1
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Heath SG, Gray SG, Hamzah EM, O'Connor KM, Bozonet SM, Botha AD, de Cordovez P, Magon NJ, Naughton JD, Goldsmith DLW, Schwartfeger AJ, Sunde M, Buell AK, Morris VK, Göbl C. Amyloid formation and depolymerization of tumor suppressor p16 INK4a are regulated by a thiol-dependent redox mechanism. Nat Commun 2024; 15:5535. [PMID: 38951545 PMCID: PMC11217399 DOI: 10.1038/s41467-024-49581-7] [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: 03/16/2023] [Accepted: 06/12/2024] [Indexed: 07/03/2024] Open
Abstract
The conversion of a soluble protein into polymeric amyloid structures is a process that is poorly understood. Here, we describe a fully redox-regulated amyloid system in which cysteine oxidation of the tumor suppressor protein p16INK4a leads to rapid amyloid formation. We identify a partially-structured disulfide-bonded dimeric intermediate species that subsequently assembles into fibrils. The stable amyloid structures disassemble when the disulfide bond is reduced. p16INK4a is frequently mutated in cancers and is considered highly vulnerable to single-point mutations. We find that multiple cancer-related mutations show increased amyloid formation propensity whereas mutations stabilizing the fold prevent transition into amyloid. The complex transition into amyloids and their structural stability is therefore strictly governed by redox reactions and a single regulatory disulfide bond.
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Affiliation(s)
- Sarah G Heath
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Shelby G Gray
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Emilie M Hamzah
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | - Karina M O'Connor
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Stephanie M Bozonet
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Alex D Botha
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Pierre de Cordovez
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Nicholas J Magon
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Jennifer D Naughton
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand
| | - Dylan L W Goldsmith
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand
| | | | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, Sydney, Australia
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800, Lyngby, Denmark
| | - Vanessa K Morris
- School of Biological Sciences, University of Canterbury, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
| | - Christoph Göbl
- Mātai Hāora - Centre for Redox Biology and Medicine, Department of Pathology and Biomedical Science, University of Otago, Christchurch, New Zealand.
- Biomolecular Interaction Centre, University of Canterbury, Christchurch, New Zealand.
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2
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Peña-Díaz S, Ferreira P, Ramos MJ, Otzen DE. Mining and engineering activity in catalytic amyloids. Methods Enzymol 2024; 697:345-422. [PMID: 38816129 DOI: 10.1016/bs.mie.2024.03.002] [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: 06/01/2024]
Abstract
This chapter describes how to test different amyloid preparations for catalytic properties. We describe how to express, purify, prepare and test two types of pathological amyloid (tau and α-synuclein) and two functional amyloid proteins, namely CsgA from Escherichia coli and FapC from Pseudomonas. We therefore preface the methods section with an introduction to these two examples of functional amyloid and their remarkable structural and kinetic properties and high physical stability, which renders them very attractive for a range of nanotechnological designs, both for structural, medical and catalytic purposes. The simplicity and high surface exposure of the CsgA amyloid is particularly useful for the introduction of new functional properties and we therefore provide a computational protocol to graft active sites from an enzyme of interest into the amyloid structure. We hope that the methods described will inspire other researchers to explore the remarkable opportunities provided by bacterial functional amyloid in biotechnology.
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Affiliation(s)
- Samuel Peña-Díaz
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark
| | - Pedro Ferreira
- Faculdade de Ciencias, Universidad do Porto, Porto, Portugal
| | | | - Daniel E Otzen
- Interdisciplinary Nanoscience Center, Aarhus University, Aarhus, Denmark; Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
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3
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Wang J, Dai L, Chen S, Zhang Z, Fang X, Zhang Z. Protein-protein interactions regulating α-synuclein pathology. Trends Neurosci 2024; 47:209-226. [PMID: 38355325 DOI: 10.1016/j.tins.2024.01.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Revised: 12/15/2023] [Accepted: 01/21/2024] [Indexed: 02/16/2024]
Abstract
Parkinson's disease (PD) is a neurodegenerative disease characterized by the degeneration of dopaminergic neurons in the substantia nigra pars compacta (SNpc) and the formation of Lewy bodies (LBs). The main proteinaceous component of LBs is aggregated α-synuclein (α-syn). However, the mechanisms underlying α-syn aggregation are not yet fully understood. Converging lines of evidence indicate that, under certain pathological conditions, various proteins can interact with α-syn and regulate its aggregation. Understanding these protein-protein interactions is crucial for unraveling the molecular mechanisms contributing to PD pathogenesis. In this review we provide an overview of the current knowledge on protein-protein interactions that regulate α-syn aggregation. Additionally, we briefly summarize the methods used to investigate the influence of protein-protein interactions on α-syn aggregation and propagation.
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Affiliation(s)
- Jiannan Wang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Lijun Dai
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Sichun Chen
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Zhaohui Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China
| | - Xin Fang
- Department of Neurology, the First Affiliated Hospital of Nanchang University, Nanchang 330000, China
| | - Zhentao Zhang
- Department of Neurology, Renmin Hospital of Wuhan University, Wuhan 430060, China; TaiKang Center for Life and Medical Sciences, Wuhan University, Wuhan 430000, China.
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4
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Katsipis G, Avgoulas DI, Geromichalos GD, Petala M, Pantazaki AA. In vitro and in silico evaluation of the serrapeptase effect on biofilm and amyloids of Pseudomonas aeruginosa. Appl Microbiol Biotechnol 2023; 107:7269-7285. [PMID: 37741938 PMCID: PMC10638192 DOI: 10.1007/s00253-023-12772-1] [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: 06/20/2023] [Revised: 08/17/2023] [Accepted: 09/02/2023] [Indexed: 09/25/2023]
Abstract
Pseudomonas aeruginosa is an emerging threat for hospitalized and cystic fibrosis patients. Biofilm, a microbial community embedded in extracellular polymeric substance, fortifies bacteria against the immune system. In biofilms, the expression of functional amyloids is linked with highly aggregative, multi-resistant strains, and chronic infections. Serrapeptase (SPT), a protease possessing similar or superior anti-microbial properties with many antibiotics, presents anti-amyloid potential. However, studies on the employment of SPT against Pseudomonas biofilms and Fap amyloid, or the possible mechanisms of action are scarce. Here, SPT inhibited biofilm formation of P. aeruginosa ATCC 27853 on both plastic and glass surfaces, with an IC50 of 11.26 µg/mL and 0.27 µg/mL, respectively. The inhibitory effect of SPT on biofilm was also verified with optical microscopy of crystal violet-stained biofilms and with confocal microscopy. Additionally, SPT caused a dose-dependent decrease of bacterial viability (IC50 of 3.07 µg/mL) as demonstrated by MTT assay. Reduction of bacterial functional amyloids was also demonstrated, employing both fluorescence microscopy with thioflavin T and photometrical determination of Congo-red-positive compounds. Both viability and functional amyloids correlated significantly with biofilm inhibition. Finally, in silico molecular docking studies provided a mechanistic insight into the interaction of SPT with FapC or FapD, proving that both peptides are possible targets of SPT. These results offer new insights into the biofilm formation of P. aeruginosa and potentiate the involvement of SPT in the prevention and eradication of Pseudomonas biofilms. KEY POINTS: • Serrapeptase inhibits biofilm formation of P. aeruginosa on plastic and glass. • Biofilm inhibition correlated with reduced viability and functional amyloid levels. • In silico studies indicated that serrapeptase may target FapC and FapD peptides.
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Affiliation(s)
- Georgios Katsipis
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece
| | - Dimitrios I Avgoulas
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece
- Laboratory of Chemical and Environmental Technology, Deparment of Chemistry, Aristotle University of Thessaloniki, 54 124, 54124, Thessaloniki, Greece
| | - George D Geromichalos
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anastasia A Pantazaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece.
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5
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Ali SA, Chung KHK, Forgham H, Olsen WP, Kakinen A, Balaji A, Otzen DE, Davis TP, Javed I. Alzheimer's Progenitor Amyloid-β Targets and Dissolves Microbial Amyloids and Impairs Biofilm Function. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2023; 10:e2301423. [PMID: 37594661 PMCID: PMC10582422 DOI: 10.1002/advs.202301423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 07/03/2023] [Indexed: 08/19/2023]
Abstract
Alzheimer's disease (AD) is a leading form of dementia where the presence of extra-neuronal plaques of Amyloid-β (Aβ) is a pathological hallmark. However, Aβ peptide is also observed in the intestinal tissues of AD patients and animal models. In this study, it is reported that Aβ monomers can target and disintegrate microbial amyloids of FapC and CsgA formed by opportunistic gut pathogens, Pseudomonas aeruginosa and Escherichia coli, explaining a potential role of Aβ in the gut-brain axis. Employing a zebrafish-based transparent in vivo system and whole-mount live-imaging, Aβ is observed to diffuse into the vasculature and subsequently localize with FapC or CsgA fibrils that were injected into the tail muscles of the fish. FapC aggregates, produced after Aβ treatment (Faβ), present selective toxicity to SH-SY5Y neuronal cells while the intestinal Caco-2 cells are shown to phagocytose Faβ in a non-toxic cellular process. After remodeling by Aβ, microbial fibrils lose their native function of cell adhesion with intestinal Caco-2 cells and Aβ dissolves and detaches the microbial fibrils already attached to the cell membrane. Taken together, this study strongly indicates an anti-biofilm role for Aβ monomers that can help aid in the future development of selective anti-Alzheimer's and anti-infective medicine.
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Affiliation(s)
- Syed Aoun Ali
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
| | - Ka Hang Karen Chung
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
| | - Helen Forgham
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
| | - William P. Olsen
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityGustav Wieds Vej 14Aarhus C8000Denmark
- Sino‐Danish Center (SDC)Eastern Yanqihu CampusUniversity of Chinese Academy of Sciences380 Huaibeizhuang, Huairou DistrictBeijing101400China
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
- Institute of BiotechnologyHiLIFEUniversity of HelsinkiHelsinki00014Finland
| | - Arunpandian Balaji
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO)Aarhus UniversityGustav Wieds Vej 14Aarhus C8000Denmark
| | - Thomas Paul Davis
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
| | - Ibrahim Javed
- Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandBrisbaneQld4072Australia
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6
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Cámara-Almirón J, Domínguez-García L, El Mammeri N, Lends A, Habenstein B, de Vicente A, Loquet A, Romero D. Molecular characterization of the N-terminal half of TasA during amyloid-like assembly and its contribution to Bacillus subtilis biofilm formation. NPJ Biofilms Microbiomes 2023; 9:68. [PMID: 37739955 PMCID: PMC10516879 DOI: 10.1038/s41522-023-00437-w] [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: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Biofilms are bacterial communities that result from a cell differentiation process leading to the secretion of an extracellular matrix (ECM) by part of the population. In Bacillus subtilis, the main protein component of the ECM is TasA, which forms a fiber-based scaffold that confers structure to the ECM. The N-terminal half of TasA is strongly conserved among Bacillus species and contains a protein domain, the rigid core (RcTasA), which is critical for the structural and functional properties of the recombinant protein. In this study, we demonstrate that recombinantly purified RcTasA in vitro retains biochemical properties previously observed for the entire protein. Further analysis of the RcTasA amino acid sequence revealed two aggregation-prone stretches and a region of imperfect amino acid repeats, which are known to contribute to functional amyloid assembly. Biochemical characterization of these stretches found in RcTasA revealed their amyloid-like capacity in vitro, contributing to the amyloid nature of RcTasA. Moreover, the study of the imperfect amino acid repeats revealed the critical role of residues D64, K68 and D69 in the structural function of TasA. Experiments with versions of TasA carrying the substitutions D64A and K68AD69A demonstrated a partial loss of function of the protein either in the assembly of the ECM or in the stability of the core and amyloid-like properties. Taken together, our findings allow us to better understand the polymerization process of TasA during biofilm formation and provide knowledge into the sequence determinants that promote the molecular behavior of protein filaments in bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, Switzerland
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Nadia El Mammeri
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV, 1006, Latvia
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Antonio de Vicente
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain.
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7
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Nowakowska AW, Wojciechowski JW, Szulc N, Kotulska M. The role of tandem repeats in bacterial functional amyloids. J Struct Biol 2023; 215:108002. [PMID: 37482232 DOI: 10.1016/j.jsb.2023.108002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration. However, recent discoveries showed that amyloid structure of a protein could also be beneficial and desired, e.g., to promote cell adhesion. Functional amyloids are proteins which differ in their characteristics from pathological amyloids, so that the fibril formation could be more under control of an organism. We propose that repeats in the sequence could regulate the aggregation propensity of these proteins. The inclusion of multiple symmetric interactions, due to the presence of the repeats, could be supporting and strengthening the desirable structural properties of functional amyloids. Our results show that tandem repeats in bacterial functional amyloids have a distinct characteristic. The pattern of repeats supports the appropriate level of fibril formation and better controllability of fibril stability. The repeats tend to be more imperfect, which attenuates excessive aggregation propensity. Their desired structure and function are also reinforced by their amino acid profile. Although in the study we focused on bacterial functional amyloids, due to their importance in biofilm formation, we propose that similar mechanisms could be employed in other functional amyloids which are designed by evolution to aggregate in a desirable manner, but not necessarily in pathological amyloids.
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Affiliation(s)
- Alicja W Nowakowska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
| | - Jakub W Wojciechowski
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland
| | - Natalia Szulc
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland; Wrocław University of Environmental and Life Sciences, Department of Physics and Biophysics, Poland; LPCT, CNRS, Universite de Lorraine, F-54000 Nancy, France
| | - Malgorzata Kotulska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
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8
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Sønderby TV, Louros NN, Khodaparast L, Khodaparast L, Madsen DJ, Olsen WP, Moonen N, Nagaraj M, Sereikaite V, Strømgaard K, Rousseau F, Schymkowitz J, Otzen DE. Sequence-targeted Peptides Divert Functional Bacterial Amyloid Towards Destabilized Aggregates and Reduce Biofilm Formation. J Mol Biol 2023; 435:168039. [PMID: 37330291 DOI: 10.1016/j.jmb.2023.168039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 02/27/2023] [Accepted: 02/27/2023] [Indexed: 06/19/2023]
Abstract
Functional bacterial amyloid provides structural stability in biofilm, making it a promising target for anti-biofilm therapeutics. Fibrils formed by CsgA, the major amyloid component in E. coli are extremely robust and can withstand very harsh conditions. Like other functional amyloids, CsgA contains relatively short aggregation-prone regions (APR) which drive amyloid formation. Here, we demonstrate the use of aggregation-modulating peptides to knock down CsgA protein into aggregates with low stability and altered morphology. Remarkably, these CsgA-peptides also modulate fibrillation of the unrelated functional amyloid protein FapC from Pseudomonas, possibly through recognition of FapC segments with structural and sequence similarity with CsgA. The peptides also reduce the level of biofilm formation in E. coli and P. aeruginosa, demonstrating the potential for selective amyloid targeting to combat bacterial biofilm.
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Affiliation(s)
- Thorbjørn V Sønderby
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Sino-Danish Center (SDC), Eastern Yanqihu Campus, University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing, China. https://twitter.com/@tvs1212
| | - Nikolaos N Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. https://twitter.com/LourosNikos
| | - Ladan Khodaparast
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. https://twitter.com/@LadanKhodapara1
| | - Laleh Khodaparast
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. https://twitter.com/@LalehKhodapara1
| | - Daniel J Madsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - William P Olsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Sino-Danish Center (SDC), Eastern Yanqihu Campus, University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing, China
| | - Nele Moonen
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Madhu Nagaraj
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Vita Sereikaite
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen Ø, Denmark. https://twitter.com/@vitasereikaite
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen Ø, Denmark. https://twitter.com/@stromgaardlab
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. https://twitter.com/@stromgaardlab
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain and Disease Research, Herestraat 49, 3000 Leuven, Belgium; Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, 3000 Leuven, Belgium. https://twitter.com/@stromgaardlab
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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9
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Frenkel A, Zecharia E, Gómez-Pérez D, Sendersky E, Yegorov Y, Jacob A, Benichou JIC, Stierhof YD, Parnasa R, Golden SS, Kemen E, Schwarz R. Cell specialization in cyanobacterial biofilm development revealed by expression of a cell-surface and extracellular matrix protein. NPJ Biofilms Microbiomes 2023; 9:10. [PMID: 36864092 PMCID: PMC9981879 DOI: 10.1038/s41522-023-00376-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 02/06/2023] [Indexed: 03/04/2023] Open
Abstract
Cyanobacterial biofilms are ubiquitous and play important roles in diverse environments, yet, understanding of the processes underlying the development of these aggregates is just emerging. Here we report cell specialization in formation of Synechococcus elongatus PCC 7942 biofilms-a hitherto unknown characteristic of cyanobacterial social behavior. We show that only a quarter of the cell population expresses at high levels the four-gene ebfG-operon that is required for biofilm formation. Almost all cells, however, are assembled in the biofilm. Detailed characterization of EbfG4 encoded by this operon revealed cell-surface localization as well as its presence in the biofilm matrix. Moreover, EbfG1-3 were shown to form amyloid structures such as fibrils and are thus likely to contribute to the matrix structure. These data suggest a beneficial 'division of labor' during biofilm formation where only some of the cells allocate resources to produce matrix proteins-'public goods' that support robust biofilm development by the majority of the cells. In addition, previous studies revealed the operation of a self-suppression mechanism that depends on an extracellular inhibitor, which supresses transcription of the ebfG-operon. Here we revealed inhibitor activity at an early growth stage and its gradual accumulation along the exponential growth phase in correlation with cell density. Data, however, do not support a threshold-like phenomenon known for quorum-sensing in heterotrophs. Together, data presented here demonstrate cell specialization and imply density-dependent regulation thereby providing deep insights into cyanobacterial communal behavior.
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Affiliation(s)
- Alona Frenkel
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Eli Zecharia
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Daniel Gómez-Pérez
- grid.10392.390000 0001 2190 1447Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Eleonora Sendersky
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Yevgeni Yegorov
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Avi Jacob
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Jennifer I. C. Benichou
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - York-Dieter Stierhof
- grid.10392.390000 0001 2190 1447Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Rami Parnasa
- grid.22098.310000 0004 1937 0503The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002 Ramat-Gan, Israel
| | - Susan S. Golden
- grid.266100.30000 0001 2107 4242Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093 USA ,grid.266100.30000 0001 2107 4242Center for Circadian Biology, University of California, San Diego, La Jolla, CA 92093 USA
| | - Eric Kemen
- grid.10392.390000 0001 2190 1447Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72074 Tübingen, Germany
| | - Rakefet Schwarz
- The Mina and Everard Goodman Faculty of Life Sciences, Bar-Ilan University, 5290002, Ramat-Gan, Israel.
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10
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Pirhaghi M, Najarzadeh Z, Moosavi-Movahedi F, Shafizadeh M, Mamashli F, Atarod D, Ghasemi A, Morshedi D, Meratan AA, Otzen DE, Saboury AA. The anti-platelet drug ticlopidine inhibits FapC fibrillation and biofilm production: Highlighting its antibiotic activity. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2023; 1871:140883. [PMID: 36455808 DOI: 10.1016/j.bbapap.2022.140883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Revised: 11/21/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022]
Abstract
Multidrug resistance of bacteria and persistent infections related to biofilms, as well as the low availability of new antibacterial drugs, make it urgent to develop new antibiotics. Here, we evaluate the antibacterial and anti-biofilm properties of ticlopidine (TP), an anti-platelet aggregation drug, TP showed antibacterial activity against both gram-positive (MRSA) and gram-negative (E. coli, and P. aeruginosa) bacteria over a long treatment period. TP significantly reduced the survival of gram-negative bacteria in human blood though impact on gram-positives was more limited. TP may cause death in MRSA by inhibiting staphyloxanthin pigment synthesis, leading to oxidative stress, while scanning electron microscopy imaging indicate a loss of membrane integrity, damage, and consequent death due to lysis in gram-negative bacteria. TP showed good anti-biofilm activity against P. aeruginosa and MRSA, and a stronger biofilm degradation activity on P. aeruginosa compared to MRSA. Measuring fluorescence of the amyloid-reporter Thioflavin T (ThT) in biofilm implicated inhibition of amyloid formation as part of TP activity. This was confirmed by assays on the purified protein in P. aeruginosa, FapC, whose fibrillation kinetics was inhibited by TP. TP prolonged the lag phase of aggregation and reduced the subsequent growth rate and prolonging the lag phase to very long times provides ample opportunity to exert TP's antibacterial effect. We conclude that TP shows activity as an antibiotic against both gram-positive and gram-negative bacteria thanks to a broad range of activities, targeting bacterial metabolic processes, cellular structures and the biofilm matrix.
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Affiliation(s)
- Mitra Pirhaghi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran; Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | | | - Mahshid Shafizadeh
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Fatemeh Mamashli
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Deyhim Atarod
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Dina Morshedi
- Department of Bioprocess Engineering, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Ali Akbar Meratan
- Department of Biological Sciences, Institute for Advanced Studies in Basic Sciences (IASBS), Zanjan, Iran
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran.
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11
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Meisl G, Xu CK, Taylor JD, Michaels TCT, Levin A, Otzen D, Klenerman D, Matthews S, Linse S, Andreasen M, Knowles TPJ. Uncovering the universality of self-replication in protein aggregation and its link to disease. SCIENCE ADVANCES 2022; 8:eabn6831. [PMID: 35960802 PMCID: PMC9374340 DOI: 10.1126/sciadv.abn6831] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
Fibrillar protein aggregates are a hallmark of a range of human disorders, from prion diseases to dementias, but are also encountered in several functional contexts. Yet, the fundamental links between protein assembly mechanisms and their functional or pathological roles have remained elusive. Here, we analyze the aggregation kinetics of a large set of proteins that self-assemble by a nucleated-growth mechanism, from those associated with disease, over those whose aggregates fulfill functional roles in biology, to those that aggregate only under artificial conditions. We find that, essentially, all such systems, regardless of their biological role, are capable of self-replication. However, for aggregates that have evolved to fulfill a structural role, the rate of self-replication is too low to be significant on the biologically relevant time scale. By contrast, all disease-related proteins are able to self-replicate quickly compared to the time scale of the associated disease. Our findings establish the ubiquity of self-replication and point to its potential importance across aggregation-related disorders.
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Affiliation(s)
- Georg Meisl
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Catherine K. Xu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Jonathan D. Taylor
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Thomas C. T. Michaels
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Aviad Levin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus DK-8000, Denmark
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- U.K. Dementia Research Institute, University of Cambridge, Cambridge CB2 0XY, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Sara Linse
- Department of Biochemistry and Structural Biology, Lund University, Lund, Sweden
- Corresponding author. (S.L.); (M.A.); (T.P.J.K.)
| | - Maria Andreasen
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Allé 3, Aarhus DK-8000, Denmark
- Corresponding author. (S.L.); (M.A.); (T.P.J.K.)
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, UK
- Corresponding author. (S.L.); (M.A.); (T.P.J.K.)
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12
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Sønderby TV, Najarzadeh Z, Otzen DE. Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies. Molecules 2022; 27:4080. [PMID: 35807329 PMCID: PMC9268375 DOI: 10.3390/molecules27134080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature's ability to get the best out of a protein fold.
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Affiliation(s)
- Thorbjørn Vincent Sønderby
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
- Sino-Danish Center (SDC), Eastern Yanqihu Campus, University of Chinese Academy of Sciences, 380 Huaibeizhuang, Huairou District, Beijing 101400, China
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus, Denmark; (T.V.S.); (Z.N.)
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13
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Akbey Ü, Andreasen M. Functional amyloids from bacterial biofilms - structural properties and interaction partners. Chem Sci 2022; 13:6457-6477. [PMID: 35756505 PMCID: PMC9172111 DOI: 10.1039/d2sc00645f] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/05/2022] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation and amyloid formation have historically been linked with various diseases such as Alzheimer's and Parkinson's disease, but recently functional amyloids have gained a great deal of interest in not causing a disease and having a distinct function in vivo. Functional bacterial amyloids form the structural scaffold in bacterial biofilms and provide a survival strategy for the bacteria along with antibiotic resistance. The formation of functional amyloids happens extracellularly which differs from most disease related amyloids. Studies of functional amyloids have revealed several distinctions compared to disease related amyloids including primary structures designed to optimize amyloid formation while still retaining a controlled assembly of the individual subunits into classical cross-β-sheet structures, along with a unique cross-α-sheet amyloid fold. Studies have revealed that functional amyloids interact with components found in the extracellular matrix space such as lipids from membranes and polymers from the biofilm. Intriguingly, a level of complexity is added as functional amyloids also interact with several disease related amyloids and a causative link has even been established between functional amyloids and neurodegenerative diseases. It is hence becoming increasingly clear that functional amyloids are not inert protein structures found in bacterial biofilms but interact with many different components including human proteins related to pathology. Gaining a clear understanding of the factors governing the interactions will lead to improved strategies to combat biofilm associated infections and the correlated antibiotic resistance. In the current review we summarize the current state of the art knowledge on this exciting and fast growing research field of biofilm forming bacterial functional amyloids, their structural features and interaction partners.
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Affiliation(s)
- Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University Wilhelm Meyers Allé 3 8000 Aarhus Denmark
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14
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Chatterjee D, Jacob RS, Ray S, Navalkar A, Singh N, Sengupta S, Gadhe L, Kadu P, Datta D, Paul A, Arunima S, Mehra S, Pindi C, Kumar S, Singru P, Senapati S, Maji SK. Co-aggregation and secondary nucleation in the life cycle of human prolactin/galanin functional amyloids. eLife 2022; 11:73835. [PMID: 35257659 PMCID: PMC8993219 DOI: 10.7554/elife.73835] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 03/03/2022] [Indexed: 11/22/2022] Open
Abstract
Synergistic-aggregation and cross-seeding by two different proteins/peptides in the amyloid aggregation are well evident in various neurological disorders including Alzheimer’s disease. Here, we show co-storage of human Prolactin (PRL), which is associated with lactation in mammals, and neuropeptide galanin (GAL) as functional amyloids in secretory granules (SGs) of the female rat. Using a wide variety of biophysical studies, we show that irrespective of the difference in sequence and structure, both hormones facilitate their synergic aggregation to amyloid fibrils. Although each hormone possesses homotypic seeding ability, a unidirectional cross-seeding of GAL aggregation by PRL seeds and the inability of cross seeding by mixed fibrils suggest tight regulation of functional amyloid formation by these hormones for their efficient storage in SGs. Further, the faster release of functional hormones from mixed fibrils compared to the corresponding individual amyloid, suggests a novel mechanism of heterologous amyloid formation in functional amyloids of SGs in the pituitary. The formation of plaques of proteins called ‘amyloids’ in the brain is one of the hallmark characteristics of both Alzheimer’s and Parkinson’s disease, but amyloids can form in many tissues and organs, often disrupting normal activity. A lot of the research into amyloids has focused on their role in disease, but it turns out that amyloids can also appear in healthy tissues. For example, some protein hormones form amyloids that act as storage depots, helping cells to release the hormone when it is needed. Normally, amyloids are made mostly of a single type of protein or protein fragment associated with a particular disease like Alzheimer's. Often, this type of amyloid promotes plaque formation in other proteins, which aggravates other diseases (for example, the amyloids that form in Alzheimer’s can lead to Parkinson’s disease or type II diabetes getting worse).The plaques start growing from small amyloid fragments called seeds. In mixed amyloids – amyloids made of two types of proteins – seeds made of one protein can trigger the formation of amyloids of the other protein. This raises the question, is this true for hormones? The body often releases more than one hormone at a time from the same tissue; for example, the pituitary gland releases prolactin and galanin simultaneously. However, these hormones have completely different structures, so whether they can form a mixed amyloid is unclear. To answer this question, Chatterjee et al. first determined that, within the pituitary gland of female rats, prolactin and galanin could be found together in the same cells, forming mixed amyloids. To understand out how this happens, Chatterjee et al. tried seeding new amyloids using either prolactin or galanin. This revealed that only prolactin seeds were able to trigger the formation of galanin amyloids. Chatterjee et al. also found that the mixed amyloids could release the hormones faster than amyloids made from either protein alone. Together, these results suggest that the collaboration between these two proteins may help maintain hormone balance in the body. Problems with hormone storage and release lead to various human diseases, including prolactinoma. Understanding amyloid storage depots could reveal new ways to control hormone levels. Further research could also help to explain more about well-studied diseases linked to amyloids, like Alzheimer's.
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Affiliation(s)
- Debdeep Chatterjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Reeba S Jacob
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Soumik Ray
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ambuja Navalkar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Namrata Singh
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Shinjinee Sengupta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Laxmikant Gadhe
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Debalina Datta
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Ajoy Paul
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Sakunthala Arunima
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Surabhi Mehra
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Chinmai Pindi
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Santosh Kumar
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
| | - Praful Singru
- School of Biological Sciences, National Institute of Science Education and Research, Bhubaneswar, India
| | - Sanjib Senapati
- Department of Biotechnology, Indian Institute of Technology Madras, Chennai, India
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Mumbai, India
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15
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Rasmussen HØ, Otzen DE, Pedersen JS. Induction, inhibition, and incorporation: Different roles for anionic and zwitterionic lysolipids in the fibrillation of the functional amyloid FapC. J Biol Chem 2022; 298:101569. [PMID: 35007533 PMCID: PMC8888460 DOI: 10.1016/j.jbc.2022.101569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 11/16/2022] Open
Abstract
Amyloid proteins are widespread in nature both as pathological species involved in several diseases and as functional entities that can provide protection and storage for the organism. Lipids have been found in amyloid deposits from various amyloid diseases and have been shown to strongly affect the formation and structure of both pathological and functional amyloid proteins. Here, we investigate how fibrillation of the functional amyloid FapC from Pseudomonas is affected by two lysolipids, the zwitterionic lipid 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine and the anionic lipid 1-myristoyl-2-hydroxy-sn-glycero-3-phospho-(1′-rac-glycerol) (LPG). Small-angle X-ray scattering, circular dichroism, dynamic light scattering, and thioflavin T fluorescence measurements were performed simultaneously on the same sample to ensure reproducibility and allow a multimethod integrated analysis. We found that LPG strongly induces fibrillation around its critical micelle concentration (cmc) by promoting formation of large structures, which mature via accumulation of intermediate fibril structures with a large cross section. At concentrations above its cmc, LPG strongly inhibits fibrillation by locking FapC in a core–shell complex. In contrast, lipid 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine induces fibrillation at concentrations above its cmc, not via strong interactions with FapC but by being incorporated during fibrillation and likely stabilizing the fibrillation nucleus to reduce the lag phase. Finally, we show that LPG is not incorporated into the fibril during assembly but rather can coat the final fibril. We conclude that lipids affect both the mechanism and outcome of fibrillation of functional amyloid, highlighting a role for lipid concentration and composition in the onset and mechanism of fibrillation in vivo.
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Affiliation(s)
- Helena Østergaard Rasmussen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Molecular Biology and Genetics, Gustav Wieds Vej 14, Aarhus University, 8000 Aarhus C, Denmark.
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark; Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark.
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16
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Interaction of membrane vesicles with the Pseudomonas functional amyloid protein FapC facilitates amyloid formation. BBA ADVANCES 2022; 2:100055. [PMID: 37082589 PMCID: PMC10074931 DOI: 10.1016/j.bbadva.2022.100055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/20/2022] Open
Abstract
Functional amyloids (FA) are proteins which are evolutionarily optimized to form highly stable fibrillar structures that strengthen the bacterial biofilm matrix. FA such as CsgA (E. coli) and FapC (Pseudomonas) are secreted to the bacterial surface where they integrate into growing fibril structures projecting from the outer membrane. FA are exposed to membrane surfaces in this process, but it remains unclear how membranes can interact with FA and potentially affect the self-assembly. Here we report the effect of different vesicles (DOPG, DMPG, DOPS, DOPC and DMPC) on the kinetics and structural endpoints of FapC fibrillation using various biophysical techniques. Particularly anionic lipids such as DMPG trigger FapC fibrillation, and the protein's second repeat sequence (R2) appears to be important for this interaction. Vesicles formed from phospholipids extracted from three different Pseudomonas strains (Δfap, ΔFapC and pfap) induce FapC fibrillation by accelerating nucleation. The general aggregation inhibitor epigallocatechin gallate (EGCG) inhibits FapC fibrillation by blocking interactions between FapC and vesicles and redirecting FapC monomers to oligomer structures. Our work indicates that biological membranes can contribute significantly to the fibrillation of functional amyloid.
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17
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Nagaraj M, Najarzadeh Z, Pansieri J, Biverstål H, Musteikyte G, Smirnovas V, Matthews S, Emanuelsson C, Johansson J, Buxbaum JN, Morozova-Roche L, Otzen DE. Chaperones mainly suppress primary nucleation during formation of functional amyloid required for bacterial biofilm formation. Chem Sci 2022; 13:536-553. [PMID: 35126986 PMCID: PMC8729806 DOI: 10.1039/d1sc05790a] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/11/2021] [Indexed: 11/21/2022] Open
Abstract
Unlike misfolding in neurodegenerative diseases, aggregation of functional amyloids involved in bacterial biofilm, e.g. CsgA (E. coli) and FapC (Pseudomonas), is carefully regulated.
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Affiliation(s)
- Madhu Nagaraj
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Jonathan Pansieri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187, Umeå, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, S – 141 83 Huddinge, Sweden
| | - Greta Musteikyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-22100 Lund, Sweden
| | - Janne Johansson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, S – 141 83 Huddinge, Sweden
| | - Joel N. Buxbaum
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
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18
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Folding Steps in the Fibrillation of Functional Amyloid: Denaturant Sensitivity Reveals Common Features in Nucleation and Elongation. J Mol Biol 2021; 434:167337. [PMID: 34748745 DOI: 10.1016/j.jmb.2021.167337] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 01/09/2023]
Abstract
Functional bacterial amyloids (FuBA) are intrinsically disordered proteins (IDPs) which rapidly and efficiently aggregate, forming extremely stable fibrils. The conversion from IDP to amyloid is evolutionarily optimized and likely couples folding to association. Many FuBA contain several imperfect repeat sequences which contribute to the stability of mature FuBA fibrils. Aggregation can be considered an intermolecular extension of the process of intramolecular protein folding which has traditionally been studied using chemical denaturants. Here we employ denaturants to investigate folding steps during fibrillation of CsgA and FapC. We quantify protein compactification (i.e. the extent of burial of otherwise exposed surface area upon association of proteins) during different stages of fibrillation based on the dependence of fibrillation rate constants on the denaturant concentration (m-values) determined from fibrillation curves. For both proteins, urea mainly affects nucleation and elongation (not fragmentation), consistent with the fact that these steps involve both intra- and intermolecular association. The two steps have similar m-values, indicating that activation steps in nucleation and elongation involve the same level of folding. Surprisingly, deletion of two or three repeats from FapC leads to larger m-values (i.e. higher compactification) during the activation step of fibril growth. This observation is extended by SAXS analysis of the fibrils which indicates that weakening of the amyloidogenic core caused by repeat deletions causes a larger portion of normally unstructured regions of the protein to be included into the amyloid backbone. We conclude that the sensitivity of fibrillation to denaturants can provide useful insight into molecular mechanisms of aggregation.
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19
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Alabresm A, Chandler SL, Benicewicz BC, Decho AW. Nanotargeting of Resistant Infections with a Special Emphasis on the Biofilm Landscape. Bioconjug Chem 2021; 32:1411-1430. [PMID: 34319073 PMCID: PMC8527872 DOI: 10.1021/acs.bioconjchem.1c00116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bacterial resistance to antimicrobial compounds is a growing concern in medical and public health circles. Overcoming the adaptable and duplicative resistance mechanisms of bacteria requires chemistry-based approaches. Engineered nanoparticles (NPs) now offer unique advantages toward this effort. However, most in situ infections (in humans) occur as attached biofilms enveloped in a protective surrounding matrix of extracellular polymers, where survival of microbial cells is enhanced. This presents special considerations in the design and deployment of antimicrobials. Here, we review recent efforts to combat resistant bacterial strains using NPs and, then, explore how NP surfaces may be specifically engineered to enhance the potency and delivery of antimicrobial compounds. Special NP-engineering challenges in the design of NPs must be overcome to penetrate the inherent protective barriers of the biofilm and to successfully deliver antimicrobials to bacterial cells. Future challenges are discussed in the development of new antibiotics and their mechanisms of action and targeted delivery via NPs.
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Affiliation(s)
- Amjed Alabresm
- Department of Environmental Health Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Biological Development of Shatt Al-Arab & N. Arabian Gulf, Marine Science Centre, University of Basrah, Basrah, Iraq
| | - Savannah L Chandler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Brian C Benicewicz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- USC NanoCenter, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Alan W Decho
- Department of Environmental Health Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
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20
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Gómez-Pérez D, Chaudhry V, Kemen A, Kemen E. Amyloid Proteins in Plant-Associated Microbial Communities. Microb Physiol 2021; 31:88-98. [PMID: 34107493 DOI: 10.1159/000516014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/17/2021] [Indexed: 11/19/2022]
Abstract
Amyloids have proven to be a widespread phenomenon rather than an exception. Many proteins presenting the hallmarks of this characteristic beta sheet-rich folding have been described to date. Particularly common are functional amyloids that play an important role in the promotion of survival and pathogenicity in prokaryotes. Here, we describe important developments in amyloid protein research that relate to microbe-microbe and microbe-host interactions in the plant microbiome. Starting with biofilms, which are a broad strategy for bacterial persistence that is extremely important for plant colonization. Microbes rely on amyloid-based mechanisms to adhere and create a protective coating that shelters them from external stresses and promotes cooperation. Another strategy generally carried out by amyloids is the formation of hydrophobic surface layers. Known as hydrophobins, these proteins coat the aerial hyphae and spores of plant pathogenic fungi, as well as certain bacterial biofilms. They contribute to plant virulence through promoting dissemination and infectivity. Furthermore, antimicrobial activity is an interesting outcome of the amyloid structure that has potential application in medicine and agriculture. There are many known antimicrobial amyloids released by animals and plants; however, those produced by bacteria or fungi remain still largely unknown. Finally, we discuss amyloid proteins with a more indirect mode of action in their host interactions. These include virulence-promoting harpins, signaling transduction that functions through amyloid templating, and root nodule bacteria proteins that promote plant-microbe symbiosis. In summary, amyloids are an interesting paradigm for their many functional mechanisms linked to bacterial survival in plant-associated microbial communities.
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Affiliation(s)
| | | | - Ariane Kemen
- ZMBP/IMIT, University of Tübingen, Tübingen, Germany
| | - Eric Kemen
- ZMBP/IMIT, University of Tübingen, Tübingen, Germany
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21
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Zaman M, Andreasen M. Cross-talk between individual phenol-soluble modulins in Staphylococcus aureus biofilm enables rapid and efficient amyloid formation. eLife 2020; 9:59776. [PMID: 33259287 PMCID: PMC7732344 DOI: 10.7554/elife.59776] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 11/30/2020] [Indexed: 12/11/2022] Open
Abstract
The infective ability of the opportunistic pathogen Staphylococcus aureus, recognized as the most frequent cause of biofilm-associated infections, is associated with biofilm-mediated resistance to host immune response. Phenol-soluble modulins (PSM) comprise the structural scaffold of S. aureus biofilms through self-assembly into functional amyloids, but the role of individual PSMs during biofilm formation remains poorly understood and the molecular pathways of PSM self-assembly are yet to be identified. Here we demonstrate high degree of cooperation between individual PSMs during functional amyloid formation. PSMα3 initiates the aggregation, forming unstable aggregates capable of seeding other PSMs resulting in stable amyloid structures. Using chemical kinetics we dissect the molecular mechanism of aggregation of individual PSMs showing that PSMα1, PSMα3 and PSMβ1 display secondary nucleation whereas PSMβ2 aggregates through primary nucleation and elongation. Our findings suggest that various PSMs have evolved to ensure fast and efficient biofilm formation through cooperation between individual peptides.
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Affiliation(s)
- Masihuz Zaman
- Aarhus University, Department of Biomedicine, Aarhus, Denmark
| | - Maria Andreasen
- Aarhus University, Department of Biomedicine, Aarhus, Denmark
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22
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Christensen LFB, Nowak JS, Sønderby TV, Frank SA, Otzen DE. Quantitating denaturation by formic acid: imperfect repeats are essential to the stability of the functional amyloid protein FapC. J Biol Chem 2020; 295:13031-13046. [PMID: 32719003 PMCID: PMC7489911 DOI: 10.1074/jbc.ra120.013396] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/11/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial functional amyloids are evolutionarily optimized to aggregate, so much so that the extreme robustness of functional amyloid makes it very difficult to examine their structure-function relationships in a detailed manner. Previous work has shown that functional amyloids are resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at high concentrations. However, systematic investigation requires a quantitative analysis of FA's ability to denature proteins. Amyloid formed by Pseudomonas sp. protein FapC provides an excellent model to investigate FA denaturation. It contains three imperfect repeats, and stepwise removal of these repeats slows fibrillation and increases fragmentation during aggregation. However, the link to stability is unclear. We first calibrated FA denaturation using three small, globular, and acid-resistant proteins. This revealed a linear relationship between the concentration of FA and the free energy of unfolding with a slope of mFA+pH (the combined contribution of FA and FA-induced lowering of pH), as well as a robust correlation between protein size and mFA+pH We then measured the solubilization of fibrils formed from different FapC variants with varying numbers of repeats as a function of the concentration of FA. This revealed a decline in the number of residues driving amyloid formation upon deleting at least two repeats. The midpoint of denaturation declined with the removal of repeats. Complete removal of all repeats led to fibrils that were solubilized at FA concentrations 2-3 orders of magnitude lower than the repeat-containing variants, showing that at least one repeat is required for the stability of functional amyloid.
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Affiliation(s)
| | - Jan Stanislaw Nowak
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | | | - Signe Andrea Frank
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark.
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23
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Javed I, Zhang Z, Adamcik J, Andrikopoulos N, Li Y, Otzen DE, Lin S, Mezzenga R, Davis TP, Ding F, Ke PC. Accelerated Amyloid Beta Pathogenesis by Bacterial Amyloid FapC. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001299. [PMID: 32999841 PMCID: PMC7509637 DOI: 10.1002/advs.202001299] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/10/2020] [Indexed: 05/03/2023]
Abstract
The gut-brain axis has attracted increasing attention in recent years, fueled by accumulating symptomatic, physiological, and pathological findings. In this study, the aggregation and toxicity of amyloid beta (Aβ), the pathogenic peptide associated with Alzheimer's disease (AD), seeded by FapC amyloid fragments (FapCS) of Pseudomonas aeruginosa that colonizes the gut microbiome through infections are examined. FapCS display favorable binding with Aβ and a catalytic capacity in seeding the peptide amyloidosis. Upon seeding, twisted Aβ fibrils assume a much-shortened periodicity approximating that of FapC fibrils, accompanied by a 37% sharp rise in the fibrillar diameter, compared with the control. The robust seeding capacity for Aβ by FapCS and the biofilm fragments derived from P. aeruginosa entail abnormal behavior pathology and immunohistology, as well as impaired cognitive function of zebrafish. Together, the data offer the first concrete evidence of structural integration and inheritance in peptide cross-seeding, a crucial knowledge gap in understanding the pathological correlations between different amyloid diseases. The catalytic role of infectious bacteria in promoting Aβ amyloidosis may be exploited as a potential therapeutic target, while the altered mesoscopic signatures of Aβ fibrils may serve as a prototype for molecular assembly and a biomarker for screening bacterial infections in AD.
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Affiliation(s)
- Ibrahim Javed
- Australian Institute for Bioengineering and NanotechnologyUniversity of QueenslandBrisbaneQLD4072Australia
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Zhenzhen Zhang
- Department of Physics and AstronomyClemson UniversityClemsonSC29634USA
| | - Jozef Adamcik
- Food & Soft MaterialsDepartment of Health Science & TechnologyETH ZurichSchmelzbergstrasse 9, LFO, E23Zurich8092Switzerland
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Yuhuan Li
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO)University of AarhusAarhus CAarhus8000Denmark
| | - Sijie Lin
- College of Environmental Science and EngineeringBiomedical Multidisciplinary Innovation Research InstituteShanghai East HospitalShanghai Institute of Pollution Control and Ecological SecurityTongji University1239 Siping RoadShanghai200092China
| | - Raffaele Mezzenga
- Food & Soft MaterialsDepartment of Health Science & TechnologyETH ZurichSchmelzbergstrasse 9, LFO, E23Zurich8092Switzerland
| | - Thomas P. Davis
- Australian Institute for Bioengineering and NanotechnologyUniversity of QueenslandBrisbaneQLD4072Australia
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Feng Ding
- Department of Physics and AstronomyClemson UniversityClemsonSC29634USA
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Zhongshan HospitalFudan University111 Yixueyuan Rd, Xuhui DistrictShanghai200032China
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24
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Ke PC, Zhou R, Serpell LC, Riek R, Knowles TPJ, Lashuel HA, Gazit E, Hamley IW, Davis TP, Fändrich M, Otzen DE, Chapman MR, Dobson CM, Eisenberg DS, Mezzenga R. Half a century of amyloids: past, present and future. Chem Soc Rev 2020; 49:5473-5509. [PMID: 32632432 PMCID: PMC7445747 DOI: 10.1039/c9cs00199a] [Citation(s) in RCA: 304] [Impact Index Per Article: 76.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Amyloid diseases are global epidemics with profound health, social and economic implications and yet remain without a cure. This dire situation calls for research into the origin and pathological manifestations of amyloidosis to stimulate continued development of new therapeutics. In basic science and engineering, the cross-β architecture has been a constant thread underlying the structural characteristics of pathological and functional amyloids, and realizing that amyloid structures can be both pathological and functional in nature has fuelled innovations in artificial amyloids, whose use today ranges from water purification to 3D printing. At the conclusion of a half century since Eanes and Glenner's seminal study of amyloids in humans, this review commemorates the occasion by documenting the major milestones in amyloid research to date, from the perspectives of structural biology, biophysics, medicine, microbiology, engineering and nanotechnology. We also discuss new challenges and opportunities to drive this interdisciplinary field moving forward.
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Affiliation(s)
- Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Zhongshan Hospital, Fudan University, 111 Yixueyuan Rd, Xuhui District, Shanghai, China
| | - Ruhong Zhou
- Institute of Quantitative Biology, Zhejiang University, Hangzhou 310058, China; Department of Chemistry, Columbia University, New York, New York, 10027, USA
| | - Louise C. Serpell
- School of Life Sciences, University of Sussex, Falmer, East Sussex BN1 9QG, UK
| | - Roland Riek
- Laboratory of Physical Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Wolfgang-Pauli-Str. 10, 8093 Zurich, Switzerland
| | - Tuomas P. J. Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
- Cavendish Laboratory, University of Cambridge, J J Thomson Avenue, CB3 0HE, Cambridge, UK
| | - Hilal A. Lashuel
- Laboratory of Molecular Neurobiology and Neuroproteomics, Brain Mind Institute, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ehud Gazit
- Department of Molecular Microbiology and Biotechnology, George S. Wise Faculty of Life Sciences; Department of Materials Science and Engineering, Iby and Aladar Fleischman Faculty of Engineering, Tel Aviv University, 69978 Tel Aviv, Israel
| | - Ian W. Hamley
- School of Chemistry, Food Biosciences and Pharmacy, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Thomas P. Davis
- ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane Qld 4072, Australia
| | - Marcus Fändrich
- Institute of Protein Biochemistry, Ulm University, 89081, Ulm, Germany
| | - Daniel Erik Otzen
- Department of Molecular Biology, Center for Insoluble Protein Structures (inSPIN), Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, Centre for Microbial Research, University of Michigan, Ann Arbor, MI 48109-1048, USA
| | - Christopher M. Dobson
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - David S. Eisenberg
- Departments of Chemistry and Biochemistry and Biological Chemistry, UCLA-DOE Institute and Howard Hughes Medical Institute, UCLA, Los Angeles, CA, USA
| | - Raffaele Mezzenga
- Department of Health Science & Technology, ETH Zurich, Schmelzbergstrasse 9, LFO, E23, 8092 Zurich, Switzerland
- Department of Materials, ETH Zurich, Wolfgang Pauli Strasse 10, 8093 Zurich, Switzerland
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25
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Alijanvand SH, Christensen MH, Christiansen G, Harikandei KB, Salehi P, Schiøtt B, Moosavi-Movahedi AA, Otzen DE. Novel noscapine derivatives stabilize the native state of insulin against fibrillation. Int J Biol Macromol 2020; 147:98-108. [DOI: 10.1016/j.ijbiomac.2020.01.061] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 01/06/2020] [Accepted: 01/06/2020] [Indexed: 12/17/2022]
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26
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Nagaraj M, Ahmed M, Lyngsø J, Vad BS, Bøggild A, Fillipsen A, Pedersen JS, Otzen DE, Akbey Ü. Predicted Loop Regions Promote Aggregation: A Study of Amyloidogenic Domains in the Functional Amyloid FapC. J Mol Biol 2020; 432:2232-2252. [DOI: 10.1016/j.jmb.2020.01.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Revised: 01/27/2020] [Accepted: 01/27/2020] [Indexed: 02/08/2023]
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27
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Abstract
When protein/peptides aggregate, they usually form the amyloid state consisting of cross β-sheet structure built by repetitively stacked β-strands forming long fibrils. Amyloids are usually associated with disease including Alzheimer's. However, amyloid has many useful features. It efficiently transforms protein from the soluble to the insoluble state in an essentially two-state process, while its repetitive structure provides high stability and a robust prion-like replication mechanism. Accordingly, amyloid is used by nature in multifaceted and ingenious ways of life, ranging from bacteria and fungi to mammals. These include (1) Structure: Templating for small chemical molecules (Pmel17), biofilm formation in bacteria (curli), assisting aerial hyphae formation in streptomycetes (chaplins) or monolayer formation at a surface (hydrophobins). (2) Reservoirs: A storage state for peptide/proteins to protect them from their surroundings or vice versa (storage of peptide hormones in mammalian secretory granules or major basic protein in eosinophils). (3) Information carriers: The fungal immune system (HET-s prion in Podospora anserina, yeast prions) or long-term memory (e.g., mnemons in yeast, cytoplasmic polyadenylation element-binding protein in aplysia). Aggregation is also used to (4) "suppress" the function of the soluble protein (e.g., Cdc19 in yeast stress granules), or (5) "signaling" through formation of oligomers (e.g., HET-s prion, necroptosis-related proteins RIP1/RIP3). This review summarizes current knowledge on functional amyloids with a focus on the amyloid systems curli in bacteria, HET-s prion in P. anserina, and peptide hormone storage in mammals together with an attempt to highlight differences between functional and disease-associated amyloids.
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Affiliation(s)
- Daniel Otzen
- iNANO, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Roland Riek
- Laboratory of Physical Chemistry, Swiss Federal Institute of Technology, CH-8093 Zürich, Switzerland
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28
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Najarzadeh Z, Mohammad-Beigi H, Nedergaard Pedersen J, Christiansen G, Sønderby TV, Shojaosadati SA, Morshedi D, Strømgaard K, Meisl G, Sutherland D, Skov Pedersen J, Otzen DE. Plant Polyphenols Inhibit Functional Amyloid and Biofilm Formation in Pseudomonas Strains by Directing Monomers to Off-Pathway Oligomers. Biomolecules 2019; 9:E659. [PMID: 31717821 PMCID: PMC6920965 DOI: 10.3390/biom9110659] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Revised: 10/19/2019] [Accepted: 10/23/2019] [Indexed: 02/07/2023] Open
Abstract
Self-assembly of proteins to β-sheet rich amyloid fibrils is commonly observed in various neurodegenerative diseases. However, amyloid also occurs in the extracellular matrix of bacterial biofilm, which protects bacteria from environmental stress and antibiotics. Many Pseudomonas strains produce functional amyloid where the main component is the highly fibrillation-prone protein FapC. FapC fibrillation may be inhibited by small molecules such as plant polyphenols, which are already known to inhibit formation of pathogenic amyloid, but the mechanism and biological impact of inhibition is unclear. Here, we elucidate how polyphenols modify the self-assembly of functional amyloid, with particular focus on epigallocatechin gallate (EGCG), penta-O-galloyl-β-d-glucose (PGG), baicalein, oleuropein, and procyanidin B2. We find EGCG and PGG to be the best inhibitors. These compounds inhibit amyloid formation by redirecting the aggregation of FapC monomers into oligomeric species, which according to small-angle X-ray scattering (SAXS) measurements organize into core-shell complexes of short axis diameters 25-26 nm consisting of ~7 monomers. Using peptide arrays, we identify EGCG-binding sites in FapC's linker regions, C and N-terminal parts, and high amyloidogenic sequences located in the R2 and R3 repeats. We correlate our biophysical observations to biological impact by demonstrating that the extent of amyloid inhibition by the different inhibitors correlated with their ability to reduce biofilm, highlighting the potential of anti-amyloid polyphenols as therapeutic agents against biofilm infections.
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Affiliation(s)
- Zahra Najarzadeh
- Biotechnology Group, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14115-143, Tehran, Iran;
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (H.M.-B.); (J.N.P.); (T.V.S.); (D.S.)
| | - Hossein Mohammad-Beigi
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (H.M.-B.); (J.N.P.); (T.V.S.); (D.S.)
| | - Jannik Nedergaard Pedersen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (H.M.-B.); (J.N.P.); (T.V.S.); (D.S.)
| | - Gunna Christiansen
- Department of Biomedicine-Medical Microbiology and Immunology, Aarhus University, 8000 Aarhus C, Denmark;
| | - Thorbjørn Vincent Sønderby
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (H.M.-B.); (J.N.P.); (T.V.S.); (D.S.)
| | - Seyed Abbas Shojaosadati
- Biotechnology Group, Faculty of Chemical Engineering, Tarbiat Modares University, P.O. Box 14115-143, Tehran, Iran;
| | - Dina Morshedi
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, P.O. Box: 1417863171, Tehran, Iran;
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen Ø, Denmark;
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, UK;
| | - Duncan Sutherland
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (H.M.-B.); (J.N.P.); (T.V.S.); (D.S.)
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (H.M.-B.); (J.N.P.); (T.V.S.); (D.S.)
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, 8000 Aarhus C, Denmark; (H.M.-B.); (J.N.P.); (T.V.S.); (D.S.)
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29
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Shanmugam N, Baker MODG, Ball SR, Steain M, Pham CLL, Sunde M. Microbial functional amyloids serve diverse purposes for structure, adhesion and defence. Biophys Rev 2019; 11:287-302. [PMID: 31049855 PMCID: PMC6557962 DOI: 10.1007/s12551-019-00526-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 04/15/2019] [Indexed: 12/22/2022] Open
Abstract
The functional amyloid state of proteins has in recent years garnered much attention for its role in serving crucial and diverse biological roles. Amyloid is a protein fold characterised by fibrillar morphology, binding of the amyloid-specific dyes Thioflavin T and Congo Red, insolubility and underlying cross-β structure. Amyloids were initially characterised as an aberrant protein fold associated with mammalian disease. However, in the last two decades, functional amyloids have been described in almost all biological systems, from viruses, to bacteria and archaea, to humans. Understanding the structure and role of these amyloids elucidates novel and potentially ancient mechanisms of protein function throughout nature. Many of these microbial functional amyloids are utilised by pathogens for invasion and maintenance of infection. As such, they offer novel avenues for therapies. This review examines the structure and mechanism of known microbial functional amyloids, with a particular focus on the pathogenicity conferred by the production of these structures and the strategies utilised by microbes to interfere with host amyloid structures. The biological importance of microbial amyloid assemblies is highlighted by their ubiquity and diverse functionality.
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Affiliation(s)
- Nirukshan Shanmugam
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Max O D G Baker
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Sarah R Ball
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Megan Steain
- Infectious Diseases and Immunology, Central Clinical School, Sydney Medical School, University of Sydney, Sydney, NSW, 2006, Australia
| | - Chi L L Pham
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia
| | - Margaret Sunde
- Discipline of Pharmacology, School of Medical Sciences, Faculty of Medicine and Health and Sydney Nano, University of Sydney, Sydney, NSW, 2006, Australia.
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30
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Kleino A, Silverman N. Regulation of the Drosophila Imd pathway by signaling amyloids. INSECT BIOCHEMISTRY AND MOLECULAR BIOLOGY 2019; 108:16-23. [PMID: 30857831 PMCID: PMC6474834 DOI: 10.1016/j.ibmb.2019.03.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Revised: 02/19/2019] [Accepted: 03/05/2019] [Indexed: 05/09/2023]
Abstract
Fruit flies elicit effective defense responses against numerous microbes. The responses against Gram-negative bacteria are mediated by the Imd pathway, an evolutionarily conserved NF-κB pathway recognizing meso-diaminopimelic acid (DAP)-type peptidoglycan from bacterial cell walls. Several reviews already provide a detailed view of ligand recognition and signal transduction during Imd signaling, but the formation and regulation of the signaling complex immediately downstream of the peptidoglycan-sensing receptors is still elusive. In this review, we focus on the formation of the Imd amyloidal signaling center and post-translational modifications in the assembly and disassembly of the Imd signaling complex.
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Affiliation(s)
- Anni Kleino
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, 8000, Aarhus C, Denmark
| | - Neal Silverman
- Division of Infectious Diseases and Immunology, Department of Medicine, University of Massachusetts Medical School, Worcester, MA, 01605, USA.
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31
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Christensen LF, Jensen KF, Nielsen J, Vad BS, Christiansen G, Otzen DE. Reducing the Amyloidogenicity of Functional Amyloid Protein FapC Increases Its Ability To Inhibit α-Synuclein Fibrillation. ACS OMEGA 2019; 4:4029-4039. [PMID: 31459612 PMCID: PMC6647998 DOI: 10.1021/acsomega.8b03590] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/11/2019] [Indexed: 05/15/2023]
Abstract
Functional amyloid (FA) proteins have evolved to assemble into fibrils with a characteristic cross-β structure, which stabilizes biofilms and contributes to bacterial virulence. Some of the most studied bacterial FAs are the curli protein CsgA, expressed in a wide range of bacteria, and FapC, produced mainly by members of the Pseudomonas genus. Though unrelated, both CsgA and FapC contain imperfect repeats believed to drive the formation of amyloid fibrils. While much is known about CsgA biogenesis and fibrillation, the mechanism of FapC fibrillation remains less explored. Here, we show that removing the three imperfect repeats of FapC (FapC ΔR1R2R3) slows down the fibrillation but does not prevent it. The increased lag phase seen for FapC ΔR1R2R3 allows for disulfide bond formation, which further delays fibrillation. Remarkably, these disulfide-bonded species of FapC ΔR1R2R3 also significantly delay the fibrillation of human α-synuclein, a key protein in Parkinson's disease pathology. This attenuation of α-synuclein fibrillation was not seen for the reduced form of FapC ΔR1R2R3. The results presented here shed light on the FapC fibrillation mechanism and emphasize how unrelated fibrillation systems may share such common fibril formation mechanisms, allowing inhibitors of one fibrillating protein to affect a completely different protein.
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Affiliation(s)
- Line Friis
Bakmann Christensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Kirstine Friis Jensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Brian Stougaard Vad
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Gunna Christiansen
- Section
for Medical Microbiology and Immunology, Department of Biomedicine, Aarhus University, Vennelyst Boulevard 4, 8000 Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
- E-mail:
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