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Petronilho EC, de Andrade GC, de Sousa GDS, Almeida FP, Mota MF, Gomes AVDS, Pinheiro CHS, da Silva MC, Arruda HRS, Marques MA, Vieira TCRG, de Oliveira GAP, Silva JL. Oncogenic p53 triggers amyloid aggregation of p63 and p73 liquid droplets. Commun Chem 2024; 7:207. [PMID: 39284933 PMCID: PMC11405828 DOI: 10.1038/s42004-024-01289-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2024] [Accepted: 08/29/2024] [Indexed: 09/20/2024] Open
Abstract
P53 Phase separation is crucial towards amyloid aggregation and p63 and p73 have enhanced expression in tumors. This study examines the phase behaviors of p53, p63, and p73. Here we show that unlike the DNA-binding domain of p53 (p53C), the p63C and p73C undergo phase separation, but do not form amyloids under physiological temperatures. Wild-type and mutant p53C form droplets at 4°C and aggregates at 37 °C with amyloid properties. Mutant p53C promotes amyloid-like states in p63C and p73C, recruiting them into membraneless organelles. Amyloid conversion is supported by thioflavin T and Congo red binding, increased light scattering, and circular dichroism. Full-length mutant p53 and p63C (or p73C) co-transfection shows reduced fluorescence recovery after photobleaching. Heparin inhibits the prion-like aggregation of p63C and p73C induced by p53C. These findings highlight the role of p53 in initiating amyloid aggregation in p63 and p73, opening avenues for targeting prion-like conversion in cancer therapy.
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Affiliation(s)
- Elaine C Petronilho
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Guilherme C de Andrade
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Gileno Dos S de Sousa
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Fernando P Almeida
- National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Michelle F Mota
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Ana Vitória Dos S Gomes
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Carlos Henrique S Pinheiro
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mylena C da Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Hiam R S Arruda
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
- National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, RJ, Brazil.
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2
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Joshi A, Avni A, Walimbe A, Rai SK, Sarkar S, Mukhopadhyay S. Hydrogen-Bonded Network of Water in Phase-Separated Biomolecular Condensates. J Phys Chem Lett 2024; 15:7724-7734. [PMID: 39042834 DOI: 10.1021/acs.jpclett.4c01153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2024]
Abstract
Biomolecular condensates formed via phase separation of intrinsically disordered proteins/regions (IDPs/IDRs) and nucleic acids are associated with cell physiology and disease. Water makes up for ∼60-70% of the condensate volume and is thought to influence the complex interplay of chain-chain and chain-solvent interactions, modulating the mesoscale properties of condensates. The behavior of water in condensates and the key roles of protein hydration water in driving the phase separation remain elusive. Here, we employ single-droplet vibrational Raman spectroscopy to illuminate the structural redistribution within protein hydration water during the phase separation of neuronal IDPs. Our Raman measurements reveal the changes in the water hydrogen bonding network during homotypic and heterotypic phase separation governed by various molecular drivers. Such single-droplet water Raman measurements offer a potent generic tool to unmask the intriguing interplay of sequence-encoded chain-chain and chain-solvent interactions governing macromolecular phase separation into membraneless organelles, synthetic condensates, and protocells.
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3
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Goto Y, Nakajima K, Yamamoto S, Yamaguchi K. Supersaturation, a Critical Factor Underlying Proteostasis of Amyloid Fibril Formation. J Mol Biol 2024; 436:168475. [PMID: 38311232 DOI: 10.1016/j.jmb.2024.168475] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/10/2024]
Abstract
From a physicochemical viewpoint, amyloid fibril formation is a phase transition from soluble to crystal-like sates limited by supersaturation. It occurs only above solubility (i.e., the solubility limit) coupled with a breakdown of supersaturation. Although many studies have examined the role of molecular chaperones in the context of proteostasis, the role of supersaturation has not been addressed. Moreover, although molecular chaperone-dependent disaggregations have been reported for preformed amyloid fibrils, amyloid fibrils will not dissolve above the solubility of monomers, even if agitations fragment long fibrils to shorter amyloid particles. On the other hand, on considering a reversible and coupled equilibrium of interactions, folding/unfolding and amyloid formation/disaggregation, molecules stabilizing native states can work as a disaggregase reversing the amyloid fibrils to monomers. It is likely that the proteostasis network has various intra- and extracellular components which disaggregate preformed amyloid fibrils as well as prevent amyloid formation. Further studies with a view of solubility and supersaturation will be essential for comprehensive understanding of proteostasis.
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Affiliation(s)
- Yuji Goto
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan.
| | - Kichitaro Nakajima
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
| | - Suguru Yamamoto
- Division of Clinical Nephrology and Rheumatology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata 951-8510, Japan
| | - Keiichi Yamaguchi
- Microsonochemistry Joint Research Chair, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka 565-0871, Japan
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4
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Garai S, Raizada A, Kumar V, Sopory SK, Pareek A, Singla-Pareek SL, Kaur C. In silico analysis of fungal prion-like proteins for elucidating their role in plant-fungi interactions. Arch Microbiol 2024; 206:308. [PMID: 38896139 DOI: 10.1007/s00203-024-04040-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Revised: 06/07/2024] [Accepted: 06/09/2024] [Indexed: 06/21/2024]
Abstract
Prion-like proteins (PrLPs) have emerged as beneficial molecules with implications in adaptive responses. These proteins possess a conserved prion-like domain (PrLD) which is an intrinsically disordered region capable of adopting different conformations upon perceiving external stimuli. Owing to changes in protein conformation, functional characteristics of proteins harboring PrLDs get altered thereby, providing a unique mode of protein-based regulation. Since PrLPs are ubiquitous in nature and involved in diverse functions, through this study, we aim to explore the role of such domains in yet another important physiological process viz. plant-microbe interactions to get insights into the mechanisms dictating cross-kingdom interactions. We have evaluated the presence and functions of PrLPs in 18 different plant-associated fungi of agricultural importance to unravel their role in plant-microbe interactions. Of the 241,997 proteins scanned, 3,820 (~ 1.6%) were identified as putative PrLPs with pathogenic fungi showing significantly higher PrLP density than their beneficial counterparts. Further, through GO enrichment analysis, we could predict several PrLPs from pathogenic fungi to be involved in virulence and formation of stress granules. Notably, PrLPs involved in (retro)transposition were observed exclusively in pathogenic fungi. We even analyzed publicly available data for the expression alterations of fungal PrLPs upon their interaction with their respective hosts which revealed perturbation in the levels of some PrLP-encoding genes during interactions with plants. Overall, our work sheds light into the probable role of prion-like candidates in plant-fungi interaction, particularly in context of pathogenesis, paving way for more focused studies for validating their role.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Avi Raizada
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Vijay Kumar
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sudhir K Sopory
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Ashwani Pareek
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India
| | - Sneh L Singla-Pareek
- Plant Stress Biology Group, International Centre for Genetic Engineering and Biotechnology, New Delhi, 110067, India
| | - Charanpreet Kaur
- National Agri-Food Biotechnology Institute, Mohali, 140306, Punjab, India.
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Litberg TJ, Horowitz S. Roles of Nucleic Acids in Protein Folding, Aggregation, and Disease. ACS Chem Biol 2024; 19:809-823. [PMID: 38477936 PMCID: PMC11149768 DOI: 10.1021/acschembio.3c00695] [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] [Indexed: 03/14/2024]
Abstract
The role of nucleic acids in protein folding and aggregation is an area of continued research, with relevance to understanding both basic biological processes and disease. In this review, we provide an overview of the trajectory of research on both nucleic acids as chaperones and their roles in several protein misfolding diseases. We highlight key questions that remain on the biophysical and biochemical specifics of how nucleic acids have large effects on multiple proteins' folding and aggregation behavior and how this pertains to multiple protein misfolding diseases.
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Affiliation(s)
- Theodore J. Litberg
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80208, USA
- Department of Pharmacology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
- Center for Synthetic Biology, Northwestern University, Evanston, IL, 60208, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry and The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, 80208, USA
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6
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Raguseo F, Wang Y, Li J, Petrić Howe M, Balendra R, Huyghebaert A, Vadukul DM, Tanase DA, Maher TE, Malouf L, Rubio-Sánchez R, Aprile FA, Elani Y, Patani R, Di Michele L, Di Antonio M. The ALS/FTD-related C9orf72 hexanucleotide repeat expansion forms RNA condensates through multimolecular G-quadruplexes. Nat Commun 2023; 14:8272. [PMID: 38092738 PMCID: PMC10719400 DOI: 10.1038/s41467-023-43872-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Accepted: 11/21/2023] [Indexed: 12/17/2023] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are neurodegenerative diseases that exist on a clinico-pathogenetic spectrum, designated ALS/FTD. The most common genetic cause of ALS/FTD is expansion of the intronic hexanucleotide repeat (GGGGCC)n in C9orf72. Here, we investigate the formation of nucleic acid secondary structures in these expansion repeats, and their role in generating condensates characteristic of ALS/FTD. We observe significant aggregation of the hexanucleotide sequence (GGGGCC)n, which we associate to the formation of multimolecular G-quadruplexes (mG4s) by using a range of biophysical techniques. Exposing the condensates to G4-unfolding conditions leads to prompt disassembly, highlighting the key role of mG4-formation in the condensation process. We further validate the biological relevance of our findings by detecting an increased prevalence of G4-structures in C9orf72 mutant human motor neurons when compared to healthy motor neurons by staining with a G4-selective fluorescent probe, revealing signal in putative condensates. Our findings strongly suggest that RNA G-rich repetitive sequences can form protein-free condensates sustained by multimolecular G-quadruplexes, highlighting their potential relevance as therapeutic targets for C9orf72 mutation-related ALS/FTD.
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Affiliation(s)
- Federica Raguseo
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yiran Wang
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Jessica Li
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Marija Petrić Howe
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Rubika Balendra
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK
| | - Anouk Huyghebaert
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Devkee M Vadukul
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Diana A Tanase
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Thomas E Maher
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Layla Malouf
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Roger Rubio-Sánchez
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK
| | - Francesco A Aprile
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK
| | - Yuval Elani
- Imperial College London, Department of Chemical Engineering, South Kensington, London, SW7 2AZ, UK
| | - Rickie Patani
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
- Department of Neuromuscular Diseases, Queen Square Institute of Neurology, University College London, London, WC1N 3BG, UK.
| | - Lorenzo Di Michele
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- University of Cambridge, Department of Chemical Engineering and Biotechnology, Philippa Fawcett Drive, Cambridge, CB3 0AS, UK.
| | - Marco Di Antonio
- Imperial College London, Department of Chemistry, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- Imperial College London, Institute of Chemical Biology, Molecular Sciences Research Hub, 82 Wood Lane, London, W12 0BZ, UK.
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK.
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7
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Younas N, Zafar S, Saleem T, Fernandez Flores LC, Younas A, Schmitz M, Zerr I. Differential interactome mapping of aggregation prone/prion-like proteins under stress: novel links to stress granule biology. Cell Biosci 2023; 13:221. [PMID: 38041189 PMCID: PMC10693047 DOI: 10.1186/s13578-023-01164-7] [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: 05/30/2023] [Accepted: 11/02/2023] [Indexed: 12/03/2023] Open
Abstract
BACKGROUND Aberrant stress granules (SGs) are emerging as prime suspects in the nucleation of toxic protein aggregates. Understanding the molecular networks linked with aggregation-prone proteins (prion protein, synuclein, and tau) under stressful environments is crucial to understand pathophysiological cascades associated with these proteins. METHODS We characterized and validated oxidative stress-induced molecular network changes of endogenous aggregation-prone proteins (prion protein, synuclein, and tau) by employing immunoprecipitation coupled with mass spectrometry analysis under basal and oxidative stress conditions. We used two different cell models (SH-SY5Y: human neuroblastoma and HeLa cell line) to induce oxidative stress using a well-known inducer (sodium arsenite) of oxidative stress. RESULTS Overall, we identified 597 proteins as potential interaction partners. Our comparative interactome mapping provides comprehensive network reorganizations of three aggregation-prone hallmark proteins, establish novel interacting partners and their dysregulation, and validates that prion protein and synuclein localize in cytoplasmic SGs. Localization of prion protein and synuclein in TIA1-positive SGs provides an important link between SG pathobiology and aggregation-prone proteins. In addition, dysregulation (downregulation) of prion protein and exportin-5 protein, and translocation of exportin-5 into the nucleus under oxidative stress shed light on nucleocytoplasmic transport defects during the stress response. CONCLUSIONS The current study contributes to our understanding of stress-mediated network rearrangements and posttranslational modifications of prion/prion-like proteins. Localization of prion protein and synuclein in the cytoplasmic SGs provides an important link between stress granule pathobiology and aggregation-prone proteins. In addition, our findings demonstrate nucleocytoplasmic transport defects after oxidative stress via dysregulation and nuclear accumulation of exportin-5.
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Affiliation(s)
- Neelam Younas
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany.
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany.
| | - Saima Zafar
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
- Biomedical Engineering and Sciences Department, School of Mechanical and Manufacturing Engineering (SMME), National University of Sciences and Technology (NUST), Islamabad, Pakistan
| | - Tayyaba Saleem
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Leticia Camila Fernandez Flores
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Abrar Younas
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Matthias Schmitz
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
| | - Inga Zerr
- Department of Neurology, University Medical Center, Georg-August-Universität, Robert-Koch-Strasse 40, 37075, Göttingen, Germany
- German Center for Neurodegenerative Diseases (DZNE), Robert-Koch-Straße 40, 37075, Göttingen, Germany
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8
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Guzman BB, Son A, Litberg TJ, Huang Z, Dominguez D, Horowitz S. Emerging roles for G-quadruplexes in proteostasis. FEBS J 2023; 290:4614-4625. [PMID: 36017725 PMCID: PMC10071977 DOI: 10.1111/febs.16608] [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: 04/05/2022] [Revised: 07/22/2022] [Accepted: 08/25/2022] [Indexed: 11/29/2022]
Abstract
How nucleic acids interact with proteins, and how they affect protein folding, aggregation, and misfolding is a still-evolving area of research. Considerable effort is now focusing on a particular structure of RNA and DNA, G-quadruplexes, and their role in protein homeostasis and disease. In this state-of-the-art review, we track recent reports on how G-quadruplexes influence protein aggregation, proteolysis, phase separation, and protein misfolding diseases, and pose currently unanswered questions in the advance of this scientific field.
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Affiliation(s)
- Bryan B Guzman
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Ahyun Son
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Theodore J Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Zijue Huang
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
| | - Daniel Dominguez
- Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA
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9
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Cordeiro Y, Freire MHO, Wiecikowski AF, do Amaral MJ. (Dys)functional insights into nucleic acids and RNA-binding proteins modulation of the prion protein and α-synuclein phase separation. Biophys Rev 2023; 15:577-589. [PMID: 37681103 PMCID: PMC10480379 DOI: 10.1007/s12551-023-01067-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 05/22/2023] [Indexed: 09/09/2023] Open
Abstract
Prion diseases are prototype of infectious diseases transmitted by a protein, the prion protein (PrP), and are still not understandable at the molecular level. Heterogenous species of aggregated PrP can be generated from its monomer. α-synuclein (αSyn), related to Parkinson's disease, has also shown a prion-like pathogenic character, and likewise PrP interacts with nucleic acids (NAs), which in turn modulate their aggregation. Recently, our group and others have characterized that NAs and/or RNA-binding proteins (RBPs) modulate recombinant PrP and/or αSyn condensates formation, and uncontrolled condensation might precede pathological aggregation. Tackling abnormal phase separation of neurodegenerative disease-related proteins has been proposed as a promising therapeutic target. Therefore, understanding the mechanism by which polyanions, like NAs, modulate phase transitions intracellularly, is key to assess their role on toxicity promotion and neuronal death. Herein we discuss data on the nucleic acids binding properties and phase separation ability of PrP and αSyn with a special focus on their modulation by NAs and RBPs. Furthermore, we provide insights into condensation of PrP and/or αSyn in the light of non-trivial subcellular locations such as the nuclear and cytosolic environments.
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Affiliation(s)
- Yraima Cordeiro
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Maria Heloisa O. Freire
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Adalgisa Felippe Wiecikowski
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
| | - Mariana Juliani do Amaral
- Faculty of Pharmacy, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho 373, bloco B, subsolo Sala 36, Rio de Janeiro, RJ 21941-902 Brazil
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10
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Silva JL, Foguel D, Ferreira VF, Vieira TCRG, Marques MA, Ferretti GDS, Outeiro TF, Cordeiro Y, de Oliveira GAP. Targeting Biomolecular Condensation and Protein Aggregation against Cancer. Chem Rev 2023. [PMID: 37379327 DOI: 10.1021/acs.chemrev.3c00131] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2023]
Abstract
Biomolecular condensates, membrane-less entities arising from liquid-liquid phase separation, hold dichotomous roles in health and disease. Alongside their physiological functions, these condensates can transition to a solid phase, producing amyloid-like structures implicated in degenerative diseases and cancer. This review thoroughly examines the dual nature of biomolecular condensates, spotlighting their role in cancer, particularly concerning the p53 tumor suppressor. Given that over half of the malignant tumors possess mutations in the TP53 gene, this topic carries profound implications for future cancer treatment strategies. Notably, p53 not only misfolds but also forms biomolecular condensates and aggregates analogous to other protein-based amyloids, thus significantly influencing cancer progression through loss-of-function, negative dominance, and gain-of-function pathways. The exact molecular mechanisms underpinning the gain-of-function in mutant p53 remain elusive. However, cofactors like nucleic acids and glycosaminoglycans are known to be critical players in this intersection between diseases. Importantly, we reveal that molecules capable of inhibiting mutant p53 aggregation can curtail tumor proliferation and migration. Hence, targeting phase transitions to solid-like amorphous and amyloid-like states of mutant p53 offers a promising direction for innovative cancer diagnostics and therapeutics.
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Affiliation(s)
- Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Debora Foguel
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Vitor F Ferreira
- Faculty of Pharmacy, Fluminense Federal University (UFF), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Tiago F Outeiro
- Department of Experimental Neurodegeneration, Center for Biostructural Imaging of Neurodegeneration, University Medical Center, 37075 Göttingen, Germany
- Max Planck Institute for Multidisciplinary Sciences, 37075 Göttingen, Germany
- Translational and Clinical Research Institute, Faculty of Medical Sciences, Newcastle University, Framlington Place, Newcastle Upon Tyne NE2 4HH, U.K
- Scientific employee with an honorary contract at Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), 37075 Göttingen, Germany
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro (UFRJ), Rio de Janeiro, RJ 21941-902, Brazil
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11
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Avni A, Joshi A, Mukhopadhyay S. Hydrogen-Deuterium Exchange Vibrational Raman Spectroscopy Distinguishes Distinct Amyloid Polymorphs Comprising Altered Core Architecture. J Phys Chem Lett 2023:5592-5601. [PMID: 37307286 DOI: 10.1021/acs.jpclett.3c01086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Amyloid fibrils are ordered protein aggregates comprising a hydrogen-bonded central cross-β core displaying a structural diversity in their supramolecular packing arrangements within the core. Such an altered packing results in amyloid polymorphism that gives rise to morphological and biological strain diversities. Here, we show that vibrational Raman spectroscopy coupled with hydrogen/deuterium (H/D) exchange discerns the key structural features that are responsible for yielding diverse amyloid polymorphs. Such a noninvasive and label-free methodology allows us to structurally distinguish distinct amyloid polymorphs displaying altered hydrogen bonding and supramolecular packing within the cross-β structural motif. By using quantitative molecular fingerprinting and multivariate statistical analysis, we analyze key Raman bands for the protein backbone and side chains that allow us to capture the conformational heterogeneity and structural distributions within distinct amyloid polymorphs. Our results delineate the key molecular factors governing the structural diversity in amyloid polymorphs and can potentially simplify studying amyloid remodeling by small molecules.
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12
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Joshi A, Mukhopadhyay S. Biophysics of biomolecular condensates. Biophys J 2023; 122:737-740. [PMID: 36791720 PMCID: PMC10027443 DOI: 10.1016/j.bpj.2023.02.002] [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: 01/15/2023] [Revised: 01/28/2023] [Accepted: 01/31/2023] [Indexed: 02/15/2023] Open
Abstract
The formation of biomolecular condensates has emerged as a new biophysical principle for subcellular compartmentalization within cells to facilitate the spatiotemporal regulation of a multitude of complex biomolecular reactions. In this Research Highlight, we summarize the findings that were published in Biophysical Journal during the past two years (2021 and 2022). These papers provided biophysical insights into the formation of biomolecular condensates via phase separation of proteins with or without nucleic acids.
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Affiliation(s)
- Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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13
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Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates. Proc Natl Acad Sci U S A 2023; 120:e2216338120. [PMID: 36595668 PMCID: PMC9986828 DOI: 10.1073/pnas.2216338120] [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] [Indexed: 01/05/2023] Open
Abstract
Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to perform a wide range of critical cellular functions by maintaining spatiotemporal regulation and organizing intracellular biochemistry. However, aberrant phase transitions are implicated in a multitude of human diseases. Here, we demonstrate that two neuronal proteins, namely tau and prion, undergo complex coacervation driven by domain-specific electrostatic interactions to yield highly dynamic, mesoscopic liquid-like droplets. The acidic N-terminal segment of tau interacts electrostatically with the polybasic N-terminal intrinsically disordered segment of the prion protein (PrP). We employed a unique combination of time-resolved tools that encompass several orders of magnitude of timescales ranging from nanoseconds to seconds. These studies unveil an intriguing symphony of molecular events associated with the formation of heterotypic condensates comprising ephemeral, domain-specific, short-range electrostatic nanoclusters. Our results reveal that these heterotypic condensates can be tuned by RNA in a stoichiometry-dependent manner resulting in reversible, multiphasic, immiscible, and ternary condensates of different morphologies ranging from core-shell to nested droplets. This ternary system exhibits a typical three-regime phase behavior reminiscent of other membraneless organelles including nucleolar condensates. We also show that upon aging, tau:PrP droplets gradually convert into solid-like co-assemblies by sequestration of persistent intermolecular interactions. Our vibrational Raman results in conjunction with atomic force microscopy and multi-color fluorescence imaging reveal the presence of amorphous and amyloid-like co-aggregates upon maturation. Our findings provide mechanistic underpinnings of overlapping neuropathology involving tau and PrP and highlight a broader biological role of complex phase transitions in physiology and disease.
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14
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Sousa Junior IP, Vieira TCRG. Enterovirus infection and its relationship with neurodegenerative diseases. Mem Inst Oswaldo Cruz 2023; 118:e220252. [PMID: 36946853 PMCID: PMC10072002 DOI: 10.1590/0074-02760220252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/24/2023] [Indexed: 03/23/2023] Open
Abstract
Neurodegenerative diseases (NDs) are increasingly common, especially in populations with higher life expectancies. They are associated mainly with protein metabolism and structure changes, leading to neuronal cell death. Viral infections affect these cellular processes and may be involved in the etiology of several neurological illnesses, particularly NDs. Enteroviruses (EVs) frequently infect the central nervous system (CNS), causing neurological disease. Inflammation, disruption of the host autophagy machinery, and deregulation and accumulation/misfolding of proteins are the main alterations observed after infection by an EV. In this perspective, we discuss the most recent findings on the subject, examining the possible role of EVs in the development of NDs, and shedding light on the putative role played by these viruses in developing NDs.
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Affiliation(s)
- Ivanildo Pedro Sousa Junior
- Fundação Oswaldo Cruz-Fiocruz, Instituto Oswaldo Cruz, Laboratório de Virologia Molecular, Rio de Janeiro, RJ, Brasil
| | - Tuane Cristine Ramos Gonçalves Vieira
- Universidade Federal do Rio de Janeiro, Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagem, Instituto de Bioquímica Médica Leopoldo de Meis, Programa de Biologia Estrutural, Rio de Janeiro, RJ, Brasil
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15
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Murakami K, Ono K. Interactions of amyloid coaggregates with biomolecules and its relevance to neurodegeneration. FASEB J 2022; 36:e22493. [PMID: 35971743 DOI: 10.1096/fj.202200235r] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/18/2022] [Accepted: 08/01/2022] [Indexed: 01/16/2023]
Abstract
The aggregation of amyloidogenic proteins is a pathological hallmark of various neurodegenerative diseases, including Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. In these diseases, oligomeric intermediates or toxic aggregates of amyloids cause neuronal damage and degeneration. Despite the substantial effort made over recent decades to implement therapeutic interventions, these neurodegenerative diseases are not yet understood at the molecular level. In many cases, multiple disease-causing amyloids overlap in a sole pathological feature or a sole disease-causing amyloid represents multiple pathological features. Various amyloid pathologies can coexist in the same brain with or without clinical presentation and may even occur in individuals without disease. From sparse data, speculation has arisen regarding the coaggregation of amyloids with disparate amyloid species and other biomolecules, which are the same characteristics that make diagnostics and drug development challenging. However, advances in research related to biomolecular condensates and structural analysis have been used to overcome some of these challenges. Considering the development of these resources and techniques, herein we review the cross-seeding of amyloidosis, for example, involving the amyloids amyloid β, tau, α-synuclein, and human islet amyloid polypeptide, and their cross-inhibition by transthyretin and BRICHOS. The interplay of nucleic acid-binding proteins, such as prions, TAR DNA-binding protein 43, fused in sarcoma/translated in liposarcoma, and fragile X mental retardation polyglycine, with nucleic acids in the pathology of neurodegeneration are also described, and we thereby highlight the potential clinical applications in central nervous system therapy.
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Affiliation(s)
- Kazuma Murakami
- Division of Food Science and Biotechnology, Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kenjiro Ono
- Department of Neurology, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
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16
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Avni A, Joshi A, Walimbe A, Pattanashetty SG, Mukhopadhyay S. Single-droplet surface-enhanced Raman scattering decodes the molecular determinants of liquid-liquid phase separation. Nat Commun 2022; 13:4378. [PMID: 35902591 PMCID: PMC9334365 DOI: 10.1038/s41467-022-32143-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 07/19/2022] [Indexed: 11/09/2022] Open
Abstract
Biomolecular condensates formed via liquid-liquid phase separation (LLPS) are involved in a myriad of critical cellular functions and debilitating neurodegenerative diseases. Elucidating the role of intrinsic disorder and conformational heterogeneity of intrinsically disordered proteins/regions (IDPs/IDRs) in these phase-separated membrane-less organelles is crucial to understanding the mechanism of formation and regulation of biomolecular condensates. Here we introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that utilizes surface-engineered, plasmonic, metal nanoparticles to unveil the inner workings of mesoscopic liquid droplets of Fused in Sarcoma (FUS) in the absence and presence of RNA. These highly sensitive measurements offer unprecedented sensitivity to capture the crucial interactions, conformational heterogeneity, and structural distributions within the condensed phase in a droplet-by-droplet manner. Such an ultra-sensitive single-droplet vibrational methodology can serve as a potent tool to decipher the key molecular drivers of biological phase transitions of a wide range of biomolecular condensates involved in physiology and disease. The authors introduce a unique single-droplet surface-enhanced Raman scattering (SERS) methodology that illuminates a wealth of molecular information within the mesoscopic liquid condensed phase of Fused in Sarcoma in the absence and presence of RNA.
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Affiliation(s)
- Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anuja Walimbe
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Swastik G Pattanashetty
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India. .,Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India. .,Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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17
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Supersaturation-Dependent Formation of Amyloid Fibrils. Molecules 2022; 27:molecules27144588. [PMID: 35889461 PMCID: PMC9321232 DOI: 10.3390/molecules27144588] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Revised: 07/11/2022] [Accepted: 07/12/2022] [Indexed: 01/27/2023] Open
Abstract
The supersaturation of a solution refers to a non-equilibrium phase in which the solution is trapped in a soluble state, even though the solute’s concentration is greater than its thermodynamic solubility. Upon breaking supersaturation, crystals form and the concentration of the solute decreases to its thermodynamic solubility. Soon after the discovery of the prion phenomena, it was recognized that prion disease transmission and propagation share some similarities with the process of crystallization. Subsequent studies exploring the structural and functional association between amyloid fibrils and amyloidoses solidified this paradigm. However, recent studies have not necessarily focused on supersaturation, possibly because of marked advancements in structural studies clarifying the atomic structures of amyloid fibrils. On the other hand, there is increasing evidence that supersaturation plays a critical role in the formation of amyloid fibrils and the onset of amyloidosis. Here, we review the recent evidence that supersaturation plays a role in linking unfolding/folding and amyloid fibril formation. We also introduce the HANABI (HANdai Amyloid Burst Inducer) system, which enables high-throughput analysis of amyloid fibril formation by the ultrasonication-triggered breakdown of supersaturation. In addition to structural studies, studies based on solubility and supersaturation are essential both to developing a comprehensive understanding of amyloid fibrils and their roles in amyloidosis, and to developing therapeutic strategies.
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18
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Shafiq M, Da Vela S, Amin L, Younas N, Harris DA, Zerr I, Altmeppen HC, Svergun D, Glatzel M. The prion protein and its ligands: Insights into structure-function relationships. BIOCHIMICA ET BIOPHYSICA ACTA. MOLECULAR CELL RESEARCH 2022; 1869:119240. [PMID: 35192891 DOI: 10.1016/j.bbamcr.2022.119240] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/23/2022] [Accepted: 01/28/2022] [Indexed: 06/14/2023]
Abstract
The prion protein is a multifunctional protein that exists in at least two different folding states. It is subject to diverse proteolytic processing steps that lead to prion protein fragments some of which are membrane-bound whereas others are soluble. A multitude of ligands bind to the prion protein and besides proteinaceous binding partners, interaction with metal ions and nucleic acids occurs. Although of great importance, information on structural and functional consequences of prion protein binding to its partners is limited. Here, we will reflect on the structure-function relationship of the prion protein and its binding partners considering the different folding states and prion protein fragments.
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Affiliation(s)
- Mohsin Shafiq
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Stefano Da Vela
- European Molecular Biology Laboratory (EMBL), Hamburg c/o German Electron Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Ladan Amin
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States
| | - Neelam Younas
- Department of Neurology, University Medical Center Goettingen, Robert-Koch-str. 40, 37075 Goettingen, Germany
| | - David A Harris
- Department of Biochemistry, Boston University School of Medicine, Boston, MA, United States
| | - Inga Zerr
- Department of Neurology, University Medical Center Goettingen, Robert-Koch-str. 40, 37075 Goettingen, Germany
| | - Hermann C Altmeppen
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany
| | - Dmitri Svergun
- European Molecular Biology Laboratory (EMBL), Hamburg c/o German Electron Synchrotron (DESY), Notkestraße 85, 22607 Hamburg, Germany
| | - Markus Glatzel
- Institute of Neuropathology, University Medical Center Hamburg-Eppendorf, Martinistraße 52, 20251 Hamburg, Germany.
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19
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Abstract
Amyloids are organized suprastructural polypeptide arrangements. The prevalence of amyloid-related processes of pathophysiological relevance has been linked to aging-related degenerative diseases. Besides the role of genetic polymorphisms on the relative risk of amyloid diseases, the contributions of nongenetic ontogenic cluster of factors remain elusive. In recent decades, mounting evidences have been suggesting the role of essential micronutrients, in particular transition metals, in the regulation of amyloidogenic processes, both directly (such as binding to amyloid proteins) or indirectly (such as regulating regulatory partners, processing enzymes, and membrane transporters). The features of transition metals as regulatory cofactors of amyloid proteins and the consequences of metal dyshomeostasis in triggering amyloidogenic processes, as well as the evidences showing amelioration of symptoms by dietary supplementation, suggest an exaptative role of metals in regulating amyloid pathways. The self- and cross-talk replicative nature of these amyloid processes along with their systemic distribution support the concept of their metastatic nature. The role of amyloidosis as nutrient sensors would act as intra- and transgenerational epigenetic metabolic programming factors determining health span and life span, viability, which could participate as an evolutive selective pressure.
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Affiliation(s)
- Luís Maurício T R Lima
- Laboratory for Pharmaceutical Biotechnology - pbiotech, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
- Laboratory for Macromolecules (LAMAC-DIMAV), National Institute of Metrology, Quality and Technology - INMETRO, Duque de Caxias, Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tháyna Sisnande
- Laboratory for Pharmaceutical Biotechnology - pbiotech, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Rio de Janeiro, Brazil
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20
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Agarwal A, Arora L, Rai SK, Avni A, Mukhopadhyay S. Spatiotemporal modulations in heterotypic condensates of prion and α-synuclein control phase transitions and amyloid conversion. Nat Commun 2022; 13:1154. [PMID: 35241680 PMCID: PMC8894376 DOI: 10.1038/s41467-022-28797-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 02/10/2022] [Indexed: 12/30/2022] Open
Abstract
Biomolecular condensation via liquid-liquid phase separation of proteins and nucleic acids is associated with a range of critical cellular functions and neurodegenerative diseases. Here, we demonstrate that complex coacervation of the prion protein and α-synuclein within narrow stoichiometry results in the formation of highly dynamic, reversible, thermo-responsive liquid droplets via domain-specific electrostatic interactions between the positively-charged intrinsically disordered N-terminal segment of prion and the acidic C-terminal tail of α-synuclein. The addition of RNA to these coacervates yields multiphasic, vesicle-like, hollow condensates. Picosecond time-resolved measurements revealed the presence of transient electrostatic nanoclusters that are stable on the nanosecond timescale and can undergo breaking-and-making of interactions on slower timescales giving rise to a liquid-like behavior in the mesoscopic regime. The liquid-to-solid transition drives a rapid conversion of complex coacervates into heterotypic amyloids. Our results suggest that synergistic prion-α-synuclein interactions within condensates provide mechanistic underpinnings of their physiological role and overlapping neuropathological features.
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Affiliation(s)
- Aishwarya Agarwal
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Sandeep K Rai
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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21
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Nucleic acid actions on abnormal protein aggregation, phase transitions and phase separation. Curr Opin Struct Biol 2022; 73:102346. [PMID: 35247749 DOI: 10.1016/j.sbi.2022.102346] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/06/2021] [Accepted: 01/28/2022] [Indexed: 12/27/2022]
Abstract
Liquid-liquid phase separation (LLPS) and phase transitions (PT) of proteins, which include the formation of gel- and solid-like species, have been characterized as physical processes related to the pathology of conformational diseases. Nucleic acid (NA)-binding proteins related to neurodegenerative disorders and cancer were shown by us and others to experience PT modulated by different NAs. Herein, we discuss recent work on phase separation and phase transitions of two amyloidogenic proteins, i.e. the prion protein (PrP) and p53, which undergo conformational changes and aggregate upon NA interaction. The role of different NAs in these processes is discussed to shed light on the relevance of PSs and PTs for both the functional and pathological roles of these mammalian proteins.
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22
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P B Gomes M, de Lima EV, G Q Barros-Aragão F, Passos YM, Lemos FS, Zamberlan DC, Ribeiro G, Macedo B, C Ferreira N, Silva JL, Figueiredo CP, Clarke JR, Cordeiro Y. Prion protein complexed to a DNA aptamer induce behavioral and synapse dysfunction in mice. Behav Brain Res 2022; 419:113680. [PMID: 34822947 DOI: 10.1016/j.bbr.2021.113680] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 11/16/2021] [Accepted: 11/18/2021] [Indexed: 01/06/2023]
Abstract
Conversion of the cellular prion protein (PrPC) into the scrapie form (PrPSc) is the leading step to the development of transmissible spongiform encephalopathies (TSEs), still incurable neurodegenerative disorders. Interaction of PrPC with cellular and synthetic ligands that induce formation of scrapie-like conformations has been deeply investigated in vitro. Different nucleic acid (NA) sequences bind PrP and convert it to β-sheet-rich or unfolded species; among such NAs, a 21-mer double-stranded DNA, D67, was shown to induce formation of PrP aggregates that were cytotoxic. However, in vivo effects of these PrP-DNA complexes were not explored. Herein, aggregates of recombinant full-length PrP (rPrP23-231) induced by interaction with the D67 aptamer were inoculated into the lateral ventricle of Swiss mice and acute effects were investigated. The aggregates had no influence on emotional, locomotor and motor behavior of mice. In contrast, mice developed cognitive impairment and hippocampal synapse loss, which was accompanied by intense activation of glial cells in this brain region. Our results suggest that the i.c.v. injection of rPrP:D67 aggregates is an interesting model to study the neurotoxicity of aggregated PrP in vivo, and that glial cell activation may be an important step for behavioral and cognitive dysfunction in prion diseases.
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Affiliation(s)
- Mariana P B Gomes
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil; Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Emanuelle V de Lima
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil
| | - Fernanda G Q Barros-Aragão
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil; Biomedical Sciences Institute, Federal University of Rio de Janeiro, RJ 21941-902, Brazil
| | - Yulli M Passos
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil
| | - Felipe S Lemos
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil; Biomedical Sciences Institute, Federal University of Rio de Janeiro, RJ 21941-902, Brazil
| | - Daniele C Zamberlan
- Department of Biochemistry and Molecular Biology, Federal University of Santa Maria, Santa Maria, RS 97105-900, Brazil
| | - Gabriel Ribeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil
| | - Bruno Macedo
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil
| | - Natalia C Ferreira
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil; IAVI Neutralizing Antibody Center, The Scripps Research Institute, La Jolla, CA, USA
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo De Meis, National Institute of Structural Biology and Bioimaging, Federal University of Rio de Janeiro, Rio de Janeiro, RJ 21941-902, Brazil
| | | | - Julia R Clarke
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil.
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, RJ 21941-902, Brazil.
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23
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Marques MA, de Andrade GC, Silva JL, de Oliveira GAP. Protein of a thousand faces: The tumor-suppressive and oncogenic responses of p53. Front Mol Biosci 2022; 9:944955. [PMID: 36090037 PMCID: PMC9452956 DOI: 10.3389/fmolb.2022.944955] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 07/18/2022] [Indexed: 12/30/2022] Open
Abstract
The p53 protein is a pleiotropic regulator working as a tumor suppressor and as an oncogene. Depending on the cellular insult and the mutational status, p53 may trigger opposing activities such as cell death or survival, senescence and cell cycle arrest or proliferative signals, antioxidant or prooxidant activation, glycolysis, or oxidative phosphorylation, among others. By augmenting or repressing specific target genes or directly interacting with cellular partners, p53 accomplishes a particular set of activities. The mechanism in which p53 is activated depends on increased stability through post-translational modifications (PTMs) and the formation of higher-order structures (HOS). The intricate cell death and metabolic p53 response are reviewed in light of gaining stability via PTM and HOS formation in health and disease.
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Affiliation(s)
- Mayra A. Marques
- *Correspondence: Mayra A. Marques, ; Guilherme A. P. de Oliveira,
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24
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Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation. J Mol Biol 2021; 434:167368. [PMID: 34808226 DOI: 10.1016/j.jmb.2021.167368] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/12/2021] [Accepted: 11/14/2021] [Indexed: 12/29/2022]
Abstract
Conformational conversion of the α-helix-rich cellular prion protein into the misfolded, β-rich, aggregated, scrapie form underlies the molecular basis of prion diseases that represent a class of invariably fatal, untreatable, and transmissible neurodegenerative diseases. However, despite the extensive and rigorous research, there is a significant gap in the understanding of molecular mechanisms that contribute to prion pathogenesis. In this review, we describe the historical perspective of the development of the prion concept and the current state of knowledge of prion biology including structural, molecular, and cellular aspects of the prion protein. We then summarize the putative functional role of the N-terminal intrinsically disordered segment of the prion protein. We next describe the ongoing efforts in elucidating the prion phase behavior and the emerging role of liquid-liquid phase separation that can have potential functional relevance and can offer an alternate non-canonical pathway involving conformational conversion into a disease-associated form. We also attempt to shed light on the evolutionary perspective of the prion protein highlighting the potential role of intrinsic disorder in prion protein biology and summarize a few important questions associated with the phase transitions of the prion protein. Delving deeper into these key aspects can pave the way for a detailed understanding of the critical molecular determinants of the prion phase transition and its relevance to physiology and neurodegenerative diseases.
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Intrinsic disorder and phase transitions: Pieces in the puzzling role of the prion protein in health and disease. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 183:1-43. [PMID: 34656326 DOI: 10.1016/bs.pmbts.2021.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
After four decades of prion protein research, the pressing questions in the literature remain similar to the common existential dilemmas. Who am I? Some structural characteristics of the cellular prion protein (PrPC) and scrapie PrP (PrPSc) remain unknown: there are no high-resolution atomic structures for either full-length endogenous human PrPC or isolated infectious PrPSc particles. Why am I here? It is not known why PrPC and PrPSc are found in specific cellular compartments such as the nucleus; while the physiological functions of PrPC are still being uncovered, the misfolding site remains obscure. Where am I going? The subcellular distribution of PrPC and PrPSc is wide (reported in 10 different locations in the cell). This complexity is further exacerbated by the eight different PrP fragments yielded from conserved proteolytic cleavages and by reversible post-translational modifications, such as glycosylation, phosphorylation, and ubiquitination. Moreover, about 55 pathological mutations and 16 polymorphisms on the PrP gene (PRNP) have been described. Prion diseases also share unique, challenging features: strain phenomenon (associated with the heterogeneity of PrPSc conformations) and the possible transmissibility between species, factors which contribute to PrP undruggability. However, two recent concepts in biochemistry-intrinsically disordered proteins and phase transitions-may shed light on the molecular basis of PrP's role in physiology and disease.
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Garai S, Citu, Singla-Pareek SL, Sopory SK, Kaur C, Yadav G. Complex Networks of Prion-Like Proteins Reveal Cross Talk Between Stress and Memory Pathways in Plants. FRONTIERS IN PLANT SCIENCE 2021; 12:707286. [PMID: 34381483 PMCID: PMC8350573 DOI: 10.3389/fpls.2021.707286] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2021] [Accepted: 06/29/2021] [Indexed: 08/01/2023]
Abstract
Prions are often considered as molecular memory devices, generating reproducible memory of a conformational change. Prion-like proteins (PrLPs) have been widely demonstrated to be present in plants, but their role in plant stress and memory remains unexplored. In this work, we report the widespread presence of PrLPs in plants through a comprehensive meta-analysis of 39 genomes representing major taxonomic groups. We find diverse functional roles associated with these proteins in various species and term the full complement of PrLPs in a genome as its "prionome." In particular, we found the rice prionome being significantly enriched in transposons/retrotransposons (Ts/RTRs) and identified over 60 rice PrLPs that were differentially regulated in stress and developmental responses. This prompted us to explore whether and to what extent PrLPs may build stress memory. By integrating the available rice interactome, transcriptome, and regulome data sets, we could find links between stress and memory pathways that would not have otherwise been discernible. Regulatory inferences derived from the superimposition of these data sets revealed a complex network and cross talk between PrLPs, transcription factors (TFs), and the genes involved in stress priming. This integrative meta-analysis connects transient and transgenerational memory mechanisms in plants with PrLPs, suggesting that plant memory may rely upon protein-based signals in addition to chromatin-based epigenetic signals. Taken together, our work provides important insights into the anticipated role of prion-like candidates in stress and memory, paving the way for more focused studies for validating the role of the identified PrLPs in memory acclimation.
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Affiliation(s)
- Sampurna Garai
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Citu
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
| | - Sneh L. Singla-Pareek
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Sudhir K. Sopory
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Charanpreet Kaur
- Plant Stress Biology, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
- Stress Physiology and Molecular Biology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India
| | - Gitanjali Yadav
- Computational Biology Laboratory, National Institute of Plant Genome Research (NIPGR), New Delhi, India
- Department of Plant Sciences, University of Cambridge, Cambridge, United Kingdom
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Angelli JN, Passos YM, Brito JMA, Silva JL, Cordeiro Y, Vieira TCRG. Rabbit PrP Is Partially Resistant to in vitro Aggregation Induced by Different Biological Cofactors. Front Neurosci 2021; 15:689315. [PMID: 34220442 PMCID: PMC8249948 DOI: 10.3389/fnins.2021.689315] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 05/14/2021] [Indexed: 02/04/2023] Open
Abstract
Prion diseases have been described in humans and other mammals, including sheep, goats, cattle, and deer. Since mice, hamsters, and cats are susceptible to prion infection, they are often used to study the mechanisms of prion infection and conversion. Mammals, such as horses and dogs, however, do not naturally contract the disease and are resistant to infection, while others, like rabbits, have exhibited low susceptibility. Infection involves the conversion of the cellular prion protein (PrPC) to the scrapie form (PrPSc), and several cofactors have already been identified as important adjuvants in this process, such as glycosaminoglycans (GAGs), lipids, and nucleic acids. The molecular mechanisms that determine transmissibility between species remain unclear, as well as the barriers to transmission. In this study, we examine the interaction of recombinant rabbit PrPC (RaPrP) with different biological cofactors such as GAGs (heparin and dermatan sulfate), phosphatidic acid, and DNA oligonucleotides (A1 and D67) to evaluate the importance of these cofactors in modulating the aggregation of rabbit PrP and explain the animal’s different degrees of resistance to infection. We used spectroscopic and chromatographic approaches to evaluate the interaction with cofactors and their effect on RaPrP aggregation, which we compared with murine PrP (MuPrP). Our data show that all cofactors induce RaPrP aggregation and exhibit pH dependence. However, RaPrP aggregated to a lesser extent than MuPrP in the presence of any of the cofactors tested. The binding affinity with cofactors does not correlate with these low levels of aggregation, suggesting that the latter are related to the stability of PrP at acidic pH. The absence of the N-terminus affected the interaction with cofactors, influencing the efficiency of aggregation. These findings demonstrate that the interaction with polyanionic cofactors is related to rabbit PrP being less susceptible to aggregation in vitro and that the N-terminal domain is important to the efficiency of conversion, increasing the interaction with cofactors. The decreased effect of cofactors in rabbit PrP likely explains its lower propensity to prion conversion.
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Affiliation(s)
- Juliana N Angelli
- Federal Institute of Rio de Janeiro, Rio de Janeiro, Brazil.,Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yulli M Passos
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Julyana M A Brito
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yraima Cordeiro
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Tuane C R G Vieira
- Federal Institute of Rio de Janeiro, Rio de Janeiro, Brazil.,Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Petronilho EC, Pedrote MM, Marques MA, Passos YM, Mota MF, Jakobus B, de Sousa GDS, Pereira da Costa F, Felix AL, Ferretti GDS, Almeida FP, Cordeiro Y, Vieira TCRG, de Oliveira GAP, Silva JL. Phase separation of p53 precedes aggregation and is affected by oncogenic mutations and ligands. Chem Sci 2021; 12:7334-7349. [PMID: 34163823 PMCID: PMC8171334 DOI: 10.1039/d1sc01739j] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF). The mechanism of the formation of the aggregates in the nucleus remains uncertain. The present study demonstrated that the DNA-binding domain of p53 (p53C) underwent phase separation (PS) on the pathway to aggregation under various conditions. p53C phase separated in the presence of the crowding agent polyethylene glycol (PEG). Similarly, mutant p53C (M237I and R249S) underwent PS; however, the process evolved to a solid-like phase transition faster than that in the case of wild-type p53C. The data obtained by microscopy of live cells indicated that transfection of mutant full-length p53 into the cells tended to result in PS and phase transition (PT) in the nuclear compartments, which are likely the cause of the GoF effects. Fluorescence recovery after photobleaching (FRAP) experiments revealed liquid characteristics of the condensates in the nucleus. Mutant p53 tended to undergo gel- and solid-like phase transitions in the nucleus and in nuclear bodies demonstrated by slow and incomplete recovery of fluorescence after photobleaching. Polyanions, such as heparin and RNA, were able to modulate PS and PT in vitro. Heparin apparently stabilized the condensates in a gel-like state, and RNA apparently induced a solid-like state of the protein even in the absence of PEG. Conditions that destabilize p53C into a molten globule conformation also produced liquid droplets in the absence of crowding. The disordered transactivation domain (TAD) modulated both phase separation and amyloid aggregation. In summary, our data provide mechanistic insight into the formation of p53 condensates and conditions that may result in the formation of aggregated structures, such as mutant amyloid oligomers, in cancer. The pathway of mutant p53 from liquid droplets to gel-like and solid-like (amyloid) species may be a suitable target for anticancer therapy. Mutant p53 tends to form aggregates with amyloid properties, especially amyloid oligomers inside the nucleus, which are believed to cause oncogenic gain-of-function (GoF).![]()
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Affiliation(s)
- Elaine C Petronilho
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Murilo M Pedrote
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Mayra A Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Yulli M Passos
- Faculty of Pharmacy, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Michelle F Mota
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Benjamin Jakobus
- Modal Informática Ltda Almeida Godinho, 19, 304 Rio de Janeiro RJ 22741-140 Brazil
| | - Gileno Dos Santos de Sousa
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Filipe Pereira da Costa
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Adriani L Felix
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Giulia D S Ferretti
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Fernando P Almeida
- National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro Rio de Janeiro Brazil
| | - Tuane C R G Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Guilherme A P de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro Rio de Janeiro RJ 21941-902 Brazil
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M Passos Y, J do Amaral M, C Ferreira N, Macedo B, Chaves JAP, E de Oliveira V, P B Gomes M, L Silva J, Cordeiro Y. The interplay between a GC-rich oligonucleotide and copper ions on prion protein conformational and phase transitions. Int J Biol Macromol 2021; 173:34-43. [PMID: 33476618 DOI: 10.1016/j.ijbiomac.2021.01.097] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/06/2021] [Accepted: 01/14/2021] [Indexed: 01/28/2023]
Abstract
The prion protein (PrP) misfolding to its infectious form is critical to the development of prion diseases, whereby various ligands are suggested to participate, such as copper and nucleic acids (NA). The PrP globular domain was shown to undergo NA-driven liquid-liquid phase separation (LLPS); this latter may precede pathological aggregation. Since Cu(II) is a physiological ligand of PrP, we argue whether it modulates phase separation altogether with nucleic acids. Using recombinant PrP, we investigate the effects of Cu(II) (at 6 M equivalents) and a previously described PrP-binding GC-rich DNA (equimolarly to protein) on PrP conformation, oligomerization, and phase transitions using a range of biophysical techniques. Raman spectroscopy data reveals the formation of the ternary complex. Microscopy suggests that phase separation is mainly driven by DNA, whereas Cu(II) has no influence. Our results show that DNA can be an adjuvant, leading to the structural conversion of PrP, even in the presence of an endogenous ligand, copper. These results provide new insights into the role of Cu(II) and NA on the phase separation, structural conversion, and aggregation of PrP, which are critical events leading to neurodegeneration.
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Affiliation(s)
- Yulli M Passos
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-590, RJ, Brazil
| | - Mariana J do Amaral
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-590, RJ, Brazil
| | - Natalia C Ferreira
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-590, RJ, Brazil; Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute for Allergy and Infectious Diseases, National Institutes of Health, MT, USA
| | - Bruno Macedo
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-590, RJ, Brazil
| | - Juliana A P Chaves
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-590, RJ, Brazil
| | - Vanessa E de Oliveira
- Departamento de Ciências da Natureza, Universidade Federal Fluminense, Rio das Ostras 28890-000, RJ, Brazil
| | - Mariana P B Gomes
- Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, FIOCRUZ, Rio de Janeiro 21040-900, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica, Centro Nacional de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-590, RJ, Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, 21941-590, RJ, Brazil.
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30
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Colnaghi L, Rondelli D, Muzi-Falconi M, Sertic S. Tau and DNA Damage in Neurodegeneration. Brain Sci 2020; 10:E946. [PMID: 33297375 PMCID: PMC7762255 DOI: 10.3390/brainsci10120946] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 11/29/2020] [Accepted: 12/02/2020] [Indexed: 12/11/2022] Open
Abstract
Neurodegenerative disorders are a family of incurable conditions. Among them, Alzheimer's disease and tauopathies are the most common. Pathological features of these two disorders are synaptic loss, neuronal cell death and increased DNA damage. A key pathological protein for the onset and progression of the conditions is the protein tau, a microtubule-binding protein highly expressed in neurons and encoded by the MAPT (microtubule-associated protein tau) gene. Tau is predominantly a cytosolic protein that interacts with numerous other proteins and molecules. Recent findings, however, have highlighted new and unexpected roles for tau in the nucleus of neuronal cells. This review summarizes the functions of tau in the metabolism of DNA, describing them in the context of the disorders.
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Affiliation(s)
- Luca Colnaghi
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, Via Negri 2, 20156 Milan, Italy
| | - Diego Rondelli
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; (D.R.); (M.M.-F.)
| | - Marco Muzi-Falconi
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; (D.R.); (M.M.-F.)
| | - Sarah Sertic
- Dipartimento di Bioscienze, Università degli Studi di Milano, Via Celoria 26, 20133 Milan, Italy; (D.R.); (M.M.-F.)
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31
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Louka A, Zacco E, Temussi PA, Tartaglia GG, Pastore A. RNA as the stone guest of protein aggregation. Nucleic Acids Res 2020; 48:11880-11889. [PMID: 33068411 PMCID: PMC7708036 DOI: 10.1093/nar/gkaa822] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/12/2020] [Accepted: 10/14/2020] [Indexed: 12/13/2022] Open
Abstract
The study of prions as infectious aggregates dates several decades. From its original formulation, the definition of a prion has progressively changed to the point that many aggregation-prone proteins are now considered bona fide prions. RNA molecules, not included in the original 'protein-only hypothesis', are also being recognized as important factors contributing to the 'prion behaviour', that implies the transmissibility of an aberrant fold. In particular, an association has recently emerged between aggregation and the assembly of prion-like proteins in RNA-rich complexes, associated with both physiological and pathological events. Here, we discuss the historical rising of the concept of prion-like domains, their relation to RNA and their role in protein aggregation. As a paradigmatic example, we present the case study of TDP-43, an RNA-binding prion-like protein associated with amyotrophic lateral sclerosis. Through this example, we demonstrate how the current definition of prions has incorporated quite different concepts making the meaning of the term richer and more stimulating. An important message that emerges from our analysis is the dual role of RNA in protein aggregation, making RNA, that has been considered for many years a 'silent presence' or the 'stone guest' of protein aggregation, an important component of the process.
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Affiliation(s)
- Alexandra Louka
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
| | - Elsa Zacco
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
| | - Piero Andrea Temussi
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
- University “Federico II’’ Napoli, via Cynthia, Napoli 80100, Italy
| | - Gian Gaetano Tartaglia
- Center for Human Technologies, Central RNA laboratory, Istituto Italiano di Tecnologia, Genova 16152, Italy
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona 08003, Spain and ICREA, 23 Passeig Lluıs Companys, Barcelona 08010, Spain
- Charles Darwin department of Biology and Biotechnology, Sapienza University of Rome, Piazzale A. Moro 5, Rome 00185, Italy
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London SE5 9RT, UK
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Holubová M, Štěpánek P, Hrubý M. Polymer materials as promoters/inhibitors of amyloid fibril formation. Colloid Polym Sci 2020. [DOI: 10.1007/s00396-020-04710-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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33
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PrPSc Oligomerization Appears Dynamic, Quickly Engendering Inherent M1000 Acute Synaptotoxicity. Biophys J 2020; 119:128-141. [PMID: 32562618 DOI: 10.1016/j.bpj.2020.04.040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2020] [Revised: 04/07/2020] [Accepted: 04/24/2020] [Indexed: 11/23/2022] Open
Abstract
Prion diseases are neurodegenerative disorders pathogenically linked to cellular prion protein (PrPC) misfolding into abnormal conformers (PrPSc), with PrPSc underpinning both transmission and synaptotoxicity. Although the biophysical features of PrPSc required to induce acute synaptic dysfunction remain incompletely defined, we recently reported that acutely synaptotoxic PrPSc appeared to be oligomeric. We herein provide further insights into the kinetic and requisite biophysical characteristics of acutely synaptotoxic ex vivo PrPSc derived from the brains of mice dying from M1000 prion disease. Pooled fractions of M1000 PrPSc located within the molecular weight range approximating monomeric PrP (mM1000) generated through size exclusion chromatography were found to harbor acute synaptotoxicity equivalent to preformed oligomeric fractions (oM1000). Subsequent investigation showed mM1000 corresponded to PrPSc rapidly concatenating in physiological buffer to exist as predominantly, closely associated, small oligomers. The oligomerization of PrP in mM1000 could be substantially mitigated by treatment with the antiaggregation compound epigallocatechin gallate, thereby maintaining the PrPSc as primarily nonoligomeric with completely abrogated acute synaptotoxicity; moreover, despite epigallocatechin gallate treatment, pooled oM1000 remained oligomeric and acutely synaptotoxic. A similar tendency to rapid formation of oligomers was observed for PrPC when monomeric fractions derived from size exclusion chromatography of normal brain homogenates (mNBH) were pooled, but neither mNBH nor preformed higher-order NBH complexes (oNBH) were acutely synaptotoxic. Oligomers formed from mNBH could be reduced to mainly monomers (<100 kDa) after enzymatic digestion of nucleic acids, whereas higher-order PrP assemblies derived from pooled mM1000, oM1000, and oNBH resisted such treatment. Collectively, these findings support that oligomerization of PrPSc into small multimeric assemblies appears to be a critical biophysical feature for engendering inherent acute synaptotoxicity, with preformed oligomers found in oM1000 appearing to be stable, tightly self-associated ensembles that coexist in dynamic equilibrium with mM1000, with the latter appearing capable of rapid aggregation, albeit initially forming smaller, weakly self-associated, acutely synaptotoxic oligomers.
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de Oliveira GAP, Petronilho EC, Pedrote MM, Marques MA, Vieira TCRG, Cino EA, Silva JL. The Status of p53 Oligomeric and Aggregation States in Cancer. Biomolecules 2020; 10:biom10040548. [PMID: 32260447 PMCID: PMC7226498 DOI: 10.3390/biom10040548] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 03/29/2020] [Accepted: 04/01/2020] [Indexed: 12/21/2022] Open
Abstract
Despite being referred to as the guardian of the genome, when impacted by mutations, p53 can lose its protective functions and become a renegade. The malignant transformation of p53 occurs on multiple levels, such as altered DNA binding properties, acquisition of novel cellular partners, or associating into different oligomeric states. The consequences of these transformations can be catastrophic. Ongoing studies have implicated different oligomeric p53 species as having a central role in cancer biology; however, the correlation between p53 oligomerization status and oncogenic activities in cancer progression remains an open conundrum. In this review, we summarize the roles of different p53 oligomeric states in cancer and discuss potential research directions for overcoming aberrant p53 function associated with them. We address how misfolding and prion-like amyloid aggregation of p53 seem to play a crucial role in cancer development. The misfolded and aggregated states of mutant p53 are prospective targets for the development of novel therapeutic strategies against tumoral diseases.
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Affiliation(s)
- Guilherme A. P. de Oliveira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-901, Brazil; (G.A.P.d.O.); (E.C.P.); (M.M.P.); (M.A.M.); (T.C.R.G.V.)
| | - Elaine C. Petronilho
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-901, Brazil; (G.A.P.d.O.); (E.C.P.); (M.M.P.); (M.A.M.); (T.C.R.G.V.)
| | - Murilo M. Pedrote
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-901, Brazil; (G.A.P.d.O.); (E.C.P.); (M.M.P.); (M.A.M.); (T.C.R.G.V.)
| | - Mayra A. Marques
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-901, Brazil; (G.A.P.d.O.); (E.C.P.); (M.M.P.); (M.A.M.); (T.C.R.G.V.)
| | - Tuane C. R. G. Vieira
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-901, Brazil; (G.A.P.d.O.); (E.C.P.); (M.M.P.); (M.A.M.); (T.C.R.G.V.)
| | - Elio A. Cino
- Department of Biochemistry and Immunology, Federal University of Minas Gerais, Belo Horizonte MG 31270-901, Brazil
- Correspondence: (J.L.S.); (E.A.C.); Tel.: +55-21-3938-6756 (J.L.S.); +55-31-3409-2613 (E.A.C.)
| | - Jerson L. Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Institute of Science and Technology for Structural Biology and Bioimaging, National Center of Nuclear Magnetic Resonance Jiri Jonas, Federal University of Rio de Janeiro, Rio de Janeiro RJ 21941-901, Brazil; (G.A.P.d.O.); (E.C.P.); (M.M.P.); (M.A.M.); (T.C.R.G.V.)
- Correspondence: (J.L.S.); (E.A.C.); Tel.: +55-21-3938-6756 (J.L.S.); +55-31-3409-2613 (E.A.C.)
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35
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Banerjee S, Ferdosh S, Ghosh AN, Barat C. Tau protein- induced sequestration of the eukaryotic ribosome: Implications in neurodegenerative disease. Sci Rep 2020; 10:5225. [PMID: 32251304 PMCID: PMC7090008 DOI: 10.1038/s41598-020-61777-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2019] [Accepted: 02/28/2020] [Indexed: 12/15/2022] Open
Abstract
The human tau is a microtubule-associated intrinsically unstructured protein that forms intraneuronal cytotoxic deposits in neurodegenerative diseases, like tauopathies. Recent studies indicate that in Alzheimer's disease, ribosomal dysfunction might be a crucial event in the disease pathology. Our earlier studies had demonstrated that amorphous protein aggregation in the presence of ribosome can lead to sequestration of the ribosomal components. The present study aims at determining the effect of incubation of the full-length tau protein (Ht40) and its microtubule binding 4-repeat domain (K18) on the eukaryotic ribosome. Our in vitro studies show that incubation of Ht40 and the K18 tau variants with isolated non-translating yeast ribosome can induce a loss of ribosome physical integrity resulting in formation of tau-rRNA-ribosomal protein aggregates. Incubation with the tau protein variants also led to a disappearance of the peak indicating the ribosome profile of the HeLa cell lysate and suppression of translation in the human in vitro translation system. The incubation of tau protein with the ribosomal RNA leads to the formation of tau-rRNA aggregates. The effect of K18 on the yeast ribosome can be mitigated in the presence of cellular polyanions like heparin and tRNA, thereby indicating the electrostatic nature of the aggregation process.
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Affiliation(s)
- Senjuti Banerjee
- Department of Biotechnology, St. Xavier's College, Park Street, Kolkata, 700016, West Bengal, India
| | - Sehnaz Ferdosh
- Department of Biotechnology, St. Xavier's College, Park Street, Kolkata, 700016, West Bengal, India
| | - Amar Nath Ghosh
- National Institute of Cholera and Enteric Diseases P-33, C.I.T. Road, Scheme XM, Beleghata, India
| | - Chandana Barat
- Department of Biotechnology, St. Xavier's College, Park Street, Kolkata, 700016, West Bengal, India.
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36
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Abstract
A hallmark feature of Alzheimer’s disease (AD) and other tauopathies is the misfolding, aggregation and cerebral accumulation of tau deposits. Compelling evidence indicates that misfolded tau aggregates are neurotoxic, producing synaptic loss and neuronal damage. Misfolded tau aggregates are able to spread the pathology from cell-to-cell by a prion like seeding mechanism. The factors implicated in the initiation and progression of tau misfolding and aggregation are largely unclear. In this study, we evaluated the effect of DNA extracted from diverse prokaryotic and eukaryotic cells in tau misfolding and aggregation. Our results show that DNA from various, unrelated gram-positive and gram-negative bacteria results in a more pronounced tau misfolding compared to eukaryotic DNA. Interestingly, a higher effect in promoting tau aggregation was observed for DNA extracted from certain bacterial species previously detected in the brain, CSF or oral cavity of patients with AD. Our findings indicate that microbial DNA may play a previously overlooked role in the propagation of tau protein misfolding and AD pathogenesis, providing a new conceptual framework that positions the compromised blood-brain and intestinal barriers as important sources of microbial DNA in the CNS, opening novel opportunities for therapeutic interventions.
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37
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Lathe R, Darlix JL. Prion protein PrP nucleic acid binding and mobilization implicates retroelements as the replicative component of transmissible spongiform encephalopathy. Arch Virol 2020; 165:535-556. [PMID: 32025859 PMCID: PMC7024060 DOI: 10.1007/s00705-020-04529-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2019] [Accepted: 12/13/2019] [Indexed: 12/21/2022]
Abstract
The existence of more than 30 strains of transmissible spongiform encephalopathy (TSE) and the paucity of infectivity of purified PrPSc, as well as considerations of PrP structure, are inconsistent with the protein-only (prion) theory of TSE. Nucleic acid is a strong contender as a second component. We juxtapose two key findings: (i) PrP is a nucleic-acid-binding antimicrobial protein that is similar to retroviral Gag proteins in its ability to trigger reverse transcription. (ii) Retroelement mobilization is widely seen in TSE disease. Given further evidence that PrP also mediates nucleic acid transport into and out of the cell, a strong case is to be made that a second element – retroelement nucleic acid – bound to PrP constitutes the second component necessary to explain the multiple strains of TSE.
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Affiliation(s)
- Richard Lathe
- Division of Infection Medicine, University of Edinburgh School of Medicine, Edinburgh, UK. .,Shemyakin and Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Pushchino, Moscow, Moscow Region, Russia.
| | - Jean-Luc Darlix
- Faculté de Pharmacie, Centre Nationale de la Recherche Scientifique (CNRS) Laboratory of Bioimaging and Pathologies (Unité Mixte de Recherche 7021), Université de Strasbourg, Illkirch, France.
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38
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Litberg TJ, Docter B, Hughes MP, Bourne J, Horowitz S. DNA Facilitates Oligomerization and Prevents Aggregation via DNA Networks. Biophys J 2019; 118:162-171. [PMID: 31839258 DOI: 10.1016/j.bpj.2019.11.022] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Revised: 10/11/2019] [Accepted: 11/05/2019] [Indexed: 12/12/2022] Open
Abstract
Previous studies have shown that nucleic acids can nucleate protein aggregation in disease-related proteins, but in other cases, they can act as molecular chaperones that prevent protein aggregation, even under extreme conditions. In this study, we describe the link between these two behaviors through a combination of electron microscopy and aggregation kinetics. We find that two different proteins become soluble under harsh conditions through oligomerization with DNA. These DNA/protein oligomers form "networks," which increase the speed of oligomerization. The cases of DNA both increasing and preventing protein aggregation are observed to stem from this enhanced oligomerization. This observation raises interesting questions about the role of nucleic acids in aggregate formation in disease states.
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Affiliation(s)
- Theodore J Litberg
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado
| | - Brianne Docter
- Cellular and Molecular Biology Program, University of Michigan, Ann Arbor, Michigan
| | - Michael P Hughes
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, California; Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, California; Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, California; Department of Energy, University of California, Los Angeles, Los Angeles, California; Institute for Genomics and Proteomics, University of California, Los Angeles, Los Angeles, California
| | - Jennifer Bourne
- Department of Cell and Developmental Biology, University of Colorado School of Medicine, Aurora, Colorado
| | - Scott Horowitz
- Department of Chemistry & Biochemistry, Knoebel Institute for Healthy Aging, University of Denver, Denver, Colorado.
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39
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Matos CO, Passos YM, do Amaral MJ, Macedo B, Tempone MH, Bezerra OCL, Moraes MO, Almeida MS, Weber G, Missailidis S, Silva JL, Uversky VN, Pinheiro AS, Cordeiro Y. Liquid-liquid phase separation and fibrillation of the prion protein modulated by a high-affinity DNA aptamer. FASEB J 2019; 34:365-385. [PMID: 31914616 DOI: 10.1096/fj.201901897r] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Revised: 10/09/2019] [Accepted: 10/15/2019] [Indexed: 01/17/2023]
Abstract
Structural conversion of cellular prion protein (PrPC) into scrapie PrP (PrPSc) and subsequent aggregation are key events associated with the onset of transmissible spongiform encephalopathies (TSEs). Experimental evidence supports the role of nucleic acids (NAs) in assisting this conversion. Here, we asked whether PrP undergoes liquid-liquid phase separation (LLPS) and if this process is modulated by NAs. To this end, two 25-mer DNA aptamers, A1 and A2, were selected against the globular domain of recombinant murine PrP (rPrP90-231) using SELEX methodology. Multiparametric structural analysis of these aptamers revealed that A1 adopts a hairpin conformation. Aptamer binding caused partial unfolding of rPrP90-231 and modulated its ability to undergo LLPS and fibrillate. In fact, although free rPrP90-231 phase separated into large droplets, aptamer binding increased the number of droplets but noticeably reduced their size. Strikingly, a modified A1 aptamer that does not adopt a hairpin structure induced formation of amyloid fibrils on the surface of the droplets. We show here that PrP undergoes LLPS, and that the PrP interaction with NAs modulates phase separation and promotes PrP fibrillation in a NA structure and concentration-dependent manner. These results shed new light on the roles of NAs in PrP misfolding and TSEs.
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Affiliation(s)
- Carolina O Matos
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yulli M Passos
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mariana J do Amaral
- Institute of Medical Biochemistry Leopoldo de Meis, National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Bruno Macedo
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Matheus H Tempone
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ohanna C L Bezerra
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Milton O Moraes
- Leprosy Laboratory, Oswaldo Cruz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Marcius S Almeida
- Institute of Medical Biochemistry Leopoldo de Meis, National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gerald Weber
- Department of Physics, Federal University of Minas Gerais, Belo Horizonte, Brazil
| | - Sotiris Missailidis
- Institute of Technology in Immunobiologics (Bio-Manguinhos), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Jerson L Silva
- Institute of Medical Biochemistry Leopoldo de Meis, National Center for Structural Biology and Bioimaging (CENABIO), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vladimir N Uversky
- Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.,Laboratory of New Methods in Biology, Institute for Biological Instrumentation, Russian Academy of Sciences, Pushchino, Russia
| | - Anderson S Pinheiro
- Department of Biochemistry, Institute of Chemistry, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
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Rha AK, Das D, Taran O, Ke Y, Mehta AK, Lynn DG. Electrostatic Complementarity Drives Amyloid/Nucleic Acid Co‐Assembly. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201907661] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Allisandra K. Rha
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Dibyendu Das
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Olga Taran
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - Yonggang Ke
- Biomedical Engineering Emory and Georgia Institute of Technology Atlanta GA 30322 USA
| | - Anil K. Mehta
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
| | - David G. Lynn
- Chemistry and Biology Emory University 1521 Dickey Drive NE Atlanta GA 30322 USA
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41
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Rha AK, Das D, Taran O, Ke Y, Mehta AK, Lynn DG. Electrostatic Complementarity Drives Amyloid/Nucleic Acid Co-Assembly. Angew Chem Int Ed Engl 2019; 59:358-363. [PMID: 31617300 DOI: 10.1002/anie.201907661] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/11/2019] [Indexed: 12/20/2022]
Abstract
Proteinaceous plaques associated with neurodegenerative diseases contain many biopolymers including the polyanions glycosaminoglycans and nucleic acids. Polyanion-induced amyloid fibrillation has been implicated in disease etiology, but structural models for amyloid/nucleic acid co-assemblies remain limited. Here we constrain nucleic acid/peptide interactions with model peptides that exploit electrostatic complementarity and define a novel amyloid/nucleic acid co-assembly. The structure provides a model for nucleic acid/amyloid co-assembly as well as insight into the energetic determinants involved in templating amyloid assembly.
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Affiliation(s)
- Allisandra K Rha
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Dibyendu Das
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Olga Taran
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - Yonggang Ke
- Biomedical Engineering, Emory and Georgia Institute of Technology, Atlanta, GA, 30322, USA
| | - Anil K Mehta
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
| | - David G Lynn
- Chemistry and Biology, Emory University, 1521 Dickey Drive NE, Atlanta, GA, 30322, USA
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42
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Modulation of p53 and prion protein aggregation by RNA. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:933-940. [DOI: 10.1016/j.bbapap.2019.02.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2019] [Revised: 02/19/2019] [Accepted: 02/25/2019] [Indexed: 02/07/2023]
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43
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de Oliveira GAP, Cordeiro Y, Silva JL, Vieira TCRG. Liquid-liquid phase transitions and amyloid aggregation in proteins related to cancer and neurodegenerative diseases. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2019; 118:289-331. [PMID: 31928729 DOI: 10.1016/bs.apcsb.2019.08.002] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Liquid-liquid phase separation (LLPS) and phase transition (LLPT) of proteins and nucleic acids have emerged as a new paradigm in cell biology. Here we will describe the recent findings about LLPS and LLPT, including the molecular and physical determinants leading to their formation, the resulting functions and their implications in cell physiology and disease. Amyloid aggregation is implicated in many neurodegenerative diseases and cancer, and LLPS of proteins involved in these diseases appear to be related to their function in different cell contexts. Amyloid formation would correspond to an irreversible liquid-to-solid transition, as clearly observed in the case of PrP, TDP43, FUS/TLS and tau protein in neurodegenerative pathologies as well as with the mutant tumor suppressor p53 in cancer. Nucleic acids play a modulatory effect on both LLPS and amyloid aggregation. Understanding the molecular events regulating how the demixing process advances to solid-like fibril materials is crucial for the development of novel therapeutic strategies against cancer and neurodegenerative maladies.
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Affiliation(s)
- Guilherme A P de Oliveira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil; Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, VA, United States
| | - Yraima Cordeiro
- Faculty of Pharmacy, Federal University of Rio de Janeiro, Rio de Janeiro-RJ, Brazil
| | - Jerson L Silva
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Tuane C R G Vieira
- Programa de Biologia Estrutural, Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Biologia Estrutural e Bioimagem, Centro Nacional de Ressonância Magnética Nuclear Jiri Jonas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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44
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Kovachev PS, Gomes MPB, Cordeiro Y, Ferreira NC, Valadão LPF, Ascari LM, Rangel LP, Silva JL, Sanyal S. RNA modulates aggregation of the recombinant mammalian prion protein by direct interaction. Sci Rep 2019; 9:12406. [PMID: 31455808 PMCID: PMC6712051 DOI: 10.1038/s41598-019-48883-x] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 08/12/2019] [Indexed: 12/22/2022] Open
Abstract
Recent studies have proposed that nucleic acids act as potential cofactors for protein aggregation and prionogenesis. By means of sedimentation, transmission electron microscopy, circular dichroism, static and dynamic light scattering, we have studied how RNA can influence the aggregation of the murine recombinant prion protein (rPrP). We find that RNA, independent of its sequence, source and size, modulates rPrP aggregation in a bimodal fashion, affecting both the extent and the rate of rPrP aggregation in a concentration dependent manner. Analogous to RNA-induced liquid-liquid phase transitions observed for other proteins implicated in neurodegenerative diseases, high protein to RNA ratios stimulate rPrP aggregation, while low ratios suppress it. However, the latter scenario also promotes formation of soluble oligomeric aggregates capable of seeding de novo rPrP aggregation. Furthermore, RNA co-aggregates with rPrP and thereby gains partial protection from RNase digestion. Our results also indicate that rPrP interacts with the RNAs with its N-terminus. In summary, this study elucidates the proposed adjuvant role of RNA in prion protein aggregation and propagation, and thus advocates an auxiliary role of the nucleic acids in protein aggregation in general.
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Affiliation(s)
- Petar Stefanov Kovachev
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden
| | - Mariana P B Gomes
- Instituto de Tecnologia em Imunobiológicos, Bio-Manguinhos, FIOCRUZ, Rio de Janeiro, 21040-900, Brazil
| | - Yraima Cordeiro
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Natália C Ferreira
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.,Laboratory of Persistent Viral Diseases, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, MT, United States of America
| | - Leticia P Felix Valadão
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Lucas M Ascari
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Luciana P Rangel
- Faculdade de Farmácia, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Jerson L Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto Nacional de Ciência Tecnologia de Biologia Estrutural e Bioimagem, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil.
| | - Suparna Sanyal
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Box-596, 75124, Sweden.
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45
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Abstract
Prion (PrPC) is an endogenous protein found mainly in the nervous system, and its misfolded isoform (PrPSc) is associated with a group of neurodegenerative disorders known as transmissible spongiform encephalopathies, or simply prion diseases. The PrPSc isoform shows an intriguing ability to self-perpetuate, acting as template for PrPC misfolding and consequent aggregation. Aggregation in vitro and in vivo follows a fibrillation processes that is associated with neurodegeneration. Therefore, it is important to investigate and understand the molecular mechanisms involved in this process; such understanding also allows investigation of the action of possible candidate molecules to inhibit this process. Here, we highlight useful in vitro methodologies and analyses that were developed using PrP as a protein model but that, as other amyloid proteins also exhibit the same behavior, may be applied to understand other "prion-like" diseases such as Alzheimer's and Parkinson's disease.
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46
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Yoo WK, Ryu BH, Kim KR, Wang Y, Le LTHL, Lee JH, Kim KK, Toth G, Ahn DR, Doohun Kim T. Modulating α-synuclein fibril formation using DNA tetrahedron nanostructures. Biochim Biophys Acta Gen Subj 2018; 1863:73-81. [PMID: 30278239 DOI: 10.1016/j.bbagen.2018.09.025] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 09/16/2018] [Accepted: 09/27/2018] [Indexed: 01/15/2023]
Abstract
The small presynaptic protein α-synuclein (α-syn) is involved in the etiology of Parkinson's disease owing to its abnormal misfolding. To date, little information is known on the role of DNA nanostructures in the formation of α-syn amyloid fibrils. Here, the effects of DNA tetrahedrons on the formation of α-syn amyloid fibrils were investigated using various biochemical and biophysical methods such as thioflavin T fluorescence assay, atomic force microscopy, light scattering, transmission electron microscopy, and cell-based cytotoxicity assay. It has been shown that DNA tetrahedrons decreased the level of oligomers and increased the level of amyloid fibrils, which corresponded to decreased cellular toxicity. The ability of DNA tetrahedron to facilitate the formation of α-syn amyloid fibrils demonstrated that structured nucleic acids such as DNA tetrahedrons could modulate the process of amyloid fibril formation. Our study suggests that DNA tetrahedrons could be used as an important facilitator toward amyloid fibril formation of α-synuclein, which may be of significance in finding therapeutic approaches to Parkinson's disease and related synucleinopathies.
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Affiliation(s)
- Wan Ki Yoo
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Bum Han Ryu
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea; Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Kyoung-Ran Kim
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Ying Wang
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Ly Thi Huong Luu Le
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea
| | - Jun Hyuck Lee
- Unit of Polar Genomics, Korea Polar Research Institute (KOPRI), Incheon 21990, Republic of Korea
| | - Kyeong Kyu Kim
- Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 16419, Republic of Korea
| | - Gergely Toth
- Molecular Imaging Chemistry Laboratory, Wolfson Brain Imaging Centre, Department of Clinical Neurosciences, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Dae-Ro Ahn
- Center for Theragnosis, Biomedical Research Institute, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.
| | - T Doohun Kim
- Department of Chemistry, College of Natural Science, Sookmyung Women's University, Seoul 04310, Republic of Korea.
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47
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Cascarina SM, Paul KR, Machihara S, Ross ED. Sequence features governing aggregation or degradation of prion-like proteins. PLoS Genet 2018; 14:e1007517. [PMID: 30005071 PMCID: PMC6059496 DOI: 10.1371/journal.pgen.1007517] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2018] [Revised: 07/25/2018] [Accepted: 06/26/2018] [Indexed: 01/12/2023] Open
Abstract
Enhanced protein aggregation and/or impaired clearance of aggregates can lead to neurodegenerative disorders such as Alzheimer's Disease, Huntington's Disease, and prion diseases. Therefore, many protein quality control factors specialize in recognizing and degrading aggregation-prone proteins. Prions, which generally result from self-propagating protein aggregates, must therefore evade or outcompete these quality control systems in order to form and propagate in a cellular context. We developed a genetic screen in yeast that allowed us to explore the sequence features that promote degradation versus aggregation of a model glutamine/asparagine (Q/N)-rich prion domain from the yeast prion protein, Sup35, and two model glycine (G)-rich prion-like domains from the human proteins hnRNPA1 and hnRNPA2. Unexpectedly, we found that aggregation propensity and degradation propensity could be uncoupled in multiple ways. First, only a subset of classically aggregation-promoting amino acids elicited a strong degradation response in the G-rich prion-like domains. Specifically, large aliphatic residues enhanced degradation of the prion-like domains, whereas aromatic residues promoted prion aggregation without enhancing degradation. Second, the degradation-promoting effect of aliphatic residues was suppressed in the context of the Q/N-rich prion domain, and instead led to a dose-dependent increase in the frequency of spontaneous prion formation. Degradation suppression correlated with Q/N content of the surrounding prion domain, potentially indicating an underappreciated activity for these residues in yeast prion domains. Collectively, these results provide key insights into how certain aggregation-prone proteins may evade protein quality control degradation systems.
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Affiliation(s)
- Sean M. Cascarina
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Kacy R. Paul
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Satoshi Machihara
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
| | - Eric D. Ross
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, United States of America
- * E-mail:
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Legname G, Virgilio T, Bistaffa E, De Luca CMG, Catania M, Zago P, Isopi E, Campagnani I, Tagliavini F, Giaccone G, Moda F. Effects of peptidyl-prolyl isomerase 1 depletion in animal models of prion diseases. Prion 2018; 12:127-137. [PMID: 29676205 DOI: 10.1080/19336896.2018.1464367] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
Pin1 is a peptidyl-prolyl isomerase that induces the cis-trans conversion of specific Ser/Thr-Pro peptide bonds in phosphorylated proteins, leading to conformational changes through which Pin1 regulates protein stability and activity. Since down-regulation of Pin1 has been described in several neurodegenerative disorders, including Alzheimer's Disease (AD), Parkinson's Disease (PD) and Huntington's Disease (HD), we investigated its potential role in prion diseases. Animals generated on wild-type (Pin1+/+), hemizygous (Pin1+/-) or knock-out (Pin1-/-) background for Pin1 were experimentally infected with RML prions. The study indicates that, neither the total depletion nor reduced levels of Pin1 significantly altered the clinical and neuropathological features of the disease.
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Affiliation(s)
- Giuseppe Legname
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy.,c ELETTRA Laboratory , Sincrotrone Trieste S.C.p.A , Basovizza, Trieste , Italy
| | - Tommaso Virgilio
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy.,d Institute for Research in Biomedicine, Università della Svizzera Italiana , Bellinzona , Switzerland
| | - Edoardo Bistaffa
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy.,b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Chiara Maria Giulia De Luca
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Marcella Catania
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Paola Zago
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy
| | - Elisa Isopi
- a Laboratory of Prion Biology, Department of Neuroscience , Scuola Internazionale Superiore di Studi Avanzati (SISSA) , Trieste , Italy
| | - Ilaria Campagnani
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Fabrizio Tagliavini
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Giorgio Giaccone
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
| | - Fabio Moda
- b Unit of Neuropathology and Neurology 5 , IRCCS Foundation Carlo Besta Neurological Institute , Milano , Italy
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Maury CPJ. Amyloid and the origin of life: self-replicating catalytic amyloids as prebiotic informational and protometabolic entities. Cell Mol Life Sci 2018; 75:1499-1507. [PMID: 29550973 PMCID: PMC5897472 DOI: 10.1007/s00018-018-2797-9] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 02/19/2018] [Accepted: 03/13/2018] [Indexed: 01/29/2023]
Abstract
A crucial stage in the origin of life was the emergence of the first molecular entity that was able to replicate, transmit information, and evolve on the early Earth. The amyloid world hypothesis posits that in the pre-RNA era, information processing was based on catalytic amyloids. The self-assembly of short peptides into β-sheet amyloid conformers leads to extraordinary structural stability and novel multifunctionality that cannot be achieved by the corresponding nonaggregated peptides. The new functions include self-replication, catalytic activities, and information transfer. The environmentally sensitive template-assisted replication cycles generate a variety of amyloid polymorphs on which evolutive forces can act, and the fibrillar assemblies can serve as scaffolds for the amyloids themselves and for ribonucleotides proteins and lipids. The role of amyloid in the putative transition process from an amyloid world to an amyloid-RNA-protein world is not limited to scaffolding and protection: the interactions between amyloid, RNA, and protein are both complex and cooperative, and the amyloid assemblages can function as protometabolic entities catalyzing the formation of simple metabolite precursors. The emergence of a pristine amyloid-based in-put sensitive, chiroselective, and error correcting information-processing system, and the evolvement of mutualistic networks were, arguably, of essential importance in the dynamic processes that led to increased complexity, organization, compartmentalization, and, eventually, the origin of life.
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Sohma Y. Toward New Direction of Peptide Research in Natural Products Chemistry. J SYN ORG CHEM JPN 2018. [DOI: 10.5059/yukigoseikyokaishi.76.466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Youhei Sohma
- Graduate School of Pharmaceutical Sciences, The University of Tokyo
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