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Hervás R, Del Carmen Fernández-Ramírez M, Galera-Prat A, Suzuki M, Nagai Y, Bruix M, Menéndez M, Laurents DV, Carrión-Vázquez M. Divergent CPEB prion-like domains reveal different assembly mechanisms for a generic amyloid-like fold. BMC Biol 2021; 19:43. [PMID: 33706787 PMCID: PMC7953810 DOI: 10.1186/s12915-021-00967-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/25/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Amyloids are ordered, insoluble protein aggregates, characterized by a cross-β sheet quaternary structure in which molecules in a β-strand conformation are stacked along the filament axis via intermolecular interactions. While amyloids are typically associated with pathological conditions, functional amyloids have also been identified and are present in a wide variety of organisms ranging from bacteria to humans. The cytoplasmic polyadenylation element-binding (CPEB) prion-like protein is an mRNA-binding translation regulator, whose neuronal isoforms undergo activity-dependent aggregation, a process that has emerged as a plausible biochemical substrate for memory maintenance. CPEB aggregation is driven by prion-like domains (PLD) that are divergent in sequence across species, and it remains unknown whether such divergent PLDs follow a similar aggregating assembly pathway. Here, we describe the amyloid-like features of the neuronal Aplysia CPEB (ApCPEB) PLD and compare them to those of the Drosophila ortholog, Orb2 PLD. RESULTS Using in vitro single-molecule and bulk biophysical methods, we find transient oligomers and mature amyloid-like filaments that suggest similarities in the late stages of the assembly pathway for both ApCPEB and Orb2 PLDs. However, while prior to aggregation the Orb2 PLD monomer remains mainly as a random coil in solution, ApCPEB PLD adopts a diversity of conformations comprising α-helical structures that evolve to coiled-coil species, indicating structural differences at the beginning of their amyloid assembly pathways. CONCLUSION Our results indicate that divergent PLDs of CPEB proteins from different species retain the ability to form a generic amyloid-like fold through different assembly mechanisms.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC, Avda. Doctor Arce 37, E-28002, Madrid, Spain. .,Present address: School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong SAR, China.
| | | | | | - Mari Suzuki
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Diabetic Neuropathy Project, Department of Sensory and Motor Systems, Tokyo Metropolitan Institute of Medical Science, Setagaya, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan.,Present address: Department of Neurology, Faculty of Medicine, Kindai University, Osaka-Sayama, Osaka, Japan
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
| | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain.,Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias (CIBERES), C/ Monforte de Lemos 3-5, 28029, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Serrano 119, E-28006, Madrid, Spain
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Belwal VK, Datta D, Chaudhary N. The β‐turn‐supporting motif in the polyglutamine binding peptide QBP1 is essential for inhibiting huntingtin aggregation. FEBS Lett 2020; 594:2894-2903. [DOI: 10.1002/1873-3468.13873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Revised: 06/05/2020] [Accepted: 06/17/2020] [Indexed: 11/11/2022]
Affiliation(s)
- Vinay Kumar Belwal
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
| | - Debika Datta
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
| | - Nitin Chaudhary
- Department of Biosciences and Bioengineering Indian Institute of Technology Guwahati India
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Mompeán M, Ramírez de Mingo D, Hervás R, Fernández-Ramírez MDC, Carrión-Vázquez M, Laurents DV. Molecular mechanism of the inhibition of TDP-43 amyloidogenesis by QBP1. Arch Biochem Biophys 2019; 675:108113. [PMID: 31568752 DOI: 10.1016/j.abb.2019.108113] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/18/2019] [Accepted: 09/22/2019] [Indexed: 12/14/2022]
Abstract
Transactive Response DNA-Binding Protein of 43 kDa (TDP-43) is an essential human protein implicated in Amyotrophic Lateral Sclerosis (ALS) and common dementias. Its C-terminal disordered region, composed of residues 264-414 includes a hydrophobic segment (residues 320-340), which drives physiological liquid/liquid phase separation and a Q/N-rich segment (residues 341-357), which is essential for pathological amyloid formation. Due to TDP-43's relevance for pathology, identifying inhibitors and characterizing their mechanism of action are important pharmacological goals. The Polyglutamine Binding Peptide 1 (QBP1), whose minimal active core is the octapeptide WGWWPGIF, strongly inhibits the aggregation of polyQ-containing amyloidogenic proteins such as Huntingtin. Rather promiscuous, this inhibitor also blocks the aggregation of other glutamine containing amyloidogenic proteins, but not Aβ, and its mechanism of action remains unknown. Using a series of spectroscopic assays and biochemical tests, we establish that QBP1 binds and inhibits amyloid formation by TDP-43's Q/N-rich region. NMR spectroscopic data evince that the aromatic rings of QBP1 accept hydrogen bonds from the HN groups of the Asn and Gln to block amyloidogenesis. This mechanism of blockage may be general to polyphenol amyloid inhibitors.
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Affiliation(s)
- Miguel Mompeán
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, Madrid, 28006, Spain
| | | | - Rubén Hervás
- Instituto Cajal, CSIC, Avda. Doctor Arce 37, Madrid, 28002, Spain
| | | | | | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, Serrano 119, Madrid, 28006, Spain.
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Galera-Prat A, Pantoja-Uceda D, Laurents DV, Carrión-Vázquez M. Solution conformation of a cohesin module and its scaffoldin linker from a prototypical cellulosome. Arch Biochem Biophys 2018; 644:1-7. [PMID: 29486159 DOI: 10.1016/j.abb.2018.02.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Revised: 02/20/2018] [Accepted: 02/23/2018] [Indexed: 11/26/2022]
Abstract
Bacterial cellulases are drawing increased attention as a means to obtain plentiful chemical feedstocks and fuels from renewable lignocellulosic biomass sources. Certain bacteria deploy a large extracellular multi-protein complex, called the cellulosome, to degrade cellulose. Scaffoldin, a key non-catalytic cellulosome component, is a large protein containing a cellulose-specific carbohydrate-binding module and several cohesin modules which bind and organize the hydrolytic enzymes. Despite the importance of the structure and protein/protein interactions of the cohesin module in the cellulosome, its structure in solution has remained unknown to date. Here, we report the backbone 1H, 13C and 15N NMR assignments of the Cohesin module 5 from the highly stable and active cellulosome from Clostridium thermocellum. These data reveal that this module adopts a tightly packed, well folded and rigid structure in solution. Furthermore, since in scaffoldin, the cohesin modules are connected by linkers we have also characterized the conformation of a representative linker segment using NMR spectroscopy. Analysis of its chemical shift values revealed that this linker is rather stiff and tends to adopt extended conformations. This suggests that the scaffoldin linkers act to minimize interactions between cohesin modules. These results pave the way towards solution studies on cohesin/dockerin's fascinating dual-binding mode.
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Affiliation(s)
| | - David Pantoja-Uceda
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 199, E-28006, Madrid, Spain
| | - Douglas V Laurents
- Instituto de Química Física "Rocasolano", CSIC, C/ Serrano 199, E-28006, Madrid, Spain.
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Protein Misfolding and Aggregation as a Therapeutic Target for Polyglutamine Diseases. Brain Sci 2017; 7:brainsci7100128. [PMID: 29019918 PMCID: PMC5664055 DOI: 10.3390/brainsci7100128] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 09/30/2017] [Accepted: 10/10/2017] [Indexed: 11/17/2022] Open
Abstract
The polyglutamine (polyQ) diseases, such as Huntington’s disease and several types of spinocerebellar ataxias, are a group of inherited neurodegenerative diseases that are caused by an abnormal expansion of the polyQ tract in disease-causative proteins. Proteins with an abnormally expanded polyQ stretch undergo a conformational transition to β-sheet rich structure, which assemble into insoluble aggregates with β-sheet rich amyloid fibrillar structures and accumulate as inclusion bodies in neurons, eventually leading to neurodegeneration. Since misfolding and aggregation of the expanded polyQ proteins are the most upstream event in the most common pathogenic cascade of the polyQ diseases, they are proposed to be one of the most ideal targets for development of disease-modifying therapies for polyQ diseases. In this review, we summarize the current understanding of the molecular pathogenic mechanisms of the polyQ diseases, and introduce therapeutic approaches targeting misfolding and aggregation of the expanded polyQ proteins, which are not only effective on a wide spectrum of polyQ diseases, but also broadly correct the functional abnormalities of multiple downstream cellular processes affected in the aggregation process of polyQ proteins. We hope that in the near future, effective therapies are developed, to bring hope to many patients suffering from currently intractable polyQ diseases.
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Zhang Q, Tsoi H, Peng S, Li PP, Lau KF, Rudnicki DD, Ngo JCK, Chan HYE. Assessing a peptidylic inhibitor-based therapeutic approach that simultaneously suppresses polyglutamine RNA- and protein-mediated toxicities in patient cells and Drosophila. Dis Model Mech 2016; 9:321-34. [PMID: 26839389 PMCID: PMC4833327 DOI: 10.1242/dmm.022350] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2015] [Accepted: 01/27/2016] [Indexed: 02/03/2023] Open
Abstract
Polyglutamine (polyQ) diseases represent a group of progressive neurodegenerative disorders that are caused by abnormal expansion of CAG triplet nucleotides in disease genes. Recent evidence indicates that not only mutant polyQ proteins, but also their corresponding mutant RNAs, contribute to the pathogenesis of polyQ diseases. Here, we describe the identification of a 13-amino-acid peptide, P3, which binds directly and preferentially to long-CAG RNA within the pathogenic range. When administered to cell and Drosophila disease models, as well as to patient-derived fibroblasts, P3 inhibited expanded-CAG-RNA-induced nucleolar stress and suppressed neurotoxicity. We further examined the combined therapeutic effect of P3 and polyQ-binding peptide 1 (QBP1), a well-characterized polyQ protein toxicity inhibitor, on neurodegeneration. When P3 and QBP1 were co-administered to disease models, both RNA and protein toxicities were effectively mitigated, resulting in a notable improvement of neurotoxicity suppression compared with the P3 and QBP1 single-treatment controls. Our findings indicate that targeting toxic RNAs and/or simultaneous targeting of toxic RNAs and their corresponding proteins could open up a new therapeutic strategy for treating polyQ degeneration.
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Affiliation(s)
- Qian Zhang
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ho Tsoi
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Shaohong Peng
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Pan P Li
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Kwok-Fai Lau
- Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Cell and Molecular Biology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Dobrila D Rudnicki
- Department of Psychiatry and Behavioral Sciences, Division of Neurobiology, Program of Cellular and Molecular Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Jacky Chi-Ki Ngo
- Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Cell and Molecular Biology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
| | - Ho Yin Edwin Chan
- Laboratory of Drosophila Research, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Biochemistry Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Cell and Molecular Biology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China Molecular Biotechnology Program, School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong SAR, China
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Hervás R, Li L, Majumdar A, Fernández-Ramírez MDC, Unruh JR, Slaughter BD, Galera-Prat A, Santana E, Suzuki M, Nagai Y, Bruix M, Casas-Tintó S, Menéndez M, Laurents DV, Si K, Carrión-Vázquez M. Molecular Basis of Orb2 Amyloidogenesis and Blockade of Memory Consolidation. PLoS Biol 2016; 14:e1002361. [PMID: 26812143 PMCID: PMC4727891 DOI: 10.1371/journal.pbio.1002361] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2015] [Accepted: 12/16/2015] [Indexed: 12/03/2022] Open
Abstract
Amyloids are ordered protein aggregates that are typically associated with neurodegenerative diseases and cognitive impairment. By contrast, the amyloid-like state of the neuronal RNA binding protein Orb2 in Drosophila was recently implicated in memory consolidation, but it remains unclear what features of this functional amyloid-like protein give rise to such diametrically opposed behaviour. Here, using an array of biophysical, cell biological and behavioural assays we have characterized the structural features of Orb2 from the monomer to the amyloid state. Surprisingly, we find that Orb2 shares many structural traits with pathological amyloids, including the intermediate toxic oligomeric species, which can be sequestered in vivo in hetero-oligomers by pathological amyloids. However, unlike pathological amyloids, Orb2 rapidly forms amyloids and its toxic intermediates are extremely transient, indicating that kinetic parameters differentiate this functional amyloid from pathological amyloids. We also observed that a well-known anti-amyloidogenic peptide interferes with long-term memory in Drosophila. These results provide structural insights into how the amyloid-like state of the Orb2 protein can stabilize memory and be nontoxic. They also provide insight into how amyloid-based diseases may affect memory processes.
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Affiliation(s)
- Rubén Hervás
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | - Liying Li
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Amitabha Majumdar
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- National Brain Research Centre, Manesar, Guragon, Haryana, India
| | | | - Jay R. Unruh
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Brian D. Slaughter
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
| | - Albert Galera-Prat
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
| | | | - Mari Suzuki
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
| | - Yoshitaka Nagai
- Department of Degenerative Neurological Diseases, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Saitama, Japan
| | - Marta Bruix
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
| | | | - Margarita Menéndez
- Instituto de Química-Física Rocasolano, IQFR-CSIC, Madrid, Spain
- Centro de Investigación Biomédica en Red sobre Enfermedades Respiratorias, Madrid, Spain
| | | | - Kausik Si
- Stowers Institute for Medical Research, Kansas City, Missouri, United States of America
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, Kansas City, Kansas, United States of America
| | - Mariano Carrión-Vázquez
- Instituto Cajal, IC-CSIC, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), Madrid, Spain
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