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Dyakin VV, Wisniewski TM, Lajtha A. Racemization in Post-Translational Modifications Relevance to Protein Aging, Aggregation and Neurodegeneration: Tip of the Iceberg. Symmetry (Basel) 2021; 13:455. [PMID: 34350031 PMCID: PMC8330555 DOI: 10.3390/sym13030455] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Homochirality of DNA and prevalent chirality of free and protein-bound amino acids in a living organism represents the challenge for modern biochemistry and neuroscience. The idea of an association between age-related disease, neurodegeneration, and racemization originated from the studies of fossils and cataract disease. Under the pressure of new results, this concept has a broader significance linking protein folding, aggregation, and disfunction to an organism's cognitive and behavioral functions. The integrity of cognitive function is provided by a delicate balance between the evolutionarily imposed molecular homo-chirality and the epigenetic/developmental impact of spontaneous and enzymatic racemization. The chirality of amino acids is the crucial player in the modulation the structure and function of proteins, lipids, and DNA. The collapse of homochirality by racemization is the result of the conformational phase transition. The racemization of protein-bound amino acids (spontaneous and enzymatic) occurs through thermal activation over the energy barrier or by the tunnel transfer effect under the energy barrier. The phase transition is achieved through the intermediate state, where the chirality of alpha carbon vanished. From a thermodynamic consideration, the system in the homo-chiral (single enantiomeric) state is characterized by a decreased level of entropy. The oscillating protein chirality is suggesting its distinct significance in the neurotransmission and flow of perceptual information, adaptive associative learning, and cognitive laterality. The common pathological hallmarks of neurodegenerative disorders include protein misfolding, aging, and the deposition of protease-resistant protein aggregates. Each of the landmarks is influenced by racemization. The brain region, cell type, and age-dependent racemization critically influence the functions of many intracellular, membrane-bound, and extracellular proteins including amyloid precursor protein (APP), TAU, PrP, Huntingtin, α-synuclein, myelin basic protein (MBP), and collagen. The amyloid cascade hypothesis in Alzheimer's disease (AD) coexists with the failure of amyloid beta (Aβ) targeting drug therapy. According to our view, racemization should be considered as a critical factor of protein conformation with the potential for inducing order, disorder, misfolding, aggregation, toxicity, and malfunctions.
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Affiliation(s)
- Victor V. Dyakin
- Virtual Reality Perception Lab (VRPL), The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
| | - Thomas M. Wisniewski
- Departments of Neurology, Pathology and Psychiatry, Center for Cognitive Neurology, New York University School of Medicine, New York, NY 10016, USA
| | - Abel Lajtha
- Center for Neurochemistry, The Nathan S. Kline Institute for Psychiatric Research (NKI), Orangeburg, NY 10962, USA
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Skretas G, Ventura S. Editorial: Protein Aggregation and Solubility in Microorganisms (Archaea, Bacteria and Unicellular Eukaryotes): Implications and Applications. Front Microbiol 2020; 11:620239. [PMID: 33329506 PMCID: PMC7734127 DOI: 10.3389/fmicb.2020.620239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Accepted: 11/12/2020] [Indexed: 11/13/2022] Open
Affiliation(s)
- Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens, Greece
| | - Salvador Ventura
- Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona, Barcelona, Spain
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3
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Abstract
Amyloids are protein polymers that were initially linked to human diseases. Across the whole Tree of Life, many disease-unrelated proteins are now emerging for which amyloids represent distinct functional states. Most bacterial amyloids described are extracellular, contributing to biofilm formation. However, only a few have been found in the bacterial cytosol. This paper reviews from the perspective of synthetic biology (SynBio) our understanding of the subtle line that separates functional from pathogenic and transmissible amyloids (prions). Amyloids are protein polymers that were initially linked to human diseases. Across the whole Tree of Life, many disease-unrelated proteins are now emerging for which amyloids represent distinct functional states. Most bacterial amyloids described are extracellular, contributing to biofilm formation. However, only a few have been found in the bacterial cytosol. This paper reviews from the perspective of synthetic biology (SynBio) our understanding of the subtle line that separates functional from pathogenic and transmissible amyloids (prions). In particular, it is focused on RepA-WH1, a functional albeit unconventional natural amyloidogenic protein domain that participates in controlling DNA replication of bacterial plasmids. SynBio approaches, including protein engineering and the design of allosteric effectors such as diverse ligands and an optogenetic module, have enabled the generation in RepA-WH1 of an intracellular cytotoxic prion-like agent in bacteria. The synthetic RepA-WH1 prion has the potential to develop into novel antimicrobials.
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Computational Assessment of Bacterial Protein Structures Indicates a Selection Against Aggregation. Cells 2019; 8:cells8080856. [PMID: 31398930 PMCID: PMC6721704 DOI: 10.3390/cells8080856] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Revised: 08/05/2019] [Accepted: 08/06/2019] [Indexed: 12/14/2022] Open
Abstract
The aggregation of proteins compromises cell fitness, either because it titrates functional proteins into non-productive inclusions or because it results in the formation of toxic assemblies. Accordingly, computational proteome-wide analyses suggest that prevention of aggregation upon misfolding plays a key role in sequence evolution. Most proteins spend their lifetimes in a folded state; therefore, it is conceivable that, in addition to sequences, protein structures would have also evolved to minimize the risk of aggregation in their natural environments. By exploiting the AGGRESCAN3D structure-based approach to predict the aggregation propensity of >600 Escherichia coli proteins, we show that the structural aggregation propensity of globular proteins is connected with their abundance, length, essentiality, subcellular location and quaternary structure. These data suggest that the avoidance of protein aggregation has contributed to shape the structural properties of proteins in bacterial cells.
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5
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Abstract
Mammalian prion proteins (PrPs) that cause transmissible spongiform encephalopathies are misfolded conformations of the host cellular PrP. The misfolded form, the scrapie PrP (PrP(Sc)), can aggregate into amyloid fibrils that progressively accumulate in the brain, evolving to a pathological phenotype. A particular characteristic of PrP(Sc) is to be found as different strains, related to the diversity of conformational states it can adopt. Prion strains are responsible for the multiple phenotypes observed in prion diseases, presenting different incubation times and diverse deposition profiles in the brain. PrP biochemical properties are also strain-dependent, such as different digestion pattern after proteolysis and different stability. Although they have long been studied, strain formation is still a major unsolved issue in prion biology. The recreation of strain-specific conformational features is of fundamental importance to study this unique pathogenic phenomenon. In our recent paper, we described that murine PrP, when expressed in bacteria, forms amyloid inclusion bodies that possess different strain-like characteristics, depending on the PrP construct. Here, we present an extra-view of these data and propose that bacteria might become a successful model to generate preparative amounts of prion strain-specific assemblies for high-resolution structural analysis as well as for addressing the determinants of infectivity and transmissibility.
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Affiliation(s)
- Bruno Macedo
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra ( Barcelona ), Spain ;,b Faculdade de Farmacia , Universidade Federal do Rio de Janeiro, Rio de Janeiro , Brazil
| | - Yraima Cordeiro
- b Faculdade de Farmacia , Universidade Federal do Rio de Janeiro, Rio de Janeiro , Brazil
| | - Salvador Ventura
- a Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular , Universitat Autonoma de Barcelona , Bellaterra ( Barcelona ), Spain
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6
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Ventura S. Editorial: Protein Solubility and Aggregation in Bacteria. Front Microbiol 2016; 7:1178. [PMID: 27524982 PMCID: PMC4965451 DOI: 10.3389/fmicb.2016.01178] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2016] [Accepted: 07/18/2016] [Indexed: 11/25/2022] Open
Affiliation(s)
- Salvador Ventura
- Departament de Bioquimica i Biologia Molecular, Institut de Biotecnologia i Biomedicina, Universitat Autònoma de Barcelona Barcelona, Spain
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7
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de Pedro-Cuesta J, Martínez-Martín P, Rábano A, Ruiz-Tovar M, Alcalde-Cabero E, Calero M. Etiologic Framework for the Study of Neurodegenerative Disorders as Well as Vascular and Metabolic Comorbidities on the Grounds of Shared Epidemiologic and Biologic Features. Front Aging Neurosci 2016; 8:138. [PMID: 27378910 PMCID: PMC4904010 DOI: 10.3389/fnagi.2016.00138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Accepted: 05/27/2016] [Indexed: 12/12/2022] Open
Abstract
Background: During the last two decades, protein aggregation at all organismal levels, from viruses to humans, has emerged from a neglected area of protein science to become a central issue in biology and biomedicine. This article constitutes a risk-based review aimed at supporting an etiologic scenario of selected, sporadic, protein-associated, i.e., conformational, neurodegenerative disorders (NDDs), and their vascular- and metabolic-associated ailments. Methods: A rationale is adopted, to incorporate selected clinical data and results from animal-model research, complementing epidemiologic evidences reported in two prior articles. Findings: Theory is formulated assuming an underlying conformational transmission mechanism, mediated either by horizontal transfer of mammalian genes coding for specific aggregation-prone proteins, or by xeno-templating between bacterial and host proteins. We build a few population-based and experimentally-testable hypotheses focusing on: (1) non-disposable surgical instruments for sporadic Creutzfeldt-Jakob disease (sCJD) and other rapid progressive neurodegenerative dementia (sRPNDd), multiple system atrophy (MSA), and motor neuron disease (MND); and (2) specific bacterial infections such as B. pertussis and E. coli for all forms, but particularly for late-life sporadic conformational, NDDs, type 2 diabetes mellitus (T2DM), and atherosclerosis where natural protein fibrils present in such organisms as a result of adaptation to the human host induce prion-like mechanisms. Conclusion: Implications for cohort alignment and experimental animal research are discussed and research lines proposed.
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Affiliation(s)
- Jesús de Pedro-Cuesta
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of HealthMadrid, Spain; Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), National Institute of Health Carlos IIIMadrid, Spain
| | - Pablo Martínez-Martín
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of HealthMadrid, Spain; Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), National Institute of Health Carlos IIIMadrid, Spain
| | - Alberto Rábano
- Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer Center Madrid, Spain
| | - María Ruiz-Tovar
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of HealthMadrid, Spain; Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), National Institute of Health Carlos IIIMadrid, Spain
| | - Enrique Alcalde-Cabero
- Department of Applied Epidemiology, National Center for Epidemiology, Carlos III Institute of HealthMadrid, Spain; Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), National Institute of Health Carlos IIIMadrid, Spain
| | - Miguel Calero
- Consortium for Biomedical Research in Neurodegenerative Diseases (CIBERNED), National Institute of Health Carlos IIIMadrid, Spain; Alzheimer Disease Research Unit, CIEN Foundation, Queen Sofia Foundation Alzheimer CenterMadrid, Spain; Chronic Disease Programme, Carlos III Institute of Health, MajadahondaMadrid, Spain
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8
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Mammalian prion protein (PrP) forms conformationally different amyloid intracellular aggregates in bacteria. Microb Cell Fact 2015; 14:174. [PMID: 26536866 PMCID: PMC4634817 DOI: 10.1186/s12934-015-0361-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 10/17/2015] [Indexed: 01/21/2023] Open
Abstract
Background An increasing number of proteins are being shown to assemble into amyloid structures that lead to pathological states. Among them, mammalian prions outstand due to their ability to transmit the pathogenic conformation, becoming thus infectious. The structural conversion of the cellular prion protein (PrPC), into its misfolded pathogenic form (PrPSc) is the central event of prion-driven pathologies. The study of the structural properties of intracellular amyloid aggregates in general and of prion-like ones in particular is a challenging task. In this context, the evidence that the inclusion bodies formed by amyloid proteins in bacteria display amyloid-like structural and functional properties make them a privileged system to model intracellular amyloid aggregation. Results Here we provide the first demonstration that recombinant murine PrP and its C-terminal domain (90–231) attain amyloid conformations inside bacteria. Moreover, the inclusions formed by these two PrP proteins display conformational diversity, since they differ in fibril morphology, binding affinity to amyloid dyes, stability, resistance to proteinase K digestion and neurotoxicity. Conclusions Overall, our results suggest that modelling PrP amyloid formation in microbial cell factories might open an avenue for a better understanding of the structural features modulating the pathogenic impact of this intriguing protein. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0361-y) contains supplementary material, which is available to authorized users.
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Navarro S, Carija A, Muñoz-Torrero D, Ventura S. A fast and specific method to screen for intracellular amyloid inhibitors using bacterial model systems. Eur J Med Chem 2015; 121:785-792. [PMID: 26608003 DOI: 10.1016/j.ejmech.2015.10.044] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Revised: 10/23/2015] [Accepted: 10/26/2015] [Indexed: 11/25/2022]
Abstract
The aggregation of a large variety of amyloidogenic proteins is linked to the onset of devastating human disorders. Therefore, there is an urgent need for effective molecules able to modulate the aggregative properties of these polypeptides in their natural environment, in order to prevent, delay or halt the progression of such diseases. On the one hand, the complexity and cost of animal models make them inefficient at early stages of drug discovery, where large chemical libraries are usually screened. On the other hand, in vitro aggregation assays in aqueous solutions hardly reproduce (patho)physiological conditions. In this context, because the formation of insoluble aggregates in bacteria shares mechanistic and functional properties with amyloid self-assembly in higher organisms, they have emerged as a promising system to model aggregation in the cell. Here we show that bacteria provide a powerful and cost-effective system to screen for amyloid inhibitors using fluorescence spectroscopy and flow cytometry, thanks to the ability of the novel red fluorescent ProteoStat dye to detect specifically intracellular amyloid-like aggregates. We validated the approach using the Alzheimer's linked Aβ40 and Aβ42 peptides and tacrine- and huprine-based aggregation inhibitors. Overall, the present method bears the potential to replace classical in vitro anti-aggregation assays.
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Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
| | - Anita Carija
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia, and Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII, 27-31, E-08028, Barcelona, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina and Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, 08193, Bellaterra, Barcelona, Spain.
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10
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Sola I, Aso E, Frattini D, López-González I, Espargaró A, Sabaté R, Di Pietro O, Luque FJ, Clos MV, Ferrer I, Muñoz-Torrero D. Novel Levetiracetam Derivatives That Are Effective against the Alzheimer-like Phenotype in Mice: Synthesis, in Vitro, ex Vivo, and in Vivo Efficacy Studies. J Med Chem 2015; 58:6018-32. [PMID: 26181606 DOI: 10.1021/acs.jmedchem.5b00624] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We have synthesized a series of heptamethylene-linked levetiracetam-huprine and levetiracetam-(6-chloro)tacrine hybrids to hit amyloid, tau, and cholinergic pathologies as well as β-amyloid (Aβ)-induced epileptiform activity, some of the mechanisms that eventually lead to cognitive deficits in Alzheimer's disease patients. These hybrids are potent inhibitors of human acetylcholinesterase and butyrylcholinesterase in vitro and moderately potent Aβ42 and tau antiaggregating agents in a simple E. coli model of amyloid aggregation. Ex vivo determination of the brain acetylcholinesterase inhibitory activity of these compounds after intraperitoneal injection to C57BL6J mice has demonstrated their ability to enter the brain. The levetiracetam-huprine hybrid 10 significantly reduced the incidence of epileptic seizures, cortical amyloid burden, and neuroinflammation in APP/PS1 mice after a 4-week treatment with a 5 mg/kg dose. Moreover, the hybrid 10 rescued transgenic mice from cognitive deficits, thereby emerging as an interesting disease-modifying anti-Alzheimer drug candidate.
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Affiliation(s)
- Irene Sola
- †Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia, and Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII 27-31, E-08028, Barcelona, Spain
| | - Ester Aso
- ‡Institut de Neuropatologia, Servei d'Anatomia Patològica, IDIBELL-Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, 08908 Barcelona, Spain.,§CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto Carlos III, Spain
| | - Daniela Frattini
- †Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia, and Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII 27-31, E-08028, Barcelona, Spain
| | - Irene López-González
- ‡Institut de Neuropatologia, Servei d'Anatomia Patològica, IDIBELL-Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, 08908 Barcelona, Spain.,§CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto Carlos III, Spain
| | - Alba Espargaró
- ∥Departament de Fisicoquímica, Facultat de Farmàcia, and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Raimon Sabaté
- ∥Departament de Fisicoquímica, Facultat de Farmàcia, and Institut de Nanociència i Nanotecnologia (IN2UB), Universitat de Barcelona, 08028 Barcelona, Spain
| | - Ornella Di Pietro
- †Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia, and Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII 27-31, E-08028, Barcelona, Spain
| | - F Javier Luque
- ⊥Departament de Fisicoquímica, Facultat de Farmàcia (Campus Torribera), and IBUB, Universitat de Barcelona, Prat de la Riba 171, E-08921, Santa Coloma de Gramenet, Spain
| | - M Victòria Clos
- #Departament de Farmacologia, de Terapèutica, i de Toxicologia, Institut de Neurociències, Universitat Autònoma de Barcelona, E-08193, Bellaterra, Barcelona, Spain
| | - Isidro Ferrer
- ‡Institut de Neuropatologia, Servei d'Anatomia Patològica, IDIBELL-Hospital Universitari de Bellvitge, Universitat de Barcelona, L'Hospitalet de Llobregat, 08908 Barcelona, Spain.,§CIBERNED, Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas, Instituto Carlos III, Spain
| | - Diego Muñoz-Torrero
- †Laboratori de Química Farmacèutica (Unitat Associada al CSIC), Facultat de Farmàcia, and Institut de Biomedicina (IBUB), Universitat de Barcelona, Av. Joan XXIII 27-31, E-08028, Barcelona, Spain
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11
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Navarro S, Marinelli P, Diaz-Caballero M, Ventura S. The prion-like RNA-processing protein HNRPDL forms inherently toxic amyloid-like inclusion bodies in bacteria. Microb Cell Fact 2015; 14:102. [PMID: 26160665 PMCID: PMC4498515 DOI: 10.1186/s12934-015-0284-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 06/16/2015] [Indexed: 01/09/2023] Open
Abstract
Background The formation of protein inclusions is connected to the onset of many human diseases. Human RNA binding proteins containing intrinsically disordered regions with an amino acid composition resembling those of yeast prion domains, like TDP-43 or FUS, are being found to aggregate in different neurodegenerative disorders. The structure of the intracellular inclusions formed by these proteins is still unclear and whether these deposits have an amyloid nature or not is a matter of debate. Recently, the aggregation of TDP-43 has been modelled in bacteria, showing that TDP-43 inclusion bodies (IBs) are amorphous but intrinsically neurotoxic. This observation raises the question of whether it is indeed the lack of an ordered structure in these human prion-like protein aggregates the underlying cause of their toxicity in different pathological states. Results Here we characterize the IBs formed by the human prion-like RNA-processing protein HNRPDL. HNRPDL is linked to the development of limb-girdle muscular dystrophy 1G and shares domain architecture with TDP-43. We show that HNRPDL IBs display characteristic amyloid hallmarks, since these aggregates bind to amyloid dyes in vitro and inside the cell, they are enriched in intermolecular β-sheet conformation and contain inner amyloid-like fibrillar structure. In addition, despite their ordered structure, HNRPDL IBs are highly neurotoxic. Conclusions Our results suggest that at least some of the disorders caused by the aggregation of human prion-like proteins would rely on the formation of classical amyloid assemblies rather than being caused by amorphous aggregates. They also illustrate the power of microbial cell factories to model amyloid aggregation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0284-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Patrizia Marinelli
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Marta Diaz-Caballero
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina, Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain.
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12
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Navarro S, Ventura S. Fluorescent dye ProteoStat to detect and discriminate intracellular amyloid-like aggregates in Escherichia coli. Biotechnol J 2014; 9:1259-66. [PMID: 25112199 DOI: 10.1002/biot.201400291] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Revised: 07/24/2014] [Accepted: 08/11/2014] [Indexed: 12/22/2022]
Abstract
The formation of amyloid aggregates is linked to the onset of an increasing number of human disorders. Thus, there is an increasing need for methodologies able to provide insights into protein deposition and its modulation. Many approaches exist to study amyloids in vitro, but the techniques available for the study of amyloid aggregation in cells are still limited and non-specific. In this study we developed a methodology for the detection of amyloid-like aggregates inside cells that discriminates these ordered assemblies from other intracellular aggregates. We chose bacteria as model system, since the inclusion bodies formed by amyloid proteins in the cytosol of bacteria resemble toxic amyloids both structurally and functionally. Using confocal microscopy, fluorescence spectroscopy, and flow cytometry, we show that the recently developed red fluorescent dye ProteoStat can detect the presence of intracellular amyloid-like deposits in living bacterial cells with high specificity, even when the target proteins are expressed at low levels. This methodology allows quantitation of the intracellular amyloid content, shows the potential to replace in vitro screenings in the search for therapeutic anti-amyloidogenic compounds, and might be useful for identifying conditions that prevent the aggregation of therapeutic recombinant proteins.
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Affiliation(s)
- Susanna Navarro
- Institut de Biotecnologia i Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Barcelona, Spain.
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13
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Abstract
The discovery that a protein could mimic viral and bacterial pathogens around 1980 by Stanley Prusiner was unexpected. Evidence shows now that Creutzfeldt-Jakob disease and related disorders are caused by prions. Prions and, for example neurodegeneratives diseases, arise from the same general disease mechanism. In each, there is abnormal unfolding and then aggregation of proteins. The protein conformational changes associated with the pathogenesis of protein misfolding disorders produce β sheet rich oligomers that are partially resistant to proteolysis and have a high tendency to form amyloid-like aggregates. It is important to distinguish between prions and amyloids: prions need not to polymerize into amyloid fibrils and can undergo self-propagation as oligomers. The prion diseases are characterized by the conformational conversion of PrP(c) to PrP(sc), the fundamental even underlying prion diseases. Despite the obvious differences between prions and conventional infectious microorganisms, prions fulfill the Koch's postulates. Meaningful treatments are likely to require cocktails of drugs that interfere with the conversion of precursor into prions and enhance the clearance of prions; such an approach may find application in the more common degenerative diseases.
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14
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Viayna E, Sola I, Bartolini M, De Simone A, Tapia-Rojas C, Serrano FG, Sabaté R, Juárez-Jiménez J, Pérez B, Luque FJ, Andrisano V, Clos MV, Inestrosa NC, Muñoz-Torrero D. Synthesis and Multitarget Biological Profiling of a Novel Family of Rhein Derivatives As Disease-Modifying Anti-Alzheimer Agents. J Med Chem 2014; 57:2549-67. [DOI: 10.1021/jm401824w] [Citation(s) in RCA: 107] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Elisabet Viayna
- Laboratori de Química Farmacèutica (Unitat
Associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
- Institut de Biomedicina
(IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Irene Sola
- Laboratori de Química Farmacèutica (Unitat
Associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
- Institut de Biomedicina
(IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Manuela Bartolini
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum University of Bologna, Via Belmeloro 6, I-40126 Bologna, Italy
| | - Angela De Simone
- Department for Life Quality Studies, University of Bologna, Corso d’Augusto 237, I-47921 Rimini, Italy
| | - Cheril Tapia-Rojas
- Centro de Envejecimiento
y Regeneración (CARE), Departamento de Biología Celular
y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, 8331150 Santiago, Chile
| | - Felipe G. Serrano
- Centro de Envejecimiento
y Regeneración (CARE), Departamento de Biología Celular
y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, 8331150 Santiago, Chile
| | - Raimon Sabaté
- Departament de Fisicoquímica,
Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
- Institut de Nanociència
i Nanotecnologia (IN2UB), Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Jordi Juárez-Jiménez
- Institut de Biomedicina
(IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain
- Departament de Fisicoquímica,
Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Belén Pérez
- Departament de Farmacologia,
de Terapèutica i de Toxicologia, Institut de Neurociències, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - F. Javier Luque
- Institut de Biomedicina
(IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain
- Departament de Fisicoquímica,
Facultat de Farmàcia, Universitat de Barcelona, E-08028 Barcelona, Spain
| | - Vincenza Andrisano
- Department for Life Quality Studies, University of Bologna, Corso d’Augusto 237, I-47921 Rimini, Italy
| | - M. Victòria Clos
- Departament de Farmacologia,
de Terapèutica i de Toxicologia, Institut de Neurociències, Universitat Autònoma de Barcelona, E-08193 Bellaterra, Barcelona, Spain
| | - Nibaldo C. Inestrosa
- Centro de Envejecimiento
y Regeneración (CARE), Departamento de Biología Celular
y Molecular, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Alameda 340, 8331150 Santiago, Chile
| | - Diego Muñoz-Torrero
- Laboratori de Química Farmacèutica (Unitat
Associada al CSIC), Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII 27-31, E-08028 Barcelona, Spain
- Institut de Biomedicina
(IBUB), Universitat de Barcelona, E-08028 Barcelona, Spain
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15
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Ramón A, Señorale-Pose M, Marín M. Inclusion bodies: not that bad…. Front Microbiol 2014; 5:56. [PMID: 24592259 PMCID: PMC3924032 DOI: 10.3389/fmicb.2014.00056] [Citation(s) in RCA: 72] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2013] [Accepted: 01/28/2014] [Indexed: 12/03/2022] Open
Abstract
The formation of inclusion bodies (IBs) constitute a frequent event during the production of heterologous proteins in bacterial hosts. Although the mechanisms leading to their formation are not completely understood, empirical data have been exploited trying to predict the aggregation propensity of specific proteins while a great number of strategies have been developed to avoid the generation of IBs. However, in many cases, the formation of such aggregates can be considered an advantage for basic research as for protein production. In this review, we focus on this positive side of IBs formation in bacteria. We present a compilation on recent advances on the understanding of IBs formation and their utilization as a model to understand protein aggregation and to explore strategies to control this process. We include recent information about their composition and structure, their use as an attractive approach to produce low cost proteins and other promising applications in Biomedicine.
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Affiliation(s)
- Ana Ramón
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mario Señorale-Pose
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Mónica Marín
- Sección Bioquímica, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
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16
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Furukawa Y. Redox environment is an intracellular factor to operate distinct pathways for aggregation of Cu,Zn-superoxide dismutase in amyotrophic lateral sclerosis. Front Cell Neurosci 2013; 7:240. [PMID: 24348334 PMCID: PMC3841916 DOI: 10.3389/fncel.2013.00240] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2013] [Accepted: 11/13/2013] [Indexed: 11/16/2022] Open
Abstract
Dominant mutations in Cu,Zn-superoxide dismutase (SOD1) cause a familial form of amyotrophic lateral sclerosis (fALS). Misfolding and aggregation of mutant SOD1 proteins are a pathological hallmark of SOD1-related fALS cases; however, the molecular mechanism of SOD1 aggregation remains controversial. Here, I have used E. coli as a model organism and shown multiple distinct pathways of SOD1 aggregation that are dependent upon its thiol-disulfide status. Overexpression of fALS-mutant SOD1s in the cytoplasm of E. coli BL21 and SHuffleTM, where redox environment is reducing and oxidizing, respectively, resulted in the formation of insoluble aggregates with notable differences; a disulfide bond of SOD1 was completely reduced in BL21 or abnormally formed between SOD1 molecules in SHuffleTM. Depending upon intracellular redox environment, therefore, mutant SOD1 is considered to misfold/aggregate through distinct pathways, which would be relevant in description of the pathological heterogeneity of SOD1-related fALS cases.
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Affiliation(s)
- Yoshiaki Furukawa
- Laboratory for Mechanistic Chemistry of Biomolecules, Department of Chemistry, Keio University Yokohama, Japan
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17
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Ferrer-Miralles N, Rodríguez-Carmona E, Corchero JL, García-Fruitós E, Vázquez E, Villaverde A. Engineering protein self-assembling in protein-based nanomedicines for drug delivery and gene therapy. Crit Rev Biotechnol 2013; 35:209-21. [DOI: 10.3109/07388551.2013.833163] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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Ami D, Natalello A, Lotti M, Doglia SM. Why and how protein aggregation has to be studied in vivo. Microb Cell Fact 2013; 12:17. [PMID: 23410248 PMCID: PMC3583745 DOI: 10.1186/1475-2859-12-17] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 02/07/2013] [Indexed: 11/10/2022] Open
Abstract
The understanding of protein aggregation is a central issue in different fields of protein science, from the heterologous protein production in biotechnology to amyloid aggregation in several neurodegenerative and systemic diseases. To this goal, it became more and more evident the crucial relevance of studying protein aggregation in the complex cellular environment, since it allows to take into account the cellular components affecting protein aggregation, such as chaperones, proteases, and molecular crowding. Here, we discuss the use of several biochemical and biophysical approaches that can be employed to monitor protein aggregation within intact cells, focusing in particular on bacteria that are widely employed as microbial cell factories.
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Affiliation(s)
- Diletta Ami
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
- Department of Physics “G. Occhialini”, University of Milano-Bicocca, Piazza della Scienza 3, 20126, Milano, Italy
| | - Antonino Natalello
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Marina Lotti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
| | - Silvia Maria Doglia
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, Piazza della Scienza 2, 20126, Milano, Italy
- Department of Physics “G. Occhialini”, University of Milano-Bicocca, Piazza della Scienza 3, 20126, Milano, Italy
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