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Peña-Díaz S, Olsen WP, Wang H, Otzen DE. Functional Amyloids: The Biomaterials of Tomorrow? ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312823. [PMID: 38308110 DOI: 10.1002/adma.202312823] [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: 11/28/2023] [Revised: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Functional amyloid (FAs), particularly the bacterial proteins CsgA and FapC, have many useful properties as biomaterials: high stability, efficient, and controllable formation of a single type of amyloid, easy availability as extracellular material in bacterial biofilm and flexible engineering to introduce new properties. CsgA in particular has already demonstrated its worth in hydrogels for stable gastrointestinal colonization and regenerative tissue engineering, cell-specific drug release, water-purification filters, and different biosensors. It also holds promise as catalytic amyloid; existing weak and unspecific activity can undoubtedly be improved by targeted engineering and benefit from the repetitive display of active sites on a surface. Unfortunately, FapC remains largely unexplored and no application is described so far. Since FapC shares many common features with CsgA, this opens the window to its development as a functional scaffold. The multiple imperfect repeats in CsgA and FapC form a platform to introduce novel properties, e.g., in connecting linkers of variable lengths. While exploitation of this potential is still at an early stage, particularly for FapC, a thorough understanding of their molecular properties will pave the way for multifunctional fibrils which can contribute toward solving many different societal challenges, ranging from CO2 fixation to hydrolysis of plastic nanoparticles.
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Affiliation(s)
- Samuel Peña-Díaz
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
| | - William Pallisgaard Olsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
| | - Huabing Wang
- Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, Clinical Laboratory Center, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Shuangyong Road 6, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus C, 8000, Denmark
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2
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Kumari S, Das S. Functional amyloid fibrils of biofilm-forming marine bacterium Pseudomonas aeruginosa PFL-P1 interact spontaneously with pyrene and augment the biodegradation. Int J Biol Macromol 2024; 266:131266. [PMID: 38556224 DOI: 10.1016/j.ijbiomac.2024.131266] [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: 02/05/2024] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Bacteria thrive in biofilms embedding in the three-dimensional extracellular polymeric substances (EPS). Functional Amyloid in Pseudomonas (Fap), a protein in EPS, efficiently sequesters polycyclic aromatic hydrocarbons (PAHs). Present study reports the characterization of Fap fibrils from Pseudomonas aeruginosa PFL-P1 and describes the interaction with pyrene to assess the impact on pyrene degradation. Overexpression of fap in E. coli BL21(DE3) cells significantly enhances biofilm formation (p < 0.0001) and amyloid production (p = 0.0002), particularly with pyrene. Defibrillated Fap analysis reveals FapC monomers and increased fibrillation with pyrene. Circular Dichroism (CD), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) unveil characteristic amyloid peaks and structural changes in Fap fibrils upon pyrene exposure. 3D-EEM analysis identifies a protein-like fluorophore in Fap fibrils, exhibiting pyrene-induced fluorescence quenching. Binding constants range from 5.23 to 7.78 M-1, with ΔG of -5.10 kJ mol-1 at 298 K, indicating spontaneous and exothermic interaction driven by hydrophobic forces. Exogenous Fap fibrils substantially increased the biofilm growth and pyrene degradation by P. aeruginosa PFL-P1 from 46 % to 64 % within 7 days (p = 0.0236). GC-MS identifies diverse metabolites, implying phthalic acid pathway in pyrene degradation. This study deepens insights into structural dynamics of Fap fibrils when exposed to pyrene, offering potential application in environmental bioremediation.
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Affiliation(s)
- Swetambari Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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3
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Byeon CH, Hansen KH, Jeffrey J, Saricayir H, Andreasen M, Akbey Ü. Intrinsically disordered Pseudomonas chaperone FapA slows down the fibrillation of major biofilm-forming functional amyloid FapC. FEBS J 2024; 291:1925-1943. [PMID: 38349812 DOI: 10.1111/febs.17084] [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: 10/23/2023] [Revised: 12/29/2023] [Accepted: 01/29/2024] [Indexed: 02/15/2024]
Abstract
Functional bacterial amyloids play a crucial role in the formation of biofilms, which mediate chronic infections and contribute to antimicrobial resistance. This study focuses on the FapC amyloid fibrillar protein from Pseudomonas, a major contributor to biofilm formation. We investigate the initial steps of FapC amyloid formation and the impact of the chaperone-like protein FapA on this process. Using solution nuclear magnetic resonance (NMR), we recently showed that both FapC and FapA are intrinsically disordered proteins (IDPs). Here, the secondary structure propensities (SSPs) are compared to alphafold (DeepMind, protein structure prediction tool/algorithm: https://alphafold.ebi.ac.uk/) models. We further demonstrate that the FapA chaperone interacts with FapC and significantly slows down the formation of FapC fibrils. Our NMR titrations reveal ~ 18% of the resonances show FapA-induced chemical shift perturbations (CSPs), which has not been previously observed, the largest being for A82, N201, C237, C240, A241, and G245. These sites may suggest a specific interaction site and/or hotspots of fibrillation inhibition/control interface at the repeat-1 (R1)/loop-2 (L2) and L2/R3 transition areas and at the C-terminus of FapC. Remarkably, ~ 90% of FapA NMR signals exhibit substantial CSPs upon titration with FapC, the largest being for S63, A69, A80, and I92. A temperature-dependent effect of FapA was observed on FapC by thioflavin T (ThT) and NMR experiments. This study provides a detailed understanding of the interaction between the FapA and FapC, shedding light on the regulation and slowing down of amyloid formation, and has important implications for the development of therapeutic strategies targeting biofilms and associated infections.
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Affiliation(s)
- Chang-Hyeock Byeon
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Kasper Holst Hansen
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Jasper Jeffrey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Hakan Saricayir
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
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Arad E, Pedersen KB, Malka O, Mambram Kunnath S, Golan N, Aibinder P, Schiøtt B, Rapaport H, Landau M, Jelinek R. Staphylococcus aureus functional amyloids catalyze degradation of β-lactam antibiotics. Nat Commun 2023; 14:8198. [PMID: 38081813 PMCID: PMC10713593 DOI: 10.1038/s41467-023-43624-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Accepted: 11/15/2023] [Indexed: 12/18/2023] Open
Abstract
Antibiotic resistance of bacteria is considered one of the most alarming developments in modern medicine. While varied pathways for bacteria acquiring antibiotic resistance have been identified, there still are open questions concerning the mechanisms underlying resistance. Here, we show that alpha phenol-soluble modulins (PSMαs), functional bacterial amyloids secreted by Staphylococcus aureus, catalyze hydrolysis of β-lactams, a prominent class of antibiotic compounds. Specifically, we show that PSMα2 and, particularly, PSMα3 catalyze hydrolysis of the amide-like bond of the four membered β-lactam ring of nitrocefin, an antibiotic β-lactam surrogate. Examination of the catalytic activities of several PSMα3 variants allowed mapping of the active sites on the amyloid fibrils' surface, specifically underscoring the key roles of the cross-α fibril organization, and the combined electrostatic and nucleophilic functions of the lysine arrays. Molecular dynamics simulations further illuminate the structural features of β-lactam association upon the fibril surface. Complementary experimental data underscore the generality of the functional amyloid-mediated catalytic phenomenon, demonstrating hydrolysis of clinically employed β-lactams by PSMα3 fibrils, and illustrating antibiotic degradation in actual S. aureus biofilms and live bacteria environments. Overall, this study unveils functional amyloids as catalytic agents inducing degradation of β-lactam antibiotics, underlying possible antibiotic resistance mechanisms associated with bacterial biofilms.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Kasper B Pedersen
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
| | - Orit Malka
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Sisira Mambram Kunnath
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
| | - Polina Aibinder
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Birgit Schiøtt
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000, Aarhus C, Denmark
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, 8000, Aarhus C, Denmark
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel
- Centre for Structural Systems Biology (CSSB), and European Molecular Biology Laboratory (EMBL), Hamburg, 22607, Germany
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
- Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel.
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Walker AC, Bhargava R, Bucher M, Brust AS, Czy DM. Identification of proteotoxic and proteoprotective bacteria that non-specifically affect proteins associated with neurodegenerative diseases. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.24.563685. [PMID: 37961318 PMCID: PMC10634778 DOI: 10.1101/2023.10.24.563685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2023]
Abstract
Neurodegenerative protein conformational diseases (PCDs), such as Alzheimer's, Parkinson's, and Huntington's, are a leading cause of death and disability worldwide and have no known cures or effective treatments. Emerging evidence suggests a role for the gut microbiota in the pathogenesis of neurodegenerative PCDs; however, the influence of specific bacteria on the culprit proteins associated with each of these diseases remains elusive, primarily due to the complexity of the microbiota. In the present study, we employed a single-strain screening approach to identify human bacterial isolates that enhance or suppress the aggregation of culprit proteins and the associated toxicity in Caenorhabditis elegans expressing Aβ1-42, α-synuclein, and polyglutamine tracts. Here, we reveal the first comprehensive analysis of the human microbiome for its effect on proteins associated with neurodegenerative diseases. Our results suggest that bacteria affect the aggregation of metastable proteins by modulating host proteostasis rather than selectively targeting specific disease-associated proteins. These results reveal bacteria that potentially influence the pathogenesis of PCDs and open new promising prevention and treatment opportunities by altering the abundance of beneficial and detrimental microbes.
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Affiliation(s)
- Alyssa C Walker
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Rohan Bhargava
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Michael Bucher
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Amanda S Brust
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
| | - Daniel M Czy
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA
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Beg AZ, Rashid F, Talat A, Haseen MA, Raza N, Akhtar K, Dueholm MKD, Khan AU. Functional Amyloids in Pseudomonas aeruginosa Are Essential for the Proteome Modulation That Leads to Pathoadaptation in Pulmonary Niches. Microbiol Spectr 2023; 11:e0307122. [PMID: 36475836 PMCID: PMC9927170 DOI: 10.1128/spectrum.03071-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Persistence and survival of Pseudomonas aeruginosa in chronic lung infections is closely linked to the biofilm lifestyle. One biofilm component, functional amyloid of P. aeruginosa (Fap), imparts structural adaptations for biofilms; however, the role of Fap in pathogenesis is still unclear. Conservation of the fap operon encoding Fap and P. aeruginosa being an opportunistic pathogen of lung infections prompted us to explore its role in lung infection. We found that Fap is essential for establishment of lung infection in rats, as its genetic exclusion led to mild focal infection with quick resolution. Moreover, without an underlying cystic fibrosis (CF) genetic disorder, overexpression of Fap reproduced the CF pathotype. The molecular basis of Fap-mediated pulmonary adaptation was explored through surface-associated proteomics in vitro. Differential proteomics positively associated Fap expression with activation of known proteins related to pulmonary pathoadaptation, attachment, and biofilm fitness. The aggregative bacterial phenotype in the pulmonary niche correlated with Fap-influenced activation of biofilm sustainability regulators and stress response regulators that favored persistence-mediated establishment of pulmonary infection. Fap overexpression upregulated proteins that are abundant in the proteome of P. aeruginosa in colonizing CF lungs. Planktonic lifestyle, defects in anaerobic pathway, and neutrophilic evasion were key factors in the absence of Fap that impaired establishment of infection. We concluded that Fap is essential for cellular equilibration to establish pulmonary infection. Amyloid-induced bacterial aggregation subverted the immune response, leading to chronic infection by collaterally damaging tissue and reinforcing bacterial persistence. IMPORTANCE Pseudomonas aeruginosa is inextricably linked with chronic lung infections. In this study, the well-conserved Fap operon was found to be essential for pathoadaptation in pulmonary infection in a rat lung model. Moreover, the presence of Fap increased pathogenesis and biofilm sustainability by modulating bacterial physiology. Hence, a pathoadaptive role of Fap in pulmonary infections can be exploited for clinical application by targeting amyloids. Furthermore, genetic conservation and extracellular exposure of Fap make it a commendable target for such interventions.
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Affiliation(s)
- Ayesha Z. Beg
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | | | - Absar Talat
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohd Azam Haseen
- Department of Cardiothoracic Surgery, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Nadeem Raza
- Department of Anaesthesiology, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Kafil Akhtar
- Pathology Department, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Asad U. Khan
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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Rasmussen HØ, Kumar A, Shin B, Stylianou F, Sewell L, Xu Y, Otzen DE, Pedersen JS, Matthews SJ. FapA is an Intrinsically Disordered Chaperone for Pseudomonas Functional Amyloid FapC. J Mol Biol 2023; 435:167878. [PMID: 36368411 DOI: 10.1016/j.jmb.2022.167878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Bacterial functional amyloids contribute to biofilm development by bacteria and provide protection from the immune system and prevent antibiotic treatment. Strategies to target amyloid formation and interrupt biofilm formation have attracted recent interest due to their antimicrobial potential. Functional amyloid in Pseudomonas (Fap) includes FapC as the major component of the fibril while FapB is a minor component suggested to function as a nucleator of FapC. The system also includes the small periplasmic protein FapA, which has been shown to regulate fibril composition and morphology. The interplay between these three components is central in Fap fibril biogenesis. Here we present a comprehensive biophysical and spectroscopy analysis of FapA, FapB and FapC and provide insight into their molecular interactions. We show that all three proteins are primarily disordered with some regions with structural propensities for α-helix and β-sheet. FapA inhibits FapC fibrillation by targeting the nucleation step, whereas for FapB the elongation step is modulated. Furthermore, FapA alters the morphology of FapC (more than FapB) fibrils. Complex formation is observed between FapA and FapC, but not between FapA and FapB, and likely involves the N-terminus of FapA. We conclude that FapA is an intrinsically disordered chaperone for FapC that guards against fibrillation within the periplasm. This new understanding of a natural protective mechanism of Pseudomonas against amyloid formations can serve as inspiration for strategies blocking biofilm formation in infections.
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Affiliation(s)
- Helena Ø Rasmussen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Amit Kumar
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Ben Shin
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Lee Sewell
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Steve J Matthews
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom.
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Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies. Molecules 2022; 27:molecules27134080. [PMID: 35807329 PMCID: PMC9268375 DOI: 10.3390/molecules27134080] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [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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Wang L, Wang H, Xu XG. Principle and applications of peak force infrared microscopy. Chem Soc Rev 2022; 51:5268-5286. [PMID: 35703031 DOI: 10.1039/d2cs00096b] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Peak force infrared (PFIR) microscopy is an emerging atomic force microscopy (AFM)-based infrared microscopy that bypasses Abbe's diffraction limit on spatial resolution. The PFIR microscopy utilizes a nanoscopically sharp AFM tip to mechanically detect the tip-enhanced infrared photothermal response of the sample in the time domain. The time-gated mechanical signals of cantilever deflections transduce the infrared absorption of the sample, delivering infrared imaging and spectroscopy capability at sub 10 nm spatial resolution. Both the infrared absorption response and mechanical properties of the sample are obtained in parallel while preserving the surface integrity of the sample. This review describes the constructions of the PFIR microscope and several variations, including multiple-pulse excitation, total internal reflection geometry, dual-color configuration, liquid-phase operations, and integrations with simultaneous surface potential measurement. Representative applications of PFIR microscopy are also included in this review. In the outlook section, we lay out several future directions of innovations in PFIR microscopy and applications in chemical and material research.
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Affiliation(s)
- Le Wang
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA.
| | - Haomin Wang
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA.
| | - Xiaoji G Xu
- Department of Chemistry, Lehigh University, Bethlehem, PA, 18015, USA.
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10
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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: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [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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11
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Hassan MN, Nabi F, Khan AN, Hussain M, Siddiqui WA, Uversky VN, Khan RH. The amyloid state of proteins: A boon or bane? Int J Biol Macromol 2022; 200:593-617. [PMID: 35074333 DOI: 10.1016/j.ijbiomac.2022.01.115] [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: 12/13/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend.
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Affiliation(s)
- Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Murtaza Hussain
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem A Siddiqui
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 10 Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy 11 of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College 13 of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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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: 4] [Impact Index Per Article: 2.0] [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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13
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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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14
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A multimethod approach for analyzing FapC fibrillation and determining mass per length. Biophys J 2021; 120:2262-2275. [PMID: 33812849 DOI: 10.1016/j.bpj.2021.03.031] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 02/12/2021] [Accepted: 03/25/2021] [Indexed: 02/05/2023] Open
Abstract
Amyloid proteins are found in a wide range of organisms owing to the high stability of the β-sheet core of the amyloid fibrils. There are both pathological amyloids involved in various diseases and functional amyloids that play a beneficial role for the organism. The aggregation process is complex and often involves many different species. Full understanding of this process requires parallel acquisition of data by complementary techniques monitoring the time course of aggregation. This is not an easy task, given the often-stochastic nature of aggregation, which can lead to significant variations in lag time. Here, we investigate the aggregation process of the functional amyloid FapC by simultaneous use of four different techniques, namely dynamic light scattering, small-angle x-ray scattering (SAXS), circular dichroism, and Thioflavin T fluorescence. All these approaches are applied to the same FapC sample just after desalting. Our data allow us to construct a master time-course graph showing the same time-course of aggregation by all techniques. This allows us to integrate insights from approaches that report on different structural and length scales. During the lag phase, loosely aggregated oligomers with random-coil structure are formed, which subsequently transform to fibrils without accumulation of additional significant species. Subsequently, the loosely associated protofilaments/subfilaments, which form side by side, mature to more compact fibrils. Furthermore, we determine the mass per length of the mature fibrils, obtaining very similar results by SAXS (33 kDa/nm) and tilted-beam transmission electron microscopy (31 kDa/nm). Transmission electron microscopy showed that the fibrils consist of primarily two protofilaments and similar dimensions of the cross section of the fibrils as revealed by SAXS modeling when the number of protofilaments per fibril was taken into account. Mass per length information underscores the general usefulness of SAXS in fibrillation analysis and provides an important constraint for further modeling the fibril structures.
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15
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Heredia-Ponce Z, Gutiérrez-Barranquero JA, Purtschert-Montenegro G, Eberl L, de Vicente A, Cazorla FM. Role of extracellular matrix components in the formation of biofilms and their contribution to the biocontrol activity of Pseudomonas chlororaphis PCL1606. Environ Microbiol 2020; 23:2086-2101. [PMID: 33314481 DOI: 10.1111/1462-2920.15355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022]
Abstract
Pseudomonas chlororaphis PCL1606 (PcPCL1606) displays plant-colonizing features and exhibits antagonistic traits against soil-borne phytopathogenic fungi. Biofilm formation could be relevant for the PcPCL1606 lifestyle, and in this study the role of some putative extracellular matrix components (EMC; Fap-like fibre, alginate and Psl-like polysaccharides) in the biofilm architecture and biocontrol activity of this bacterium were determined. EMC such as the Fap-like fibre and alginate polysaccharide play secondary roles in biofilm formation in PcPCL1606, because they are not fundamental to its biofilm architecture in flow cell chamber, but synergistically they have shown to favour bacterial competition during biofilm formation. Conversely, studies on Psl-like polysaccharide have revealed that it may contain mannose, and that it is strongly involved in the PcPCL1606 biofilm architecture and niche competition. Furthermore, the Fap-like fibre and Psl-like exopolysaccharide play roles in early surface attachment and contribute to biocontrol activity against the white root rot disease caused by Rosellinia necatrix in avocado plants. These results constitute the first report regarding the study of the extracellular matrix of the PcPCL1606 strain and highlight the importance of a putative Fap-like fibre and Psl-like exopolysaccharide produced by PcPCL1606 in the biofilm formation process and interactions with the host plant root.
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Affiliation(s)
- Zaira Heredia-Ponce
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - José Antonio Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | | | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
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16
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Kosolapova AO, Antonets KS, Belousov MV, Nizhnikov AA. Biological Functions of Prokaryotic Amyloids in Interspecies Interactions: Facts and Assumptions. Int J Mol Sci 2020; 21:E7240. [PMID: 33008049 PMCID: PMC7582709 DOI: 10.3390/ijms21197240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Amyloids are fibrillar protein aggregates with an ordered spatial structure called "cross-β". While some amyloids are associated with development of approximately 50 incurable diseases of humans and animals, the others perform various crucial physiological functions. The greatest diversity of amyloids functions is identified within prokaryotic species where they, being the components of the biofilm matrix, function as adhesins, regulate the activity of toxins and virulence factors, and compose extracellular protein layers. Amyloid state is widely used by different pathogenic bacterial species in their interactions with eukaryotic organisms. These amyloids, being functional for bacteria that produce them, are associated with various bacterial infections in humans and animals. Thus, the repertoire of the disease-associated amyloids includes not only dozens of pathological amyloids of mammalian origin but also numerous microbial amyloids. Although the ability of symbiotic microorganisms to produce amyloids has recently been demonstrated, functional roles of prokaryotic amyloids in host-symbiont interactions as well as in the interspecies interactions within the prokaryotic communities remain poorly studied. Here, we summarize the current findings in the field of prokaryotic amyloids, classify different interspecies interactions where these amyloids are involved, and hypothesize about their real occurrence in nature as well as their roles in pathogenesis and symbiosis.
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Affiliation(s)
- Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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17
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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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18
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Moshynets O, Chernii S, Chernii V, Losytskyy M, Karakhim S, Czerwieniec R, Pekhnyo V, Yarmoluk S, Kovalska V. Fluorescent β-ketoenole AmyGreen dye for visualization of amyloid components of bacterial biofilms. Methods Appl Fluoresc 2020; 8:035006. [PMID: 32375137 DOI: 10.1088/2050-6120/ab90e0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Green-emitting water-soluble amino-ketoenole dye AmyGreen is proposed as an efficient fluorescent stain for visualization of bacterial amyloids in biofilms and the detection of pathological amyloids in vitro. This dye is almost non-fluorescent in solution, displays strong green emission in the presence of amyloid fibril of proteins. AmyGreen is also weakly fluorescent in presence to biomolecules that are components of cells, extracellular matrix or medium: nucleic acids, polysaccharides, lipids, and proteins. Thus, the luminescence turn-on behavior of AmyGreen can be utilized for visualization of amyloid components of bacterial biofilm extracellular matrix. Herein we report the application of AmyGreen for fluorescent staining of a number of amyloid-contained bacteria biofilms produced by Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Bordetella avium, and Staphylococcus aureus. The effectiveness of AmyGreen was compared to traditional amyloid sensitive dye Thioflavine T. The main advantage of AmyGreen (concentration 10-5 M) is a higher sensitivity in the visualization of amyloid biofilm components over Thioflavine T (10-4 M) as it was revealed when staining E. coli and K. pneumoniae bacterial biofilms. Besides, AmyGreen displays lower cross-selectivity to nucleic acids as demonstrated both in in-solution experiments and upon staining of eukaryotic human mesenchymal stem cells used as amyloid-free negative control over amyloid-rich bacterial biofilms. The results point to a lower risk of false-positive response upon determination of amyloid components of bacterial biofilm using AmyGreen. Co-staining of biofilm by AmyGreen and cellulose sensitive dye Calcofluor White show difference in their staining patterns and localization, indicating separation of polysaccharide-rich and amyloid-rich regions of investigated biofilms. Thus, we suggest the new AmyGreen stain for visualization and differentiation of amyloid fibrils in bacterial biofilms to be used solely and in combination with other stains for confocal and fluorescence microscopy analysis.
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Affiliation(s)
- Olena Moshynets
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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19
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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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20
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Jerdan R, Kuśmierska A, Petric M, Spiers AJ. Penetrating the air-liquid interface is the key to colonization and wrinkly spreader fitness. MICROBIOLOGY-SGM 2020; 165:1061-1074. [PMID: 31436522 DOI: 10.1099/mic.0.000844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
In radiating populations of Pseudomonas fluorescens SBW25, adaptive wrinkly spreader (WS) mutants are able to gain access to the air-liquid (A-L) interface of static liquid microcosms and achieve a significant competitive fitness advantage over other non-biofilm-forming competitors. Aerotaxis and flagella-based swimming allows SBW25 cells to move into the high-O2 region located at the top of the liquid column and maintain their position by countering the effects of random cell diffusion, convection and disturbance (i.e. physical displacement). However, wild-type cells showed significantly lower levels of enrichment in this region compared to the archetypal WS, indicating that WS cells employ an additional mechanism to transfer to the A-L interface where displacement is no longer an issue and a biofilm can develop at the top of the liquid column. Preliminary experiments suggest that this might be achieved through the expression of an as yet unidentified surface active agent that is weakly associated with WS cells and alters liquid surface tension, as determined by quantitative tensiometry. The effect of physical displacement on the colonization of the high-O2 region and A-L interface was reduced through the addition of agar or polyethylene glycol to increase liquid viscosity, and under these conditions the competitive fitness of the WS was significantly reduced. These observations suggest that the ability to transfer to the A-L interface from the high-O2 region and remain there without further expenditure of energy (through, for example, the deployment of flagella) is a key evolutionary innovation of the WS, as it allows subsequent biofilm development and significant population increase, thereby affording these adaptive mutants a competitive fitness advantage over non-biofilm-forming competitors located within the liquid column.
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Affiliation(s)
- Robyn Jerdan
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kuśmierska
- Department of Industrial Microbiology and Biotechnology, Faculty of Biology and Environmental Protection, University of Łódź, Łódź, Poland.,School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Marija Petric
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
| | - Andrew J Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
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21
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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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22
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Sureda A, Daglia M, Argüelles Castilla S, Sanadgol N, Fazel Nabavi S, Khan H, Belwal T, Jeandet P, Marchese A, Pistollato F, Forbes-Hernandez T, Battino M, Berindan-Neagoe I, D'Onofrio G, Nabavi SM. Oral microbiota and Alzheimer's disease: Do all roads lead to Rome? Pharmacol Res 2019; 151:104582. [PMID: 31794871 DOI: 10.1016/j.phrs.2019.104582] [Citation(s) in RCA: 70] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Revised: 11/28/2019] [Accepted: 11/29/2019] [Indexed: 12/19/2022]
Abstract
Alzheimer's disease (AD) is a progressive neurodegenerative pathology affecting milions of people worldwide associated with deposition of senile plaques. While the genetic and environmental risk factors associated with the onset and consolidation of late onset AD are heterogeneous and sporadic, growing evidence also suggests a potential link between some infectious diseases caused by oral microbiota and AD. Oral microbiota dysbiosis is purported to contribute either directly to amyloid protein production, or indirectly to neuroinflammation, occurring as a consequence of bacterial invasion. Over the last decade, the development of Human Oral Microbiome database (HOMD) has deepened our understanding of oral microbes and their different roles during the human lifetime. Oral pathogens mostly cause caries, periodontal disease, and edentulism in aged population, and, in particular, alterations of the oral microbiota causing chronic periodontal disease have been associated with the risk of AD. Here we describe how different alterations of the oral microbiota may be linked to AD, highlighting the importance of a good oral hygiene for the prevention of oral microbiota dysbiosis.
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Affiliation(s)
- Antoni Sureda
- Research Group on Community Nutrition and Oxidative Stress, University of Balearic Islands, CIBEROBN (Physiopathology of Obesity and Nutrition), and IdisBa, Palma de Mallorca, Balearic Islands, Spain.
| | - Maria Daglia
- Department of Pharmacy, University of Naples Federico II, Naples, Italy; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang, China
| | | | - Nima Sanadgol
- Department of Biology, Faculty of Sciences, University of Zabol, Zabol, Iran; Department of Physics and Chemistry, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto-SP, Brazil
| | - Seyed Fazel Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Haroon Khan
- Department of Pharmacy, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Tarun Belwal
- Zhejiang University, College of Biosystems Engineering and Food Science, Zhejiang Key Laboratory for Agri-Food Processing, Key Laboratory of Agro-Products Postharvest Handling of Ministry of Agriculture and Rural Affairs, Hangzhou, People's Republic of China
| | - Philippe Jeandet
- Induced Resistance and Plant Bioprotection, Faculty of Sciences, University of Reims Champagne-Ardenne, Reims Cedex 51687, France
| | | | - Francesca Pistollato
- Centre for Health & Nutrition, Universidad Europea del Atlantico, Santander, Spain
| | - Tamara Forbes-Hernandez
- Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo - Vigo Campus, Vigo, Spain
| | - Maurizio Battino
- Nutrition and Food Science Group, Department of Analytical and Food Chemistry, CITACA, CACTI, University of Vigo - Vigo Campus, Vigo, Spain; Dept of Clinical Sciences, Università Politecnica delle Marche, Ancona, Italy; International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
| | - Ioana Berindan-Neagoe
- MEDFUTURE - Research Center for Advanced Medicine, "Iuliu-Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, Cluj-Napoca, Romania; Research Center for Functional Genomics, Biomedicine and Translational Medicine, "Iuliu Hatieganu" University of Medicine and Pharmacy, 23 Marinescu Street, 400337 Cluj-Napoca, Romania; Department of Functional Genomics and Experimental Pathology, The Oncology Institute "Prof. Dr. Ion Chiricuta", 34-36 Republicii Street, Cluj-Napoca, Romania
| | - Grazia D'Onofrio
- Unit of Geriatrics, Department of Medical Sciences, Fondazione Casa Sollievo della sofferenza, San Giovanni Rotondo, Italy
| | - Seyed Mohammad Nabavi
- Applied Biotechnology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran.
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23
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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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24
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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: 47] [Impact Index Per Article: 9.4] [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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25
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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: 22] [Impact Index Per Article: 4.4] [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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26
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Dean DN, Lee JC. pH-Dependent fibril maturation of a Pmel17 repeat domain isoform revealed by tryptophan fluorescence. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:961-969. [PMID: 30716507 DOI: 10.1016/j.bbapap.2019.01.012] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2018] [Revised: 01/24/2019] [Accepted: 01/28/2019] [Indexed: 11/19/2022]
Abstract
The pre-melanosomal protein (Pmel17) aggregates within melanosomes to form functional amyloid fibrils that facilitate melanin polymerization. The repeat domain (RPT) of Pmel17 fibrillates under strict acidic melanosomal pH. Alternative splicing results in a shortened repeat domain (sRPT), which also forms amyloid fibrils. Here, we explored the effects of pH and protein concentration on sRPT aggregation by monitoring the intrinsic fluorescence of the sole tryptophan at position 381 (381W). 381W emission properties revealed changes of local environment polarity for sRPT fibrils formed at different pH. At pH 4, fibrils formed rapidly with no lag phase. A high 381W intensity was observed with a slight blue shift (10 nm). These fibrils underwent further structural rearrangements at intermediate pH (5-6), mirroring that of melanosome maturation, which initiates at pH 4 and increases to near neutral pH. In contrast, typical sigmoidal kinetics were observed at pH 6 with slower rates and 381W exhibited quenched emission. Interestingly, biphasic kinetics were observed at pH 5 in a protein concentration-dependent manner. A large 381W blue shift (23 nm) was measured, indicating a more hydrophobic environment for fibrils made at pH 5. Consistent with 381W fluorescence, Raman spectroscopy revealed molecular level perturbations in sRPT fibrils that were not evident from circular dichroism, transmission electron microscopy, or limited proteolysis analysis. Finally, sRPT fibrils did not form at pH ≥7 and preformed fibrils rapidly disaggregated under these solution conditions. Collectively, this work yields mechanistic insights into pH-dependent sRPT aggregation in the context of melanosome maturation.
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Affiliation(s)
- Dexter N Dean
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States
| | - Jennifer C Lee
- Laboratory of Protein Conformation and Dynamics, Biochemistry and Biophysics Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, United States.
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27
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Rasmussen CB, Christiansen G, Vad BS, Lynggaard C, Enghild JJ, Andreasen M, Otzen D. Imperfect repeats in the functional amyloid protein FapC reduce the tendency to fragment during fibrillation. Protein Sci 2019; 28:633-642. [PMID: 30592554 DOI: 10.1002/pro.3566] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/25/2018] [Accepted: 12/26/2018] [Indexed: 12/14/2022]
Abstract
Functional amyloid (FA) is widespread in bacteria and serves multiple purposes such as strengthening of biofilm and contact with eukaryotic hosts. Unlike pathological amyloid, FA has been subjected to evolutionary optimization which is likely to be reflected in the aggregation mechanism. FA from different bacteria, including Escherichia coli (CsgA) and Pseudomonas (FapC), contains a number of imperfect repeats which may be key to efficient aggregation. Here we report on the aggregative behavior of FapC constructs which represent all single, double, and triple deletions of the protein's three imperfect repeats. Analysis of the fibrillation kinetics by the program Amylofit reveals that the removal of these repeats increases the tendency of the growing fibrils to fragment and also generally increases aggregation half-times. Remarkably, even the mutant lacking all three repeats was able to fibrillate, although fibrillation was much more irregular and led to significantly altered and destabilized fibrils. We conclude that imperfect repeats can promote fibrillation efficiency thanks to their modular design, though the context of the imperfect repeats also plays a significant role.
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Affiliation(s)
- Casper B Rasmussen
- Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | | | - Brian S Vad
- Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus, Denmark
| | - Carina Lynggaard
- Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus, Denmark
| | - Jan J Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Daniel Otzen
- Interdisciplinary Nanoscience Centre, Aarhus University, Aarhus, Denmark.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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28
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Abstract
A wide range of bacterial pathogens have been shown to form biofilms, which significantly increase their resistance to environmental stresses, such as antibiotics, and are thus of central importance in the context of bacterial diseases. One of the major structural components of these bacterial biofilms are amyloid fibrils, yet the mechanism of fibril assembly and its importance for biofilm formation are currently not fully understood. By studying fibril formation in vitro, in a model system of two common but unrelated biofilm-forming proteins, FapC from Pseudomonas fluorescens and CsgA from Escherichia coli, we found that the two proteins have a common aggregation mechanism. In both systems, fibril formation proceeds via nucleated growth of linear fibrils exhibiting similar measured rates of elongation, with negligible fibril self-replication. These similarities between two unrelated systems suggest that convergent evolution plays a key role in tuning the assembly kinetics of functional amyloid fibrils and indicates that only a narrow window of mechanisms and assembly rates allows for successful biofilm formation. Thus, the amyloid assembly reaction is likely to represent a means for controlling biofilm formation, both by the organism and by possible inhibitory drugs.IMPORTANCE Biofilms are generated by bacteria, embedded in the formed extracellular matrix. The biofilm's function is to improve the survival of a bacterial colony through, for example, increased resistance to antibiotics or other environmental stresses. Proteins secreted by the bacteria act as a major structural component of this extracellular matrix, as they self-assemble into highly stable amyloid fibrils, making the biofilm very difficult to degrade by physical and chemical means once formed. By studying the self-assembly mechanism of the fibrils from their monomeric precursors in two unrelated bacteria, our experimental and theoretical approaches shed light on the mechanism of functional amyloid assembly in the context of biofilm formation. Our results suggest that fibril formation may be a rate-limiting step in biofilm formation, which in turn has implications on the protein self-assembly reaction as a target for potential antibiotic drugs.
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29
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Bacterial Amyloids: Biogenesis and Biomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:113-159. [DOI: 10.1007/978-981-13-9791-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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30
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Mohammad-Beigi H, Kjaer L, Eskandari H, Aliakbari F, Christiansen G, Ruvo G, Ward JL, Otzen DE. A Possible Connection Between Plant Longevity and the Absence of Protein Fibrillation: Basis for Identifying Aggregation Inhibitors in Plants. FRONTIERS IN PLANT SCIENCE 2019; 10:148. [PMID: 30815009 PMCID: PMC6381023 DOI: 10.3389/fpls.2019.00148] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/28/2019] [Indexed: 05/08/2023]
Abstract
The ability of proteins to aggregate to form well-organized β-sheet rich amyloid fibrils is increasingly viewed as a general if regrettable property of the polypeptide chain. Aggregation leads to diseases such as amyloidosis and neurodegeneration in humans and various mammalian species but is also found in a functional variety in both animals and microbes. However, there are to our knowledge no reports of amyloid formation in plants. Plants are also the source of a large number of aggregation-inhibiting compounds. We reasoned that the two phenomena could be connected and that one of (many) preconditions for plant longevity is the ability to suppress unwanted protein aggregation. In support of this, we show that while protein extracts from the sugar maple tree Acer saccharum fibrillate readily on their own, this process is efficiently abolished by addition of small molecule extracts from the same plant. Further analysis of 44 plants showed a correlation between plant longevity and ability to inhibit protein aggregation. Extracts from the best performing plant, the sugar maple, were subjected to chromatographic fractionation, leading to the identification of a large number of compounds, many of which were shown to inhibit aggregation in vitro. One cautious interpretation is that it may have been advantageous for plants to maintain an efficient collection of aggregation-inhibiting metabolites as long as they do not impair metabolite function. From a practical perspective, our results indicate that long-lived plants may be particularly appropriate sources of new anti-aggregation compounds with therapeutic potential.
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Affiliation(s)
| | - Lars Kjaer
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Hoda Eskandari
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
| | - Farhang Aliakbari
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology, Tehran, Iran
| | - Gunna Christiansen
- Department of Biomedicine-Medical Microbiology and Immunology, Aarhus University, Aarhus, Denmark
| | - Gianluca Ruvo
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, United Kingdom
| | - Jane L. Ward
- Computational and Analytical Sciences Department, Rothamsted Research, Harpenden, United Kingdom
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Aarhus, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
- *Correspondence: Daniel Erik Otzen,
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31
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Christensen LFB, Hansen LM, Finster K, Christiansen G, Nielsen PH, Otzen DE, Dueholm MS. The Sheaths of Methanospirillum Are Made of a New Type of Amyloid Protein. Front Microbiol 2018; 9:2729. [PMID: 30483237 PMCID: PMC6242892 DOI: 10.3389/fmicb.2018.02729] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/25/2018] [Indexed: 12/12/2022] Open
Abstract
The genera Methanospirillum and Methanosaeta contain species of anaerobic archaea that grow and divide within proteinaceous tubular sheaths that protect them from environmental stressors. The sheaths of Methanosaeta thermophila PT are composed of the 60.9 kDa major sheath protein MspA. In this study we show that sheaths purified from Methanospirillum hungatei JF-1 are regularly striated tubular structures with amyloid-like properties similar to those of M. thermophila PT. Depolymerizing the sheaths from M. hungatei JF-1 allowed us to identify a 40.6 kDa protein (WP_011449234.1) that shares 23% sequence similarity to MspA from M. thermophila PT (ABK14853.1), indicating that they might be distant homologs. The genome of M. hungatei JF-1 encodes six homologs of the identified MspA protein. Several homologs also exist in the related strains Methanospirillum stamsii Pt1 (7 homologs, 28–66% sequence identity), M. lacunae Ki8-1 C (15 homologs, 29–60% sequence identity) and Methanolinea tarda NOBI-1 (2 homologs, 31% sequence identity). The MspA protein discovered here could accordingly represent a more widely found sheath protein than the MspA from M. thermophila PT, which currently has no homologs in the NCBI Reference Sequence database (RefSeq).
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Affiliation(s)
- Line Friis Bakmann Christensen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Lonnie Maria Hansen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Kai Finster
- Section for Microbiology, Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Gunna Christiansen
- Section for Medical Microbiology and Immunology, Department of Biomedicine, Aarhus University, Aarhus, Denmark
| | - Per Halkjær Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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32
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Cámara-Almirón J, Caro-Astorga J, de Vicente A, Romero D. Beyond the expected: the structural and functional diversity of bacterial amyloids. Crit Rev Microbiol 2018; 44:653-666. [PMID: 30354913 DOI: 10.1080/1040841x.2018.1491527] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Intense research has confirmed the formerly theoretical distribution of amyloids in nature, and studies on different systems have illustrated the role of these proteins in microbial adaptation and in interactions with the environment. Two lines of research are expanding our knowledge on functional amyloids: (i) structural studies providing insights into the molecular machineries responsible for the transition from monomer to fibers and (ii) studies showing the way in which these proteins might participate in the microbial fitness in natural settings. Much is known about how amyloids play a role in the social behavior of bacteria, or biofilm formation, and in the adhesion of bacteria to surfaces; however, we are still in the initial stages of understanding a complementary involvement of amyloids in bacteria-host interactions. This review will cover the following two topics: first, the key aspects of the microbial platforms dedicated to the assembly of the fibers, and second, the mechanisms by which bacteria utilize the morphological and biochemical variability of amyloids to modulate the immunological response of the host, plants and humans, contributing to (i) infection, in the case of pathogenic bacteria or (ii) promotion of the health of the host, in the case of beneficial bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Joaquin Caro-Astorga
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Antonio de Vicente
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
| | - Diego Romero
- a Instituto de Hortofruticultura Subtropical y Mediterránea ''La Mayora'' - Departamento de Microbiología , Universidad de Málaga , Málaga , Spain
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33
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Rouse SL, Matthews SJ, Dueholm MS. Ecology and Biogenesis of Functional Amyloids in Pseudomonas. J Mol Biol 2018; 430:3685-3695. [PMID: 29753779 PMCID: PMC6173800 DOI: 10.1016/j.jmb.2018.05.004] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 05/03/2018] [Accepted: 05/04/2018] [Indexed: 12/02/2022]
Abstract
Functional amyloids can be found in the extracellular matrix produced by many bacteria during biofilm growth. They mediate the initial attachment of bacteria to surfaces and provide stability and functionality to mature biofilms. Efficient amyloid biogenesis requires a highly coordinated system of amyloid subunits, molecular chaperones and transport systems. The functional amyloid of Pseudomonas (Fap) represents such a system. Here, we review the phylogenetic diversification of the Fap system, its potential ecological role and the dedicated machinery required for Fap biogenesis, with a particular focus on the amyloid exporter FapF, the structure of which has been recently resolved. We also present a sequence covariance-based in silico model of the FapC fiber-forming subunit. Finally, we highlight key questions that remain unanswered and we believe deserve further attention by the scientific community.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen J Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark.
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34
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Van Gerven N, Van der Verren SE, Reiter DM, Remaut H. The Role of Functional Amyloids in Bacterial Virulence. J Mol Biol 2018; 430:3657-3684. [PMID: 30009771 PMCID: PMC6173799 DOI: 10.1016/j.jmb.2018.07.010] [Citation(s) in RCA: 95] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 07/05/2018] [Accepted: 07/06/2018] [Indexed: 12/14/2022]
Abstract
Amyloid fibrils are best known as a product of human and animal protein misfolding disorders, where amyloid formation is associated with cytotoxicity and disease. It is now evident that for some proteins, the amyloid state constitutes the native structure and serves a functional role. These functional amyloids are proving widespread in bacteria and fungi, fulfilling diverse functions as structural components in biofilms or spore coats, as toxins and surface-active fibers, as epigenetic material, peptide reservoirs or adhesins mediating binding to and internalization into host cells. In this review, we will focus on the role of functional amyloids in bacterial pathogenesis. The role of functional amyloids as virulence factor is diverse but mostly indirect. Nevertheless, functional amyloid pathways deserve consideration for the acute and long-term effects of the infectious disease process and may form valid antimicrobial targets. Functional amyloids are widespread in bacteria, pathogenic and non-pathogenic. Bacterial biofilms most commonly function as structural support in the extracellular matrix of biofilms or spore coats, and in cell–cell and cell-surface adherence. The amyloid state can be the sole structured and functional state, or can be facultative, as a secondary state to folded monomeric subunits. Bacterial amyloids can enhance virulence by increasing persistence, cell adherence and invasion, intracellular survival, and pathogen spread by increased environmental survival. Bacterial amyloids may indirectly inflict disease by triggering inflammation, contact phase activation and possibly induce or aggravate human pathological aggregation disorders.
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Affiliation(s)
- Nani Van Gerven
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Sander E Van der Verren
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Dirk M Reiter
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium; Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium.
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35
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Bleem A, Christiansen G, Madsen DJ, Maric H, Strømgaard K, Bryers JD, Daggett V, Meyer RL, Otzen DE. Protein Engineering Reveals Mechanisms of Functional Amyloid Formation in Pseudomonas aeruginosa Biofilms. J Mol Biol 2018; 430:3751-3763. [PMID: 29964047 DOI: 10.1016/j.jmb.2018.06.043] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 06/22/2018] [Accepted: 06/25/2018] [Indexed: 11/25/2022]
Abstract
Amyloids are typically associated with neurodegenerative diseases, but recent research demonstrates that several bacteria utilize functional amyloid fibrils to fortify the biofilm extracellular matrix and thereby resist antibiotic treatments. In Pseudomonas aeruginosa, these fibrils are composed predominantly of FapC, a protein with high-sequence conservation among the genera. Previous studies established FapC as the major amyloid subunit, but its mechanism of fibril formation in P. aeruginosa remained largely unexplored. Here, we examine the FapC sequence in greater detail through a combination of bioinformatics and protein engineering, and we identify specific motifs that are implicated in amyloid formation. Sequence regions of high evolutionary conservation tend to coincide with regions of high amyloid propensity, and mutation of amyloidogenic motifs to a designed, non-amyloidogenic motif suppresses fibril formation in a pH-dependent manner. We establish the particular significance of the third repeat motif in promoting fibril formation and also demonstrate emergence of soluble oligomer species early in the aggregation pathway. The insights reported here expand our understanding of the mechanism of amyloid polymerization in P. aeruginosa, laying the foundation for development of new amyloid inhibitors to combat recalcitrant biofilm infections.
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Affiliation(s)
- Alissa Bleem
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Gunna Christiansen
- Department of Biomedicine-Medical Microbiology and Immunology, Aarhus University, 8000 Aarhus C, Denmark
| | - Daniel J Madsen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Hans Maric
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - Kristian Strømgaard
- Department of Drug Design and Pharmacology, University of Copenhagen, 2100 Copenhagen Ø, Denmark
| | - James D Bryers
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Valerie Daggett
- Department of Bioengineering, University of Washington, Seattle, WA 98195, USA
| | - Rikke L Meyer
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, 8000 Aarhus C, Denmark.
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36
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Markande AR, Vemuluri VR, Shouche YS, Nerurkar AS. Characterization ofSolibacillus silvestrisstrain AM1 that produces amyloid bioemulsifier. J Basic Microbiol 2018; 58:523-531. [DOI: 10.1002/jobm.201700685] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/04/2018] [Accepted: 03/29/2018] [Indexed: 11/06/2022]
Affiliation(s)
- Anoop R. Markande
- Faculty of Science, Department of Microbiology and Biotechnology Centre; The Maharaja Sayajirao University of Baroda; Vadodara Gujarat India
- C.G. Bhakta Institute of Biotechnology, Uka Tarsadia University; Maliba Campus; Bardoli Gujarat India
| | - Venkata R. Vemuluri
- Microbial Culture Collection (MCC); National Center for Cell Science (NCCS); Pune University Campus; Pune India
| | - Yogesh S. Shouche
- Microbial Culture Collection (MCC); National Center for Cell Science (NCCS); Pune University Campus; Pune India
| | - Anuradha S. Nerurkar
- Faculty of Science, Department of Microbiology and Biotechnology Centre; The Maharaja Sayajirao University of Baroda; Vadodara Gujarat India
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37
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Brothers HM, Gosztyla ML, Robinson SR. The Physiological Roles of Amyloid-β Peptide Hint at New Ways to Treat Alzheimer's Disease. Front Aging Neurosci 2018; 10:118. [PMID: 29922148 PMCID: PMC5996906 DOI: 10.3389/fnagi.2018.00118] [Citation(s) in RCA: 204] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 04/06/2018] [Indexed: 12/11/2022] Open
Abstract
Amyloid-ß (Aß) is best known as the misfolded peptide that is involved in the pathogenesis of Alzheimer's disease (AD), and it is currently the primary therapeutic target in attempts to arrest the course of this disease. This notoriety has overshadowed evidence that Aß serves several important physiological functions. Aß is present throughout the lifespan, it has been found in all vertebrates examined thus far, and its molecular sequence shows a high degree of conservation. These features are typical of a factor that contributes significantly to biological fitness, and this suggestion has been supported by evidence of functions that are beneficial for the brain. The putative roles of Aß include protecting the body from infections, repairing leaks in the blood-brain barrier, promoting recovery from injury, and regulating synaptic function. Evidence for these beneficial roles comes from in vitro and in vivo studies, which have shown that the cellular production of Aß rapidly increases in response to a physiological challenge and often diminishes upon recovery. These roles are further supported by the adverse outcomes of clinical trials that have attempted to deplete Aß in order to treat AD. We suggest that anti-Aß therapies will produce fewer adverse effects if the known triggers of Aß deposition (e.g., pathogens, hypertension, and diabetes) are addressed first.
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Affiliation(s)
- Holly M Brothers
- Department of Psychology, The Ohio State University Columbus, Columbus, OH, United States
| | - Maya L Gosztyla
- Department of Neuroscience, The Ohio State University Columbus, Columbus, OH, United States
| | - Stephen R Robinson
- Discipline of Psychology, School of Health and Biomedical Sciences, RMIT University, Melbourne, VIC, Australia
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38
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Koza A, Kusmierska A, McLaughlin K, Moshynets O, Spiers AJ. Adaptive radiation of Pseudomonas fluorescens SBW25 in experimental microcosms provides an understanding of the evolutionary ecology and molecular biology of A-L interface biofilm formation. FEMS Microbiol Lett 2018; 364:3850210. [PMID: 28535292 DOI: 10.1093/femsle/fnx109] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Accepted: 05/22/2017] [Indexed: 12/17/2022] Open
Abstract
Combined experimental evolutionary and molecular biology approaches have been used to investigate the adaptive radiation of Pseudomonas fluorescens SBW25 in static microcosms leading to the colonisation of the air-liquid interface by biofilm-forming mutants such as the Wrinkly Spreader (WS). In these microcosms, the ecosystem engineering of the early wild-type colonists establishes the niche space for subsequent WS evolution and colonisation. Random WS mutations occurring in the developing population that deregulate diguanylate cyclases and c-di-GMP homeostasis result in cellulose-based biofilms at the air-liquid interface. These structures allow Wrinkly Spreaders to intercept O2 diffusing into the liquid column and limit the growth of competitors lower down. As the biofilm matures, competition increasingly occurs between WS lineages, and niche divergence within the biofilm may support further diversification before system failure when the structure finally sinks. A combination of pleiotropic and epistasis effects, as well as secondary mutations, may explain variations in WS phenotype and fitness. Understanding how mutations subvert regulatory networks to express intrinsic genome potential and key innovations providing a selective advantage in novel environments is key to understanding the versatility of bacteria, and how selection and ecological opportunity can rapidly lead to substantive changes in phenotype and in community structure and function.
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Affiliation(s)
- Anna Koza
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Anna Kusmierska
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Kimberley McLaughlin
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
| | - Olena Moshynets
- Institute of Molecular Biology and Genetics of the National Academy of Sciences of Ukraine, Kiev 03143, Ukraine
| | - Andrew J Spiers
- School of Science, Engineering and Technology, Abertay University, Dundee DD1 1HG, UK
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39
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Danielsen HN, Hansen SH, Herbst FA, Kjeldal H, Stensballe A, Nielsen PH, Dueholm MS. Direct Identification of Functional Amyloid Proteins by Label-Free Quantitative Mass Spectrometry. Biomolecules 2017; 7:biom7030058. [PMID: 28777328 PMCID: PMC5618239 DOI: 10.3390/biom7030058] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Revised: 07/30/2017] [Accepted: 07/31/2017] [Indexed: 11/16/2022] Open
Abstract
Functional amyloids are important structural and functional components of many biofilms, yet our knowledge of these fascinating polymers is limited to a few examples for which the native amyloids have been isolated in pure form. Isolation of the functional amyloids from other cell components represents a major bottleneck in the search for new functional amyloid systems. Here we present a label-free quantitative mass spectrometry method that allows identification of amyloid proteins directly in cell lysates. The method takes advantage of the extreme structural stability and polymeric nature of functional amyloids and the ability of concentrated formic acid to depolymerize the amyloids. An automated data processing pipeline that provides a short list of amyloid protein candidates was developed based on an amyloid-specific sigmoidal abundance signature in samples treated with increasing concentrations of formic acid. The method was evaluated using the Escherichiacoli curli and the Pseudomonas Fap system. It confidently identified the major amyloid subunit for both systems, as well as the minor subunit for the curli system. A few non-amyloid proteins also displayed the sigmoidal abundance signature. However, only one of these contained a sec-dependent signal peptide, which characterizes most of all secreted proteins, including all currently known functional bacterial amyloids.
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Affiliation(s)
- Heidi N Danielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
| | - Susan H Hansen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
| | - Henrik Kjeldal
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, 9220 Aalborg, Denmark.
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
| | - Morten S Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9220 Aalborg, Denmark.
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40
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Markande AR, Nerurkar AS. Bioemulsifier (BE-AM1) produced by Solibacillus silvestris AM1 is a functional amyloid that modulates bacterial cell-surface properties. BIOFOULING 2016; 32:1153-1162. [PMID: 27669827 DOI: 10.1080/08927014.2016.1232716] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Accepted: 08/29/2016] [Indexed: 06/06/2023]
Abstract
A novel estuarine bacterial strain, Solibacillus silvestris AM1, produces an extracellular, thermostable and fibrous, glycoprotein bioemulsifier (BE-AM1). The amyloid nature of the bioemulsifier (BE-AM1) was confirmed by biophysical techniques (Congo red based polarization microscopy, ThioflavinS based fluorescent microscopy, fibrous arrangement in transmission electron microscopy and secondary structure measurement by FTIR and CD spectrum analysis). Cell-bound BE-AM1 production by S. silvestris AM1 during the mid-logarithmic phase of growth coincided with a decrease in cell surface hydrophobicity, and an increase in cell autoaggregation and biofilm formation. It was observed that the total interfacial interaction energy ([Formula: see text]) for the surface of the bioemulsifier producing S. silvestris AM1 and different derivatized surfaces of polystyrene (silanized and sulfonated) was found to support biofilm formation. This study has revealed that the BE-AM1, a bacterial bioemulsifier, is a functional amyloid and has a role in biofilm formation and cell surface modulation in S. silvestris AM1.
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Affiliation(s)
- A R Markande
- a Department of Microbiology and Biotechnology Centre, Faculty of Science , The Maharaja Sayajirao University of Baroda , Vadodara , India
| | - A S Nerurkar
- a Department of Microbiology and Biotechnology Centre, Faculty of Science , The Maharaja Sayajirao University of Baroda , Vadodara , India
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41
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Stenvang M, Dueholm MS, Vad BS, Seviour T, Zeng G, Geifman-Shochat S, Søndergaard MT, Christiansen G, Meyer RL, Kjelleberg S, Nielsen PH, Otzen DE. Epigallocatechin Gallate Remodels Overexpressed Functional Amyloids in Pseudomonas aeruginosa and Increases Biofilm Susceptibility to Antibiotic Treatment. J Biol Chem 2016; 291:26540-26553. [PMID: 27784787 DOI: 10.1074/jbc.m116.739953] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 10/07/2016] [Indexed: 01/09/2023] Open
Abstract
Epigallocatechin-3-gallate (EGCG) is the major polyphenol in green tea. It has antimicrobial properties and disrupts the ordered structure of amyloid fibrils involved in human disease. The antimicrobial effect of EGCG against the opportunistic pathogen Pseudomonas aeruginosa has been shown to involve disruption of quorum sensing (QS). Functional amyloid fibrils in P. aeruginosa (Fap) are able to bind and retain quorum-sensing molecules, suggesting that EGCG interferes with QS through structural remodeling of amyloid fibrils. Here we show that EGCG inhibits the ability of Fap to form fibrils; instead, EGCG stabilizes protein oligomers. Existing fibrils are remodeled by EGCG into non-amyloid aggregates. This fibril remodeling increases the binding of pyocyanin, demonstrating a mechanism by which EGCG can affect the QS function of functional amyloid. EGCG reduced the amyloid-specific fluorescent thioflavin T signal in P. aeruginosa biofilms at concentrations known to exert an antimicrobial effect. Nanoindentation studies showed that EGCG reduced the stiffness of biofilm containing Fap fibrils but not in biofilm with little Fap. In a combination treatment with EGCG and tobramycin, EGCG had a moderate effect on the minimum bactericidal eradication concentration against wild-type P. aeruginosa biofilms, whereas EGCG had a more pronounced effect when Fap was overexpressed. Our results provide a direct molecular explanation for the ability of EGCG to disrupt P. aeruginosa QS and modify its biofilm and strengthens the case for EGCG as a candidate in multidrug treatment of persistent biofilm infections.
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Affiliation(s)
- Marcel Stenvang
- From the Interdisciplinary Nanoscience Center (iNANO).,Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN).,the Sino-Danish Centre for Education and Research (SDC), 8000 Aarhus C, Denmark
| | - Morten S Dueholm
- the Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9000 Aalborg, Denmark
| | - Brian S Vad
- From the Interdisciplinary Nanoscience Center (iNANO).,Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN)
| | - Thomas Seviour
- the Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Singapore 637551, Singapore
| | | | - Susana Geifman-Shochat
- the School of Biological Sciences, Nanyang Technological University, Singapore 637551, Singapore, and
| | - Mads T Søndergaard
- the Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9000 Aalborg, Denmark
| | | | - Rikke Louise Meyer
- From the Interdisciplinary Nanoscience Center (iNANO).,the Department of Bioscience, Aarhus University, 8000 Aarhus C, Denmark
| | - Staffan Kjelleberg
- the Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Singapore 637551, Singapore.,the Centre for Marine Bio-innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Mosman, New South Wales 2088, Australia
| | - Per Halkjær Nielsen
- the Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, 9000 Aalborg, Denmark.,the Singapore Centre on Environmental Life Sciences Engineering (SCELSE), Singapore 637551, Singapore
| | - Daniel E Otzen
- From the Interdisciplinary Nanoscience Center (iNANO), .,Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN)
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42
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Abstract
Recent insights into bacterial biofilm matrix structures have induced a paradigm shift toward the recognition of amyloid fibers as common building block structures that confer stability to the exopolysaccharide matrix. Here we describe the functional amyloid systems related to biofilm matrix formation in both Gram-negative and Gram-positive bacteria and recent knowledge regarding the interaction of amyloids with other biofilm matrix components such as extracellular DNA (eDNA) and the host immune system. In addition, we summarize the efforts to identify compounds that target amyloid fibers for therapeutic purposes and recent developments that take advantage of the amyloid structure to engineer amyloid fibers of bacterial biofilm matrices for biotechnological applications.
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43
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Zeng G, Vad BS, Dueholm MS, Christiansen G, Nilsson M, Tolker-Nielsen T, Nielsen PH, Meyer RL, Otzen DE. Functional bacterial amyloid increases Pseudomonas biofilm hydrophobicity and stiffness. Front Microbiol 2015; 6:1099. [PMID: 26500638 PMCID: PMC4595789 DOI: 10.3389/fmicb.2015.01099] [Citation(s) in RCA: 110] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Accepted: 09/22/2015] [Indexed: 12/20/2022] Open
Abstract
The success of Pseudomonas species as opportunistic pathogens derives in great part from their ability to form stable biofilms that offer protection against chemical and mechanical attack. The extracellular matrix of biofilms contains numerous biomolecules, and it has recently been discovered that in Pseudomonas one of the components includes β-sheet rich amyloid fibrils (functional amyloid) produced by the fap operon. However, the role of the functional amyloid within the biofilm has not yet been investigated in detail. Here we investigate how the fap-based amyloid produced by Pseudomonas affects biofilm hydrophobicity and mechanical properties. Using atomic force microscopy imaging and force spectroscopy, we show that the amyloid renders individual cells more resistant to drying and alters their interactions with hydrophobic probes. Importantly, amyloid makes Pseudomonas more hydrophobic and increases biofilm stiffness 20-fold. Deletion of any one of the individual members of in the fap operon (except the putative chaperone FapA) abolishes this ability to increase biofilm stiffness and correlates with the loss of amyloid. We conclude that amyloid makes major contributions to biofilm mechanical robustness.
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Affiliation(s)
- Guanghong Zeng
- Interdisciplinary Nanoscience Centre, Aarhus UniversityAarhus, Denmark
| | - Brian S. Vad
- Interdisciplinary Nanoscience Centre, Aarhus UniversityAarhus, Denmark
| | - Morten S. Dueholm
- Center for Microbial Communities, Aalborg UniversityAalborg, Denmark
| | - Gunna Christiansen
- Department of Biomedicine-Medical Microbiology and Immunology, Aarhus UniversityAarhus, Denmark
| | - Martin Nilsson
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Tim Tolker-Nielsen
- Department of Immunology and Microbiology, Costerton Biofilm Center, Faculty of Health and Medical Sciences, University of CopenhagenCopenhagen, Denmark
| | - Per H. Nielsen
- Center for Microbial Communities, Aalborg UniversityAalborg, Denmark
| | - Rikke L. Meyer
- Interdisciplinary Nanoscience Centre, Aarhus UniversityAarhus, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Centre, Aarhus UniversityAarhus, Denmark
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44
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Dueholm MS, Larsen P, Finster K, Stenvang MR, Christiansen G, Vad BS, Bøggild A, Otzen DE, Nielsen PH. The Tubular Sheaths Encasing Methanosaeta thermophila Filaments Are Functional Amyloids. J Biol Chem 2015; 290:20590-600. [PMID: 26109065 DOI: 10.1074/jbc.m115.654780] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2015] [Indexed: 11/06/2022] Open
Abstract
Archaea are renowned for their ability to thrive in extreme environments, although they can be found in virtually all habitats. Their adaptive success is linked to their unique cell envelopes that are extremely resistant to chemical and thermal denaturation and that resist proteolysis by common proteases. Here we employ amyloid-specific conformation antibodies and biophysical techniques to show that the extracellular cell wall sheaths encasing the methanogenic archaea Methanosaeta thermophila PT are functional amyloids. Depolymerization of sheaths and subsequent MS/MS analyses revealed that the sheaths are composed of a single major sheath protein (MspA). The amyloidogenic nature of MspA was confirmed by in vitro amyloid formation of recombinant MspA under a wide range of environmental conditions. This is the first report of a functional amyloid from the archaeal domain of life. The amyloid nature explains the extreme resistance of the sheath, the elastic properties that allow diffusible substrates to penetrate through expandable hoop boundaries, and how the sheaths are able to split and elongate outside the cell. The archaeal sheath amyloids do not share homology with any of the currently known functional amyloids and clearly represent a new function of the amyloid protein fold.
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Affiliation(s)
- Morten S Dueholm
- From the Center for Microbial Communities, Department of Chemistry and Biosciences, Aalborg University, 9220 Aalborg, Denmark
| | - Poul Larsen
- From the Center for Microbial Communities, Department of Chemistry and Biosciences, Aalborg University, 9220 Aalborg, Denmark
| | | | - Marcel R Stenvang
- the Interdisciplinary Nanoscience Center (iNANO) and Center for Insoluble Protein Structures (inSPIN), the Department of Molecular Biology and Genetics, and
| | | | - Brian S Vad
- the Interdisciplinary Nanoscience Center (iNANO) and Center for Insoluble Protein Structures (inSPIN), the Department of Molecular Biology and Genetics, and
| | | | - Daniel E Otzen
- the Interdisciplinary Nanoscience Center (iNANO) and Center for Insoluble Protein Structures (inSPIN), the Department of Molecular Biology and Genetics, and
| | - Per Halkjær Nielsen
- From the Center for Microbial Communities, Department of Chemistry and Biosciences, Aalborg University, 9220 Aalborg, Denmark,
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45
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Seviour T, Hansen SH, Yang L, Yau YH, Wang VB, Stenvang MR, Christiansen G, Marsili E, Givskov M, Chen Y, Otzen DE, Nielsen PH, Geifman-Shochat S, Kjelleberg S, Dueholm MS. Functional amyloids keep quorum-sensing molecules in check. J Biol Chem 2015; 290:6457-69. [PMID: 25586180 DOI: 10.1074/jbc.m114.613810] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The mechanism by which extracellular metabolites, including redox mediators and quorum-sensing signaling molecules, traffic through the extracellular matrix of biofilms is poorly explored. We hypothesize that functional amyloids, abundant in natural biofilms and possessing hydrophobic domains, retain these metabolites. Using surface plasmon resonance, we demonstrate that the quorum-sensing (QS) molecules, 2-heptyl-3-hydroxy-4(1H)-quinolone and N-(3-oxododecanoyl)-l-homoserine lactone, and the redox mediator pyocyanin bind with transient affinity to functional amyloids from Pseudomonas (Fap). Their high hydrophobicity predisposes them to signal-amyloid interactions, but specific interactions also play a role. Transient interactions allow for rapid association and dissociation kinetics, which make the QS molecules bioavailable and at the same time secure within the extracellular matrix as a consequence of serial bindings. Retention of the QS molecules was confirmed using Pseudomonas aeruginosa PAO1-based 2-heptyl-3-hydroxy-4(1H)-quinolone and N-(3-oxododecanoyl)-l-homoserine lactone reporter assays, showing that Fap fibrils pretreated with the QS molecules activate the reporters even after sequential washes. Pyocyanin retention was validated by electrochemical analysis of pyocyanin-pretreated Fap fibrils subjected to the same washing process. Results suggest that QS molecule-amyloid interactions are probably important in the turbulent environments commonly encountered in natural habitats.
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Affiliation(s)
- Thomas Seviour
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and
| | - Susan Hove Hansen
- the Center for Microbial Communities, Aalborg University, 9220 Aalborg East, Denmark
| | - Liang Yang
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and
| | - Yin Hoe Yau
- the School of Biological Sciences (SBS), Nanyang Technological University, Singapore 637551, Singapore
| | - Victor Bochuan Wang
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and the School of Materials Science and Engineering (MSE), Nanyang Technological University, Singapore 639798
| | - Marcel R Stenvang
- the Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN), and
| | - Gunna Christiansen
- the Department of Biomedicine, Aarhus University, 8000 Aarhus C, Denmark
| | - Enrico Marsili
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and
| | - Michael Givskov
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and the Department of International Health, Immunology and Microbiology, University of Copenhagen, 1165 Copenhagen, Denmark, and
| | - Yicai Chen
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and
| | - Daniel E Otzen
- the Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Center for Insoluble Protein Structures (inSPIN), and
| | - Per Halkjær Nielsen
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and the Center for Microbial Communities, Aalborg University, 9220 Aalborg East, Denmark
| | - Susana Geifman-Shochat
- the School of Biological Sciences (SBS), Nanyang Technological University, Singapore 637551, Singapore
| | - Staffan Kjelleberg
- From the Singapore Centre on Environmental Life Sciences Engineering (SCELSE) and the Centre for Marine Bio-innovation and School of Biotechnology and Biomolecular Science, University of New South Wales, Mosman, New South Wales 2088, Australia
| | - Morten S Dueholm
- the Center for Microbial Communities, Aalborg University, 9220 Aalborg East, Denmark
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46
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Complete Genome Sequence of Pseudomonas sp. UK4, a Model Organism for Studies of Functional Amyloids in Pseudomonas. GENOME ANNOUNCEMENTS 2014; 2:2/5/e00898-14. [PMID: 25212622 PMCID: PMC4161751 DOI: 10.1128/genomea.00898-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Here, we present the complete genome of Pseudomonas sp. UK4. This bacterium was the first Pseudomonas strain shown to produce functional amyloids, and it represents a model organism for studies of functional amyloids in Pseudomonas (Fap).
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47
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Complete Genome Sequences of Pseudomonas monteilii SB3078 and SB3101, Two Benzene-, Toluene-, and Ethylbenzene-Degrading Bacteria Used for Bioaugmentation. GENOME ANNOUNCEMENTS 2014; 2:2/3/e00524-14. [PMID: 24874689 PMCID: PMC4038894 DOI: 10.1128/genomea.00524-14] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Pseudomonas monteilii SB3078 and SB3101 are benzene-, toluene-, and ethylbenzene-degrading strains used for bioaugmentation in relation to treatment of wastewater contaminated with petrochemical hydrocarbons. Complete genome sequencing of the bioaugmentation strains confirms that they are very closely related (100.0% average nucleotide identity). Both strains contain extensive integration of phage elements, with the main difference being insertion of additional phage elements in the SB3078 genome.
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