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Candelise N, Caissutti D, Zenuni H, Nesci V, Scaricamazza S, Salvatori I, Spinello Z, Mattei V, Garofalo T, Ferri A, Valle C, Misasi R. Different Chronic Stress Paradigms Converge on Endogenous TDP43 Cleavage and Aggregation. Mol Neurobiol 2023; 60:6346-6361. [PMID: 37450246 PMCID: PMC10533643 DOI: 10.1007/s12035-023-03455-z] [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: 02/01/2023] [Accepted: 06/17/2023] [Indexed: 07/18/2023]
Abstract
The TAR-DNA binding protein (TDP43) is a nuclear protein whose cytoplasmic inclusions are hallmarks of Amyotrophic Lateral Sclerosis (ALS). Acute stress in cells causes TDP43 mobilization to the cytoplasm and its aggregation through different routes. Although acute stress elicits a strong phenotype, is far from recapitulating the years-long aggregation process. We applied different chronic stress protocols and described TDP43 aggregation in a human neuroblastoma cell line by combining solubility assays, thioflavin-based microscopy and flow cytometry. This approach allowed us to detect, for the first time to our knowledge in vitro, the formation of 25 kDa C-terminal fragment of TDP43, a pathogenic hallmark of ALS. Our results indicate that chronic stress, compared to the more common acute stress paradigm, better recapitulates the cell biology of TDP43 proteinopathies. Moreover, we optimized a protocol for the detection of bona fide prions in living cells, suggesting that TDP43 may form amyloids as a stress response.
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Affiliation(s)
- Niccolò Candelise
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
| | - Daniela Caissutti
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
| | - Henri Zenuni
- Department of Systems Medicine, Tor Vergata" University of Rome, 00133, Rome, Italy
| | - Valentina Nesci
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
- Department of Systems Medicine, Tor Vergata" University of Rome, 00133, Rome, Italy
| | | | - Illari Salvatori
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
| | - Zaira Spinello
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
| | - Vincenzo Mattei
- Biomedicine and Advanced Technologies Rieti Center, Sabina Universitas, 02100, Rieti, Italy
| | - Tina Garofalo
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy
| | - Alberto Ferri
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale Delle Ricerche (CNR), 00185, Rome, Italy
| | - Cristiana Valle
- IRCCS Fondazione Santa Lucia, 00179, Rome, Italy.
- Institute of Translational Pharmacology (IFT), Consiglio Nazionale Delle Ricerche (CNR), 00185, Rome, Italy.
| | - Roberta Misasi
- Department of Experimental Medicine, University La Sapienza, 00185, Rome, Italy.
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2
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Patra P, Rani A, Sharma N, Mukherjee C, Jha HC. Unraveling the Connection of Epstein-Barr Virus and Its Glycoprotein M 146-157 Peptide with Neurological Ailments. ACS Chem Neurosci 2023. [PMID: 37290090 DOI: 10.1021/acschemneuro.3c00231] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023] Open
Abstract
Epstein-Barr virus (EBV) is known to be associated with several cancers along with neurological modalities like Alzheimer's disease (AD) and multiple sclerosis (MS). Previous study from our group revealed that a 12 amino acid peptide fragment (146SYKHVFLSAFVY157) of EBV glycoprotein M (gM) exhibits amyloid-like self-aggregative properties. In the current study, we have investigated its effect on Aβ42 aggregation along with its effect on neural cell immunology and disease markers. EBV virion was also considered for the above-mentioned investigation. An increase in the aggregation of Aβ42 peptide was observed upon incubation with gM146-157. Further, the exposure of EBV and gM146-157 onto neuronal cells indicated the upregulation of inflammatory molecules like IL-1β, IL-6, TNF-α, and TGF-β that suggested neuroinflammation. Besides, host cell factors like mitochondrial potential and calcium ion signaling play a crucial role in cellular homeostasis and alterations in these factors aid in neurodegeneration. Changes in mitochondrial membrane potential manifested a decrease while elevation in the level of total Ca2+ ions was observed. Amelioration of Ca2+ ions triggers excitotoxicity in neurons. Subsequently, neurological disease-associated genes APP, ApoE4, and MBP were found to be increased at the protein level. Additionally, demyelination of neurons is a hallmark of MS and the myelin sheath consists of ∼70% of lipid/cholesterol-associated moieties. Hereby, genes associated with cholesterol metabolism indicated changes at the mRNA level. Enhanced expression of neurotropic factors like NGF and BDNF was discerned postexposure to EBV and gM146-157. Altogether, this study delineates a direct connection of EBV and its peptide gM146-157 with neurological illnesses.
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Affiliation(s)
- Priyanka Patra
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, Madhya Pradesh, India
| | - Annu Rani
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, Madhya Pradesh, India
| | - Neha Sharma
- Department of Atomic Energy, Optical Coatings Laboratory, High Energy Lasers & Optics Section, Laser Technology Division, Laser Group, Raja Ramanna Centre for Advanced Technology, Indore 452013, Madhya Pradesh, India
| | - Chandrachur Mukherjee
- Department of Atomic Energy, Optical Coatings Laboratory, High Energy Lasers & Optics Section, Laser Technology Division, Laser Group, Raja Ramanna Centre for Advanced Technology, Indore 452013, Madhya Pradesh, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore 453552, Madhya Pradesh, India
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3
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MacKeigan TP, Morgan ML, Stys PK. Quantitation of Tissue Amyloid via Fluorescence Spectroscopy Using Controlled Concentrations of Thioflavin-S. Molecules 2023; 28:molecules28114483. [PMID: 37298959 DOI: 10.3390/molecules28114483] [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: 05/04/2023] [Revised: 05/24/2023] [Accepted: 05/29/2023] [Indexed: 06/12/2023] Open
Abstract
Amyloids are misfolded proteins that aggregate into fibrillar structures, the accumulation of which is associated with the pathogenesis of many neurodegenerative diseases, such as Alzheimer's disease (AD). Early, sensitive detection of these misfolded aggregates is of great interest to the field, as amyloid deposition begins well before the presentation of clinical symptoms. Thioflavin-S (ThS) is a fluorescent probe commonly used to detect amyloid pathology. Protocols for ThS staining vary, but they often use high staining concentrations followed by differentiation, which causes varying levels of non-specific staining and potentially leaves more subtle amyloid deposition unidentified. In this study, we developed an optimized ThS staining protocol for the sensitive detection of β-amyloids in the widely used 5xFAD Alzheimer's mouse model. Controlled dye concentrations together with fluorescence spectroscopy and advanced analytical methods enabled not only the visualization of plaque pathology, but also the detection of subtle and widespread protein misfolding throughout the 5xFAD white matter and greater parenchyma. Together, these findings demonstrate the efficacy of a controlled ThS staining protocol and highlight the potential use of ThS for the detection of protein misfolding that precedes clinical manifestation of disease.
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Affiliation(s)
- Tatiana P MacKeigan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Megan L Morgan
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, 3330 Hospital Drive NW, Calgary, AB T2N 4N1, Canada
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4
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Wang J, Liu J, Dong Q, An Y, Su J, Xie H, Sun B, Liu J. The Influence of Heparan Sulfate on Breast Amyloidosis and the Toxicity of the Pre-fibrils Formed by β-casein. Protein J 2022; 41:543-549. [PMID: 35962883 DOI: 10.1007/s10930-022-10071-8] [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] [Accepted: 07/31/2022] [Indexed: 11/27/2022]
Abstract
Heparan sulfate (HS) as a mediator is usually involved in both inflammation and fibrosis. Besides, pre-fibrils are the intermediates of amyloid fibrils that usually cause cell death and tissue damage, like the amyloid-β in Alzheimer's disease, α-synuclein in Parkinson disease and islet amyloid polypeptide in type II diabetes mellitus. However, the related study was involved rarely in breast. Therefore, the combing technologies including hematoxylin-eosin staining and thioflavin S staining were used to investigate the influence of HS on breast amyloidosis. To further study the toxicity of the pre-fibrils formed by β-casein on the HC11 cells and the breast mammary gland, the combing technologies including pentamer formyl thiophene acetic acid fluorescence analysis, MTT assay, Annexin V/PI staining and hematoxylin-eosin staining were performed. The results demonstrated that HS, acted as an endogenous molecule, induced the inflammation and amyloid fibril formation at the same time, and there was a close relationship between inflammation and fibrosis of breast. In addition, the pre-fibrils formed by β-casein were toxic because they induced the death and apoptosis of HC11 cells, as well as the inflammation of mammary gland of rats. Therefore, the early examination and identify of the pre-fibrils in the breast were worth considering to prevent the disease development, and it was interesting to explore the HS mimetics to impair the breast amyloidosis and attenuate the inflammatory response in the future.
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Affiliation(s)
- Jia Wang
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Jiayin Liu
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Qinghai Dong
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Yang An
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Jun Su
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Hongliu Xie
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Bo Sun
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China
| | - Jihua Liu
- Department of Natural Product Chemistry, Pharmacy College, Jilin University, 1266 Fujin Street, 130021, Changchun, PR China.
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5
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Zacco E, Kantelberg O, Milanetti E, Armaos A, Panei FP, Gregory J, Jeacock K, Clarke DJ, Chandran S, Ruocco G, Gustincich S, Horrocks MH, Pastore A, Tartaglia GG. Probing TDP-43 condensation using an in silico designed aptamer. Nat Commun 2022; 13:3306. [PMID: 35739092 PMCID: PMC9226187 DOI: 10.1038/s41467-022-30944-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Accepted: 05/23/2022] [Indexed: 12/03/2022] Open
Abstract
Aptamers are artificial oligonucleotides binding to specific molecular targets. They have a promising role in therapeutics and diagnostics but are often difficult to design. Here, we exploited the catRAPID algorithm to generate aptamers targeting TAR DNA-binding protein 43 (TDP-43), whose aggregation is associated with Amyotrophic Lateral Sclerosis. On the pathway to forming insoluble inclusions, TDP-43 adopts a heterogeneous population of assemblies, many smaller than the diffraction-limit of light. We demonstrated that our aptamers bind TDP-43 and used the tightest interactor, Apt-1, as a probe to visualize TDP-43 condensates with super-resolution microscopy. At a resolution of 10 nanometers, we tracked TDP-43 oligomers undetectable by standard approaches. In cells, Apt-1 interacts with both diffuse and condensed forms of TDP-43, indicating that Apt-1 can be exploited to follow TDP-43 phase transition. The de novo generation of aptamers and their use for microscopy opens a new page to study protein condensation.
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Affiliation(s)
- Elsa Zacco
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Owen Kantelberg
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Edoardo Milanetti
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Alexandros Armaos
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Francesco Paolo Panei
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
| | - Jenna Gregory
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Kiani Jeacock
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - David J Clarke
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK
| | - Siddharthan Chandran
- UK Dementia Research Institute at University of Edinburgh, University of Edinburgh, Edinburgh bioQuarter, Chancellor's Building, 49 Little F, Edinburgh, UK
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- Euan MacDonald Centre for MND Research, University of Edinburgh, Edinburgh, UK
| | - Giancarlo Ruocco
- Department of Physics, Sapienza University, Piazzale Aldo Moro 5, 00185, Rome, Italy
- Center for Life Nanoscience, Istituto Italiano di Tecnologia, Viale Regina Elena 291, 00161, Rome, Italy
| | - Stefano Gustincich
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy
| | - Mathew H Horrocks
- EaStCHEM School of Chemistry, University of Edinburgh, Edinburgh, EH9 3FJ, UK.
| | - Annalisa Pastore
- UK Dementia Research Institute at the Maurice Wohl Institute of King's College London, London, SE5 9RT, UK.
| | - Gian Gaetano Tartaglia
- Centre for Human Technologies (CHT), Istituto Italiano di Tecnologia (IIT), Via Enrico Melen, 83, 16152, Genova, Italy.
- Centre for Genomic Regulation (CRG), Dr. Aiguader 88, 08003, Barcelona, Spain.
- Catalan Institution for Research and Advanced Studies, ICREA, Passeig Lluís Companys 23, 08010, Barcelona, Spain.
- Department of Biology 'Charles Darwin', Sapienza University of Rome, P.le A. Moro 5, Rome, 00185, Italy.
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6
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Caballero AB, Gamez P, Sabate R, Espargaró A. Anti-Amyloid Drug Screening Methods Using Bacterial Inclusion Bodies. Methods Mol Biol 2022; 2538:165-188. [PMID: 35951300 DOI: 10.1007/978-1-0716-2529-3_12] [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] [Indexed: 06/15/2023]
Abstract
Amyloid aggregation is linked to a number of human disorders that range from non-neurological illnesses such as type 2 diabetes to neurodegenerative diseases such as Alzheimer's and Parkinson's diseases. The formation of insoluble protein aggregates with amyloid conformation inside bacteria, namely, in bacterial inclusion bodies, offers the possibility to use bacteria as simple models to study amyloid aggregation processes and potential effects of both anti-amyloid drugs and/or pro-aggregative compounds. This chapter describes fast, simple, inexpensive, highly reproducible, and tunable in vitro and in cellulo methods that use bacterial inclusion bodies as preliminary screening tools for anti-amyloid drugs.
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Affiliation(s)
- Ana B Caballero
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
| | - Patrick Gamez
- NanoBIC, Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, Barcelona, Catalonia, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Catalan Institution for Research and Advanced Studies, Passeig Lluís Companys 23, Barcelona, Catalonia, Spain
| | - Raimon Sabate
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain
| | - Alba Espargaró
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, Barcelona, Catalonia, Spain.
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, Barcelona, Catalonia, Spain.
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7
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Prats-Ejarque G, Lorente H, Villalba C, Anguita R, Lu L, Vázquez-Monteagudo S, Fernández-Millán P, Boix E. Structure-Based Design of an RNase Chimera for Antimicrobial Therapy. Int J Mol Sci 2021; 23:95. [PMID: 35008522 PMCID: PMC8745102 DOI: 10.3390/ijms23010095] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/16/2022] Open
Abstract
Bacterial resistance to antibiotics urges the development of alternative therapies. Based on the structure-function of antimicrobial members of the RNase A superfamily, we have developed a hybrid enzyme. Within this family, RNase 1 exhibits the highest catalytic activity and the lowest cytotoxicity; in contrast, RNase 3 shows the highest bactericidal action, alas with a reduced catalytic activity. Starting from both parental proteins, we designed a first RNase 3/1-v1 chimera. The construct had a catalytic activity much higher than RNase 3, unfortunately without reaching an equivalent antimicrobial activity. Thus, two new versions were created with improved antimicrobial properties. Both of these versions (RNase 3/1-v2 and -v3) incorporated an antimicrobial loop characteristic of RNase 3, while a flexible RNase 1-specific loop was removed in the latest construct. RNase 3/1-v3 acquired both higher antimicrobial and catalytic activities than previous versions, while retaining the structural determinants for interaction with the RNase inhibitor and displaying non-significant cytotoxicity. Following, we tested the constructs' ability to eradicate macrophage intracellular infection and observed an enhanced ability in both RNase 3/1-v2 and v3. Interestingly, the inhibition of intracellular infection correlates with the variants' capacity to induce autophagy. We propose RNase 3/1-v3 chimera as a promising lead for applied therapeutics.
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Affiliation(s)
- Guillem Prats-Ejarque
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Helena Lorente
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Clara Villalba
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Raúl Anguita
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Lu Lu
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 625014, China
| | - Sergi Vázquez-Monteagudo
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Pablo Fernández-Millán
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
| | - Ester Boix
- Department of Biochemistry and Molecular Biology, Faculty of Biosciences, Universitat Autònoma de Barcelona, 08193 Cerdanyola del Vallès, Spain; (H.L.); (C.V.); (R.A.); (L.L.); (S.V.-M.); (P.F.-M.)
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8
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Nikoo S, Maghari A, Habibi-Rezaei M, Moosavi-Movahedi AA. Mechanistic study of lysozyme glycation by fructose and modulation by curcumin derivatives. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.117917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Tiwari D, Singh VK, Baral B, Pathak DK, Jayabalan J, Kumar R, Tapryal S, Jha HC. Indication of Neurodegenerative Cascade Initiation by Amyloid-like Aggregate-Forming EBV Proteins and Peptide in Alzheimer's Disease. ACS Chem Neurosci 2021; 12:3957-3967. [PMID: 34609141 DOI: 10.1021/acschemneuro.1c00584] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The neurotropic potential of the Epstein-Barr virus (EBV) was demonstrated quite recently; however, the mechanistic details are yet to be explored. Therefore, the effects of EBV infection in the neural milieu remain underexplored. Previous reports have suggested the potential role of virus-derived peptides in seeding the amyloid-β aggregation cascade, which lies at the center of Alzheimer's disease (AD) pathophysiology. However, no such study has been undertaken to explore the role of EBV peptides in AD. In our research, ∼100 EBV proteins were analyzed for their aggregation proclivity in silico using bioinformatic tools, followed by the prediction of 20S proteasomal cleavage sites using online algorithms NetChop ver. 3.1 and Pcleavage, thereby mimicking the cellular proteasomal cleavage activity generating short antigenic peptides of viral origin. Our study reports a high aggregate-forming tendency of a 12-amino-acid-long (146SYKHVFLSAFVY157) peptide derived from EBV glycoprotein M (EBV-gM). The in vitro analysis of aggregate formation done using Congo red and Thioflavin-S assays demonstrated dose- and time-dependent kinetics. Thereafter, Raman spectroscopy was used to validate the formation of secondary structures (α helix, β sheets) in the aggregates. Additionally, cytotoxicity assay revealed that even a low concentration of these aggregates has a lethal effect on neuroblastoma cells. The findings of this study provide insights into the mechanistic role of EBV in AD and open up new avenues to explore in the future.
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Affiliation(s)
- Deeksha Tiwari
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Vikas Kumar Singh
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Budhadev Baral
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Devesh Kumar Pathak
- Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Jesumony Jayabalan
- Nano Science Laboratory, MSS, Raja Ramanna Centre for Advanced Technology, Indore 452013, India
- Homi Bhabha National Institute, Training School
Complex, Anushakti Nagar, Mumbai 400094, India
| | - Rajesh Kumar
- Discipline of Physics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
- Centre for Advanced Electronics, Indian Institute of Technology Indore, Simrol, Indore 453552, India
| | - Suman Tapryal
- Department of Biotechnology, School of Life Sciences, Central University of Rajasthan, Ajmer 305817, Rajasthan, India
| | - Hem Chandra Jha
- Department of Biosciences and Biomedical Engineering, Indian Institute of Technology Indore, Simrol, Indore 453552, India
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10
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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11
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Ebo JS, Saunders JC, Devine PWA, Gordon AM, Warwick AS, Schiffrin B, Chin SE, England E, Button JD, Lloyd C, Bond NJ, Ashcroft AE, Radford SE, Lowe DC, Brockwell DJ. An in vivo platform to select and evolve aggregation-resistant proteins. Nat Commun 2020; 11:1816. [PMID: 32286330 PMCID: PMC7156504 DOI: 10.1038/s41467-020-15667-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Accepted: 03/19/2020] [Indexed: 02/06/2023] Open
Abstract
Protein biopharmaceuticals are highly successful, but their utility is compromised by their propensity to aggregate during manufacture and storage. As aggregation can be triggered by non-native states, whose population is not necessarily related to thermodynamic stability, prediction of poorly-behaving biologics is difficult, and searching for sequences with desired properties is labour-intensive and time-consuming. Here we show that an assay in the periplasm of E. coli linking aggregation directly to antibiotic resistance acts as a sensor for the innate (un-accelerated) aggregation of antibody fragments. Using this assay as a directed evolution screen, we demonstrate the generation of aggregation resistant scFv sequences when reformatted as IgGs. This powerful tool can thus screen and evolve ‘manufacturable’ biopharmaceuticals early in industrial development. By comparing the mutational profiles of three different immunoglobulin scaffolds, we show the applicability of this method to investigate protein aggregation mechanisms important to both industrial manufacture and amyloid disease. Protein aggregation remains a significant challenge for manufacturing of protein biopharmaceuticals. Here, the authors demonstrate the use of directed evolution and an assay for in vivo innate protein aggregation-propensity to generate aggregation-resistant scFv fragments.
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Affiliation(s)
- Jessica S Ebo
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Janet C Saunders
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.,AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK.,AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK
| | - Paul W A Devine
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.,AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK
| | - Alice M Gordon
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Amy S Warwick
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Bob Schiffrin
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | | | | | | | | | | | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK
| | - David C Lowe
- AstraZeneca, Granta Park, Cambridge, CB21 6GH, UK.
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK. .,School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, LS2 9JT, UK.
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12
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Wang S, Cho YK. Yeast surface display of full-length human microtubule-associated protein tau. Biotechnol Prog 2019; 36:e2920. [PMID: 31581367 DOI: 10.1002/btpr.2920] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 08/15/2019] [Accepted: 09/16/2019] [Indexed: 12/24/2022]
Abstract
Microtubule-associated protein tau is an intrinsically disordered, highly soluble protein found primarily in neurons. Under normal conditions, tau regulates the stability of axonal microtubules and intracellular vesicle transport. However, in patients of neurodegeneration such as Alzheimer's disease (AD), tau forms neurofibrillary deposits, which correlates well with the disease progression. Identifying molecular signatures in tau, such as posttranslational modification, truncation, and conformational change has great potential to detect earliest signs of neurodegeneration and develop therapeutic strategies. Here, we show that full-length human tau, including the longest isoform found in the adult brain, can be robustly displayed on the surface of yeast Saccharomyces cerevisiae. Yeast-displayed tau binds to anti-tau antibodies that cover epitopes ranging from the N-terminus to the 4R repeat region. Unlike tau expressed in the yeast cytosol, surface-displayed tau was not phosphorylated at sites found in AD patients (probed by antibodies AT8, AT270, AT180, and PHF-1). However, yeast-displayed tau showed clear binding to paired helical filament (PHF) tau conformation-specific antibodies Alz-50, MC-1, and Tau-2. Although the tau possessed a conformation found in PHFs, oligomerization or aggregation into larger filaments was undetected. Taken together, yeast-displayed tau enables robust measurement of protein interactions and is of particular interest for characterizing conformational change.
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Affiliation(s)
- Shiyao Wang
- Department of Chemical and Biomolecular Engineering, Institute for Systems Genomics, CT Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT
| | - Yong Ku Cho
- Department of Chemical and Biomolecular Engineering, Institute for Systems Genomics, CT Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT.,Department of Biomedical Engineering, Institute for Systems Genomics, CT Institute for the Brain and Cognitive Sciences, University of Connecticut, Storrs, CT
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13
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Delivoria DC, Chia S, Habchi J, Perni M, Matis I, Papaevgeniou N, Reczko M, Chondrogianni N, Dobson CM, Vendruscolo M, Skretas G. Bacterial production and direct functional screening of expanded molecular libraries for discovering inhibitors of protein aggregation. SCIENCE ADVANCES 2019; 5:eaax5108. [PMID: 31663025 PMCID: PMC6795521 DOI: 10.1126/sciadv.aax5108] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 09/25/2019] [Indexed: 05/17/2023]
Abstract
Protein misfolding and aggregation are associated with a many human disorders, including Alzheimer's and Parkinson's diseases. Toward increasing the effectiveness of early-stage drug discovery for these conditions, we report a bacterial platform that enables the biosynthesis of molecular libraries with expanded diversities and their direct functional screening for discovering protein aggregation inhibitors. We illustrate this approach by performing, what is to our knowledge, the largest functional screen of small-size molecular entities described to date. We generated a combinatorial library of ~200 million drug-like, cyclic peptides and rapidly screened it for aggregation inhibitors against the amyloid-β peptide (Aβ42), linked to Alzheimer's disease. Through this procedure, we identified more than 400 macrocyclic compounds that efficiently reduce Aβ42 aggregation and toxicity in vitro and in vivo. Finally, we applied a combination of deep sequencing and mutagenesis analyses to demonstrate how this system can rapidly determine structure-activity relationships and define consensus motifs required for bioactivity.
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Affiliation(s)
- Dafni C. Delivoria
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- School of Chemical Engineering, National Technical University of Athens, Athens 15780, Greece
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Perni
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Ilias Matis
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Nikoletta Papaevgeniou
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Faculty of Biology and Pharmacy, Institute of Nutrition, Friedrich Schiller University of Jena, Jena 07743, Germany
| | - Martin Reczko
- Institute for Fundamental Biomedical Science, Biomedical Sciences Research Center “Alexander Fleming,” Athens 16672, Greece
| | - Niki Chondrogianni
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
| | - Christopher M. Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK
| | - Georgios Skretas
- Institute of Chemical Biology, National Hellenic Research Foundation, Athens 11635, Greece
- Corresponding author.
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14
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Caballero AB, Espargaró A, Pont C, Busquets MA, Estelrich J, Muñoz-Torrero D, Gamez P, Sabate R. Bacterial Inclusion Bodies for Anti-Amyloid Drug Discovery: Current and Future Screening Methods. Curr Protein Pept Sci 2019; 20:563-576. [PMID: 30924417 DOI: 10.2174/1389203720666190329120007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 03/20/2019] [Accepted: 03/22/2019] [Indexed: 11/22/2022]
Abstract
Amyloid aggregation is linked to an increasing number of human disorders from nonneurological pathologies such as type-2 diabetes to neurodegenerative ones such as Alzheimer or Parkinson's diseases. Thirty-six human proteins have shown the capacity to aggregate into pathological amyloid structures. To date, it is widely accepted that amyloid folding/aggregation is a universal process present in eukaryotic and prokaryotic cells. In the last decade, several studies have unequivocally demonstrated that bacterial inclusion bodies - insoluble protein aggregates usually formed during heterologous protein overexpression in bacteria - are mainly composed of overexpressed proteins in amyloid conformation. This fact shows that amyloid-prone proteins display a similar aggregation propensity in humans and bacteria, opening the possibility to use bacteria as simple models to study amyloid aggregation process and the potential effect of both anti-amyloid drugs and pro-aggregative compounds. Under these considerations, several in vitro and in cellulo methods, which exploit the amyloid properties of bacterial inclusion bodies, have been proposed in the last few years. Since these new methods are fast, simple, inexpensive, highly reproducible, and tunable, they have aroused great interest as preliminary screening tools in the search for anti-amyloid (beta-blocker) drugs for conformational diseases. The aim of this mini-review is to compile recently developed methods aimed at tracking amyloid aggregation in bacteria, discussing their advantages and limitations, and the future potential applications of inclusion bodies in anti-amyloid drug discovery.
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Affiliation(s)
- Ana B Caballero
- Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Alba Espargaró
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Maria Antònia Busquets
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Joan Estelrich
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Patrick Gamez
- Department of Inorganic and Organic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain.,Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, 08010 Barcelona, Spain
| | - Raimon Sabate
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain.,Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
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15
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Formation of Cross-Beta Supersecondary Structure by Soft-Amyloid Cores: Strategies for Their Prediction and Characterization. Methods Mol Biol 2019. [PMID: 30945222 DOI: 10.1007/978-1-4939-9161-7_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/08/2023]
Abstract
Proteins with prion-like behavior are attracting an increasing interest, since accumulating evidences indicate that they play relevant roles both in health and disease. The self-assembly of these proteins into insoluble aggregates is associated with severe neuropathological processes such as amyotrophic lateral sclerosis (ALS). However, in normal conditions, they are known to accomplish a wide range of functional roles. The conformational duality of prion-like proteins is often encoded in specific protein regions, named prion-like domains (PrLDs). PrLDs are usually long and disordered regions of low complexity. We have shown that PrLDs might contain soft-amyloid cores that contribute significantly to trigger their aggregation, as well as to support their propagation. Further exploration of the role of these sequences in the conformational conversion of prion-like proteins might provide novel insights into the mechanism of action and regulation of these polypeptides, enabling the future development of therapeutic strategies. Here, we describe a set of methodologies aimed to identify and characterize these short amyloid stretches in a protein or proteome of interest, ranging from in silico detection to in vitro and in vivo evaluation and validation.
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16
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Espargaró A, Pont C, Gamez P, Muñoz-Torrero D, Sabate R. Amyloid Pan-inhibitors: One Family of Compounds To Cope with All Conformational Diseases. ACS Chem Neurosci 2019; 10:1311-1317. [PMID: 30380841 DOI: 10.1021/acschemneuro.8b00398] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Amyloids are ubiquitous protein aggregates sharing common internal structural features; they are present in all organisms, from prokaryotes to eukaryotes, where they play physiological or pathological roles. Importantly, amyloids, which are generated by aggregation of a range of distinct proteins, could be a key factor in a number of major human disorders, the so-called conformational diseases. Because all amyloids exhibit similar cross-β motifs, one may envisage that molecules capable of blocking the formation of β-sheet structures could abolish aggregation of all amyloid proteins, albeit with different efficacies. Herein, two different β-sheet blockers were tested against a selection of amyloidogenic proteins, encompassing all the major types of amyloid-based disorders. Analysis of their blocking efficiency, using a simple but contrasted cell-based screening procedure, unequivocally confirms that they indeed behave as aggregation pan-inhibitors. The significant inhibitory effects observed for these compounds against all tested amyloidogenic proteins could spur a broader biological evaluation of other known and new amyloid aggregation inhibitors to further determine the potential use of this class of compounds for the universal treatment of conformational diseases.
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Affiliation(s)
- Alba Espargaró
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Caterina Pont
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
| | - Patrick Gamez
- Department of Organic and Inorganic Chemistry, Faculty of Chemistry, University of Barcelona, E-08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), E-08010 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
| | - Diego Muñoz-Torrero
- Laboratory of Pharmaceutical Chemistry (CSIC Associated Unit), Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Biomedicine (IBUB), University of Barcelona, E-08028 Barcelona, Spain
| | - Raimon Sabate
- Department of Pharmacy and Pharmaceutical Technology and Physical-Chemistry, Faculty of Pharmacy and Food Sciences, University of Barcelona, E-08028 Barcelona, Spain
- Institute of Nanoscience and Nanotechnology (IN2UB), University of Barcelona, E-08028 Barcelona, Spain
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17
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Abstract
Protein misfolding and aggregation into amyloid conformations have been described to underlie the onset of several human neurodegenerative diseases. Although a large number of biophysical approaches are available to study amyloids in vitro, we still need robust methods to address their self-assembly in living cells. In this context, simple cellular models, like bacteria and yeast, expressing recombinant amyloidogenic proteins are emerging as convenient systems for studying the formation of protein inclusions, their toxicity, propagation, and interactions. We describe here a simple and fast flow cytometry method able to detect intracellular inclusions, as well as to analyze the distribution of the amyloidogenic protein of interest in intact cells. Using specific fluorescent amyloid-dyes, such as thioflavin-S and ProteoStat, or the fusion of fluorescent molecules, such as GFP, the technique can be applied in the quantification of intracellular amyloid content, for the screening of antiamyloidogenic compounds, and to test epigenetic or environmental conditions able to modulate amyloid deposition in vivo.
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18
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Sadler JC, Currin A, Kell DB. Ultra-high throughput functional enrichment of large monoamine oxidase (MAO-N) libraries by fluorescence activated cell sorting. Analyst 2018; 143:4747-4755. [PMID: 30199078 PMCID: PMC6156879 DOI: 10.1039/c8an00851e] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022]
Abstract
Directed evolution enables the improvement and optimisation of enzymes for particular applications and is a valuable tool for biotechnology and synthetic biology. However, studies are often limited in their scope by the inability to screen very large numbers of variants to identify improved enzymes. One class of enzyme for which a universal, operationally simple ultra-high throughput (>106 variants per day) assay is not available is flavin adenine dinucleotide (FAD) dependent oxidases. The current high throughput assay involves a visual, colourimetric, colony-based screen, however this is not suitable for very large libraries and does not enable quantification of the relative fitness of variants. To address this, we describe an optimised method for the sensitive detection of oxidase activity within single Escherichia coli (E. coli) cells, using the monoamine oxidase from Aspergillus niger, MAO-N, as a model system. In contrast to other methods for the screening of oxidase activity in vivo, this method does not require cell surface expression, emulsion formation or the addition of an extracellular peroxidase. Furthermore, we show that fluorescence activated cell sorting (FACS) of large libraries derived from MAO-N under the assay conditions can enrich the library in functional variants at much higher rates than via the colony-based method. We demonstrate its use for directed evolution by identifying a new mutant of MAO-N with improved activity towards a novel secondary amine substrate. This work demonstrates, for the first time, an ultra-high throughput screening methodology widely applicable for the directed evolution of FAD dependent oxidases in E. coli.
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Affiliation(s)
- Joanna C. Sadler
- School of Chemistry
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
- The Manchester Institute of Biotechnology
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
- Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM)
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
.
;
;
; http://dbkgroup.org/@dbkell
| | - Andrew Currin
- School of Chemistry
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
- The Manchester Institute of Biotechnology
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
- Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM)
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
.
;
;
; http://dbkgroup.org/@dbkell
| | - Douglas B. Kell
- School of Chemistry
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
- The Manchester Institute of Biotechnology
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
- Centre for the Synthetic Biology of Fine and Speciality Chemicals (SYNBIOCHEM)
, The University of Manchester
,
131 Princess St
, Manchester M1 7DN
, UK
.
;
;
; http://dbkgroup.org/@dbkell
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19
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Muralidharan A, Josyula VR, Hariharapura RC. Exploring the potential of marine microbes in clinical management of Alzheimer's disease: A road map for bioprospecting and identifying promising isolates. Life Sci 2018; 208:149-160. [PMID: 30031811 DOI: 10.1016/j.lfs.2018.07.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 07/18/2018] [Indexed: 10/28/2022]
Abstract
Pervasiveness of Alzheimer's disease (AD) across the globe is on rise, devitalizing the essential brain functions of the afflicted individual. Multiple neurological pathways viz., cholinergic, amyloidogenic and tau protein pathways underlying the disease and interdependence make it more complex to develop effective treatment strategies. Existing drug treatments for Alzheimer's disease majorly belong to the class of cholinergic inhibitors which improve the behavioral symptoms. But there are no drugs that could arrest the disease progression. Inhibition of beta secretase enzyme could prevent the deposition of amyloid plaques in the neurons, thereby arresting the disease progression. Search for novel drugs to treat the underlying pathogenesis of the disease is pivotal in this day and age. The source of most active lead molecules discovered recently is from the nature. Marine ecosystem provides a plethora of pharmacologically lead molecules from various living organisms inhabiting the sea. Among all, marine microbes are the most under-explored and indispensable source of many bioactive metabolites. Studies have been reported on potent metabolites from marine microbes which could inhibit the key enzymes involved in the AD pathogenesis. The advancement in microbial bioprospecting and molecular biology techniques have eased the process of cultivation and identification of microbes, isolation of novel bioactive metabolites of clinical use. Exploring such marine natural resources for pharmacological lead molecules could give a breakthrough in the drug discovery domain for treating AD such debilitating diseases. In this review, a comprehensive account of bioprospecting methods and reports of marine microbial isolates are discussed.
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Affiliation(s)
- Anuraag Muralidharan
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Udupi, Karnataka, India
| | - Venkata Rao Josyula
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Udupi, Karnataka, India.
| | - Raghu Chandrashekhar Hariharapura
- Department of Pharmaceutical Biotechnology, Manipal College of Pharmaceutical Sciences, Manipal Academy of Higher Education, Manipal, 576104 Udupi, Karnataka, India
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20
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Kaur G, Kapoor S, Thakur KG. Bacillus subtilis HelD, an RNA Polymerase Interacting Helicase, Forms Amyloid-Like Fibrils. Front Microbiol 2018; 9:1934. [PMID: 30186259 PMCID: PMC6111841 DOI: 10.3389/fmicb.2018.01934] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Accepted: 07/30/2018] [Indexed: 12/26/2022] Open
Abstract
HelD, an RNA polymerase binding protein from Bacillus subtilis, stimulates transcription and helps in timely adaptation of cells under diverse environmental conditions. At present, no structural information is available for HelD. In the current study, we performed size exclusion chromatography coupled to small angle X-ray scattering (SEC-SAXS) which suggests that HelD is predominantly monomeric and globular in solution. Using combination of size exclusion chromatography and analytical ultracentrifugation, we also show that HelD has a tendency to form higher order oligomers in solution. CD experiments suggest that HelD has both α-helical (∼35%) and β sheet (∼26%) secondary structural elements. Thermal melting experiments suggest that even at 90°C, there is only about 30% loss in secondary structural contents with Tm of 44°C. However, with the increase in temperature, there was a gain in the β-sheet content and significant irreversible loss of α-helical content. Using a combination of X-ray fiber diffraction analysis, and dye based assays including Thioflavin-T based fluorescence and Congo red binding assays, we discovered that HelD forms amyloid-like fibrils at physiologically relevant conditions in vitro. Using confocal imaging, we further show that HelD forms amyloid inclusions in Escherichia coli. Bioinformatics-based sequence analysis performed using three independent web-based servers suggests that HelD has more than 20 hot-spots spread across the sequence that may aid the formation of amyloid-like fibrils. This discovery adds one more member to the growing list of amyloid or amyloid-like fibril forming cytosolic proteins in bacteria. Future studies aimed at resolving the function of amyloid-like fibrils or amyloid inclusions may help better understand their role, if any, in the bacterial physiology.
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Affiliation(s)
- Gundeep Kaur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Srajan Kapoor
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
| | - Krishan G Thakur
- Structural Biology Laboratory, G. N. Ramachandran Protein Centre, Council of Scientific and Industrial Research-Institute of Microbial Technology, Chandigarh, India
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21
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Cereghetti G, Saad S, Dechant R, Peter M. Reversible, functional amyloids: towards an understanding of their regulation in yeast and humans. Cell Cycle 2018; 17:1545-1558. [PMID: 29963943 DOI: 10.1080/15384101.2018.1480220] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Protein aggregates, and in particular amyloids, are generally considered to be inherently irreversible aberrant clumps, and are often associated with pathologies, such as Alzheimer's disease, Parkinson's disease, or systemic amyloidosis. However, recent evidence demonstrates that some aggregates are not only fully reversible, but also perform essential physiological functions. Despite these new findings, very little is known about how these functional protein aggregates are regulated in a physiological context. Here, we take the yeast pyruvate kinase Cdc19 as an example of a protein forming functional, reversible, solid, amyloid-like aggregates in response to stress conditions. Cdc19 aggregation is regulated via an aggregation-prone low complexity region (LCR). In favorable growth conditions, this LCR is prevented from aggregating by phosphorylation or oligomerization, while upon glucose starvation it becomes exposed and allows aggregation. We suggest that LCR phosphorylation, oligomerization or partner-binding may be general and widespread mechanisms regulating LCR-mediated reversible protein aggregation. Moreover, we show that, as predicted by computational tools, Cdc19 forms amyloid-like aggregates in vitro. Interestingly, we also observe striking similarities between Cdc19 and its mammalian counterpart, PKM2. Indeed, also PKM2 harbors a LCR and contains several peptides with high amyloidogenic propensity, which coincide with known phosphorylation sites. Thus, we speculate that the formation of reversible, amyloid-like aggregates may be a general physiological mechanism for cells to adapt to stress conditions, and that the underlying regulatory mechanisms may be conserved from yeast to humans.
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Affiliation(s)
- Gea Cereghetti
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland.,b Life Science Zürich , Molecular Life Sciences , Zürich , Switzerland
| | - Shady Saad
- c Department of Chemical and Systems Biology , Stanford University , Stanford, CA , USA
| | - Reinhard Dechant
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
| | - Matthias Peter
- a Institute of Biochemistry, Department of Biology , ETH Zürich , Zürich , Switzerland
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22
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Mycobacterium tuberculosis CarD, an essential global transcriptional regulator forms amyloid-like fibrils. Sci Rep 2018; 8:10124. [PMID: 29973616 PMCID: PMC6031611 DOI: 10.1038/s41598-018-28290-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 06/21/2018] [Indexed: 02/06/2023] Open
Abstract
CarD is an essential global transcription regulator from Mycobacterium tuberculosis (Mtb) that binds RNA polymerase and activates transcription by stabilizing the transcription initiation complex. Available crystal structures have captured two distinct, monomeric and domain-swapped homodimeric, oligomeric states of CarD. However, the actual oligomeric state of CarD in solution and its biological relevance has remained unclear. Here, we confirm the presence of the homodimeric state of CarD in solution by using synchrotron-based small-angle X-ray scattering. Furthermore, by using biochemical and biophysical experiments, in addition to mass-spectrometry, transmission electron microscopy, and confocal imaging, we show that CarD is the first soluble cytosolic protein in Mtb which displays the tendency to form amyloid-like fibrils both in vitro as well as in vivo. We demonstrate that the deletion of the fourteen N-terminal residues involved in domain-swapping hampers amyloid formation, thus, suggesting that domain-swapping is crucial in amyloidogenesis. The discovery of the amyloidogenic property of an essential cytosolic global transcription regulator, CarD, in a pathogenic bacteria will further open up new frontiers in research.
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23
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Huang RYC, Iacob RE, Sankaranarayanan S, Yang L, Ahlijanian M, Tao L, Tymiak AA, Chen G. Probing Conformational Dynamics of Tau Protein by Hydrogen/Deuterium Exchange Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:174-182. [PMID: 28971440 DOI: 10.1007/s13361-017-1815-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 09/12/2017] [Accepted: 09/13/2017] [Indexed: 06/07/2023]
Abstract
Fibrillization of the microtubule-associated protein tau has been recognized as one of the signature pathologies of the nervous system in Alzheimer's disease, progressive supranuclear palsy, and other tauopathies. The conformational transition of tau in the fibrillization process, tau monomer to soluble aggregates to fibrils in particular, remains unclear. Here we report on the use of hydrogen/deuterium exchange mass spectrometry (HDX-MS) in combination with other biochemical approaches, including Thioflavin S fluorescence measurements, enzyme-linked immunosorbent assay (ELISA), and Western blotting to understand the heparin-induced tau's fibrillization. HDX-MS studies including anti-tau antibody epitope mapping experiments provided molecular level details of the full-length tau's conformational dynamics and its regional solvent accessibility upon soluble aggregates formation. The results demonstrate that R3 region in the full-length tau's microtubule binding repeat region (MTBR) is stabilized in the aggregation process, leaving both N and C terminal regions to be solvent exposed in the soluble aggregates and fibrils. The findings also illustrate the practical utility of orthogonal analytical methodologies for the characterization of protein higher order structure. Graphical Abstract ᅟ.
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Affiliation(s)
- Richard Y-C Huang
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Roxana E Iacob
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, MA, USA
| | - Sethu Sankaranarayanan
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Ling Yang
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Michael Ahlijanian
- Discovery Biology, Research and Development, Bristol-Myers Squibb Company, Wallingford, CT, USA
| | - Li Tao
- Biologics Development, Global Product Development and Supply, Bristol-Myers Squibb Company, Hopewell, NJ, USA
| | - Adrienne A Tymiak
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA
| | - Guodong Chen
- Bioanalytical and Discovery Analytical Sciences, Pharmaceutical Candidate Optimization, Research and Development, Bristol-Myers Squibb Company, Princeton, NJ, USA.
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24
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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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25
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Vasilescu A, Boulahneche S, Chekin F, Gáspár S, Medjram MS, Diagne AA, Singh SK, Kurungot S, Boukherroub R, Szunerits S. Porous reduced graphene oxide modified electrodes for the analysis of protein aggregation. Part 1: Lysozyme aggregation at pH 2 and 7.4. Electrochim Acta 2017. [DOI: 10.1016/j.electacta.2017.09.083] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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26
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Hoarau M, Malbert Y, Irague R, Hureau C, Faller P, Gras E, André I, Remaud-Siméon M. A Robust and Efficient Production and Purification Procedure of Recombinant Alzheimers Disease Methionine-Modified Amyloid-β Peptides. PLoS One 2016; 11:e0161209. [PMID: 27532547 PMCID: PMC4988814 DOI: 10.1371/journal.pone.0161209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 08/01/2016] [Indexed: 01/29/2023] Open
Abstract
An improved production and purification method for Alzheimer’s disease related methionine-modified amyloid-β 1–40 and 1–42 peptides is proposed, taking advantage of the formation of inclusion body in Escherichia coli. A Thioflavin-S assay was set-up to evaluate inclusion body formation during growth and optimize culture conditions for amyloid-β peptides production. A simple and fast purification protocol including first the isolation of the inclusion bodies and second, two cycles of high pH denaturation/ neutralization combined with an ultrafiltration step on 30-kDa cut-off membrane was established. Special attention was paid to purity monitoring based on a rational combination of UV spectrophotometry and SDS-PAGE analyses at the various stages of the process. It revealed that this chromatography-free protocol affords good yield of high quality peptides in term of purity. The resulting peptides were fully characterized and are appropriate models for highly reproducible in vitro aggregation studies.
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Affiliation(s)
- Marie Hoarau
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, INPT, Toulouse, France
| | - Yannick Malbert
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Romain Irague
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Christelle Hureau
- Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, INPT, Toulouse, France
| | - Peter Faller
- Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, INPT, Toulouse, France
| | - Emmanuel Gras
- Laboratoire de Chimie de Coordination, CNRS, Université de Toulouse, INPT, Toulouse, France
| | - Isabelle André
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Magali Remaud-Siméon
- Laboratoire d’Ingénierie des Systèmes Biologiques et Procédés, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
- * E-mail:
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27
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Ultra rapid in vivo screening for anti-Alzheimer anti-amyloid drugs. Sci Rep 2016; 6:23349. [PMID: 27000658 PMCID: PMC4802339 DOI: 10.1038/srep23349] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 03/02/2016] [Indexed: 12/20/2022] Open
Abstract
More than 46 million people worldwide suffer from Alzheimer’s disease. A
large number of potential treatments have been proposed; among these, the inhibition
of the aggregation of amyloid β-peptide (Aβ), considered one
of the main culprits in Alzheimer’s disease. Limitations in monitoring
the aggregation of Aβ in cells and tissues restrict the screening of
anti-amyloid drugs to in vitro studies in most cases. We have developed a
simple but powerful method to track Aβ aggregation in vivo in
real-time, using bacteria as in vivo amyloid reservoir. We use the specific
amyloid dye Thioflavin-S (Th-S) to stain bacterial inclusion bodies (IBs), in this
case mainly formed of Aβ in amyloid conformation. Th-S binding to
amyloids leads to an increment of fluorescence that can be monitored. The
quantification of the Th-S fluorescence along the time allows tracking
Aβ aggregation and the effect of potential anti-aggregating agents.
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28
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Ude C, Ben-Dov N, Jochums A, Li Z, Segal E, Scheper T, Beutel S. Online analysis of protein inclusion bodies produced in E. coli by monitoring alterations in scattered and reflected light. Appl Microbiol Biotechnol 2016; 100:4147-59. [PMID: 26940052 DOI: 10.1007/s00253-016-7403-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 02/15/2016] [Accepted: 02/17/2016] [Indexed: 12/29/2022]
Abstract
The online monitoring of recombinant protein aggregate inclusion bodies during microbial cultivation is an immense challenge. Measurement of scattered and reflected light offers a versatile and non-invasive measurement technique. Therefore, we investigated two methods to detect the formation of inclusion bodies and monitor their production: (1) online 180° scattered light measurement (λ = 625 nm) using a sensor platform during cultivation in shake flask and (2) online measurement of the light reflective interference using a porous Si-based optical biosensor (SiPA). It could be shown that 180° scattered light measurement allows monitoring of alterations in the optical properties of Escherichia coli BL21 cells, associated with the formation of inclusion bodies during cultivation. A reproducible linear correlation between the inclusion body concentration of the non-fluorescent protein human leukemia inhibitory factor (hLIF) carrying a thioredoxin tag and the shift ("Δamp") in scattered light signal intensity was observed. This was also observed for the glutathione-S-transferase-tagged green fluorescent protein (GFP-GST). Continuous online monitoring of reflective interference spectra reveals a significant increase in the bacterium refractive index during hLIF production in comparison to a non-induced reference that coincide with the formation of inclusion bodies. These online monitoring techniques could be applied for fast and cost-effective screening of different protein expression systems.
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Affiliation(s)
- Christian Ude
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Nadav Ben-Dov
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - André Jochums
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Zhaopeng Li
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Ester Segal
- Department of Biotechnology and Food Engineering, Technion-Israel Institute of Technology, 32000, Haifa, Israel
| | - Thomas Scheper
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany
| | - Sascha Beutel
- Institut für Technische Chemie, Gottfried Wilhelm Leibniz Universität Hannover, Callinstraße 5, 30167, Hannover, Germany.
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29
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Aguilera P, Marcoleta A, Lobos-Ruiz P, Arranz R, Valpuesta JM, Monasterio O, Lagos R. Identification of Key Amino Acid Residues Modulating Intracellular and In vitro Microcin E492 Amyloid Formation. Front Microbiol 2016; 7:35. [PMID: 26858708 PMCID: PMC4729943 DOI: 10.3389/fmicb.2016.00035] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/11/2016] [Indexed: 12/30/2022] Open
Abstract
Microcin E492 (MccE492) is a pore-forming bacteriocin produced and exported by Klebsiella pneumoniae RYC492. Besides its antibacterial activity, excreted MccE492 can form amyloid fibrils in vivo as well as in vitro. It has been proposed that bacterial amyloids can be functional playing a biological role, and in the particular case of MccE492 it would control the antibacterial activity. MccE492 amyloid fibril's morphology and formation kinetics in vitro have been well-characterized, however, it is not known which amino acid residues determine its amyloidogenic propensity, nor if it forms intracellular amyloid inclusions as has been reported for other bacterial amyloids. In this work we found the conditions in which MccE492 forms intracellular amyloids in Escherichia coli cells, that were visualized as round-shaped inclusion bodies recognized by two amyloidophilic probes, 2-4'-methylaminophenyl benzothiazole and thioflavin-S. We used this property to perform a flow cytometry-based assay to evaluate the aggregation propensity of MccE492 mutants, that were designed using an in silico prediction of putative aggregation hotspots. We established that the predicted amino acid residues 54-63, effectively act as a pro-amyloidogenic stretch. As in the case of other amyloidogenic proteins, this region presented two gatekeeper residues (P57 and P59), which disfavor both intracellular and in vitro MccE492 amyloid formation, preventing an uncontrolled aggregation. Mutants in each of these gatekeeper residues showed faster in vitro aggregation and bactericidal inactivation kinetics, and the two mutants were accumulated as dense amyloid inclusions in more than 80% of E. coli cells expressing these variants. In contrast, the MccE492 mutant lacking residues 54-63 showed a significantly lower intracellular aggregation propensity and slower in vitro polymerization kinetics. Electron microscopy analysis of the amyloids formed in vitro by these mutants revealed that, although with different efficiency, all formed fibrils morphologically similar to wild-type MccE492. The physiological implication of MccE492 intracellular amyloid formation is probably similar to the inactivation process observed for extracellular amyloids, and could be used as a mean of sequestering potentially toxic species inside the cell when this bacteriocin is produced in large amounts.
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Affiliation(s)
- Paulina Aguilera
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Andrés Marcoleta
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Pablo Lobos-Ruiz
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Rocío Arranz
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - José M Valpuesta
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas Madrid, Spain
| | - Octavio Monasterio
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
| | - Rosalba Lagos
- Laboratorio de Biología Estructural y Molecular, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Santiago, Chile
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30
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Saunders JC, Young LM, Mahood RA, Jackson MP, Revill CH, Foster RJ, Smith DA, Ashcroft AE, Brockwell DJ, Radford SE. An in vivo platform for identifying inhibitors of protein aggregation. Nat Chem Biol 2015; 12:94-101. [PMID: 26656088 PMCID: PMC4720988 DOI: 10.1038/nchembio.1988] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 10/30/2015] [Indexed: 02/07/2023]
Abstract
Protein aggregation underlies an array of human diseases, yet only one small-molecule therapeutic targeting this process has been successfully developed to date. Here, we introduce an in vivo system, based on a β-lactamase tripartite fusion construct, that is capable of identifying aggregation-prone sequences in the periplasm of Escherichia coli and inhibitors that prevent their aberrant self-assembly. We demonstrate the power of the system using a range of proteins, from small unstructured peptides (islet amyloid polypeptide and amyloid β) to larger, folded immunoglobulin domains. Configured in a 48-well format, the split β-lactamase sensor readily differentiates between aggregation-prone and soluble sequences. Performing the assay in the presence of 109 compounds enabled a rank ordering of inhibition and revealed a new inhibitor of islet amyloid polypeptide aggregation. This platform can be applied to both amyloidogenic and other aggregation-prone systems, independent of sequence or size, and can identify small molecules or other factors able to ameliorate or inhibit protein aggregation.
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Affiliation(s)
- Janet C Saunders
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Lydia M Young
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Rachel A Mahood
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Matthew P Jackson
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Charlotte H Revill
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, LS2 9JT, UK
| | - Richard J Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Chemistry, University of Leeds, LS2 9JT, UK
| | | | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - David J Brockwell
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds, LS2 9JT, UK.,School of Molecular and Cellular Biology, University of Leeds, Leeds, LS2 9JT, UK
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31
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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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32
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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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33
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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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Telikepalli S, Shinogle HE, Thapa PS, Kim JH, Deshpande M, Jawa V, Middaugh CR, Narhi LO, Joubert MK, Volkin DB. Physical characterization and in vitro biological impact of highly aggregated antibodies separated into size-enriched populations by fluorescence-activated cell sorting. J Pharm Sci 2015; 104:1575-91. [PMID: 25753756 DOI: 10.1002/jps.24379] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/19/2014] [Accepted: 01/14/2015] [Indexed: 12/17/2022]
Abstract
An IgG2 monoclonal antibody (mAb) solution was subjected to stirring, generating high concentrations of nanometer and subvisible particles, which were then successfully size-enriched into different size bins by low-speed centrifugation or a combination of gravitational sedimentation and fluorescence-activated cell sorting (FACS). The size-fractionated mAb particles were assessed for their ability to elicit the release of cytokines from a population of donor-derived human peripheral blood mononuclear cells (PBMC) at two phases of the immune response. Fractions enriched in nanometer-sized particles showed a lower response than those enriched in micron-sized particles in this assay. Particles of 5-10 μm in size displayed elevated cytokine release profiles compared with other size ranges. Stir-stressed mAb particles had amorphous morphology, contained protein with partially altered secondary structure, elevated surface hydrophobicity (compared with controls), and trace levels of elemental fluorine. FACS size-enriched the mAb particle samples, yet did not notably alter the overall morphology or composition of particles as measured by microflow imaging, transmission electron microscopy, and scanning electron microscopy-energy dispersive X-ray spectroscopy. The utility and limitations of FACS for size separation of mAb particles and potential of in vitro PBMC studies to rank-order the immunogenic potential of various types of mAb particles are discussed.
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Affiliation(s)
- Srivalli Telikepalli
- Department of Pharmaceutical Chemistry, Macromolecule and Vaccine Stabilization Center, University of Kansas, Lawrence, Kansas, 66047
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35
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Villar-Pique A, Navarro S, Ventura S. Characterization of amyloid-like properties in bacterial intracellular aggregates. Methods Mol Biol 2015; 1258:99-122. [PMID: 25447861 DOI: 10.1007/978-1-4939-2205-5_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Protein aggregation into amyloid conformations is associated with more than 50 different human disorders. Recent studies demonstrate that the expression in bacteria of amyloid proteins results in the formation of intracellular aggregates structurally related to those underlying human diseases. The ease with which prokaryotic organisms can be genetically and biochemically manipulated makes them useful systems for studying how and why protein aggregates inside the cell, providing a tractable environment to rationally model in vivo amyloid formation. In this chapter we present an overview of the methods used to characterize the kinetic, structural, and functional properties of amyloid-like bacterial intracellular aggregates and how they can be employed to screen for lead compounds that might modulate amyloid deposition.
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Affiliation(s)
- Anna Villar-Pique
- Departament de Bioquímica i Biologia Molecular, Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Cerdanyola del Vallés, 08193, Barcelona, Spain
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36
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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: 38] [Impact Index Per Article: 3.8] [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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37
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McLean D, Cooke MJ, Albay R, Glabe C, Shoichet MS. Positron emission tomography imaging of fibrillar parenchymal and vascular amyloid-β in TgCRND8 mice. ACS Chem Neurosci 2013; 4:613-23. [PMID: 23509918 DOI: 10.1021/cn300226q] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Few quantitative diagnostic and monitoring, tools are available to clinicians treating patients with Alzheimer's disease. Further, many of the promising quantitative imaging tools under development lack clear specificity toward different types of Amyloid-β (Aβ) pathology such as vascular or oligomeric species. Antibodies offer an opportunity to image specific types of Aβ pathology because of their excellent specificity. In this study, we developed a method to translate a panel of anti-Aβ antibodies, which show excellent histological performance, into live animal imaging contrast agents. In the TgCRND8 mouse model of Alzheimer's disease, we tested two antibodies, M64 and M116, that target parenchyma aggregated Aβ plaques and one antibody, M31, that targets vascular Aβ. All three antibodies were administered intravenously after labeling with both poly(ethylene glycol) to enhance circulation and (64)Cu to allow detection via positron emission tomography (PET) imaging. We were clearly able to differentiate TgCRND8 mice from wild type controls by PET imaging using either M116, the anti-Aβ antibody targeting parenchymal Aβ or M31, the antivascular Aβ antibody. To confirm the validity of the noninvasive imaging of specific Aβ pathology, brains were examined after imaging and showed clear evidence of binding to Aβ plaques.
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Affiliation(s)
- Daniel McLean
- Department of Chemical
Engineering
and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
| | - Michael J. Cooke
- Department of Chemical
Engineering
and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
| | - Ricardo Albay
- Department of Molecular Biology
and Biochemistry, School of Biological Sciences, University of California at Irvine, Irvine, California, United
States
| | - Charles Glabe
- Department of Molecular Biology
and Biochemistry, School of Biological Sciences, University of California at Irvine, Irvine, California, United
States
| | - Molly S. Shoichet
- Department of Chemical
Engineering
and Applied Chemistry, University of Toronto, Toronto, Ontario M5S 3E5, Canada
- Institute of Biomaterials and
Biomedical Engineering, University of Toronto, Toronto, Ontario M5S 3G9, Canada
- Department of Chemistry University of Toronto, Toronto, Ontario M5S 3H6, Canada
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38
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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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Villar-Piqué A, Ventura S. Modeling amyloids in bacteria. Microb Cell Fact 2012; 11:166. [PMID: 23272903 PMCID: PMC3539947 DOI: 10.1186/1475-2859-11-166] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2012] [Accepted: 12/23/2012] [Indexed: 11/17/2022] Open
Abstract
An increasing number of proteins are being shown to assemble into amyloid structures, self-seeding fibrillar aggregates that may lead to pathological states or play essential biological functions in organisms. Bacterial cell factories have raised as privileged model systems to understand the mechanisms behind amyloid assembly and the cellular fitness cost associated to the formation of these aggregates. In the near future, these bacterial systems will allow implementing high-throughput screening approaches to identify effective modulators of amyloid aggregation.
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