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Guo M, Tan S, Wu Y, Zheng C, Du P, Zhu J, Sun A, Liu X. BrfA functions as a bacterial enhancer-binding protein to regulate functional amyloid Fap-dependent biofilm formation in Pseudomonas fluorescens by sensing cyclic diguanosine monophosphate. Microbiol Res 2024; 287:127864. [PMID: 39116779 DOI: 10.1016/j.micres.2024.127864] [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: 04/18/2024] [Revised: 07/04/2024] [Accepted: 07/07/2024] [Indexed: 08/10/2024]
Abstract
The functional amyloid of Pseudomonas (Fap) is essential for the formation of macrocolony biofilms, pellicles, and solid surface-associated (SSA) biofilms of Pseudomonas fluorescens PF07, an isolate from refrigerated marine fish. However, limited information on the expression regulation of fap genes is available. Herein, we found that a novel bacterial enhancer-binding protein (bEBP), BrfA, regulated Fap-dependent biofilm formation by directly sensing cyclic diguanosine monophosphate (c-di-GMP). Our in vivo data showed that the REC domain deletion of BrfA promoted fap gene expression and biofilm formation, and c-di-GMP positively regulated the transcription of fapA in a BrfA-dependent manner. In in vitro experiments, we found that the ATPase activity of BrfA was inhibited by the REC domain and was activated by c-di-GMP. BrfA and the sigma factor RpoN bound to the upstream region of fapA, and the binding ability of BrfA was not affected by either deletion of the REC domain or c-di-GMP. BrfA specifically bound to the three enhancer sites upstream of the fapA promoter, which contain the consensus sequence CA-(N4)-TGA(A/T)ACACC. In vivo experiments using a lacZ fusion reporter indicated that all three BrfA enhancer sites were essential for the activation of fapA transcription. Overall, these findings reveal that BrfA is a new type of c-di-GMP-responsive transcription factor that directly controls the transcription of Fap biosynthesis genes in P. fluorescens. Fap functional amyloids and BrfA-type transcription factors are widespread in Pseudomonas species. The novel insights into the c-di-GMP- and BrfA-dependent expression regulation of fap provided by this work will contribute to the development of antibiofilm strategies.
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Affiliation(s)
- Miao Guo
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China; School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China; Zouping Center for Disease Control and Prevention, Zouping, Shandong, 256200, China
| | - Siqi Tan
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China; School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China
| | - Yinying Wu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China; School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China
| | - Chongni Zheng
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China; School of Public Health, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China
| | - Peng Du
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, Zhejiang, 310018, China
| | - Aihua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China.
| | - Xiaoxiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, Zhejiang, 310053, China.
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2
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Dürvanger Z, Bencs F, Menyhárd DK, Horváth D, Perczel A. Solvent induced amyloid polymorphism and the uncovering of the elusive class 3 amyloid topology. Commun Biol 2024; 7:968. [PMID: 39122990 PMCID: PMC11316126 DOI: 10.1038/s42003-024-06621-8] [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: 12/01/2023] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Aggregation-prone-motifs (APRs) of proteins are short segments, which - as isolated peptides - form diverse amyloid-like crystals. We introduce two APRs - designed variants of the incretin mimetic Exendin-4 - that both display crystal-phase polymorphism. Crystallographic and spectroscopic analysis revealed that a single amino-acid substitution can greatly reduce topological variability: while LYIQWL can form both parallel and anti-parallel β-sheets, LYIQNL selects only the former. We also found that the parallel/anti-parallel switch of LYIQWL can be induced by simply changing the crystallization temperature. One crystal form of LYIQNL was found to belong to the class 3 topology, an arrangement previously not encountered among proteinogenic systems. We also show that subtle environmental changes lead to crystalline assemblies with different topologies, but similar interfaces. Spectroscopic measurements showed that polymorphism is already apparent in the solution state. Our results suggest that the temperature-, sequence- and environmental sensitivity of physiological amyloids is reflected in assemblies of the APR segments, which, complete with the new class 3 crystal form, effectively sample all the originally proposed basic topologies of amyloid-like aggregates.
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Affiliation(s)
- Zsolt Dürvanger
- Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
- HUN-REN-ELTE Protein Modeling Research Group, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
| | - Fruzsina Bencs
- Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
- Hevesy György PhD School of Chemistry, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
| | - Dóra K Menyhárd
- Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
- HUN-REN-ELTE Protein Modeling Research Group, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
| | - Dániel Horváth
- Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
- HUN-REN-ELTE Protein Modeling Research Group, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary
| | - András Perczel
- Laboratory of Structural Chemistry and Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary.
- HUN-REN-ELTE Protein Modeling Research Group, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/A, H-1117, Budapest, Hungary.
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3
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Fernández-Calvet A, Matilla-Cuenca L, Izco M, Navarro S, Serrano M, Ventura S, Blesa J, Herráiz M, Alkorta-Aranburu G, Galera S, Ruiz de Los Mozos I, Mansego ML, Toledo-Arana A, Alvarez-Erviti L, Valle J. Gut microbiota produces biofilm-associated amyloids with potential for neurodegeneration. Nat Commun 2024; 15:4150. [PMID: 38755164 PMCID: PMC11099085 DOI: 10.1038/s41467-024-48309-x] [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: 11/06/2023] [Accepted: 04/26/2024] [Indexed: 05/18/2024] Open
Abstract
Age-related neurodegenerative diseases involving amyloid aggregation remain one of the biggest challenges of modern medicine. Alterations in the gastrointestinal microbiome play an active role in the aetiology of neurological disorders. Here, we dissect the amyloidogenic properties of biofilm-associated proteins (BAPs) of the gut microbiota and their implications for synucleinopathies. We demonstrate that BAPs are naturally assembled as amyloid-like fibrils in insoluble fractions isolated from the human gut microbiota. We show that BAP genes are part of the accessory genomes, revealing microbiome variability. Remarkably, the abundance of certain BAP genes in the gut microbiome is correlated with Parkinson's disease (PD) incidence. Using cultured dopaminergic neurons and Caenorhabditis elegans models, we report that BAP-derived amyloids induce α-synuclein aggregation. Our results show that the chaperone-mediated autophagy is compromised by BAP amyloids. Indeed, inoculation of BAP fibrils into the brains of wild-type mice promote key pathological features of PD. Therefore, our findings establish the use of BAP amyloids as potential targets and biomarkers of α-synucleinopathies.
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Affiliation(s)
- Ariadna Fernández-Calvet
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Leticia Matilla-Cuenca
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - María Izco
- Laboratory of Molecular Neurobiology, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Susanna Navarro
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Miriam Serrano
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina and Departament de Bioquimica i Biologia Molecular, Universitat Autónoma de Barcelona, Bellaterra, Spain
| | - Javier Blesa
- HM CINAC (Centro Integral de Neurociencias Abarca Campal), Hospital Universitario HM Puerta del Sur, HM Hospitales, Madrid, Spain
- Instituto de Investigación Sanitaria, HM Hospitales, Madrid, Spain
| | - Maite Herráiz
- Department of Gastroenterology, Clínica Universitaria and Medical School, University of Navarra, Navarra, Spain
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
| | - Gorka Alkorta-Aranburu
- IdiSNA, Instituto de Investigación Sanitaria de Navarra, Pamplona, Spain
- CIMA LAB Diagnostics, University of Navarra, Pamplona, Spain
| | - Sergio Galera
- Department of Personalized Medicine, NASERTIC, Government of Navarra, Pamplona, Spain
| | | | - María Luisa Mansego
- Translational Bioinformatics Unit, Navarrabiomed, Complejo Hospitalario de Navarra (CHN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Alejandro Toledo-Arana
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain
| | - Lydia Alvarez-Erviti
- Laboratory of Molecular Neurobiology, Center for Biomedical Research of La Rioja, Logroño, Spain
| | - Jaione Valle
- Instituto de Agrobiotecnología (IDAB). CSIC-Gobierno de Navarra, Avenida Pamplona 123, Mutilva, 31192, Spain.
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4
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Szulc N, Gąsior-Głogowska M, Żyłka P, Szefczyk M, Wojciechowski JW, Żak AM, Dyrka W, Kaczorowska A, Burdukiewicz M, Tarek M, Kotulska M. Structural effects of charge destabilization and amino acid substitutions in amyloid fragments of CsgA. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2024; 313:124094. [PMID: 38503257 DOI: 10.1016/j.saa.2024.124094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 02/20/2024] [Accepted: 02/27/2024] [Indexed: 03/21/2024]
Abstract
The most studied functional amyloid is the CsgA, major curli subunit protein, which is produced by numerous strains of Enterobacteriaceae. Although CsgA sequences are highly conserved, they exhibit species diversity, which reflects the specific evolutionary and functional adaptability of the major curli subunit. Herein, we performed bioinformatics analyses to uncover the differences in the amyloidogenic properties of the R4 fragments in Escherichia coli and Salmonella enterica and proposed four mutants for more detailed studies: M1, M2, M3, and M4. The mutated sequences were characterized by various experimental techniques, such as circular dichroism, ATR-FTIR, FT-Raman, thioflavin T, transmission electron microscopy and confocal microscopy. Additionally, molecular dynamics simulations were performed to determine the role of buffer ions in the aggregation process. Our results demonstrated that the aggregation kinetics, fibril morphology, and overall structure of the peptide were significantly affected by the positions of charged amino acids within the repeat sequences of CsgA. Notably, substituting glycine with lysine resulted in the formation of distinctive spherically packed globular aggregates. The differences in morphology observed are attributed to the influence of phosphate ions, which disrupt the local electrostatic interaction network of the polypeptide chains. This study provides knowledge on the preferential formation of amyloid fibrils based on charge states within the polypeptide chain.
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Affiliation(s)
- Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; CNRS, University of Lorraine, F-5400 Nancy, France; Department of Physics and Biophysics, Faculty of Biotechnology and Food Science, Wrocław University of Environmental and Life Sciences, Norwida 25, 50-375 Wrocław, Poland
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Paweł Żyłka
- Department of Electrical Engineering Fundamentals, Faculty of Electrical Engineering, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Jakub W Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Andrzej M Żak
- Institute of Advanced Materials, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Witold Dyrka
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland
| | - Aleksandra Kaczorowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland; Laboratory of Cytobiochemistry, Faculty of Biotechnology, University of Wroclaw, F. Joliot-Curie 14a, 50-383 Wroclaw, Poland
| | - Michał Burdukiewicz
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Campus Universitat Autònoma de Barcelona Plaça Cívica Bellaterra, s/n, 08193 Cerdanyola del Vallès, Barcelona, Spain; Clinical Research Centre, Medical University of Bialystok, Jana Kilinskiego 1, 15-089 Bialystok, Poland
| | - Mounir Tarek
- CNRS, University of Lorraine, F-5400 Nancy, France.
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeze Wyspianskiego 27, 50-370 Wroclaw, Poland.
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5
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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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6
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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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7
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Dabirmanesh B, Khajeh K, Uversky VN. The hidden world of protein aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:473-494. [PMID: 38811088 DOI: 10.1016/bs.pmbts.2024.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Though the book's journey into The Hidden World of Protein Aggregation has come to an end, the search for knowledge, the development of healthier lives, and the discovery of nature's mysteries continue, promising new horizons and discoveries yet to be discovered. The intricacies of protein misfolding and aggregation remain a mystery in cellular biology, despite advances made in unraveling them. In this chapter, we will summarize the specific conclusions from the previous chapters and explore the persistent obstacles and unanswered questions that motivate scientists to pursue exploration of protein misfolding and aggregation.
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Affiliation(s)
- Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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8
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Khalili K, Farzam F, Dabirmanesh B, Khajeh K. Prediction of protein aggregation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:229-263. [PMID: 38811082 DOI: 10.1016/bs.pmbts.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
The scientific community is very interested in protein aggregation because of its involvement in several neurodegenerative diseases and its significance in industry. Remarkably, fibrillar aggregates are utilized naturally for constructing structural scaffolds or creating biological switches and may be intentionally designed to construct versatile nanomaterials. Consequently, there is a significant need to rationalize and predict protein aggregation. Researchers have developed various computational methodologies and algorithms to predict protein aggregation and understand its underlying mechanics. This chapter aims to summarize the significant advancements in computational methods, accessible resources, and prospective developments in the field of in silico research. We assess the existing computational tools for predicting protein aggregation propensities, detecting areas that are prone to sequential and structural aggregation, analyzing the effects of mutations on protein aggregation, or identifying prion-like domains.
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Affiliation(s)
- Kavyan Khalili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Farnoosh Farzam
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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9
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Bu F, Dee DR, Liu B. Structural insight into Escherichia coli CsgA amyloid fibril assembly. mBio 2024; 15:e0041924. [PMID: 38501920 PMCID: PMC11005368 DOI: 10.1128/mbio.00419-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Accepted: 03/04/2024] [Indexed: 03/20/2024] Open
Abstract
The discovery of functional amyloids in bacteria dates back several decades, and our understanding of the Escherichia coli curli biogenesis system has gradually expanded over time. However, due to its high aggregation propensity and intrinsically disordered nature, CsgA, the main structural component of curli fibrils, has eluded comprehensive structural characterization. Recent advancements in cryo-electron microscopy (cryo-EM) offer a promising tool to achieve high-resolution structural insights into E. coli CsgA fibrils. In this study, we outline an approach to addressing the colloidal instability challenges associated with CsgA, achieved through engineering and electrostatic repulsion. Then, we present the cryo-EM structure of CsgA fibrils at 3.62 Å resolution. This structure provides new insights into the cross-β structure of E. coli CsgA. Additionally, our study identifies two distinct spatial arrangements within several CsgA fibrils, a 2-CsgA-fibril pair and a 3-CsgA-fibril bundle, shedding light on the intricate hierarchy of the biofilm extracellular matrix and laying the foundation for precise manipulation of CsgA-derived biomaterials.IMPORTANCEThe visualization of the architecture of Escherichia coli CsgA amyloid fibril has been a longstanding research question, for which a high-resolution structure is still unavailable. CsgA serves as a major subunit of curli, the primary component of the extracellular matrix generated by bacteria. The support provided by this extracellular matrix enables bacterial biofilms to resist antibiotic treatment, significantly impacting human health. CsgA has been identified in members of Enterobacteriaceae, with pathogenic E. coli being the most well-known model system. Our novel insights into the structure of E. coli CsgA protofilaments form the basis for drug design targeting diseases associated with biofilms. Additionally, CsgA is widely researched in biomaterials due to its self-assembly characteristics. The resolved spatial arrangements of CsgA amyloids revealed in our study will further enhance the precision design of functional biomaterials. Therefore, our study uniquely contributes to the understanding of CsgA amyloids for both microbiology and material science.
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Affiliation(s)
- Fan Bu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Pharmacology, University of Minnesota Medical School, Minneapolis, Minnesota, USA
| | - Derek R. Dee
- Faculty of Land and Food Systems, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Bin Liu
- The Hormel Institute, University of Minnesota, Austin, Minnesota, USA
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10
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Mirza Agha M, Tavili E, Dabirmanesh B. Functional amyloids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:389-434. [PMID: 38811086 DOI: 10.1016/bs.pmbts.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
While amyloid has traditionally been viewed as a harmful formation, emerging evidence suggests that amyloids may also play a functional role in cell biology, contributing to normal physiological processes that have been conserved throughout evolution. Functional amyloids have been discovered in several creatures, spanning from bacteria to mammals. These amyloids serve a multitude of purposes, including but not limited to, forming biofilms, melanin synthesis, storage, information transfer, and memory. The functional role of amyloids has been consistently validated by the discovery of more functional amyloids, indicating a conceptual convergence. The biology of amyloids is well-represented by non-pathogenic amyloids, given the numerous ones already identified and the ongoing rate of new discoveries. In this chapter, functional amyloids in microorganisms, animals, and plants are described.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elaheh Tavili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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11
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Dabirmanesh B, Khajeh K, Uversky VN. Protein aggregation: An overview. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:1-10. [PMID: 38811077 DOI: 10.1016/bs.pmbts.2024.03.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
In order for an ordered protein to perform its specific function, it must have a specific molecular structure. Information about this structure is encoded in the protein's amino acid sequence. The unique functional state is achieved as a result of a specific process, known as protein folding. However, as a result of partial or complete unfolding of the polypeptide chain, proteins may misfold and aggregate, leading to the formation of various aggregated structures, such as like amyloid aggregates with the cross-β structure. A variety of cellular biological processes can be affected by protein aggregates that consume essential factors necessary for maintaining proteostasis, which leads to the proteostasis imbalance and further accumulation of protein aggregates, often resulting in age-related neurodegenerative disease progression and aging. However, in addition to their well-established pathological effects, amyloids also play various physiological roles, and many important biological processes involve such 'functional amyloids'. This chapter represents a brief overview of the protein aggregation phenomenon outlines a timeline provides of some key discoveries in this exciting field.
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Affiliation(s)
- Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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12
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Carrillo D, Duran-Meza E, Castillo-Caceres C, Alarcon DE, Guzman H, Diaz-Espinoza R. Catalytic amyloids for nucleotide hydrolysis. Methods Enzymol 2024; 697:269-291. [PMID: 38816126 DOI: 10.1016/bs.mie.2024.01.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
The design of small peptides that assemble into catalytically active intermolecular structures has proven to be a successful strategy towards developing minimalistic catalysts that exhibit some of the unique functional features of enzymes. Among these, catalytic amyloids have emerged as a fruitful source to unravel many different activities. These assemblies can potentially have broad applications that range from biotechnology to prebiotic chemistry. Although many peptides that assemble into catalytic amyloids have been developed in recent years, the elucidation of convergent mechanistic aspects of the catalysis and the structure/function relationship is still a challenge. Novel catalytic activities are necessary to better address these issues and expand the current repertoire of applicability. In this chapter, we described a methodology to produce catalytic amyloids that are specifically active towards the hydrolysis of phosphoanhydride bonds of nucleotides. The design of potentially active amyloid-prone peptide sequences is explored using as template the active site of enzymes with nucleotidyltransferase activity. The procedures include an approach for sequence design, in vitro aggregation assays, morphological characterization of the amyloid state and a comprehensive methodology to measure activity in vitro using nucleoside and deoxynucleosides triphosphates as model substrates. The proposed strategy can also be implemented to explore different types of activities for the design of future catalytic amyloids.
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Affiliation(s)
- Daniel Carrillo
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Eva Duran-Meza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile; Departamento de Biología, Facultad de Ciencias, Universidad de Chile, Chile
| | - Claudio Castillo-Caceres
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Diego Eduardo Alarcon
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Hardy Guzman
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile
| | - Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Chile.
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13
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Arad E, Jelinek R. Catalytic physiological amyloids. Methods Enzymol 2024; 697:77-112. [PMID: 38816136 DOI: 10.1016/bs.mie.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Amyloid fibrils have been identified in many protein systems, mostly linked to progression and cytotoxicity in neurodegenerative diseases and other pathologies, but have also been observed in normal physiological systems. A growing body of work has shown that amyloid fibrils can catalyze chemical reactions. Most studies have focused on catalysis by de-novo synthetic amyloid-like peptides; however, recent studies reveal that physiological, native amyloids are catalytic as well. Here, we discuss methodologies and major experimental aspects pertaining to physiological catalytic amyloids. We highlight analyzes of kinetic parameters related to the catalytic activities of amyloid fibrils, structure-function considerations, characterization of the catalytic active sites, and deciphering of catalytic mechanisms.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel; Department of Chemical Engineering, Columbia University in the City of New York, New York, NY, United States.
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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14
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Le NTK, Kang EJ, Park JH, Kang K. Catechol-Amyloid Interactions. Chembiochem 2023; 24:e202300628. [PMID: 37850717 DOI: 10.1002/cbic.202300628] [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: 09/13/2023] [Revised: 10/17/2023] [Accepted: 10/18/2023] [Indexed: 10/19/2023]
Abstract
This review introduces multifaceted mutual interactions between molecules containing a catechol moiety and aggregation-prone proteins. The complex relationships between these two molecular species have previously been elucidated primarily in a unidirectional manner, as demonstrated in cases involving the development of catechol-based inhibitors for amyloid aggregation and the elucidation of the role of functional amyloid fibers in melanin biosynthesis. This review aims to consolidate scattered clues pertaining to catechol-based amyloid inhibitors, functional amyloid scaffold of melanin biosynthesis, and chemically designed peptide fibers for providing chemical insights into the role of the local three-dimensional orientation of functional groups in manifesting such interactions. These orientations may play crucial, yet undiscovered, roles in various supramolecular structures.
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Affiliation(s)
- Nghia T K Le
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Eun Joo Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
| | - Ji Hun Park
- Department of Science Education, Ewha Womans University, Seoul, 03760, South Korea
| | - Kyungtae Kang
- Department of Applied Chemistry, Kyung Hee University, Yongin, Gyeonggi, 17104, South Korea
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15
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Rahman S, Das AK. Staphylococcal superantigen-like protein 10 enhances the amyloidogenic biofilm formation in Staphylococcus aureus. BMC Microbiol 2023; 23:390. [PMID: 38062361 PMCID: PMC10701973 DOI: 10.1186/s12866-023-03134-y] [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: 05/31/2023] [Accepted: 11/22/2023] [Indexed: 12/18/2023] Open
Abstract
Staphylococcus aureus is a highly infectious pathogen that represents a significant burden on the current healthcare system. Bacterial attachment to medical implants and host tissue, and the establishment of a mature biofilm, play an important role in chronic diseases such as endocarditis, osteomyelitis and wound infections. These biofilms decrease bacterial susceptibility to antibiotics and immune defences, making the infections challenging to treatment. S. aureus produces numerous exotoxins that contribute to the pathogenesis of the bacteria. In this study, we have identified a novel function of staphylococcal superantigen-like protein 10 (SSL10) in enhancing the formation of staphylococcal biofilms. Biofilm biomass is significantly increased when SSL10 is added exogenously to bacterial cultures, whereas SSL2 and SSL12 are found to be less active. Exogenously added SSL10 mask the surface charge of the bacterial cells and lowers their zeta potential, leading to the aggregation of the cells. Moreover, the biofilm formation by SSL10 is governed by amyloid aggregation, as evident from spectroscopic and microscopic studies. These findings thereby give the first overview of the SSL-mediated amyloid-based biofilm formation and further drive the future research in identifying potential molecules for developing new antibacterial therapies against Staphylococcus aureus.
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Affiliation(s)
- Shakilur Rahman
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India
| | - Amit Kumar Das
- Department of Biotechnology, Indian Institute of Technology Kharagpur, Kharagpur, 721302, West Bengal, India.
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16
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Sampson T. Microbial amyloids in neurodegenerative amyloid diseases. FEBS J 2023:10.1111/febs.17023. [PMID: 38041542 PMCID: PMC11144261 DOI: 10.1111/febs.17023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023]
Abstract
Human-disease associated amyloidogenic proteins are not unique in their ability to form amyloid fibrillar structures. Numerous microbes produce amyloidogenic proteins that have distinct functions for their physiology in their amyloid form, rather than solely detrimental. Emerging data indicate associations between various microbial organisms, including those which produce functional amyloids, with neurodegenerative diseases. Here, we review some of the evidence suggesting that microbial amyloids impact amyloid disease in host organisms. Experimental data are building a foundation for continued lines of enquiry and suggest that that direct or indirect interactions between microbial and host amyloids may be a contributor to amyloid pathologies. Inhibiting microbial amyloids or their interactions with the host may therefore represent a tangible target to limit various amyloid pathologies.
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Affiliation(s)
- Timothy Sampson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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17
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Louros N, Schymkowitz J, Rousseau F. Mechanisms and pathology of protein misfolding and aggregation. Nat Rev Mol Cell Biol 2023; 24:912-933. [PMID: 37684425 DOI: 10.1038/s41580-023-00647-2] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/28/2023] [Indexed: 09/10/2023]
Abstract
Despite advances in machine learning-based protein structure prediction, we are still far from fully understanding how proteins fold into their native conformation. The conventional notion that polypeptides fold spontaneously to their biologically active states has gradually been replaced by our understanding that cellular protein folding often requires context-dependent guidance from molecular chaperones in order to avoid misfolding. Misfolded proteins can aggregate into larger structures, such as amyloid fibrils, which perpetuate the misfolding process, creating a self-reinforcing cascade. A surge in amyloid fibril structures has deepened our comprehension of how a single polypeptide sequence can exhibit multiple amyloid conformations, known as polymorphism. The assembly of these polymorphs is not a random process but is influenced by the specific conditions and tissues in which they originate. This observation suggests that, similar to the folding of native proteins, the kinetics of pathological amyloid assembly are modulated by interactions specific to cells and tissues. Here, we review the current understanding of how intrinsic protein conformational propensities are modulated by physiological and pathological interactions in the cell to shape protein misfolding and aggregation pathology.
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Affiliation(s)
- Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Leuven, Belgium.
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium.
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18
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Cheng Y, Han J, Song M, Zhang S, Cao Q. Serine peptidase Vpr forms enzymatically active fibrils outside Bacillus bacteria revealed by cryo-EM. Nat Commun 2023; 14:7503. [PMID: 37980359 PMCID: PMC10657474 DOI: 10.1038/s41467-023-43359-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 11/08/2023] [Indexed: 11/20/2023] Open
Abstract
Bacteria develop a variety of extracellular fibrous structures crucial for their survival, such as flagella and pili. In this study, we use cryo-EM to identify protein fibrils surrounding lab-cultured Bacillus amyloiquefaciens and discover an unreported fibril species in addition to the flagellar fibrils. These previously unknown fibrils are composed of Vpr, an extracellular serine peptidase. We find that Vpr assembles into fibrils in an enzymatically active form, potentially representing a strategy of enriching Vpr activities around bacterial cells. Vpr fibrils are also observed under other culture conditions and around other Bacillus bacteria, such as Bacillus subtilis, which may suggest a general mechanism across all Bacillus bacterial groups. Taken together, our study reveals fibrils outside the bacterial cell and sheds light on the physiological role of these extracellular fibrils.
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Affiliation(s)
- Yijia Cheng
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jianting Han
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Meinai Song
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Shuqin Zhang
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qin Cao
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China.
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19
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Sinha A, Kummer N, Wu T, De France KJ, Pinotsi D, Thoma JL, Fischer P, Campioni S, Nyström G. Nanocellulose aerogels as 3D amyloid templates. NANOSCALE 2023; 15:17785-17792. [PMID: 37909800 PMCID: PMC10653027 DOI: 10.1039/d3nr02109b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 08/23/2023] [Indexed: 11/03/2023]
Abstract
Proteins in solution tend to coat solid surfaces upon exposure. Depending on the nature of the surface, the environmental conditions, and the nature of the protein these adsorbed proteins may self-assemble into ordered, fibre-like structures called amyloids. Nanoparticulate surfaces, with their high surface to volume ratio, are particularly favourable to amyloid formation. Most prior research has focussed on either inorganic or organic nanoparticles in solution. In this research, we instead focus on aerogels created from TEMPO-oxidized cellulose nanofibers (TO-CNF) to serve as bio-based, three-dimensional amyloid templates with a tuneable surface chemistry. Previous research on the use of cellulose as a protein adsorption template has shown no evidence of a change in the secondary protein structure. Herein, however, with the aid of the reducing agent TCEP, we were able to induce the formation of amyloid-like 'worms' on the surface of TO-CNF aerogels. Furthermore, we demonstrate that the addition of the TO-CNF aerogel can also induce bulk aggregation under conditions where it previously did not exist. Finally, we show that the addition of the aerogel increases the rate of 'worm' formation in conditions where previous research has found a long lag-phase. Therefore, TO-CNF aerogels are shown to be excellent templates for inducing ordered protein aggregation.
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Affiliation(s)
- Ashutosh Sinha
- Laboratory for Cellulose and Wood Materials, Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Nico Kummer
- Laboratory for Cellulose and Wood Materials, Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Tingting Wu
- Laboratory for Cellulose and Wood Materials, Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
| | - Kevin J De France
- Laboratory for Cellulose and Wood Materials, Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
| | - Dorothea Pinotsi
- Scientific Centre for Optical and Electron Microscopy, ETH Zurich, 8093, Zurich, Switzerland
| | - Janine L Thoma
- Laboratory for Cellulose and Wood Materials, Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
| | - Peter Fischer
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
| | - Silvia Campioni
- Laboratory for Cellulose and Wood Materials, Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
| | - Gustav Nyström
- Laboratory for Cellulose and Wood Materials, Empa, Überlandstrasse 129, 8600 Dübendorf, Switzerland.
- Institute of Food Nutrition and Health, ETH Zürich, Schmelzbergstrasse 7, 8092 Zürich, Switzerland
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20
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Marichal L, Bagnard L, Sire O, Vendrely C, Bruckert F, Weidenhaupt M. Phenol-soluble modulins form amyloids in contact with multiple surface chemistries. Biochim Biophys Acta Gen Subj 2023; 1867:130450. [PMID: 37640168 DOI: 10.1016/j.bbagen.2023.130450] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2023] [Revised: 08/24/2023] [Accepted: 08/25/2023] [Indexed: 08/31/2023]
Abstract
Functional amyloids are commonly produced by many microorganisms and their biological functions are numerous. Staphylococcus aureus can secrete a group of peptides named phenol-soluble modulins (PSMs) in their biofilm extracellular matrix. PSMs have been found inside biofilms both in their soluble form and assembled into amyloid structures. Yet, the actual biological function of these amyloids has been highly debated. Here, we assessed the ability of PSMs to form amyloids in contact with different abiotic surfaces to unravel a potential unknown bioadhesive and/or biofilm stabilization function. We combined surface plasmon resonance imaging, fluorescence aggregation kinetics, and FTIR spectroscopy in order to evaluate the PSM adsorption as well as amyloid formation properties in the presence of various surface chemistries. Overall, PSMs adsorb even on low-binding surfaces, making them highly adaptable adsorbants in the context of bioadhesion. Moreover, the PSM aggregation potential to form amyloid aggregates is not impacted by the presence of the surface chemistries tested. This versatility regarding adsorption and amyloid formation may imply a possible role of PSMs in biofilm adhesion and/or structure integrity.
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Affiliation(s)
- Laurent Marichal
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
| | - Lucie Bagnard
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
| | - Olivier Sire
- IRDL, UMR CNRS 6027, Université Bretagne Sud, Vannes, France
| | - Charlotte Vendrely
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
| | - Franz Bruckert
- Université Grenoble Alpes, CNRS, Grenoble-INP LMGP, Grenoble F-38000, France
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21
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Franco EM, Alves LA, Naveed H, Freitas VAA, Bastos DC, Mattos-Graner RO. Amyloid Fibrils Produced by Streptococcus sanguinis Contribute to Biofilm Formation and Immune Evasion. Int J Mol Sci 2023; 24:15686. [PMID: 37958670 PMCID: PMC10647432 DOI: 10.3390/ijms242115686] [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: 10/06/2023] [Accepted: 10/20/2023] [Indexed: 11/15/2023] Open
Abstract
Bacterial surface proteins assembled into amyloids contribute to biofilm formation and host immune evasion. Streptococcus sanguinis, a pioneer colonizer of teeth commonly involved in cardiovascular infections, expresses about thirty-three proteins anchored to the cell wall by sortase A. Here, we characterized the production of amyloid in S. sanguinis strains differing in biofilm and immune evasion phenotypes and investigated the role of sortase A in amyloidogenesis. Amyloid was identified in biofilms formed by nine strains, using Congo red (CR) staining and cross-polarized light microscopy. Additionally, EGCG, an amyloid inhibitor, impaired biofilm maturation in a strain-specific fashion. The amounts of amyloid-like components quantified in culture fluids of nine strains using thioflavin T and fluorimetry negatively correlated with bacterial binding to complement-activating proteins (SAP, C1q), C3b deposition and rates of opsonophagocytosis in PMNs, implying amyloid production in immune evasion. The deletion of the sortase A gene (srtA) in strain SK36 compromised amyloid production and sucrose-independent biofilm maturation. The srtA mutant further showed increased susceptibility to C3b deposition and altered interactions with PMNs as well as reduced persistence in human blood. These findings highlight the contribution of amyloids to biofilm formation and host immune evasion in S. sanguinis strains, further indicating the participation of sortase A substrates in amyloidogenesis.
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Affiliation(s)
- Eduardo M. Franco
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas, Piracicaba 13414-903, SP, Brazil; (E.M.F.); (L.A.A.); (H.N.); (V.A.A.F.)
| | - Lívia A. Alves
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas, Piracicaba 13414-903, SP, Brazil; (E.M.F.); (L.A.A.); (H.N.); (V.A.A.F.)
- School of Dentistry, Cruzeiro do Sul University (UNICSUL), São Paulo 01506-000, SP, Brazil
| | - Hassan Naveed
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas, Piracicaba 13414-903, SP, Brazil; (E.M.F.); (L.A.A.); (H.N.); (V.A.A.F.)
| | - Victor A. A. Freitas
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas, Piracicaba 13414-903, SP, Brazil; (E.M.F.); (L.A.A.); (H.N.); (V.A.A.F.)
| | - Débora C. Bastos
- Department of Biosciences, Piracicaba Dental School, State University of Campinas, Piracicaba 13414-903, SP, Brazil;
- São Leopoldo Mandic Medical School, Campinas 13045-755, SP, Brazil
| | - Renata O. Mattos-Graner
- Department of Oral Diagnosis, Piracicaba Dental School, State University of Campinas, Piracicaba 13414-903, SP, Brazil; (E.M.F.); (L.A.A.); (H.N.); (V.A.A.F.)
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22
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Aguilera P, Berríos-Pastén C, Veloso M, Gálvez-Silva M, Turbant F, Lagos R, Wien F, Arluison V, Marcoleta AE. The Green Tea Polyphenol Epigallocatechin-Gallate (EGCG) Interferes with Microcin E492 Amyloid Formation. Molecules 2023; 28:7262. [PMID: 37959682 PMCID: PMC10648153 DOI: 10.3390/molecules28217262] [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: 09/22/2023] [Revised: 10/09/2023] [Accepted: 10/17/2023] [Indexed: 11/15/2023] Open
Abstract
Microcin E492 (MccE492) is an antimicrobial peptide and proposed virulence factor produced by some Klebsiella pneumoniae strains, which, under certain conditions, form amyloid fibers, leading to the loss of its antibacterial activity. Although this protein has been characterized as a model functional amyloid, the secondary structure transitions behind its formation, and the possible effect of molecules that inhibit this process, have not been investigated. In this study, we examined the ability of the green tea flavonoid epigallocatechin gallate (EGCG) to interfere with MccE492 amyloid formation. Aggregation kinetics followed by thioflavin T binding were used to monitor amyloid formation in the presence or absence of EGCG. Additionally, synchrotron radiation circular dichroism (SRCD) and transmission electron microscopy (TEM) were used to study the secondary structure, thermal stability, and morphology of microcin E492 fibers. Our results showed that EGCG significantly inhibited the formation of the MccE492 amyloid, resulting in mainly amorphous aggregates and small oligomers. However, these aggregates retained part of the β-sheet SRCD signal and a high resistance to heat denaturation, suggesting that the aggregation process is sequestered or deviated at some stage but not completely prevented. Thus, EGCG is an interesting inhibitor of the amyloid formation of MccE492 and other bacterial amyloids.
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Affiliation(s)
- Paulina Aguilera
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Marcelo Veloso
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Matías Gálvez-Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Florian Turbant
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.)
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
| | - Frank Wien
- Synchrotron SOLEIL, L’Orme des Merisiers, Saint Aubin BP48, 91192 Gif-sur-Yvette, France; (F.T.); (F.W.)
| | - Veronique Arluison
- Laboratoire Léon Brillouin LLB, CEA, CNRS UMR12, Université Paris-Saclay, CEA Saclay, 91191 Gif-sur-Yvette, France
- UFR Sciences du Vivant, Université Paris Cité, 75006 Paris, France
| | - Andrés E. Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425 Ñuñoa, Santiago 7800003, Chile; (P.A.); (C.B.-P.); (M.V.); (M.G.-S.); (R.L.)
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23
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Parladé E, Sánchez JM, López-Laguna H, Unzueta U, Villaverde A, Vázquez E. Protein features instruct the secretion dynamics from metal-supported synthetic amyloids. Int J Biol Macromol 2023; 250:126164. [PMID: 37549767 DOI: 10.1016/j.ijbiomac.2023.126164] [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: 05/16/2023] [Revised: 08/03/2023] [Accepted: 08/04/2023] [Indexed: 08/09/2023]
Abstract
Hexahistidine-tagged proteins can be clustered by divalent cations into self-containing, dynamic protein depots at the microscale, which under physiological conditions leak functional protein. While such protein granules show promise in clinics as time-sustained drug delivery systems, little is known about how the nature of their components, that is, the protein and the particular cation used as cross-linker, impact on the disintegration of the material and on its secretory performance. By using four model proteins and four different cation formulations to control aggregation, we have here determined a moderate influence of the used cation and a potent impact of some protein properties on the release kinetics and on the final fraction of releasable protein. In particular, the electrostatic charge at the amino terminus and the instability and hydropathicity indexes determine the disintegration profile of the depot. These data offer clues for the fabrication of efficient and fully exploitable secretory granules that being biocompatible and chemically homogenous allow their tailored use as drug delivery platforms in biological systems.
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Affiliation(s)
- Eloi Parladé
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
| | - Julieta M Sánchez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departamento de Química, Cátedra de Química Biológica, Facultad de Ciencias Exactas, Físicas y Naturales, ICTA, Universidad Nacional de Córdoba, Av. Vélez Sársfield 1611, Córdoba 5016, Argentina; Instituto de Investigaciones Biológicas y Tecnológicas (IIByT), CONICET-Universidad Nacional de Córdoba, Córdoba 5016, Argentina
| | - Hèctor López-Laguna
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ugutz Unzueta
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut d'Investigació Biomèdica Sant Pau (IIB SANT PAU), Sant Quintí 77-79, 08041 Barcelona, Spain; Josep Carreras Leukaemia Research Institute, 08025 Barcelona, Spain
| | - Antonio Villaverde
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Esther Vázquez
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN, ISCIII), Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
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24
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Cámara-Almirón J, Domínguez-García L, El Mammeri N, Lends A, Habenstein B, de Vicente A, Loquet A, Romero D. Molecular characterization of the N-terminal half of TasA during amyloid-like assembly and its contribution to Bacillus subtilis biofilm formation. NPJ Biofilms Microbiomes 2023; 9:68. [PMID: 37739955 PMCID: PMC10516879 DOI: 10.1038/s41522-023-00437-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Biofilms are bacterial communities that result from a cell differentiation process leading to the secretion of an extracellular matrix (ECM) by part of the population. In Bacillus subtilis, the main protein component of the ECM is TasA, which forms a fiber-based scaffold that confers structure to the ECM. The N-terminal half of TasA is strongly conserved among Bacillus species and contains a protein domain, the rigid core (RcTasA), which is critical for the structural and functional properties of the recombinant protein. In this study, we demonstrate that recombinantly purified RcTasA in vitro retains biochemical properties previously observed for the entire protein. Further analysis of the RcTasA amino acid sequence revealed two aggregation-prone stretches and a region of imperfect amino acid repeats, which are known to contribute to functional amyloid assembly. Biochemical characterization of these stretches found in RcTasA revealed their amyloid-like capacity in vitro, contributing to the amyloid nature of RcTasA. Moreover, the study of the imperfect amino acid repeats revealed the critical role of residues D64, K68 and D69 in the structural function of TasA. Experiments with versions of TasA carrying the substitutions D64A and K68AD69A demonstrated a partial loss of function of the protein either in the assembly of the ECM or in the stability of the core and amyloid-like properties. Taken together, our findings allow us to better understand the polymerization process of TasA during biofilm formation and provide knowledge into the sequence determinants that promote the molecular behavior of protein filaments in bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, Switzerland
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Nadia El Mammeri
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV, 1006, Latvia
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Antonio de Vicente
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain.
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25
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Pitocchi R, Stanzione I, Illiano A, Amoresano A, Tarallo O, Cicatiello P, Piscitelli A, Giardina P. Evidence of Small Fungal Cysteine-Rich Proteins Acting as Biosurfactants and Self-Assembling into Large Fibers. Int J Mol Sci 2023; 24:13843. [PMID: 37762146 PMCID: PMC10531366 DOI: 10.3390/ijms241813843] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 09/04/2023] [Accepted: 09/06/2023] [Indexed: 09/29/2023] Open
Abstract
Fungi produce surface-active proteins, among which hydrophobins are the most characterized and attractive also for their ability to form functional amyloids. Our most recent findings show that these abilities are shared with other classes of fungal proteins. Indeed, in this paper, we compared the characteristics of a class I hydrophobin (Vmh2 from Pleurotus ostreatus) and an unknown protein (named PAC3), extracted from the marine fungal strain Acremonium sclerotigenum, which does not belong to the same protein family based on its sequence features. They both proved to be good biosurfactants, stabilizing emulsions in several conditions (concentration, pH, and salinity) and decreasing surface tension to a comparable value to that of some synthetic surfactants. After that, we observed for both Vmh2 and PAC3 the formation of giant fibers without the need for harsh conditions or long incubation time, a remarkable ability herein reported for the first time.
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Affiliation(s)
| | | | | | | | | | - Paola Cicatiello
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia, 80126 Naples, Italy; (R.P.); (I.S.); (A.I.); (A.A.); (O.T.); (A.P.); (P.G.)
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26
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Nowakowska AW, Wojciechowski JW, Szulc N, Kotulska M. The role of tandem repeats in bacterial functional amyloids. J Struct Biol 2023; 215:108002. [PMID: 37482232 DOI: 10.1016/j.jsb.2023.108002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/05/2023] [Accepted: 07/20/2023] [Indexed: 07/25/2023]
Abstract
Repetitivity and modularity of proteins are two related notions incorporated into multiple evolutionary concepts. We discuss whether they may also be essential for functional amyloids. Amyloids are proteins that create very regular and usually highly insoluble fibrils, which are often associated with neurodegeneration. However, recent discoveries showed that amyloid structure of a protein could also be beneficial and desired, e.g., to promote cell adhesion. Functional amyloids are proteins which differ in their characteristics from pathological amyloids, so that the fibril formation could be more under control of an organism. We propose that repeats in the sequence could regulate the aggregation propensity of these proteins. The inclusion of multiple symmetric interactions, due to the presence of the repeats, could be supporting and strengthening the desirable structural properties of functional amyloids. Our results show that tandem repeats in bacterial functional amyloids have a distinct characteristic. The pattern of repeats supports the appropriate level of fibril formation and better controllability of fibril stability. The repeats tend to be more imperfect, which attenuates excessive aggregation propensity. Their desired structure and function are also reinforced by their amino acid profile. Although in the study we focused on bacterial functional amyloids, due to their importance in biofilm formation, we propose that similar mechanisms could be employed in other functional amyloids which are designed by evolution to aggregate in a desirable manner, but not necessarily in pathological amyloids.
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Affiliation(s)
- Alicja W Nowakowska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
| | - Jakub W Wojciechowski
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland
| | - Natalia Szulc
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland; Wrocław University of Environmental and Life Sciences, Department of Physics and Biophysics, Poland; LPCT, CNRS, Universite de Lorraine, F-54000 Nancy, France
| | - Malgorzata Kotulska
- Wrocław University of Science and Technology, Department of Biomedical Engineering, Poland.
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27
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Álamo P, Parladé E, Favaro MTP, Gallardo A, Mendoza R, Ferreira LC, Roher N, Mangues R, Villaverde A, Vázquez E. Probing the Biosafety of Implantable Artificial Secretory Granules for the Sustained Release of Bioactive Proteins. ACS APPLIED MATERIALS & INTERFACES 2023; 15:39167-39175. [PMID: 37614001 PMCID: PMC10450642 DOI: 10.1021/acsami.3c08643] [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: 06/15/2023] [Accepted: 07/27/2023] [Indexed: 08/25/2023]
Abstract
Among bio-inspired protein materials, secretory protein microparticles are of clinical interest as self-contained, slow protein delivery platforms that mimic secretory granules of the human endocrine system, in which the protein is both the drug and the scaffold. Upon subcutaneous injection, their progressive disintegration results in the sustained release of the building block polypeptides, which reach the bloodstream for systemic distribution and subsequent biological effects. Such entities are easily fabricated in vitro by Zn-assisted cross-molecular coordination of histidine residues. Using cationic Zn for the assembly of selected pure protein species and in the absence of any heterologous holding material, these granules are expected to be nontoxic and therefore adequate for different clinical uses. However, such presumed biosafety has not been so far confirmed and the potential protein dosage threshold not probed yet. By selecting the receptor binding domain (RBD) from the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein as a model protein and using a mouse lab model, we have explored the toxicity of RBD-made secretory granules at increasing doses up to ∼100 mg/kg of animal weight. By monitoring body weight and biochemical blood markers and through the histological scrutiny of main tissues and organs, we have not observed systemic toxicity. Otherwise, the bioavailability of the material was demonstrated by the induction of specific antibody responses. The presented data confirm the intrinsic biosafety of artificial secretory granules made by recombinant proteins and prompt their further clinical development as self-contained and dynamic protein reservoirs.
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Affiliation(s)
- Patricia Álamo
- Institut
d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- Josep
Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
| | - Eloi Parladé
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Marianna T. P. Favaro
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Instituto
de Ciências Biomédicas, Universidade
de São Paulo, São
Paulo 05508-000, Brazil
| | - Alberto Gallardo
- Institut
d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- Department
of Pathology, Hospital de la Santa Creu
i Sant Pau, 08025 Barcelona, Spain
| | - Rosa Mendoza
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Luís C.
S. Ferreira
- Instituto
de Ciências Biomédicas, Universidade
de São Paulo, São
Paulo 05508-000, Brazil
| | - Nerea Roher
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Department
of Cell Biology, Animal Physiology and Immunology, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Ramón Mangues
- Institut
d’Investigació Biomèdica Sant Pau (IIB SANT PAU), 08041 Barcelona, Spain
- Josep
Carreras Leukaemia Research Institute (IJC), 08916 Badalona, Spain
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
| | - Antonio Villaverde
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
| | - Esther Vázquez
- CIBER
de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN,
ISCIII), Universitat Autònoma de
Barcelona, 08193 Bellaterra, Spain
- Institut
de Biotecnologia i de Biomedicina, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
- Departament
de Genètica i de Microbiologia, Universitat
Autònoma de Barcelona, 08193 Bellaterra, Spain
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28
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Sulatsky MI, Belousov MV, Kosolapova AO, Mikhailova EV, Romanenko MN, Antonets KS, Kuznetsova IM, Turoverov KK, Nizhnikov AA, Sulatskaya AI. Amyloid Fibrils of Pisum sativum L. Vicilin Inhibit Pathological Aggregation of Mammalian Proteins. Int J Mol Sci 2023; 24:12932. [PMID: 37629113 PMCID: PMC10454621 DOI: 10.3390/ijms241612932] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/10/2023] [Accepted: 08/15/2023] [Indexed: 08/27/2023] Open
Abstract
Although incurable pathologies associated with the formation of highly ordered fibrillar protein aggregates called amyloids have been known for about two centuries, functional roles of amyloids have been studied for only two decades. Recently, we identified functional amyloids in plants. These amyloids formed using garden pea Pisum sativum L. storage globulin and vicilin, accumulated during the seed maturation and resisted treatment with gastric enzymes and canning. Thus, vicilin amyloids ingested with food could interact with mammalian proteins. In this work, we analyzed the effects of vicilin amyloids on the fibril formation of proteins that form pathological amyloids. We found that vicilin amyloids inhibit the fibrillogenesis of these proteins. In particular, vicilin amyloids decrease the number and length of lysozyme amyloid fibrils; the length and width of β-2-microglobulin fibrils; the number, length and the degree of clustering of β-amyloid fibrils; and, finally, they change the structure and decrease the length of insulin fibrils. Such drastic influences of vicilin amyloids on the pathological amyloids' formation cause the alteration of their toxicity for mammalian cells, which decreases for all tested amyloids with the exception of insulin. Taken together, our study, for the first time, demonstrates the anti-amyloid effect of vicilin fibrils and suggests the mechanisms underlying this phenomenon.
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Affiliation(s)
- Maksim I. Sulatsky
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (M.I.S.); (E.V.M.); (I.M.K.); (K.K.T.)
| | - Mikhail V. Belousov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anastasiia O. Kosolapova
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Ekaterina V. Mikhailova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (M.I.S.); (E.V.M.); (I.M.K.); (K.K.T.)
| | - Maria N. Romanenko
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Irina M. Kuznetsova
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (M.I.S.); (E.V.M.); (I.M.K.); (K.K.T.)
| | - Konstantin K. Turoverov
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (M.I.S.); (E.V.M.); (I.M.K.); (K.K.T.)
| | - Anton A. Nizhnikov
- All-Russia Research Institute for Agricultural Microbiology, 196608 St. Petersburg, Russia; (M.V.B.); (A.O.K.); (M.N.R.); (K.S.A.)
- Faculty of Biology, St. Petersburg State University, 199034 St. Petersburg, Russia
| | - Anna I. Sulatskaya
- Institute of Cytology, Russian Academy of Sciences, 194064 St. Petersburg, Russia; (M.I.S.); (E.V.M.); (I.M.K.); (K.K.T.)
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29
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Naskar S, Gour N. Realization of Amyloid-like Aggregation as a Common Cause for Pathogenesis in Diseases. Life (Basel) 2023; 13:1523. [PMID: 37511898 PMCID: PMC10381831 DOI: 10.3390/life13071523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 06/27/2023] [Accepted: 07/05/2023] [Indexed: 07/30/2023] Open
Abstract
Amyloids were conventionally referred to as extracellular and intracellular accumulation of Aβ42 peptide, which causes the formation of plaques and neurofibrillary tangles inside the brain leading to the pathogenesis in Alzheimer's disease. Subsequently, amyloid-like deposition was found in the etiology of prion diseases, Parkinson's disease, type II diabetes, and cancer, which was attributed to the aggregation of prion protein, α-Synuclein, islet amyloid polypeptide protein, and p53 protein, respectively. Hence, traditionally amyloids were considered aggregates formed exclusively by proteins or peptides. However, since the last decade, it has been discovered that other metabolites, like single amino acids, nucleobases, lipids, glucose derivatives, etc., have a propensity to form amyloid-like toxic assemblies. Several studies suggest direct implications of these metabolite assemblies in the patho-physiology of various inborn errors of metabolisms like phenylketonuria, tyrosinemia, cystinuria, and Gaucher's disease, to name a few. In this review, we present a comprehensive literature overview that suggests amyloid-like structure formation as a common phenomenon for disease progression and pathogenesis in multiple syndromes. The review is devoted to providing readers with a broad knowledge of the structure, mode of formation, propagation, and transmission of different extracellular amyloids and their implications in the pathogenesis of diseases. We strongly believe a review on this topic is urgently required to create awareness about the understanding of the fundamental molecular mechanism behind the origin of diseases from an amyloid perspective and possibly look for a common therapeutic strategy for the treatment of these maladies by designing generic amyloid inhibitors.
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Affiliation(s)
- Soumick Naskar
- Department of Chemistry, Indrashil University, Kadi, Mehsana 382740, Gujarat, India
| | - Nidhi Gour
- Department of Chemistry, Indrashil University, Kadi, Mehsana 382740, Gujarat, India
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30
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Indig RY, Landau M. Designed inhibitors to reduce amyloid virulence and cytotoxicity and combat neurodegenerative and infectious diseases. Curr Opin Chem Biol 2023; 75:102318. [PMID: 37196450 DOI: 10.1016/j.cbpa.2023.102318] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2023] [Revised: 04/10/2023] [Accepted: 04/14/2023] [Indexed: 05/19/2023]
Abstract
The review highlights the role of amyloids in various diseases and the challenges associated with targeting human amyloids in therapeutic development. However, due to the better understanding of microbial amyloids' role as virulence factors, there is a growing interest in repurposing and designing anti-amyloid compounds for antivirulence therapy. The identification of amyloid inhibitors has not only significant clinical implications but also provides valuable insights into the structure and function of amyloids. The review showcases small molecules and peptides that specifically target amyloids in both humans and microbes, reducing cytotoxicity and biofilm formation, respectively. The review emphasizes the importance of further research on amyloid structures, mechanisms, and interactions across all life forms to yield new drug targets and improve the design of selective treatments. Overall, the review highlights the potential for amyloid inhibitors in therapeutic development for both human diseases and microbial infections.
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Affiliation(s)
- Rinat Yona Indig
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel; Centre for Structural Systems Biology (CSSB) and Deutsches Elektronen-Synchrotron DESY, Hamburg, Germany; Universitätsklinikum Hamburg-Eppendorf (UKE), Hamburg, Germany; European Molecular Biology Laboratory (EMBL), Hamburg, Germany.
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31
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,School of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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Haider HI, Zafar I, Ain QU, Noreen A, Nazir A, Javed R, Sehgal SA, Khan AA, Rahman MM, Rashid S, Garai S, Sharma R. Synthesis and characterization of copper oxide nanoparticles: its influence on corn (Z. mays) and wheat (Triticum aestivum) plants by inoculation of Bacillus subtilis. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:37370-37385. [PMID: 36571685 DOI: 10.1007/s11356-022-24877-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 12/15/2022] [Indexed: 06/17/2023]
Abstract
Nanotechnology is now playing an emerging role in green synthesis in agriculture as nanoparticles (NPs) are used for various applications in plant growth and development. Copper is a plant micronutrient; the amount of copper oxide nanoparticles (CuONPs) in the soil determines whether it has positive or adverse effects. CuONPs can be used to grow corn and wheat plants by combining Bacillus subtilis. In this research, CuONPs were synthesized by precipitation method using different precursors such as sodium hydroxide (0.1 M) and copper nitrate (Cu(NO3)2) having 0.1 M concentration with a post-annealing method. The NPs were characterized through X-ray diffraction (XRD), scanning electron microscope (SEM), and ultraviolet (UV) visible spectroscopy. Bacillus subtilis is used as a potential growth promoter for microbial inoculation due to its prototrophic nature. The JAR experiment was conducted, and the growth parameter of corn (Z. mays) and wheat (Triticum aestivum) was recorded after 5 days. The lab assay evaluated the germination in JARs with and without microbial inoculation under CuONP stress at different concentrations (25 and 50 mg). The present study aimed to synthesize CuONPs and systematically investigate the particle size effects of copper (II) oxide (CuONPs) (< 50 nm) on Triticum aestivum and Z. mays. In our results, the XRD pattern of CuONPs at 500 °C calcination temperature with monoclinic phase is observed, with XRD peak intensity slightly increasing. The XRD patterns showed that the prepared CuONPs were extremely natural, crystal-like, and nano-shaped. We used Scherrer's formula to calculate the average size of the particle, indicated as 23 nm. The X-ray diffraction spectrum of synthesized materials and SEM analysis show that the particles of CuONPs were spherical in nature. The results revealed that the synthesized CuONPs combined with Bacillus subtilis used in a field study provided an excellent result, where growth parameters of Z. Mays and Triticum aestivum such as root length, shoot length, and plant biomass was improved as compared to the control group.
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Affiliation(s)
| | - Imran Zafar
- Department of Bioinformatics and Computational Biology, Virtual University of Pakistan, Lahore, Pakistan
| | - Qurat Ul Ain
- Department of Chemistry, Government College Women University, Faisalabad, Pakistan
| | - Asifa Noreen
- Department of Chemistry, Riphah International University, Faisalabad Campus, , Faisalabad, Pakistan
| | - Aamna Nazir
- Department of Chemistry, University of Lahore, Sargodha Campus, Sargodha, Pakistan
| | - Rida Javed
- Department of Chemistry, University of Sargodha, Sargodha, Pakistan
| | - Sheikh Arslan Sehgal
- Department of Bioinformatics, University of Okara, Okara, Pakistan
- Department of Bioinformatics, Institute of Biochemistry, Biotechnology and Bioinformatics, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Md Mominur Rahman
- Department of Pharmacy, Faculty of Allied Health Sciences, Daffodil International University, Dhaka, 1207, Bangladesh
| | - Summya Rashid
- Department of Pharmacology & Toxicology, College of Pharmacy, Prince Sattam Bin Abdulaziz University, P.O. Box 173, Al-Kharj, 11942, Saudi Arabia
| | - Somenath Garai
- Department of Chemistry, Institute of Science, Banaras Hindu University, Varanasi, 221005, India
| | - Rohit Sharma
- Department of Rasa Shastra and Bhaishajya Kalpana, Faculty of Ayurveda, Institute of Medical Science, Banaras Hindu University, Varanasi, 221005, India.
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Flemming HC, van Hullebusch ED, Neu TR, Nielsen PH, Seviour T, Stoodley P, Wingender J, Wuertz S. The biofilm matrix: multitasking in a shared space. Nat Rev Microbiol 2023; 21:70-86. [PMID: 36127518 DOI: 10.1038/s41579-022-00791-0] [Citation(s) in RCA: 161] [Impact Index Per Article: 161.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 01/20/2023]
Abstract
The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates - in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.
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Affiliation(s)
- Hans-Curt Flemming
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.
| | | | - Thomas R Neu
- Department of River Ecology, Helmholtz Centre for Environmental Research - UFZ, Magdeburg, Germany
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Thomas Seviour
- Aarhus University Centre for Water Technology, Department of Biological and Chemical Engineering, Aarhus University, Aarhus, Denmark
| | - Paul Stoodley
- Department of Microbial Infection and Immunity, The Ohio State University, Columbus, OH, USA.,Department of Orthopaedics, The Ohio State University, Columbus, OH, USA
| | - Jost Wingender
- University of Duisburg-Essen, Biofilm Centre, Department of Aquatic Microbiology, Essen, Germany
| | - Stefan Wuertz
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
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34
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Diaz-Espinoza R. Catalytically Active Amyloids as Future Bionanomaterials. NANOMATERIALS (BASEL, SWITZERLAND) 2022; 12:3802. [PMID: 36364578 PMCID: PMC9656882 DOI: 10.3390/nano12213802] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/14/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Peptides and proteins can aggregate into highly ordered and structured conformations called amyloids. These supramolecular structures generally have convergent features, such as the formation of intermolecular beta sheets, that lead to fibrillary architectures. The resulting fibrils have unique mechanical properties that can be exploited to develop novel nanomaterials. In recent years, sequences of small peptides have been rationally designed to self-assemble into amyloids that catalyze several chemical reactions. These amyloids exhibit reactive surfaces that can mimic the active sites of enzymes. In this review, I provide a state-of-the-art summary of the development of catalytically active amyloids. I will focus especially on catalytic activities mediated by hydrolysis, which are the most studied examples to date, as well as novel types of recently reported activities that promise to expand the possible repertoires. The combination of mechanical properties with catalytic activity in an amyloid scaffold has great potential for the development of future bionanomaterials aimed at specific applications.
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Affiliation(s)
- Rodrigo Diaz-Espinoza
- Departamento de Biología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago 3363, Chile
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Yarmola E, Ishkov IP, di Cologna NM, Menashe M, Whitener RL, Long JR, Abranches J, Hagen SJ, Brady LJ. Amyloid Aggregates Are Localized to the Nonadherent Detached Fraction of Aging Streptococcus mutans Biofilms. Microbiol Spectr 2022; 10:e0166122. [PMID: 35950854 PMCID: PMC9431626 DOI: 10.1128/spectrum.01661-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 07/21/2022] [Indexed: 11/23/2022] Open
Abstract
The number of bacterial species recognized to utilize purposeful amyloid aggregation within biofilms continues to grow. The oral pathogen Streptococcus mutans produces several amyloidogenic proteins, including adhesins P1 (also known as AgI/II, PAc) and WapA, whose truncation products, namely, AgII and AgA, respectively, represent the amyloidogenic moieties. Amyloids demonstrate common biophysical properties, including recognition by Thioflavin T (ThT) and Congo red (CR) dyes that bind to the cross β-sheet quaternary structure of amyloid aggregates. Previously, we observed amyloid formation to occur only after 60 h or more of S. mutans biofilm growth. Here, we extend those findings to investigate where amyloid is detected within 1- and 5-day-old biofilms, including within tightly adherent compared with those in nonadherent fractions. CR birefringence and ThT uptake demonstrated amyloid within nonadherent material removed from 5-day-old cultures but not within 1-day-old or adherent samples. These experiments were done in conjunction with confocal microscopy and immunofluorescence staining with AgII- and AgA-reactive antibodies, including monoclonal reagents shown to discriminate between monomeric protein and amyloid aggregates. These results also localized amyloid primarily to the nonadherent fraction of biofilms. Lastly, we show that the C-terminal region of P1 loses adhesive function following amyloidogenesis and is no longer able to competitively inhibit binding of S. mutans to its physiologic substrate, salivary agglutinin. Taken together, our results provide new evidence that amyloid aggregation negatively impacts the functional activity of a widely studied S. mutans adhesin and are consistent with a model in which amyloidogenesis of adhesive proteins facilitates the detachment of aging biofilms. IMPORTANCE Streptococcus mutans is a keystone pathogen and causative agent of human dental caries, commonly known as tooth decay, the most prevalent infectious disease in the world. Like many pathogens, S. mutans causes disease in biofilms, which for dental decay begins with bacterial attachment to the salivary pellicle coating the tooth surface. Some strains of S. mutans are also associated with bacterial endocarditis. Amyloid aggregation was initially thought to represent only a consequence of protein mal-folding, but now, many microorganisms are known to produce functional amyloids with biofilm environments. In this study, we learned that amyloid formation diminishes the activity of a known S. mutans adhesin and that amyloid is found within the nonadherent fraction of older biofilms. This finding suggests that the transition from adhesin monomer to amyloid facilitates biofilm detachment. Knowing where and when S. mutans produces amyloid will help in developing therapeutic strategies to control tooth decay and other biofilm-related diseases.
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Affiliation(s)
- Elena Yarmola
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Ivan P. Ishkov
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | | | - Megan Menashe
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Robert L. Whitener
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
| | - Joanna R. Long
- Department of Biochemistry and Molecular Biology, University of Florida, Gainesville, Florida, USA
| | | | - Stephen J. Hagen
- Department of Physics, University of Florida, Gainesville, Florida, USA
| | - L. Jeannine Brady
- Department of Oral Biology, University of Florida, Gainesville, Florida, USA
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36
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Azam MW, Khan AU. CRISPRi -mediated suppression of E. coli Nissle 1917 virulence factors: A strategy for creating an engineered probiotic using csgD gene suppression. Front Nutr 2022; 9:938989. [PMID: 35978963 PMCID: PMC9376613 DOI: 10.3389/fnut.2022.938989] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 06/29/2022] [Indexed: 11/13/2022] Open
Abstract
Background Biofilm formation is a complex phenomenon, and it is the causative agent of several human infections. Bacterial amyloids are involved in biofilm formation leading to infection persistence. Due to antibiotic resistance, their treatment is a great challenge for physicians. Probiotics, especially E. coli Nissle 1917 (EcN), are used to treat human intestinal disorders and ulcerative colitis. It also expresses virulence factors associated with biofilm and amyloid formation. EcN produces biofilm equivalent to the pathogenic UPEC strains. Methods CRISPRi was used to create the knockdown mutants of the csgD gene (csgD-KD). The qRT-PCR was performed to assess the expression of the csgD gene in csgD-KD cells. The csgD-KD cells were also evaluated for the expression of csgA, csgB, fimA, fimH, ompR, luxS, and bolA genes. The gene expression data obtained was further confirmed by spectroscopic, microscopic, and other assays to validate our study. Results CRISPRi-mediated knockdown of csgD gene shows reduction in curli amyloid formation, biofilm formation, and suppression of genes (csgA, csgB, fimA, fimH, ompR, bolA, and luxS) involved in virulence factors production. Conclusion Curli amyloid fibers and fimbriae fibers play a critical role in biofilm formation leading to pathogenicity. CsgD protein is the master regulator of curli synthesis in E. coli. Hence, curli amyloid inhibition through the csgD gene may be used to improve the EcN and different probiotic strains by suppressing virulence factors.
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Affiliation(s)
- Mohd W Azam
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
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37
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Arad E, Jelinek R. Catalytic amyloids. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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38
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Liu M, Meng P, Chen G, Guan Y, Liu G. Correlation of structural extracellular polymeric substances in the mesh biofilms with solids retention time and biofilm hydraulic resistance in dynamic membrane bioreactors. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 832:155000. [PMID: 35381253 DOI: 10.1016/j.scitotenv.2022.155000] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 03/19/2022] [Accepted: 03/30/2022] [Indexed: 06/14/2023]
Abstract
Dynamic membrane bioreactor (DMBR), which mainly relied on the in-situ formed biofilms on support materials with large aperture (e.g., nylon mesh) to separate fine particles in wastewater, has attracted a lot of attentions due to low cost. The filtration performance of DMBR is mainly determined by the structure and hydraulic resistance of biofilms formed on the mesh. Therefore, understanding the correlation of operation conditions with mesh biofilm compositions and permeability are critically important for optimizing DMBR operation. In present study, how structural extracellular polymeric substances, including alginate-like extracellular polysaccharide (ALE) and amyloid-like protein (AP), in mesh biofilms correlate to solids retention time (SRT) and biofilm structures was explored in DMBRs. At 5d-SRT, compact and gel-like mesh biofilms were formed with a high specific filtration resistance (SFR) of 459 × 109 m/g, while at 40d-SRT porous mesh biofilms were developed with a low SFR of 24 × 109 m/g. Consequently, the 5d-SRT MBR experienced more rapid rise in transmembrane pressure. Further studies found that the 5d-SRT mesh biofilms had a higher AP content, which was positively correlated to biofilm hydraulic resistance. On the contrary, the 40d-SRT mesh biofilms contained a higher content of ALE, suggesting that ALE was negatively correlated to biofilm hydraulic resistance. Therefore, AP instead of ALE likely played a more important role in the formation of compact and gel-like mesh biofilms.
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Affiliation(s)
- Mai Liu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Peipei Meng
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Guichang Chen
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China
| | - Ying Guan
- Department of Biostatistics, School of Public Health, Southern Medical University, Guangzhou 510515, China.
| | - Guoqiang Liu
- School of Environment, Guangdong Engineering Research Center of Water Treatment Processes and Materials, Guangdong Key Laboratory of Environmental Pollution and Health, Jinan University, Guangzhou 510632, China.
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39
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Bücker R, Seuring C, Cazey C, Veith K, García-Alai M, Grünewald K, Landau M. The Cryo-EM structures of two amphibian antimicrobial cross-β amyloid fibrils. Nat Commun 2022; 13:4356. [PMID: 35896552 PMCID: PMC9329304 DOI: 10.1038/s41467-022-32039-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2022] [Accepted: 07/13/2022] [Indexed: 12/14/2022] Open
Abstract
The amyloid-antimicrobial link hypothesis is based on antimicrobial properties found in human amyloids involved in neurodegenerative and systemic diseases, along with amyloidal structural properties found in antimicrobial peptides (AMPs). Supporting this hypothesis, we here determined the fibril structure of two AMPs from amphibians, uperin 3.5 and aurein 3.3, by cryogenic electron microscopy (cryo-EM), revealing amyloid cross-β fibrils of mated β-sheets at atomic resolution. Uperin 3.5 formed a 3-blade symmetrical propeller of nine peptides per fibril layer including tight β-sheet interfaces. This cross-β cryo-EM structure complements the cross-α fibril conformation previously determined by crystallography, substantiating a secondary structure switch mechanism of uperin 3.5. The aurein 3.3 arrangement consisted of six peptides per fibril layer, all showing kinked β-sheets allowing a rounded compactness of the fibril. The kinked β-sheets are similar to LARKS (Low-complexity, Amyloid-like, Reversible, Kinked Segments) found in human functional amyloids. In this work the authors provide high-resolution structural support for the amyloid-antimicrobial link via functional amyloids displaying propeller-like and kinked cross-β fibrils.
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Affiliation(s)
- Robert Bücker
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Rigaku Europe SE, Neu-Isenburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Carolin Seuring
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany.,Leibniz Institute of Virology, Hamburg, Germany
| | - Cornelia Cazey
- Centre for Structural Systems Biology, Hamburg, Germany.,Department of Chemistry, University of Hamburg, Hamburg, Germany
| | - Katharina Veith
- European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Maria García-Alai
- Centre for Structural Systems Biology, Hamburg, Germany.,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany
| | - Kay Grünewald
- Centre for Structural Systems Biology, Hamburg, Germany. .,Department of Chemistry, University of Hamburg, Hamburg, Germany. .,Leibniz Institute of Virology, Hamburg, Germany. .,Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
| | - Meytal Landau
- Centre for Structural Systems Biology, Hamburg, Germany. .,European Molecular Biology Laboratory, EMBL Hamburg, Hamburg, Germany. .,Department of Biology, Technion-Israel Institute of Technology, Haifa, 3200003, Israel.
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40
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Golan N, Engelberg Y, Landau M. Structural Mimicry in Microbial and Antimicrobial Amyloids. Annu Rev Biochem 2022; 91:403-422. [PMID: 35729071 DOI: 10.1146/annurev-biochem-032620-105157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The remarkable variety of microbial species of human pathogens and microbiomes generates significant quantities of secreted amyloids, which are structured protein fibrils that serve diverse functions related to virulence and interactions with the host. Human amyloids are associated largely with fatal neurodegenerative and systemic aggregation diseases, and current research has put forward the hypothesis that the interspecies amyloid interactome has physiological and pathological significance. Moreover, functional and molecular-level connections between antimicrobial activity and amyloid structures suggest a neuroimmune role for amyloids that are otherwise known to be pathological. Compared to the extensive structural information that has been accumulated for human amyloids, high-resolution structures of microbial and antimicrobial amyloids are only emerging. These recent structures reveal both similarities and surprising departures from the typical amyloid motif, in accordance with their diverse activities, and advance the discovery of novel antivirulence and antimicrobial agents. In addition, the structural information has led researchers to postulate that amyloidogenic sequences are natural targets for structural mimicry, for instance in host-microbe interactions. Microbial amyloid research could ultimately be used to fight aggressive infections and possibly processes leading to autoimmune and neurodegenerative diseases.
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Affiliation(s)
- Nimrod Golan
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Yizhaq Engelberg
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel;
| | - Meytal Landau
- Department of Biology, Technion-Israel Institute of Technology, Haifa, Israel; .,European Molecular Biology Laboratory (EMBL) and Center for Structural Systems Biology (CSSB), Hamburg, Germany
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41
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Akbey Ü, Andreasen M. Functional amyloids from bacterial biofilms - structural properties and interaction partners. Chem Sci 2022; 13:6457-6477. [PMID: 35756505 PMCID: PMC9172111 DOI: 10.1039/d2sc00645f] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [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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42
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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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43
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Computational methods to predict protein aggregation. Curr Opin Struct Biol 2022; 73:102343. [PMID: 35240456 DOI: 10.1016/j.sbi.2022.102343] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 12/20/2021] [Accepted: 01/17/2022] [Indexed: 01/13/2023]
Abstract
In most cases, protein aggregation stems from the establishment of non-native intermolecular contacts. The formation of insoluble protein aggregates is associated with many human diseases and is a major bottleneck for the industrial production of protein-based therapeutics. Strikingly, fibrillar aggregates are naturally exploited for structural scaffolding or to generate molecular switches and can be artificially engineered to build up multi-functional nanomaterials. Thus, there is a high interest in rationalizing and forecasting protein aggregation. Here, we review the available computational toolbox to predict protein aggregation propensities, identify sequential or structural aggregation-prone regions, evaluate the impact of mutations on aggregation or recognize prion-like domains. We discuss the strengths and limitations of these algorithms and how they can evolve in the next future.
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44
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Vendrell-Fernández S, Lozano-Picazo P, Cuadros-Sánchez P, Tejero-Ojeda MM, Giraldo R. Conversion of the OmpF Porin into a Device to Gather Amyloids on the E. coli Outer Membrane. ACS Synth Biol 2022; 11:655-667. [PMID: 34852197 DOI: 10.1021/acssynbio.1c00347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein amyloids are ubiquitous in natural environments. They typically originate from microbial secretions or spillages from mammals infected by prions, currently raising concerns about their infectivity and toxicity in contexts such as gut microbiota or soils. Exploiting the self-assembly potential of amyloids for their scavenging, here, we report the insertion of an amyloidogenic sequence stretch from a bacterial prion-like protein (RepA-WH1) in one of the extracellular loops (L5) of the abundant Escherichia coli outer membrane porin OmpF. The expression of this grafted porin enables bacterial cells to trap on their envelopes the same amyloidogenic sequence when provided as an extracellular free peptide. Conversely, when immobilized on a surface as bait, the full-length prion-like protein including the amyloidogenic peptide can catch bacteria displaying the L5-grafted OmpF. Polyphenolic molecules known to inhibit amyloid assembly interfere with peptide recognition by the engineered OmpF, indicating that this is compatible with the kind of homotypic interactions expected for amyloid assembly. Our study suggests that synthetic porins may provide suitable scaffolds for engineering biosensor and clearance devices to tackle the threat posed by pathogenic amyloids.
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Affiliation(s)
- Sol Vendrell-Fernández
- Department of Microbial Biotechnology, National Centre for Biotechnology (CSIC), c/ Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain
| | - Paloma Lozano-Picazo
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), c/ Ramiro de Maeztu 9, Campus Moncloa, 28040 Madrid, Spain
| | - Paula Cuadros-Sánchez
- Department of Microbial Biotechnology, National Centre for Biotechnology (CSIC), c/ Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain
| | - María M. Tejero-Ojeda
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), c/ Ramiro de Maeztu 9, Campus Moncloa, 28040 Madrid, Spain
| | - Rafael Giraldo
- Department of Microbial Biotechnology, National Centre for Biotechnology (CSIC), c/ Darwin 3, Campus Cantoblanco, 28049 Madrid, Spain
- Department of Cellular and Molecular Biology, Centro de Investigaciones Biológicas (CSIC), c/ Ramiro de Maeztu 9, Campus Moncloa, 28040 Madrid, Spain
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Abstract
This mini-review represents a brief, disorder-centric consideration of the interplay between order and disorder in proteins. The goal here is to show that inside the cell, folding, non-folding, and misfolding of proteins are interlinked on multiple levels. This is evidenced by the highly heterogeneous spatio-temporal structural organization of a protein molecule, where one can find differently (dis)ordered components that can undergo local or global order-to-disorder and disorder-to-order transitions needed for functionality. This is further illustrated by the fact that at particular moments of their life, most notably during their synthesis and degradation, all proteins are at least partially disordered. In addition to these intrinsic forms of disorder, proteins are constantly facing extrinsic disorder, which is intrinsic disorder in their functional partners. All this comprises the multileveled protein disorder cycle.
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Affiliation(s)
- Vladimir N Uversky
- Department of Molecular Medicine and Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612 USA
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Kubiak K, Gaffke L, Pierzynowska K, Cyske Z, Grabowski Ł, Kosznik-Kwaśnicka K, Jaroszewicz W, Węgrzyn A, Węgrzyn G. Determination of Effects and Mechanisms of Action of Bacterial Amyloids on Antibiotic Resistance. Methods Mol Biol 2022; 2538:189-205. [PMID: 35951301 DOI: 10.1007/978-1-0716-2529-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial functional amyloids, apart from their many other functions, can influence the resistance of bacteria to antibiotics and other antibacterial agents. Mechanisms of modulation of susceptibility of bacterial cells to antimicrobials can be either indirect or direct. The former mechanisms are exemplified by the contribution of functional amyloids to biofilm formation, which may effectively prevent the penetration of various compounds into bacterial cells. The direct mechanisms include the effects of bacterial proteins revealing amyloid-like structures, like the C-terminal region of the Escherichia coli Hfq protein, on the expression of genes involved in antibiotic resistance. Therefore, in this paper, we describe methods by which effects and mechanisms of action of bacterial amyloids on antibiotic resistance can be studied. Assessment of formation of biofilms, determination of the efficiency of antibiotic resistance in solid and liquid media, and determination of the effects on gene expression at levels of mRNA abundance and stability and protein abundance are described.
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Affiliation(s)
- Krzysztof Kubiak
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | | | - Zuzanna Cyske
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdansk, Poland
| | - Katarzyna Kosznik-Kwaśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdansk, Poland
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | | | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland.
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47
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Vestergaard B, Langkilde AE. Protein fibrillation from another small angle: Sample preparation and SAXS data collection. Methods Enzymol 2022; 677:291-321. [DOI: 10.1016/bs.mie.2022.08.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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48
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Kang SY, Pokhrel A, Bratsch S, Benson JJ, Seo SO, Quin MB, Aksan A, Schmidt-Dannert C. Engineering Bacillus subtilis for the formation of a durable living biocomposite material. Nat Commun 2021; 12:7133. [PMID: 34880257 PMCID: PMC8654922 DOI: 10.1038/s41467-021-27467-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 11/17/2021] [Indexed: 01/23/2023] Open
Abstract
Engineered living materials (ELMs) are a fast-growing area of research that combine approaches in synthetic biology and material science. Here, we engineer B. subtilis to become a living component of a silica material composed of self-assembling protein scaffolds for functionalization and cross-linking of cells. B. subtilis is engineered to display SpyTags on polar flagella for cell attachment to SpyCatcher modified secreted scaffolds. We engineer endospore limited B. subtilis cells to become a structural component of the material with spores for long-term storage of genetic programming. Silica biomineralization peptides are screened and scaffolds designed for silica polymerization to fabricate biocomposite materials with enhanced mechanical properties. We show that the resulting ELM can be regenerated from a piece of cell containing silica material and that new functions can be incorporated by co-cultivation of engineered B. subtilis strains. We believe that this work will serve as a framework for the future design of resilient ELMs.
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Affiliation(s)
- Sun-Young Kang
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Anaya Pokhrel
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Sara Bratsch
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Joey J. Benson
- grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Seung-Oh Seo
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Maureen B. Quin
- grid.17635.360000000419368657Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN 55455 USA ,grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA
| | - Alptekin Aksan
- grid.17635.360000000419368657BioTechnology Institute, University of Minnesota, St. Paul, MN 55108 USA ,grid.17635.360000000419368657Department of Mechanical Engineering, University of Minnesota, Minneapolis, MN 55455 USA
| | - Claudia Schmidt-Dannert
- Department of Biochemistry, Molecular Biology & Biochemistry, University of Minnesota, Minneapolis, MN, 55455, USA. .,BioTechnology Institute, University of Minnesota, St. Paul, MN, 55108, USA.
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Damour A, Robin B, Deroche L, Broutin L, Bellin N, Verdon J, Lina G, Leclère FM, Garcia M, Cremniter J, Lévêque N, Bodet C. Phenol-soluble modulins α are major virulence factors of Staphylococcus aureus secretome promoting inflammatory response in human epidermis. Virulence 2021; 12:2474-2492. [PMID: 34516337 PMCID: PMC8451463 DOI: 10.1080/21505594.2021.1975909] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 08/03/2021] [Accepted: 08/25/2021] [Indexed: 11/10/2022] Open
Abstract
Staphylococcus aureus is a skin commensal microorganism commonly colonizing healthy humans. Nevertheless, S. aureus can also be responsible for cutaneous infections and contribute to flare-up of inflammatory skin diseases such as atopic dermatitis (AD), which is characterized by dysbiosis of the skin microbiota with S. aureus as the predominant species. However, the role of major virulence factors of this pathogen such as phenol-soluble modulin (PSM) toxins in epidermal inflammation remains poorly understood. Stimulation of primary human keratinocytes with sublytic concentrations of synthetic and purified PSM α3 resulted in upregulation of a large panel of pro-inflammatory chemokine and cytokine gene expression, including CXCL1, CXCL2, CXCL3, CXCL5, CXCL8, CCL20, IL-1α, IL-1β, IL-6, IL-36γ and TNF-α, while inducing the release of CXCL8, CCL20, TNF-α and IL-6. In addition, using S. aureus culture supernatant from mutants deleted from genes encoding either α-type PSMs or all PSM production, PSMs were shown to be the main factors of S. aureus secretome responsible for pro-inflammatory mediator induction in human keratinocytes. On the other hand, α-type PSM-containing supernatant triggered an intense induction of pro-inflammatory mediator expression and secretion during both topical and basal layer stimulation of an ex vivo model of human skin explants, a physiologically relevant model of pluristratified epidermis. Taken together, the results of this study show that PSMs and more specifically α-type PSMs are major virulence factors of S. aureus inducing a potent inflammatory response during infection of the human epidermis and could thereby contribute to AD flare-up through exacerbation of skin inflammation.
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Affiliation(s)
- Alexia Damour
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
| | - Brandon Robin
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
| | - Luc Deroche
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
| | - Lauranne Broutin
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
- Laboratoire De Bactériologie, CHU de Poitiers, Poitiers, France
| | - Nicolas Bellin
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
| | - Julien Verdon
- Laboratoire Ecologie et Biologie des Interactions, UMR CNRS 7267, Université De Poitiers, Poitiers, France
| | - Gérard Lina
- CIRI Centre International de Recherche en Infectiologie, Inserm U1111, Université Lyon 1, Ecole Normale Supérieure de Lyon, Lyon, France
- Centre National de Référence des Staphylocoques, Institut des Agent Infectieux, Hôpital de La Croix Rousse, Hospices Civils de Lyon, Lyon, France
| | - Franck Marie Leclère
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
- Département de Chirurgie Plastique, Reconstructive et Esthétique, CHU de Poitiers, Poitiers, France
| | - Magali Garcia
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Julie Cremniter
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
- Laboratoire De Bactériologie, CHU de Poitiers, Poitiers, France
| | - Nicolas Lévêque
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
- Laboratoire de Virologie et Mycobactériologie, CHU de Poitiers, Poitiers, France
| | - Charles Bodet
- Laboratoire Inflammation Tissus Epithéliaux et Cytokines EA 4331, Université De Poitiers, Poitiers, France
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50
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Matilla-Cuenca L, Toledo-Arana A, Valle J. Anti-Biofilm Molecules Targeting Functional Amyloids. Antibiotics (Basel) 2021; 10:antibiotics10070795. [PMID: 34210036 PMCID: PMC8300730 DOI: 10.3390/antibiotics10070795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
The choice of an effective therapeutic strategy in the treatment of biofilm-related infections is a significant issue. Amyloids, which have been historically related to human diseases, are now considered to be prevailing structural components of the biofilm matrix in a wide range of bacteria. This assumption creates the potential for an exciting research area, in which functional amyloids are considered to be attractive targets for drug development to dissemble biofilm structures. The present review describes the best-characterized bacterial functional amyloids and focuses on anti-biofilm agents that target intrinsic and facultative amyloids. This study provides a better understanding of the different modes of actions of the anti-amyloid molecules to inhibit biofilm formation. This information can be further exploited to improve the therapeutic strategies to combat biofilm-related infections.
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