril polymorphisms, including fibrils composed of varying numbers of protofilaments. Our results allow us to speculate on how the flanking domains are organized around the polyglutamine core of the fibril and provide insight into how they might affect the huntingtin fibril structure and polymorphism. The removal of the first 17 amino acids at the N-terminus resulted in surprising intra-fibril structural heterogeneity and reduced fibril's propensity to lateral associations. Overall, this work provides valuable insights that could help guide future mechanistic studies to elucidate the sequence and structural determinants of huntingtin aggregation, as well as for cryo-EM and structural studies of fibrils derived from huntingtin protein and other disease-associated polyglutamine-containing proteins.
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Affiliation(s)
- Sergey Nazarov
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland.,BioEM Core Facility and Technology Platform, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Driss Boudeffa
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, School of Life Sciences, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
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21
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Sinnige T. Molecular mechanisms of amyloid formation in living systems. Chem Sci 2022; 13:7080-7097. [PMID: 35799826 PMCID: PMC9214716 DOI: 10.1039/d2sc01278b] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 05/14/2022] [Indexed: 12/28/2022] Open
Abstract
Fibrillar protein aggregation is a hallmark of a variety of human diseases. Examples include the deposition of amyloid-β and tau in Alzheimer's disease, and that of α-synuclein in Parkinson's disease. The molecular mechanisms by which soluble proteins form amyloid fibrils have been extensively studied in the test tube. These investigations have revealed the microscopic steps underlying amyloid formation, and the role of factors such as chaperones that modulate these processes. This perspective explores the question to what extent the mechanisms of amyloid formation elucidated in vitro apply to human disease. The answer is not yet clear, and may differ depending on the protein and the associated disease. Nevertheless, there are striking qualitative similarities between the aggregation behaviour of proteins in vitro and the development of the related diseases. Limited quantitative data obtained in model organisms such as Caenorhabditis elegans support the notion that aggregation mechanisms in vivo can be interpreted using the same biophysical principles established in vitro. These results may however be biased by the high overexpression levels typically used in animal models of protein aggregation diseases. Molecular chaperones have been found to suppress protein aggregation in animal models, but their mechanisms of action have not yet been quantitatively analysed. Several mechanisms are proposed by which the decline of protein quality control with organismal age, but also the intrinsic nature of the aggregation process may contribute to the kinetics of protein aggregation observed in human disease. The molecular mechanisms of amyloid formation have been studied extensively in test tube reactions. This perspective article addresses the question to what extent these mechanisms apply to the complex situation in living cells and organisms.![]()
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Affiliation(s)
- Tessa Sinnige
- Bijvoet Centre for Biomolecular Research, Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands
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22
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Wan Q, Mouton SN, Veenhoff LM, Boersma AJ. A FRET-based method for monitoring structural transitions in protein self-organization. CELL REPORTS METHODS 2022; 2:100184. [PMID: 35475219 PMCID: PMC8960284 DOI: 10.1016/j.crmeth.2022.100184] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 08/12/2021] [Accepted: 02/24/2022] [Indexed: 11/04/2022]
Abstract
Proteins assemble into a variety of dynamic and functional structures. Their structural transitions are often challenging to distinguish inside cells, particularly with a high spatiotemporal resolution. Here, we present a fluorescence resonance energy transfer (FRET)-based method for continuous and high-throughput monitoring of protein self-assemblies to reveal well-resolved transient intermediate states. Intermolecular FRET with both the donor and acceptor proteins at the same target protein provides high sensitivity while retaining the advantage of straightforward ratiometric imaging. We apply this method to monitor self-assembly of three proteins. We show that the mutant Huntingtin exon1 (mHttex1) first forms less-ordered assemblies, which develop into fibril-like aggregates, and demonstrate that the chaperone protein DNAJB6b increases the critical saturation concentration of mHttex1. We also monitor the structural changes in fused in sarcoma (FUS) condensates. This method adds to the toolbox for protein self-assembly structure and kinetics determination, and implementation with native or non-native proteins can inform studies involving protein condensation or aggregation.
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Affiliation(s)
- Qi Wan
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
- Department of Biochemistry, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, the Netherlands
| | - Sara N. Mouton
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Liesbeth M. Veenhoff
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Arnold J. Boersma
- DWI – Leibniz Institute for Interactive Materials, Forckenbeckstr. 50, 52056 Aachen, Germany
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23
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Riera-Tur I, Schäfer T, Hornburg D, Mishra A, da Silva Padilha M, Fernández-Mosquera L, Feigenbutz D, Auer P, Mann M, Baumeister W, Klein R, Meissner F, Raimundo N, Fernández-Busnadiego R, Dudanova I. Amyloid-like aggregating proteins cause lysosomal defects in neurons via gain-of-function toxicity. Life Sci Alliance 2021; 5:5/3/e202101185. [PMID: 34933920 PMCID: PMC8711852 DOI: 10.26508/lsa.202101185] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 12/02/2021] [Accepted: 12/03/2021] [Indexed: 01/02/2023] Open
Abstract
Using cryo-ET, cell biology, and proteomics, this study shows that aggregating proteins impair the autophagy-lysosomal pathway in neurons by sequestering a subunit of the AP-3 adaptor complex. The autophagy-lysosomal pathway is impaired in many neurodegenerative diseases characterized by protein aggregation, but the link between aggregation and lysosomal dysfunction remains poorly understood. Here, we combine cryo-electron tomography, proteomics, and cell biology studies to investigate the effects of protein aggregates in primary neurons. We use artificial amyloid-like β-sheet proteins (β proteins) to focus on the gain-of-function aspect of aggregation. These proteins form fibrillar aggregates and cause neurotoxicity. We show that late stages of autophagy are impaired by the aggregates, resulting in lysosomal alterations reminiscent of lysosomal storage disorders. Mechanistically, β proteins interact with and sequester AP-3 μ1, a subunit of the AP-3 adaptor complex involved in protein trafficking to lysosomal organelles. This leads to destabilization of the AP-3 complex, missorting of AP-3 cargo, and lysosomal defects. Restoring AP-3μ1 expression ameliorates neurotoxicity caused by β proteins. Altogether, our results highlight the link between protein aggregation, lysosomal impairments, and neurotoxicity.
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Affiliation(s)
- Irene Riera-Tur
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Martinsried, Germany.,Molecular Neurodegeneration Group, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Tillman Schäfer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Hornburg
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Experimental Systems Immunology Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Archana Mishra
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Miguel da Silva Padilha
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Martinsried, Germany.,Molecular Neurodegeneration Group, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Lorena Fernández-Mosquera
- The William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, UK
| | - Dennis Feigenbutz
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Martinsried, Germany.,Molecular Neurodegeneration Group, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Patrick Auer
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Martinsried, Germany.,Molecular Neurodegeneration Group, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Rüdiger Klein
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Martinsried, Germany
| | - Felix Meissner
- Experimental Systems Immunology Group, Max Planck Institute of Biochemistry, Martinsried, Germany.,Department of Systems Immunology and Proteomics, Institute of Innate Immunity, Medical Faculty, University of Bonn, Bonn, Germany
| | - Nuno Raimundo
- Department of Cellular and Molecular Physiology, Penn State College of Medicine, Hershey, PA, USA
| | - Rubén Fernández-Busnadiego
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany .,Institute of Neuropathology, University Medical Center Goettingen, Goettingen, Germany.,Cluster of Excellence "Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells" (MBExC), University of Goettingen, Goettingen, Germany
| | - Irina Dudanova
- Department of Molecules-Signaling-Development, Max Planck Institute of Neurobiology, Martinsried, Germany .,Molecular Neurodegeneration Group, Max Planck Institute of Neurobiology, Martinsried, Germany
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24
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Papagiannidis D, Bircham PW, Lüchtenborg C, Pajonk O, Ruffini G, Brügger B, Schuck S. Ice2 promotes ER membrane biogenesis in yeast by inhibiting the conserved lipin phosphatase complex. EMBO J 2021; 40:e107958. [PMID: 34617598 PMCID: PMC8591542 DOI: 10.15252/embj.2021107958] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 09/01/2021] [Accepted: 09/03/2021] [Indexed: 11/30/2022] Open
Abstract
Cells dynamically adapt organelle size to current physiological demand. Organelle growth requires membrane biogenesis and therefore needs to be coordinated with lipid metabolism. The endoplasmic reticulum (ER) can undergo massive expansion, but the underlying regulatory mechanisms are largely unclear. Here, we describe a genetic screen for factors involved in ER membrane expansion in budding yeast and identify the ER transmembrane protein Ice2 as a strong hit. We show that Ice2 promotes ER membrane biogenesis by opposing the phosphatidic acid phosphatase Pah1, called lipin in metazoa. Specifically, Ice2 inhibits the conserved Nem1‐Spo7 complex and thus suppresses the dephosphorylation and activation of Pah1. Furthermore, Ice2 cooperates with the transcriptional regulation of lipid synthesis genes and helps to maintain cell homeostasis during ER stress. These findings establish the control of the lipin phosphatase complex as an important mechanism for regulating ER membrane biogenesis.
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Affiliation(s)
- Dimitrios Papagiannidis
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Peter W Bircham
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany
| | | | - Oliver Pajonk
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Giulia Ruffini
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
| | - Sebastian Schuck
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance and Cell Networks Cluster of Excellence, Heidelberg, Germany.,Heidelberg University Biochemistry Center (BZH), Heidelberg, Germany
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25
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Nuclear and cytoplasmic huntingtin inclusions exhibit distinct biochemical composition, interactome and ultrastructural properties. Nat Commun 2021; 12:6579. [PMID: 34772920 PMCID: PMC8589980 DOI: 10.1038/s41467-021-26684-z] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/11/2021] [Indexed: 12/20/2022] Open
Abstract
Despite the strong evidence linking the aggregation of the Huntingtin protein (Htt) to the pathogenesis of Huntington's disease (HD), the mechanisms underlying Htt aggregation and neurodegeneration remain poorly understood. Herein, we investigated the ultrastructural properties and protein composition of Htt cytoplasmic and nuclear inclusions in mammalian cells and primary neurons overexpressing mutant exon1 of the Htt protein. Our findings provide unique insight into the ultrastructural properties of cytoplasmic and nuclear Htt inclusions and their mechanisms of formation. We show that Htt inclusion formation and maturation are complex processes that, although initially driven by polyQ-dependent Htt aggregation, also involve the polyQ and PRD domain-dependent sequestration of lipids and cytoplasmic and cytoskeletal proteins related to HD dysregulated pathways; the recruitment and accumulation of remodeled or dysfunctional membranous organelles, and the impairment of the protein quality control and degradation machinery. We also show that nuclear and cytoplasmic Htt inclusions exhibit distinct biochemical compositions and ultrastructural properties, suggesting different mechanisms of aggregation and toxicity.
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26
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Hommen F, Bilican S, Vilchez D. Protein clearance strategies for disease intervention. J Neural Transm (Vienna) 2021; 129:141-172. [PMID: 34689261 PMCID: PMC8541819 DOI: 10.1007/s00702-021-02431-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 10/10/2021] [Indexed: 02/06/2023]
Abstract
Protein homeostasis, or proteostasis, is essential for cell function and viability. Unwanted, damaged, misfolded and aggregated proteins are degraded by the ubiquitin–proteasome system (UPS) and the autophagy-lysosome pathway. Growing evidence indicates that alterations in these major proteolytic mechanisms lead to a demise in proteostasis, contributing to the onset and development of distinct diseases. Indeed, dysregulation of the UPS or autophagy is linked to several neurodegenerative, infectious and inflammatory disorders as well as cancer. Thus, modulation of protein clearance pathways is a promising approach for therapeutics. In this review, we discuss recent findings and open questions on how targeting proteolytic mechanisms could be applied for disease intervention.
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Affiliation(s)
- Franziska Hommen
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - Saygın Bilican
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany
| | - David Vilchez
- Cologne Excellence Cluster for Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Joseph Stelzmann Strasse 26, 50931, Cologne, Germany. .,Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany. .,Faculty of Medicine, University Hospital Cologne, Cologne, Germany.
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27
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Deryusheva EI, Machulin AV, Galzitskaya OV. Structural, Functional, and Evolutionary Characteristics of Proteins with Repeats. Mol Biol 2021. [DOI: 10.1134/s0026893321040038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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28
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Vieweg S, Mahul-Mellier AL, Ruggeri FS, Riguet N, DeGuire SM, Chiki A, Cendrowska U, Dietler G, Lashuel HA. The Nt17 Domain and its Helical Conformation Regulate the Aggregation, Cellular Properties and Neurotoxicity of Mutant Huntingtin Exon 1. J Mol Biol 2021; 433:167222. [PMID: 34492254 DOI: 10.1016/j.jmb.2021.167222] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 08/25/2021] [Accepted: 08/26/2021] [Indexed: 11/29/2022]
Abstract
Converging evidence points to the N-terminal domain comprising the first 17 amino acids of the Huntingtin protein (Nt17) as a key regulator of its aggregation, cellular properties and toxicity. In this study, we further investigated the interplay between Nt17 and the polyQ domain repeat length in regulating the aggregation and inclusion formation of exon 1 of the Huntingtin protein (Httex1). In addition, we investigated the effect of removing Nt17 or modulating its local structure on the membrane interactions, neuronal uptake, and toxicity of monomeric or fibrillar Httex1. Our results show that the polyQ and Nt17 domains synergistically modulate the aggregation propensity of Httex1 and that the Nt17 domain plays important roles in shaping the surface properties of mutant Httex1 fibrils and regulating their poly-Q-dependent growth, lateral association and neuronal uptake. Removal of Nt17 or disruption of its transient helical conformations slowed the aggregation of monomeric Httex1 in vitro, reduced inclusion formation in cells, enhanced the neuronal uptake and nuclear accumulation of monomeric Httex1 proteins, and was sufficient to prevent cell death induced by Httex1 72Q overexpression. Finally, we demonstrate that the uptake of Httex1 fibrils into primary neurons and the resulting toxicity are strongly influenced by mutations and phosphorylation events that influence the local helical propensity of Nt17. Altogether, our results demonstrate that the Nt17 domain serves as one of the key master regulators of Htt aggregation, internalization, and toxicity and represents an attractive target for inhibiting Htt aggregate formation, inclusion formation, and neuronal toxicity.
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Affiliation(s)
- Sophie Vieweg
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anne-Laure Mahul-Mellier
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Francesco S Ruggeri
- Laboratory of the Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Nathan Riguet
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Sean M DeGuire
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Anass Chiki
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland
| | - Urszula Cendrowska
- Laboratory of the Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Giovanni Dietler
- Laboratory of the Physics of Living Matter, EPFL, 1015 Lausanne, Switzerland
| | - Hilal A Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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29
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Pigazzini ML, Lawrenz M, Margineanu A, Kaminski Schierle GS, Kirstein J. An Expanded Polyproline Domain Maintains Mutant Huntingtin Soluble in vivo and During Aging. Front Mol Neurosci 2021; 14:721749. [PMID: 34720872 PMCID: PMC8554126 DOI: 10.3389/fnmol.2021.721749] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2021] [Accepted: 08/30/2021] [Indexed: 02/02/2023] Open
Abstract
Huntington's disease is a dominantly inherited neurodegenerative disorder caused by the expansion of a CAG repeat, encoding for the amino acid glutamine (Q), present in the first exon of the protein huntingtin. Over the threshold of Q39 HTT exon 1 (HTTEx1) tends to misfold and aggregate into large intracellular structures, but whether these end-stage aggregates or their on-pathway intermediates are responsible for cytotoxicity is still debated. HTTEx1 can be separated into three domains: an N-terminal 17 amino acid region, the polyglutamine (polyQ) expansion and a C-terminal proline rich domain (PRD). Alongside the expanded polyQ, these flanking domains influence the aggregation propensity of HTTEx1: with the N17 initiating and promoting aggregation, and the PRD modulating it. In this study we focus on the first 11 amino acids of the PRD, a stretch of pure prolines, which are an evolutionary recent addition to the expanding polyQ region. We hypothesize that this proline region is expanding alongside the polyQ to counteract its ability to misfold and cause toxicity, and that expanding this proline region would be overall beneficial. We generated HTTEx1 mutants lacking both flanking domains singularly, missing the first 11 prolines of the PRD, or with this stretch of prolines expanded. We then followed their aggregation landscape in vitro with a battery of biochemical assays, and in vivo in novel models of C. elegans expressing the HTTEx1 mutants pan-neuronally. Employing fluorescence lifetime imaging we could observe the aggregation propensity of all HTTEx1 mutants during aging and correlate this with toxicity via various phenotypic assays. We found that the presence of an expanded proline stretch is beneficial in maintaining HTTEx1 soluble over time, regardless of polyQ length. However, the expanded prolines were only advantageous in promoting the survival and fitness of an organism carrying a pathogenic stretch of Q48 but were extremely deleterious to the nematode expressing a physiological stretch of Q23. Our results reveal the unique importance of the prolines which have and still are evolving alongside expanding glutamines to promote the function of HTTEx1 and avoid pathology.
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Affiliation(s)
- Maria Lucia Pigazzini
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- NeuroCure Cluster of Excellence, Charité Universitätsmedizin Berlin, Berlin, Germany
| | - Mandy Lawrenz
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
| | - Anca Margineanu
- Advanced Light Microscopy, Max-Delbrück Centrum for Molecular Medicine (MDC), Berlin, Germany
| | - Gabriele S. Kaminski Schierle
- Molecular Neuroscience Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, United Kingdom
| | - Janine Kirstein
- Department of Molecular Physiology and Cell Biology, Leibniz Research Institute for Molecular Pharmacology in the Forschungsverbund Berlin e.V. (FMP), Berlin, Germany
- Department of Cell Biology, University of Bremen, Bremen, Germany
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30
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Cryo-electron tomography provides topological insights into mutant huntingtin exon 1 and polyQ aggregates. Commun Biol 2021; 4:849. [PMID: 34239038 PMCID: PMC8266869 DOI: 10.1038/s42003-021-02360-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2020] [Accepted: 06/15/2021] [Indexed: 01/27/2023] Open
Abstract
Huntington disease (HD) is a neurodegenerative trinucleotide repeat disorder caused by an expanded poly-glutamine (polyQ) tract in the mutant huntingtin (mHTT) protein. The formation and topology of filamentous mHTT inclusions in the brain (hallmarks of HD implicated in neurotoxicity) remain elusive. Using cryo-electron tomography and subtomogram averaging, here we show that mHTT exon 1 and polyQ-only aggregates in vitro are structurally heterogenous and filamentous, similar to prior observations with other methods. Yet, we find filaments in both types of aggregates under ~2 nm in width, thinner than previously reported, and regions forming large sheets. In addition, our data show a prevalent subpopulation of filaments exhibiting a lumpy slab morphology in both aggregates, supportive of the polyQ core model. This provides a basis for future cryoET studies of various aggregated mHTT and polyQ constructs to improve their structure-based modeling as well as their identification in cells without fusion tags.
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31
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Schlagowski AM, Knöringer K, Morlot S, Sánchez Vicente A, Flohr T, Krämer L, Boos F, Khalid N, Ahmed S, Schramm J, Murschall LM, Haberkant P, Stein F, Riemer J, Westermann B, Braun RJ, Winklhofer KF, Charvin G, Herrmann JM. Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol. EMBO J 2021; 40:e107913. [PMID: 34191328 PMCID: PMC8365258 DOI: 10.15252/embj.2021107913] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/25/2021] [Accepted: 05/31/2021] [Indexed: 12/11/2022] Open
Abstract
The formation of protein aggregates is a hallmark of neurodegenerative diseases. Observations on patient samples and model systems demonstrated links between aggregate formation and declining mitochondrial functionality, but causalities remain unclear. We used Saccharomyces cerevisiae to analyze how mitochondrial processes regulate the behavior of aggregation‐prone polyQ protein derived from human huntingtin. Expression of Q97‐GFP rapidly led to insoluble cytosolic aggregates and cell death. Although aggregation impaired mitochondrial respiration only slightly, it considerably interfered with the import of mitochondrial precursor proteins. Mutants in the import component Mia40 were hypersensitive to Q97‐GFP, whereas Mia40 overexpression strongly suppressed the formation of toxic Q97‐GFP aggregates both in yeast and in human cells. Based on these observations, we propose that the post‐translational import of mitochondrial precursor proteins into mitochondria competes with aggregation‐prone cytosolic proteins for chaperones and proteasome capacity. Mia40 regulates this competition as it has a rate‐limiting role in mitochondrial protein import. Therefore, Mia40 is a dynamic regulator in mitochondrial biogenesis that can be exploited to stabilize cytosolic proteostasis.
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Affiliation(s)
| | | | - Sandrine Morlot
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
| | - Ana Sánchez Vicente
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Tamara Flohr
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Lena Krämer
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Nabeel Khalid
- German Research Center for Artificial Intelligence DFKI, Kaiserslautern, Germany
| | - Sheraz Ahmed
- German Research Center for Artificial Intelligence DFKI, Kaiserslautern, Germany
| | - Jana Schramm
- Cell Biology, University of Bayreuth, Bayreuth, Germany
| | | | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Jan Riemer
- Biochemistry, University of Cologne, Cologne, Germany
| | | | - Ralf J Braun
- Cell Biology, University of Bayreuth, Bayreuth, Germany.,Neurodegeneration, Danube Private University, Krems/Donau, Austria
| | - Konstanze F Winklhofer
- Department of Molecular Cell Biology, Institute of Biochemistry and Pathobiochemistry, Ruhr University Bochum, Bochum, Germany
| | - Gilles Charvin
- Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France.,Centre National de la Recherche Scientifique, UMR7104, Illkirch, France.,Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France.,Université de Strasbourg, Illkirch, France
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Kuang X, Nunn K, Jiang J, Castellano P, Hardikar U, Horgan A, Kong J, Tan Z, Dai W. Structural insight into transmissive mutant huntingtin species by correlative light and electron microscopy and cryo-electron tomography. Biochem Biophys Res Commun 2021; 560:99-104. [PMID: 33984771 DOI: 10.1016/j.bbrc.2021.04.124] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 02/07/2023]
Abstract
Aggregates of mutant huntingtin (mHTT) containing an expanded polyglutamine (polyQ) tract are hallmarks of Huntington's Disease (HD). Studies have shown that mHTT can spread between cells, leading to the propagation of misfolded protein pathology. However, the structure of transmissive mHTT species, and the molecular mechanisms underlying their transmission remain unknown. Using correlative light and electron microscopy (CLEM) and cryo-electron tomography (cryo-ET), we identified two types of aggregation-prone granules in conditioned medium from PC12 cells expressing a mHTT N-terminal fragment: densities enclosed by extracellular vesicles (EVs), and uncoated, amorphous meshworks of heterogeneous oligomers that co-localize with clusters of EVs. In vitro assays confirmed that liposomes induce condensation of polyQ oligomers into higher-order assemblies, resembling the uncoated meshworks observed in PC12 conditioned medium. Our findings provide novel insights into formation and architecture of transmissive mHTT proteins, and highlight the potential role of EVs as both carriers and modulators of transmissive mHTT proteins.
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Affiliation(s)
- Xuyuan Kuang
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Department of Hyperbaric Oxygen, Xiangya Hospital, Central South University, Changsha, Hunan, 410008, China
| | - Kyle Nunn
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Jennifer Jiang
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Paul Castellano
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Uttara Hardikar
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Arianna Horgan
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; School of Environmental and Biological Sciences, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Joyce Kong
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Ernest Mario School of Pharmacy, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA
| | - Zhiqun Tan
- Department of Anatomy and Neurobiology, University of California Irvine School of Medicine, Irvine, CA, 29697, USA; Institute for Memory Impairment and Neurological Disorders, University of California-Irvine, Irvine, CA, 29697, USA.
| | - Wei Dai
- Department of Cell Biology and Neuroscience, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA; Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, 08854, USA.
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33
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Zhou Y, Peskett TR, Landles C, Warner JB, Sathasivam K, Smith EJ, Chen S, Wetzel R, Lashuel HA, Bates GP, Saibil HR. Correlative light and electron microscopy suggests that mutant huntingtin dysregulates the endolysosomal pathway in presymptomatic Huntington's disease. Acta Neuropathol Commun 2021; 9:70. [PMID: 33853668 PMCID: PMC8048291 DOI: 10.1186/s40478-021-01172-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/28/2021] [Indexed: 12/18/2022] Open
Abstract
Huntington's disease (HD) is a late onset, inherited neurodegenerative disorder for which early pathogenic events remain poorly understood. Here we show that mutant exon 1 HTT proteins are recruited to a subset of cytoplasmic aggregates in the cell bodies of neurons in brain sections from presymptomatic HD, but not wild-type, mice. This occurred in a disease stage and polyglutamine-length dependent manner. We successfully adapted a high-resolution correlative light and electron microscopy methodology, originally developed for mammalian and yeast cells, to allow us to correlate light microscopy and electron microscopy images on the same brain section within an accuracy of 100 nm. Using this approach, we identified these recruitment sites as single membrane bound, vesicle-rich endolysosomal organelles, specifically as (1) multivesicular bodies (MVBs), or amphisomes and (2) autolysosomes or residual bodies. The organelles were often found in close-proximity to phagophore-like structures. Immunogold labeling localized mutant HTT to non-fibrillar, electron lucent structures within the lumen of these organelles. In presymptomatic HD, the recruitment organelles were predominantly MVBs/amphisomes, whereas in late-stage HD, there were more autolysosomes or residual bodies. Electron tomograms indicated the fusion of small vesicles with the vacuole within the lumen, suggesting that MVBs develop into residual bodies. We found that markers of MVB-related exocytosis were depleted in presymptomatic mice and throughout the disease course. This suggests that endolysosomal homeostasis has moved away from exocytosis toward lysosome fusion and degradation, in response to the need to clear the chronically aggregating mutant HTT protein, and that this occurs at an early stage in HD pathogenesis.
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Affiliation(s)
- Ya Zhou
- Huntington’s Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London, UK
| | - Thomas R. Peskett
- Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX UK
- Present Address: Department of Biology, Institute of Biochemistry, ETH Zurich, Otto-Stern-Weg 3, 8093 Zurich, Switzerland
| | - Christian Landles
- Huntington’s Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London, UK
| | - John B. Warner
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Kirupa Sathasivam
- Huntington’s Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London, UK
| | - Edward J. Smith
- Huntington’s Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London, UK
| | - Shu Chen
- Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX UK
| | - Ronald Wetzel
- Department of Structural Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA 15260 USA
| | - Hilal A. Lashuel
- Laboratory of Molecular and Chemical Biology of Neurodegeneration, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), Lausanne, Switzerland
| | - Gillian P. Bates
- Huntington’s Disease Centre, Department of Neurodegenerative Disease and UK Dementia Research Institute at UCL, Queen Square Institute of Neurology, University College London, London, UK
| | - Helen R. Saibil
- Institute of Structural and Molecular Biology, Birkbeck College, London, WC1E 7HX UK
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34
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Goetz SK, Mahamid J. Visualizing Molecular Architectures of Cellular Condensates: Hints of Complex Coacervation Scenarios. Dev Cell 2021; 55:97-107. [PMID: 33049214 DOI: 10.1016/j.devcel.2020.09.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Revised: 08/15/2020] [Accepted: 09/05/2020] [Indexed: 02/09/2023]
Abstract
In the last decade, liquid-liquid phase separation has emerged as a fundamental principle in the organization of crowded cellular environments into functionally distinct membraneless compartments. It is now established that biomolecules can condense into various physical phases, traditionally defined for simple polymer systems, and more recently elucidated by techniques employed in life sciences. We review pioneering cryo-electron tomography studies that have begun to unravel a wide spectrum of molecular architectures, ranging from amorphous to crystalline assemblies, that underlie cellular condensates. These observations bring into question current interpretations of microscopic phase behavior. Furthermore, by examining emerging concepts of non-classical phase separation pathways in small-molecule crystallization, we draw parallels with biomolecular condensation that highlight aspects not yet fully explored. In particular, transient and metastable intermediates that might be challenging to capture experimentally inside cells could be probed through computational simulations and enable a multi-scale understanding of the subcellular organization governed by distinct phases.
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Affiliation(s)
- Sara Kathrin Goetz
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany; Collaboration for Joint PhD Degree between EMBL and Heidelberg University, Faculty of Biosciences, Im Neuenheimer Feld 234, 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstrasse 1, 69117 Heidelberg, Germany.
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35
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Krämer L, Groh C, Herrmann JM. The proteasome: friend and foe of mitochondrial biogenesis. FEBS Lett 2020; 595:1223-1238. [PMID: 33249599 DOI: 10.1002/1873-3468.14010] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 10/26/2020] [Accepted: 11/01/2020] [Indexed: 01/06/2023]
Abstract
Most mitochondrial proteins are synthesized in the cytosol and subsequently translocated as unfolded polypeptides into mitochondria. Cytosolic chaperones maintain precursor proteins in an import-competent state. This post-translational import reaction is under surveillance of the cytosolic ubiquitin-proteasome system, which carries out several distinguishable activities. On the one hand, the proteasome degrades nonproductive protein precursors from the cytosol and nucleus, import intermediates that are stuck in mitochondrial translocases, and misfolded or damaged proteins from the outer membrane and the intermembrane space. These surveillance activities of the proteasome are essential for mitochondrial functionality, as well as cellular fitness and survival. On the other hand, the proteasome competes with mitochondria for nonimported cytosolic precursor proteins, which can compromise mitochondrial biogenesis. In order to balance the positive and negative effects of the cytosolic protein quality control system on mitochondria, mitochondrial import efficiency directly regulates the capacity of the proteasome via transcription factor Rpn4 in yeast and nuclear respiratory factor (Nrf) 1 and 2 in animal cells. In this review, we provide a thorough overview of how the proteasome regulates mitochondrial biogenesis.
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Affiliation(s)
- Lena Krämer
- Cell Biology, University of Kaiserslautern, Germany
| | - Carina Groh
- Cell Biology, University of Kaiserslautern, Germany
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36
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Klaips CL, Gropp MHM, Hipp MS, Hartl FU. Sis1 potentiates the stress response to protein aggregation and elevated temperature. Nat Commun 2020; 11:6271. [PMID: 33293525 PMCID: PMC7722728 DOI: 10.1038/s41467-020-20000-x] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 11/10/2020] [Indexed: 12/13/2022] Open
Abstract
Cells adapt to conditions that compromise protein conformational stability by activating various stress response pathways, but the mechanisms used in sensing misfolded proteins remain unclear. Moreover, aggregates of disease proteins often fail to induce a productive stress response. Here, using a yeast model of polyQ protein aggregation, we identified Sis1, an essential Hsp40 co-chaperone of Hsp70, as a critical sensor of proteotoxic stress. At elevated levels, Sis1 prevented the formation of dense polyQ inclusions and directed soluble polyQ oligomers towards the formation of permeable condensates. Hsp70 accumulated in a liquid-like state within this polyQ meshwork, resulting in a potent activation of the HSF1 dependent stress response. Sis1, and the homologous DnaJB6 in mammalian cells, also regulated the magnitude of the cellular heat stress response, suggesting a general role in sensing protein misfolding. Sis1/DnaJB6 functions as a limiting regulator to enable a dynamic stress response and avoid hypersensitivity to environmental changes.
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Affiliation(s)
- Courtney L Klaips
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
| | - Michael H M Gropp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany
| | - Mark S Hipp
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Antonius Deusinglaan 1, 9713 AV, Groningen, The Netherlands
- School of Medicine and Health Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152, Martinsried, Germany.
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37
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Investigating the Structure of Neurotoxic Protein Aggregates Inside Cells. Trends Cell Biol 2020; 30:951-966. [PMID: 32981805 DOI: 10.1016/j.tcb.2020.08.007] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 08/13/2020] [Accepted: 08/17/2020] [Indexed: 12/22/2022]
Abstract
Neurodegenerative diseases affect the lives of millions of people across the world, being particularly prevalent in the aging population. Despite huge research efforts, conclusive insights into the disease mechanisms are still lacking. Therefore, therapeutic strategies are limited to symptomatic treatments. A common histopathological hallmark of many neurodegenerative diseases is the presence of large pathognomonic protein aggregates, but their role in the disease pathology is unclear and subject to controversy. Here, we discuss imaging methods allowing investigation of these structures within their cellular environment: conventional electron microscopy (EM), super-resolution light microscopy (SR-LM), and cryo-electron tomography (cryo-ET). Multidisciplinary approaches are key for understanding neurodegenerative diseases and may contribute to the development of effective treatments. For simplicity, we focus on huntingtin aggregates, characteristic of Huntington's disease.
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38
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Nakamura S, Kibria MG, Unzai S, Kuroda Y, Kidokoro SI. Reversible Oligomerization and Reverse Hydrophobic Effect Induced by Isoleucine Tags Attached at the C-Terminus of a Simplified BPTI Variant. Biochemistry 2020; 59:3660-3668. [PMID: 32924442 DOI: 10.1021/acs.biochem.0c00436] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Protein amorphous aggregation has become the focus of great attention, as it can impair the ability of cells to function properly. Here, we evaluated the effects of three peptide tags, consisting of one, three, and five consecutive isoleucines attached at the C-terminus end of a simplified bovine pancreatic trypsin inhibitor (BPTI) variant, BPTI-19A, on the thermal stability and oligomerization by circular dichroism spectrometry and differential scanning calorimetry in detail. All of the BPTI-19A variants exhibited a reversible and apparently two-state thermal transition like BPTI-19A at pH 4.7. The thermal transition of the five-isoleucine-tagged variant showed clear protein-concentration dependence, where the apparent denaturation temperature decreased as the protein concentration increased. Quantitative analysis indicated that this phenomenon originated from the presence of reversibly oligomerized (RO) states at high temperatures. The results also illustrated that the thermodynamic stability difference between the native and the monomeric denatured state in all the proteins was destabilized by the hydrophobic tags and was well explained by the reverse hydrophobic effect due to the tags. The existence of the RO states was confirmed by both analytical ultracentrifugation and dynamic light scattering. This indicated that the five-isoleucine hydrophobic tag is strong enough to induce intermolecular hydrophobic contact among the denatured molecules leading to oligomerization, and even one- or three-isoleucine tags are effective enough to generate intramolecular hydrophobic contact, thus provoking denaturation through the reverse hydrophobic effect.
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Affiliation(s)
- Shigeyoshi Nakamura
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan.,Department of General Education, National Institute of Technology, Ube College, 2-14-1 Tokiwadai, Ube, Yamaguchi 755-8555, Japan
| | - Md Golam Kibria
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Satoru Unzai
- Department of Frontier Bioscience, Faculty of Bioscience and Applied Chemistry, Hosei University, 3-7-2 Kajino-cho, Koganei, Tokyo 184-8584, Japan
| | - Yutaka Kuroda
- Department of Biotechnology and Life Science, Graduate School of Engineering, Tokyo University of Agriculture and Technology, 2-24-15 Nakamachi, Koganei, Tokyo 184-8588, Japan
| | - Shun-Ichi Kidokoro
- Department of Bioengineering, Nagaoka University of Technology, 1603-1 Kamitomioka, Nagaoka, Niigata 940-2188, Japan
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Chavali S, Singh AK, Santhanam B, Babu MM. Amino acid homorepeats in proteins. Nat Rev Chem 2020; 4:420-434. [PMID: 37127972 DOI: 10.1038/s41570-020-0204-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/04/2020] [Indexed: 12/16/2022]
Abstract
Amino acid homorepeats, or homorepeats, are polypeptide segments found in proteins that contain stretches of identical amino acid residues. Although abnormal homorepeat expansions are linked to pathologies such as neurodegenerative diseases, homorepeats are prevalent in eukaryotic proteomes, suggesting that they are important for normal physiology. In this Review, we discuss recent advances in our understanding of the biological functions of homorepeats, which range from facilitating subcellular protein localization to mediating interactions between proteins across diverse cellular pathways. We explore how the functional diversity of homorepeat-containing proteins could be linked to the ability of homorepeats to adopt different structural conformations, an ability influenced by repeat composition, repeat length and the nature of flanking sequences. We conclude by highlighting how an understanding of homorepeats will help us better characterize and develop therapeutics against the human diseases to which they contribute.
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Affiliation(s)
- Sreenivas Chavali
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India.
| | - Anjali K Singh
- Department of Biology, Indian Institute of Science Education and Research (IISER) Tirupati, Tirupati, India
| | - Balaji Santhanam
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - M Madan Babu
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge, UK.
- Department of Structural Biology and Center for Data Driven Discovery, St. Jude Children's Research Hospital, Memphis, TN, USA.
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40
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Chernoff YO, Grizel AV, Rubel AA, Zelinsky AA, Chandramowlishwaran P, Chernova TA. Application of yeast to studying amyloid and prion diseases. ADVANCES IN GENETICS 2020; 105:293-380. [PMID: 32560789 PMCID: PMC7527210 DOI: 10.1016/bs.adgen.2020.01.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Amyloids are fibrous cross-β protein aggregates that are capable of proliferation via nucleated polymerization. Amyloid conformation likely represents an ancient protein fold and is linked to various biological or pathological manifestations. Self-perpetuating amyloid-based protein conformers provide a molecular basis for transmissible (infectious or heritable) protein isoforms, termed prions. Amyloids and prions, as well as other types of misfolded aggregated proteins are associated with a variety of devastating mammalian and human diseases, such as Alzheimer's, Parkinson's and Huntington's diseases, transmissible spongiform encephalopathies (TSEs), amyotrophic lateral sclerosis (ALS) and transthyretinopathies. In yeast and fungi, amyloid-based prions control phenotypically detectable heritable traits. Simplicity of cultivation requirements and availability of powerful genetic approaches makes yeast Saccharomyces cerevisiae an excellent model system for studying molecular and cellular mechanisms governing amyloid formation and propagation. Genetic techniques allowing for the expression of mammalian or human amyloidogenic and prionogenic proteins in yeast enable researchers to capitalize on yeast advantages for characterization of the properties of disease-related proteins. Chimeric constructs employing mammalian and human aggregation-prone proteins or domains, fused to fluorophores or to endogenous yeast proteins allow for cytological or phenotypic detection of disease-related protein aggregation in yeast cells. Yeast systems are amenable to high-throughput screening for antagonists of amyloid formation, propagation and/or toxicity. This review summarizes up to date achievements of yeast assays in application to studying mammalian and human disease-related aggregating proteins, and discusses both limitations and further perspectives of yeast-based strategies.
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Affiliation(s)
- Yury O Chernoff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, United States; Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia.
| | - Anastasia V Grizel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Aleksandr A Rubel
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia; Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russia; Sirius University of Science and Technology, Sochi, Russia
| | - Andrew A Zelinsky
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | | | - Tatiana A Chernova
- Department of Biochemistry, Emory University School of Medicine, Atlanta, GA, United States
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41
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Boos F, Labbadia J, Herrmann JM. How the Mitoprotein-Induced Stress Response Safeguards the Cytosol: A Unified View. Trends Cell Biol 2020; 30:241-254. [DOI: 10.1016/j.tcb.2019.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/09/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
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42
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Laidou S, Alanis-Lobato G, Pribyl J, Raskó T, Tichy B, Mikulasek K, Tsagiopoulou M, Oppelt J, Kastrinaki G, Lefaki M, Singh M, Zink A, Chondrogianni N, Psomopoulos F, Prigione A, Ivics Z, Pospisilova S, Skladal P, Izsvák Z, Andrade-Navarro MA, Petrakis S. Nuclear inclusions of pathogenic ataxin-1 induce oxidative stress and perturb the protein synthesis machinery. Redox Biol 2020; 32:101458. [PMID: 32145456 PMCID: PMC7058924 DOI: 10.1016/j.redox.2020.101458] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Revised: 01/29/2020] [Accepted: 02/06/2020] [Indexed: 12/20/2022] Open
Abstract
Spinocerebellar ataxia type-1 (SCA1) is caused by an abnormally expanded polyglutamine (polyQ) tract in ataxin-1. These expansions are responsible for protein misfolding and self-assembly into intranuclear inclusion bodies (IIBs) that are somehow linked to neuronal death. However, owing to lack of a suitable cellular model, the downstream consequences of IIB formation are yet to be resolved. Here, we describe a nuclear protein aggregation model of pathogenic human ataxin-1 and characterize IIB effects. Using an inducible Sleeping Beauty transposon system, we overexpressed the ATXN1(Q82) gene in human mesenchymal stem cells that are resistant to the early cytotoxic effects caused by the expression of the mutant protein. We characterized the structure and the protein composition of insoluble polyQ IIBs which gradually occupy the nuclei and are responsible for the generation of reactive oxygen species. In response to their formation, our transcriptome analysis reveals a cerebellum-specific perturbed protein interaction network, primarily affecting protein synthesis. We propose that insoluble polyQ IIBs cause oxidative and nucleolar stress and affect the assembly of the ribosome by capturing or down-regulating essential components. The inducible cell system can be utilized to decipher the cellular consequences of polyQ protein aggregation. Our strategy provides a broadly applicable methodology for studying polyQ diseases.
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Affiliation(s)
- Stamatia Laidou
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Gregorio Alanis-Lobato
- Faculty of Biology, Johannes Gutenberg University Mainz, 55122, Mainz, Germany; Human Embryo and Stem Cell Laboratory, The Francis Crick Institute, NW1 1AT, London, UK
| | - Jan Pribyl
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Tamás Raskó
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - Boris Tichy
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Kamil Mikulasek
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic; National Centre for Biomolecular Research, Faculty of Science, Masaryk University, 62500, Brno, Czech Republic
| | - Maria Tsagiopoulou
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Jan Oppelt
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Georgia Kastrinaki
- Aerosol and Particle Technology Laboratory/Chemical Process & Energy Resources Institute/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece
| | - Maria Lefaki
- Institute of Biology, Medicinal Chemistry & Biotechnology/National Hellenic Research Foundation, 11365, Athens, Greece
| | - Manvendra Singh
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany
| | - Annika Zink
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany; Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Niki Chondrogianni
- Institute of Biology, Medicinal Chemistry & Biotechnology/National Hellenic Research Foundation, 11365, Athens, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece; Department of Molecular Medicine and Surgery, Karolinska Institutet, 17177, Stockholm, Sweden
| | - Alessandro Prigione
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany; Department of General Pediatrics, Neonatology and Pediatric Cardiology, University Children's Hospital, Heinrich Heine University, 40225, Düsseldorf, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich-Institute, 63225, Langen, Germany
| | - Sarka Pospisilova
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Petr Skladal
- Central European Institute of Technology, Masaryk University, 62500, Brno, Czech Republic
| | - Zsuzsanna Izsvák
- Max-Delbrueck-Center for Molecular Medicine in the Helmholtz Association, Berlin, 13125, Germany.
| | | | - Spyros Petrakis
- Institute of Applied Biosciences/Centre for Research and Technology Hellas, 57001, Thessaloniki, Greece.
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43
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Hu LD, Wang J, Chen XJ, Yan YB. Lanosterol modulates proteostasis via dissolving cytosolic sequestosomes/aggresome-like induced structures. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1867:118617. [DOI: 10.1016/j.bbamcr.2019.118617] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 11/17/2019] [Accepted: 11/25/2019] [Indexed: 01/06/2023]
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Abstract
Mitochondria are essential organelles of eukaryotic cells. They consist of hundreds of different proteins that exhibit crucial activities in respiration, catabolic metabolism and the synthesis of amino acids, lipids, heme and iron-sulfur clusters. With the exception of a handful of hydrophobic mitochondrially encoded membrane proteins, all these proteins are synthesized on cytosolic ribosomes, targeted to receptors on the mitochondrial surface, and transported across or inserted into the outer and inner mitochondrial membrane before they are folded and assembled into their final native structure. This review article provides a comprehensive overview of the mechanisms and components of the mitochondrial protein import systems with a particular focus on recent developments in the field.
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Affiliation(s)
- Katja G Hansen
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrödinger-Strasse 13, 67663, Kaiserslautern, Germany.
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45
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Lévy E, El Banna N, Baïlle D, Heneman-Masurel A, Truchet S, Rezaei H, Huang ME, Béringue V, Martin D, Vernis L. Causative Links between Protein Aggregation and Oxidative Stress: A Review. Int J Mol Sci 2019; 20:ijms20163896. [PMID: 31405050 PMCID: PMC6719959 DOI: 10.3390/ijms20163896] [Citation(s) in RCA: 104] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 07/30/2019] [Accepted: 08/01/2019] [Indexed: 01/17/2023] Open
Abstract
Compelling evidence supports a tight link between oxidative stress and protein aggregation processes, which are noticeably involved in the development of proteinopathies, such as Alzheimer’s disease, Parkinson’s disease, and prion disease. The literature is tremendously rich in studies that establish a functional link between both processes, revealing that oxidative stress can be either causative, or consecutive, to protein aggregation. Because oxidative stress monitoring is highly challenging and may often lead to artefactual results, cutting-edge technical tools have been developed recently in the redox field, improving the ability to measure oxidative perturbations in biological systems. This review aims at providing an update of the previously known functional links between oxidative stress and protein aggregation, thereby revisiting the long-established relationship between both processes.
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Affiliation(s)
- Elise Lévy
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Nadine El Banna
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Dorothée Baïlle
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Amélie Heneman-Masurel
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Sandrine Truchet
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Human Rezaei
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Meng-Er Huang
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France
| | - Vincent Béringue
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France
| | - Davy Martin
- Molecular Virology and Immunology Unit (VIM-UR892), INRA, Université Paris-Saclay, 78352 Jouy-en-Josas, France.
| | - Laurence Vernis
- Institut Curie, PSL Research University, CNRS UMR3348, Université Paris-Sud, Université Paris-Saclay, 91400 Orsay, France.
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46
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Abstract
Lipid droplets (LDs), important organelles for energy storage and involved in the development of metabolic disorders, are extremely dynamic and interact with many other cellular compartments to orchestrate lipid metabolism. Little is known about how these organelle contacts are changed according to cellular needs and functions under different metabolic and pathological conditions and which proteins regulate this. Here, we summarize recent exciting discoveries about the reorganization of organelle contacts in steatotic liver, including the identification of novel LD contact site proteins in cell lines and in animals. We also discuss state of the art proteomics workflows that enable the characterization of LD-organelle contacts and tethering proteins and give an outlook how this can inform obesity research.
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Affiliation(s)
- Natalie Krahmer
- Institute for Diabetes and Obesity, Helmholtz Zentrum München, Munich-Neuherberg, Germany.,Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany.,Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Denmark
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47
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Abstract
The spinocerebellar ataxias (SCAs) are a genetically heterogeneous group of autosomal dominantly inherited progressive disorders, the clinical hallmark of which is loss of balance and coordination accompanied by slurred speech; onset is most often in adult life. Genetically, SCAs are grouped as repeat expansion SCAs, such as SCA3/Machado-Joseph disease (MJD), and rare SCAs that are caused by non-repeat mutations, such as SCA5. Most SCA mutations cause prominent damage to cerebellar Purkinje neurons with consecutive cerebellar atrophy, although Purkinje neurons are only mildly affected in some SCAs. Furthermore, other parts of the nervous system, such as the spinal cord, basal ganglia and pontine nuclei in the brainstem, can be involved. As there is currently no treatment to slow or halt SCAs (many SCAs lead to premature death), the clinical care of patients with SCA focuses on managing the symptoms through physiotherapy, occupational therapy and speech therapy. Intense research has greatly expanded our understanding of the pathobiology of many SCAs, revealing that they occur via interrelated mechanisms (including proteotoxicity, RNA toxicity and ion channel dysfunction), and has led to the identification of new targets for treatment development. However, the development of effective therapies is hampered by the heterogeneity of the SCAs; specific therapeutic approaches may be required for each disease.
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48
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Rencus-Lazar S, DeRowe Y, Adsi H, Gazit E, Laor D. Yeast Models for the Study of Amyloid-Associated Disorders and Development of Future Therapy. Front Mol Biosci 2019; 6:15. [PMID: 30968029 PMCID: PMC6439353 DOI: 10.3389/fmolb.2019.00015] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/01/2019] [Indexed: 12/28/2022] Open
Abstract
First described almost two decades ago, the pioneering yeast models of neurodegenerative disorders, including Alzheimer's, Parkinson's, and Huntington's diseases, have become well-established research tools, providing both basic mechanistic insights as well as a platform for the development of therapeutic agents. These maladies are associated with the formation of aggregative amyloid protein structures showing common characteristics, such as the assembly of soluble oligomeric species, binding of indicative dyes, and apoptotic cytotoxicity. The canonical yeast models have recently been expanded by the establishment of a model for type II diabetes, a non-neurological amyloid-associated disease. While these model systems require the exogenous expression of mammalian proteins in yeast, an additional amyloid-associated disease model, comprising solely mutations of endogenous yeast genes, has been recently described. Mutated in the adenine salvage pathway, this yeast model exhibits adenine accumulation, thereby recapitulating adenine inborn error of metabolism disorders. Moreover, in line with the recent extension of the amyloid hypothesis to include metabolite amyloids, in addition to protein-associated ones, the intracellular assembly of adenine amyloid-like structures has been demonstrated using this yeast model. In this review, we describe currently available yeast models of diverse amyloid-associated disorders, as well as their impact on our understanding of disease mechanisms and contribution to future potential drug development.
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Affiliation(s)
- Sigal Rencus-Lazar
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Yasmin DeRowe
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Hanaa Adsi
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel.,BLAVATNIK CENTER for Drug Discovery, Tel Aviv University, Tel Aviv, Israel.,Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, Tel Aviv, Israel
| | - Dana Laor
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
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49
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Rawat S, Anusha V, Jha M, Sreedurgalakshmi K, Raychaudhuri S. Aggregation of Respiratory Complex Subunits Marks the Onset of Proteotoxicity in Proteasome Inhibited Cells. J Mol Biol 2019; 431:996-1015. [DOI: 10.1016/j.jmb.2019.01.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Revised: 01/10/2019] [Accepted: 01/11/2019] [Indexed: 01/04/2023]
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50
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Tuite MF. Yeast models of neurodegenerative diseases. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2019; 168:351-379. [DOI: 10.1016/bs.pmbts.2019.07.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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