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Peña-Díaz S, Olsen WP, Wang H, Otzen DE. Functional Amyloids: The Biomaterials of Tomorrow? ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2024; 36:e2312823. [PMID: 38308110 DOI: 10.1002/adma.202312823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 01/22/2024] [Indexed: 02/04/2024]
Abstract
Functional amyloid (FAs), particularly the bacterial proteins CsgA and FapC, have many useful properties as biomaterials: high stability, efficient, and controllable formation of a single type of amyloid, easy availability as extracellular material in bacterial biofilm and flexible engineering to introduce new properties. CsgA in particular has already demonstrated its worth in hydrogels for stable gastrointestinal colonization and regenerative tissue engineering, cell-specific drug release, water-purification filters, and different biosensors. It also holds promise as catalytic amyloid; existing weak and unspecific activity can undoubtedly be improved by targeted engineering and benefit from the repetitive display of active sites on a surface. Unfortunately, FapC remains largely unexplored and no application is described so far. Since FapC shares many common features with CsgA, this opens the window to its development as a functional scaffold. The multiple imperfect repeats in CsgA and FapC form a platform to introduce novel properties, e.g., in connecting linkers of variable lengths. While exploitation of this potential is still at an early stage, particularly for FapC, a thorough understanding of their molecular properties will pave the way for multifunctional fibrils which can contribute toward solving many different societal challenges, ranging from CO2 fixation to hydrolysis of plastic nanoparticles.
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Affiliation(s)
- Samuel Peña-Díaz
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
| | - William Pallisgaard Olsen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
| | - Huabing Wang
- Guangxi Key Laboratory of Enhanced Recovery after Surgery for Gastrointestinal Cancer, Clinical Laboratory Center, Department of Clinical Laboratory, The First Affiliated Hospital of Guangxi Medical University, Shuangyong Road 6, Guangxi Zhuang Autonomous Region, Nanning, 530021, China
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, Aarhus C, DK - 8000, Denmark
- Department of Molecular Biology and Genetics, Aarhus University, Universitetsbyen 81, Aarhus C, 8000, Denmark
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2
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Kumari S, Das S. Functional amyloid fibrils of biofilm-forming marine bacterium Pseudomonas aeruginosa PFL-P1 interact spontaneously with pyrene and augment the biodegradation. Int J Biol Macromol 2024; 266:131266. [PMID: 38556224 DOI: 10.1016/j.ijbiomac.2024.131266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 03/13/2024] [Accepted: 03/28/2024] [Indexed: 04/02/2024]
Abstract
Bacteria thrive in biofilms embedding in the three-dimensional extracellular polymeric substances (EPS). Functional Amyloid in Pseudomonas (Fap), a protein in EPS, efficiently sequesters polycyclic aromatic hydrocarbons (PAHs). Present study reports the characterization of Fap fibrils from Pseudomonas aeruginosa PFL-P1 and describes the interaction with pyrene to assess the impact on pyrene degradation. Overexpression of fap in E. coli BL21(DE3) cells significantly enhances biofilm formation (p < 0.0001) and amyloid production (p = 0.0002), particularly with pyrene. Defibrillated Fap analysis reveals FapC monomers and increased fibrillation with pyrene. Circular Dichroism (CD), Fourier Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) unveil characteristic amyloid peaks and structural changes in Fap fibrils upon pyrene exposure. 3D-EEM analysis identifies a protein-like fluorophore in Fap fibrils, exhibiting pyrene-induced fluorescence quenching. Binding constants range from 5.23 to 7.78 M-1, with ΔG of -5.10 kJ mol-1 at 298 K, indicating spontaneous and exothermic interaction driven by hydrophobic forces. Exogenous Fap fibrils substantially increased the biofilm growth and pyrene degradation by P. aeruginosa PFL-P1 from 46 % to 64 % within 7 days (p = 0.0236). GC-MS identifies diverse metabolites, implying phthalic acid pathway in pyrene degradation. This study deepens insights into structural dynamics of Fap fibrils when exposed to pyrene, offering potential application in environmental bioremediation.
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Affiliation(s)
- Swetambari Kumari
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India
| | - Surajit Das
- Laboratory of Environmental Microbiology and Ecology (LEnME), Department of Life Science, National Institute of Technology, Rourkela 769008, Odisha, India.
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3
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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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4
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Bakalakos M, Ampadiotaki MM, Vlachos C, Sipsas N, Pneumaticos S, Vlamis J. Molecular Mechanisms of Biofilm Formation on Orthopaedic Implants: Review of the Literature. MAEDICA 2024; 19:129-136. [PMID: 38736937 PMCID: PMC11079743 DOI: 10.26574/maedica.2021.19.1.129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/14/2024]
Abstract
Orthopaedic implant-associated infections (OIAIs) is one of the most catastrophic complications following joint arthroplasty or fracture fixation. Given the increasing number of orthopaedic implants which are used annually, periprosthetic infections emerge as a global problem. Their diagnosis and consequent therapeutic management remain challenging for clinicians. Biofilm formation is a complex and only partially understood process that has not been extensively studied. Understanding the underlying mechanisms involved in biofilm formation is crucial in the amelioration of both diagnosis and therapeutic management of OIAIs. We performed a literature review of the molecular mechanisms of biofilm formation and discussed the four most common and thoroughly researched microbes of biofilm-related OIAIs.
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Affiliation(s)
- Matthaios Bakalakos
- 3rd Orthopaedic Department, National and Kapodistrian University of Athens, KAT General Hospital, Athens, Greece
| | | | - Christos Vlachos
- 3rd Orthopaedic Department, National and Kapodistrian University of Athens, KAT General Hospital, Athens, Greece
| | - Nikolaos Sipsas
- Infectious Diseases, National and Kapodistrian University of Athens, Athens, Greece
| | - Spiros Pneumaticos
- 3rd Orthopaedic Department, National and Kapodistrian University of Athens, KAT General Hospital, Athens, Greece
| | - John Vlamis
- 3rd Orthopaedic Department, National and Kapodistrian University of Athens, KAT General Hospital, Athens, Greece
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5
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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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Böhning J, Tarafder AK, Bharat TA. The role of filamentous matrix molecules in shaping the architecture and emergent properties of bacterial biofilms. Biochem J 2024; 481:245-263. [PMID: 38358118 PMCID: PMC10903470 DOI: 10.1042/bcj20210301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 01/29/2024] [Accepted: 01/31/2024] [Indexed: 02/16/2024]
Abstract
Numerous bacteria naturally occur within spatially organised, multicellular communities called biofilms. Moreover, most bacterial infections proceed with biofilm formation, posing major challenges to human health. Within biofilms, bacterial cells are embedded in a primarily self-produced extracellular matrix, which is a defining feature of all biofilms. The biofilm matrix is a complex, viscous mixture primarily composed of polymeric substances such as polysaccharides, filamentous protein fibres, and extracellular DNA. The structured arrangement of the matrix bestows bacteria with beneficial emergent properties that are not displayed by planktonic cells, conferring protection against physical and chemical stresses, including antibiotic treatment. However, a lack of multi-scale information at the molecular level has prevented a better understanding of this matrix and its properties. Here, we review recent progress on the molecular characterisation of filamentous biofilm matrix components and their three-dimensional spatial organisation within biofilms.
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Affiliation(s)
- Jan Böhning
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Abul K. Tarafder
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
| | - Tanmay A.M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, U.K
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Blanco-Romero E, Garrido-Sanz D, Durán D, Rybtke M, Tolker-Nielsen T, Redondo-Nieto M, Rivilla R, Martín M. Role of extracellular matrix components in biofilm formation and adaptation of Pseudomonas ogarae F113 to the rhizosphere environment. Front Microbiol 2024; 15:1341728. [PMID: 38333580 PMCID: PMC10850567 DOI: 10.3389/fmicb.2024.1341728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 01/11/2024] [Indexed: 02/10/2024] Open
Abstract
Regulating the transition of bacteria from motile to sessile lifestyles is crucial for their ability to compete effectively in the rhizosphere environment. Pseudomonas are known to rely on extracellular matrix (ECM) components for microcolony and biofilm formation, allowing them to adapt to a sessile lifestyle. Pseudomonas ogarae F113 possesses eight gene clusters responsible for the production of ECM components. These gene clusters are tightly regulated by AmrZ, a major transcriptional regulator that influences the cellular levels of c-di-GMP. The AmrZ-mediated transcriptional regulation of ECM components is primarily mediated by the signaling molecule c-di-GMP and the flagella master regulator FleQ. To investigate the functional role of these ECM components in P. ogarae F113, we performed phenotypic analyses using mutants in genes encoding these ECM components. These analyses included assessments of colony morphology, dye-staining, static attachment to abiotic surfaces, dynamic biofilm formation on abiotic surfaces, swimming motility, and competitive colonization assays of the rhizosphere. Our results revealed that alginate and PNAG polysaccharides, along with PsmE and the fimbrial low molecular weight protein/tight adherence (Flp/Tad) pilus, are the major ECM components contributing to biofilm formation. Additionally, we found that the majority of these components and MapA are needed for a competitive colonization of the rhizosphere in P. ogarae F113.
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Affiliation(s)
- Esther Blanco-Romero
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Daniel Garrido-Sanz
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - David Durán
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, University of Copenhagen, Copenhagen, Denmark
| | - Miguel Redondo-Nieto
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Rafael Rivilla
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
| | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, Madrid, Spain
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Katsipis G, Avgoulas DI, Geromichalos GD, Petala M, Pantazaki AA. In vitro and in silico evaluation of the serrapeptase effect on biofilm and amyloids of Pseudomonas aeruginosa. Appl Microbiol Biotechnol 2023; 107:7269-7285. [PMID: 37741938 PMCID: PMC10638192 DOI: 10.1007/s00253-023-12772-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 08/17/2023] [Accepted: 09/02/2023] [Indexed: 09/25/2023]
Abstract
Pseudomonas aeruginosa is an emerging threat for hospitalized and cystic fibrosis patients. Biofilm, a microbial community embedded in extracellular polymeric substance, fortifies bacteria against the immune system. In biofilms, the expression of functional amyloids is linked with highly aggregative, multi-resistant strains, and chronic infections. Serrapeptase (SPT), a protease possessing similar or superior anti-microbial properties with many antibiotics, presents anti-amyloid potential. However, studies on the employment of SPT against Pseudomonas biofilms and Fap amyloid, or the possible mechanisms of action are scarce. Here, SPT inhibited biofilm formation of P. aeruginosa ATCC 27853 on both plastic and glass surfaces, with an IC50 of 11.26 µg/mL and 0.27 µg/mL, respectively. The inhibitory effect of SPT on biofilm was also verified with optical microscopy of crystal violet-stained biofilms and with confocal microscopy. Additionally, SPT caused a dose-dependent decrease of bacterial viability (IC50 of 3.07 µg/mL) as demonstrated by MTT assay. Reduction of bacterial functional amyloids was also demonstrated, employing both fluorescence microscopy with thioflavin T and photometrical determination of Congo-red-positive compounds. Both viability and functional amyloids correlated significantly with biofilm inhibition. Finally, in silico molecular docking studies provided a mechanistic insight into the interaction of SPT with FapC or FapD, proving that both peptides are possible targets of SPT. These results offer new insights into the biofilm formation of P. aeruginosa and potentiate the involvement of SPT in the prevention and eradication of Pseudomonas biofilms. KEY POINTS: • Serrapeptase inhibits biofilm formation of P. aeruginosa on plastic and glass. • Biofilm inhibition correlated with reduced viability and functional amyloid levels. • In silico studies indicated that serrapeptase may target FapC and FapD peptides.
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Affiliation(s)
- Georgios Katsipis
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece
| | - Dimitrios I Avgoulas
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece
- Laboratory of Chemical and Environmental Technology, Deparment of Chemistry, Aristotle University of Thessaloniki, 54 124, 54124, Thessaloniki, Greece
| | - George D Geromichalos
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece
- Department of General and Inorganic Chemistry, Faculty of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Maria Petala
- Laboratory of Environmental Engineering & Planning, Department of Civil Engineering, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Anastasia A Pantazaki
- Laboratory of Biochemistry, Department of Chemistry, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece.
- Center for Interdisciplinary Research and Innovation, Laboratory of Neurodegenerative Diseases (LND), Thermi, 57001, Thessaloniki, Greece.
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9
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Galkin AP, Sysoev EI, Valina AA. Amyloids and prions in the light of evolution. Curr Genet 2023; 69:189-202. [PMID: 37165144 DOI: 10.1007/s00294-023-01270-6] [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: 04/14/2023] [Revised: 05/02/2023] [Accepted: 05/04/2023] [Indexed: 05/12/2023]
Abstract
Functional amyloids have been identified in a wide variety of organisms including bacteria, fungi, plants, and vertebrates. Intracellular and extracellular amyloid fibrils of different proteins perform storage, protective, structural, and regulatory functions. The structural organization of amyloid fibrils determines their unique physical and biochemical properties. The formation of these fibrillar structures can provide adaptive advantages that are picked up by natural selection. Despite the great interest in functional and pathological amyloids, questions about the conservatism of the amyloid properties of proteins and the regularities in the appearance of these fibrillar structures in evolution remain almost unexplored. Using bioinformatics approaches and summarizing the data published previously, we have shown that amyloid fibrils performing similar functions in different organisms have been arising repeatedly and independently in the course of evolution. On the other hand, we show that the amyloid properties of a number of bacterial and eukaryotic proteins are evolutionarily conserved. We also discuss the role of protein-based inheritance in the evolution of microorganisms. Considering that missense mutations and the emergence of prions cause the same consequences, we propose the concept that the formation of prions, similarly to mutations, generally causes a negative effect, although it can also lead to adaptations in rare cases. In general, our analysis revealed certain patterns in the emergence and spread of amyloid fibrillar structures in the course of evolution.
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Affiliation(s)
- Alexey P Galkin
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russian Federation, 199034.
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034.
| | - Evgeniy I Sysoev
- Vavilov Institute of General Genetics, St. Petersburg Branch, Russian Academy of Sciences, St. Petersburg, Russian Federation, 199034
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034
| | - Anna A Valina
- Department of Genetics and Biotechnology, St. Petersburg State University, St. Petersburg, Russian Federation, 199034
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10
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Bonincontro G, Scuderi SA, Marino A, Simonetti G. Synergistic Effect of Plant Compounds in Combination with Conventional Antimicrobials against Biofilm of Staphylococcus aureus, Pseudomonas aeruginosa, and Candida spp. Pharmaceuticals (Basel) 2023; 16:1531. [PMID: 38004397 PMCID: PMC10675371 DOI: 10.3390/ph16111531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2023] [Revised: 10/20/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Bacterial and fungal biofilm has increased antibiotic resistance and plays an essential role in many persistent diseases. Biofilm-associated chronic infections are difficult to treat and reduce the efficacy of medical devices. This global problem has prompted extensive research to find alternative strategies to fight microbial chronic infections. Plant bioactive metabolites with antibiofilm activity are known to be potential resources to alleviate this problem. The phytochemical screening of some medicinal plants showed different active groups, such as stilbenes, tannins, alkaloids, terpenes, polyphenolics, flavonoids, lignans, quinones, and coumarins. Synergistic effects can be observed in the interaction between plant compounds and conventional drugs. This review analyses and summarises the current knowledge on the synergistic effects of plant metabolites in combination with conventional antimicrobials against biofilms of Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans. The synergism of conventional antimicrobials with plant compounds can modify and inhibit the mechanisms of acquired resistance, reduce undesirable effects, and obtain an appropriate therapeutic effect at lower doses. A deeper knowledge of these combinations and of their possible antibiofilm targets is needed to develop next-generation novel antimicrobials and/or improve current antimicrobials to fight drug-resistant infections attributed to biofilm.
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Affiliation(s)
- Graziana Bonincontro
- Department of Environmental Biology, Sapienza University of Rome, P.le Aldo Moro, 5, 00185 Roma, Italy;
| | - Sarah Adriana Scuderi
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 98100 Messina, Italy;
| | - Andreana Marino
- Department of Chemical, Biological, Pharmaceutical and Environmental Sciences, University of Messina, Viale Ferdinando Stagno D’Alcontres, 98100 Messina, Italy;
| | - Giovanna Simonetti
- Department of Environmental Biology, Sapienza University of Rome, P.le Aldo Moro, 5, 00185 Roma, Italy;
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Master NG, Markande AR. Importance of microbial amphiphiles: interaction potential of biosurfactants, amyloids, and other exo-polymeric-substances. World J Microbiol Biotechnol 2023; 39:320. [PMID: 37747579 DOI: 10.1007/s11274-023-03751-9] [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: 02/01/2023] [Accepted: 09/04/2023] [Indexed: 09/26/2023]
Abstract
Microorganisms produce a diverse group of biomolecules having amphipathic nature (amphiphiles). Microbial amphiphiles, including amyloids, bio-surfactants, and other exo-polymeric substances, play a crucial role in various biological processes and have gained significant attention recently. Although diverse in biochemical composition, these amphiphiles have been reported for common microbial traits like biofilm formation and pathogenicity due to their ability to act as surface active agents with active interfacial properties essential for microbes to grow in various niches. This enables microbes to reduce surface tension, emulsification, dispersion, and attachment at the interface. In this report, the ecological importance and biotechnological usage of important amphiphiles have been discussed. The low molecular weight amphiphiles like biosurfactants, siderophores, and peptides showing helical and antimicrobial activities have been extensively reported for their ability to work as quorum-sensing mediators. While high molecular weight amphiphiles make up amyloid fibers, exopolysaccharides, liposomes, or magnetosomes have been shown to have a significant influence in deciding microbial physiology and survival. In this report, we have discussed the functional similarities and biochemical variations of several amphipathic biomolecules produced by microbes, and the present report shows these amphiphiles showing polyphyletic and ecophysiological groups of microorganisms and hence can `be replaced in biotechnological applications depending on the compatibility of the processes.
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Affiliation(s)
- Nishita G Master
- Department of Biological Sciences, P.D. Patel Institute of Applied Sciences (PDPIAS), Charotar University of Science and Technology (CHARUSAT), Changa, Anand, Gujarat, 388421, India
| | - Anoop R Markande
- Department of Biological Sciences, P.D. Patel Institute of Applied Sciences (PDPIAS), Charotar University of Science and Technology (CHARUSAT), Changa, Anand, Gujarat, 388421, India.
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12
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Jimoh AA, Booysen E, van Zyl L, Trindade M. Do biosurfactants as anti-biofilm agents have a future in industrial water systems? Front Bioeng Biotechnol 2023; 11:1244595. [PMID: 37781531 PMCID: PMC10540235 DOI: 10.3389/fbioe.2023.1244595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/04/2023] [Indexed: 10/03/2023] Open
Abstract
Biofilms are bacterial communities embedded in exopolymeric substances that form on the surfaces of both man-made and natural structures. Biofilm formation in industrial water systems such as cooling towers results in biofouling and biocorrosion and poses a major health concern as well as an economic burden. Traditionally, biofilms in industrial water systems are treated with alternating doses of oxidizing and non-oxidizing biocides, but as resistance increases, higher biocide concentrations are needed. Using chemically synthesized surfactants in combination with biocides is also not a new idea; however, these surfactants are often not biodegradable and lead to accumulation in natural water reservoirs. Biosurfactants have become an essential bioeconomy product for diverse applications; however, reports of their use in combating biofilm-related problems in water management systems is limited to only a few studies. Biosurfactants are powerful anti-biofilm agents and can act as biocides as well as biodispersants. In laboratory settings, the efficacy of biosurfactants as anti-biofilm agents can range between 26% and 99.8%. For example, long-chain rhamnolipids isolated from Burkholderia thailandensis inhibit biofilm formation between 50% and 90%, while a lipopeptide biosurfactant from Bacillus amyloliquefaciens was able to inhibit biofilms up to 96% and 99%. Additionally, biosurfactants can disperse preformed biofilms up to 95.9%. The efficacy of antibiotics can also be increased by between 25% and 50% when combined with biosurfactants, as seen for the V9T14 biosurfactant co-formulated with ampicillin, cefazolin, and tobramycin. In this review, we discuss how biofilms are formed and if biosurfactants, as anti-biofilm agents, have a future in industrial water systems. We then summarize the reported mode of action for biosurfactant molecules and their functionality as biofilm dispersal agents. Finally, we highlight the application of biosurfactants in industrial water systems as anti-fouling and anti-corrosion agents.
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Affiliation(s)
| | | | | | - Marla Trindade
- Department of Biotechnology, Institute for Microbial Biotechnology and Metagenomics (IMBM), University of the Western Cape, Cape Town, South Africa
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13
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Espinosa-Urgel M, Ramos-González MI. Becoming settlers: Elements and mechanisms for surface colonization by Pseudomonas putida. Environ Microbiol 2023; 25:1575-1593. [PMID: 37045787 DOI: 10.1111/1462-2920.16385] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 03/31/2023] [Indexed: 04/14/2023]
Abstract
Pseudomonads are considered to be among the most widespread culturable bacteria in mesophilic environments. The evolutive success of Pseudomonas species can be attributed to their metabolic versatility, in combination with a set of additional functions that enhance their ability to colonize different niches. These include the production of secondary metabolites involved in iron acquisition or having a detrimental effect on potential competitors, different types of motility, and the capacity to establish and persist within biofilms. Although biofilm formation has been extensively studied using the opportunistic pathogen Pseudomonas aeruginosa as a model organism, a significant body of knowledge is also becoming available for non-pathogenic Pseudomonas. In this review, we focus on the mechanisms that allow Pseudomonas putida to colonize biotic and abiotic surfaces and adapt to sessile life, as a relevant persistence strategy in the environment. This species is of particular interest because it includes plant-beneficial strains, in which colonization of plant surfaces may be relevant, and strains used for environmental and biotechnological applications, where the design and functionality of biofilm-based bioreactors, for example, also have to take into account the efficiency of bacterial colonization of solid surfaces. This work reviews the current knowledge of mechanistic and regulatory aspects of biofilm formation by P. putida and pinpoints the prospects in this field.
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Affiliation(s)
- Manuel Espinosa-Urgel
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Granada, Spain
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14
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Mesdaghi S, Price RM, Madine J, Rigden DJ. Deep Learning-based structure modelling illuminates structure and function in uncharted regions of β-solenoid fold space. J Struct Biol 2023; 215:108010. [PMID: 37544372 DOI: 10.1016/j.jsb.2023.108010] [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: 04/26/2023] [Revised: 07/19/2023] [Accepted: 08/03/2023] [Indexed: 08/08/2023]
Abstract
Repeat proteins are common in all domains of life and exhibit a wide range of functions. One class of repeat protein contains solenoid folds where the repeating unit consists of β-strands separated by tight turns. β-solenoids have distinguishing structural features such as handedness, twist, oligomerisation state, coil shape and size which give rise to their diversity. Characterised β-solenoid repeat proteins are known to form regions in bacterial and viral virulence factors, antifreeze proteins and functional amyloids. For many of these proteins, the experimental structure has not been solved, as they are difficult to crystallise or model. Here we use various deep learning-based structure-modelling methods to discover novel predicted β-solenoids, perform structural database searches to mine further structural neighbours and relate their predicted structure to possible functions. We find both eukaryotic and prokaryotic adhesins, confirming a known functional linkage between adhesin function and the β-solenoid fold. We further identify exceptionally long, flat β-solenoid folds as possible structures of mucin tandem repeat regions and unprecedentedly small β-solenoid structures. Additionally, we characterise a novel β-solenoid coil shape, the FapC Greek key β-solenoid as well as plausible complexes between it and other proteins involved in Pseudomonas functional amyloid fibres.
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Affiliation(s)
- Shahram Mesdaghi
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom; Computational Biology Facility, MerseyBio, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Rebecca M Price
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom
| | - Jillian Madine
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom.
| | - Daniel J Rigden
- The University of Liverpool, Institute of Systems, Molecular & Integrative Biology, Biosciences Building, Crown Street, Liverpool L69 7ZB, United Kingdom.
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15
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Beg AZ, Rashid F, Talat A, Haseen MA, Raza N, Akhtar K, Dueholm MKD, Khan AU. Functional Amyloids in Pseudomonas aeruginosa Are Essential for the Proteome Modulation That Leads to Pathoadaptation in Pulmonary Niches. Microbiol Spectr 2023; 11:e0307122. [PMID: 36475836 PMCID: PMC9927170 DOI: 10.1128/spectrum.03071-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 11/14/2022] [Indexed: 12/13/2022] Open
Abstract
Persistence and survival of Pseudomonas aeruginosa in chronic lung infections is closely linked to the biofilm lifestyle. One biofilm component, functional amyloid of P. aeruginosa (Fap), imparts structural adaptations for biofilms; however, the role of Fap in pathogenesis is still unclear. Conservation of the fap operon encoding Fap and P. aeruginosa being an opportunistic pathogen of lung infections prompted us to explore its role in lung infection. We found that Fap is essential for establishment of lung infection in rats, as its genetic exclusion led to mild focal infection with quick resolution. Moreover, without an underlying cystic fibrosis (CF) genetic disorder, overexpression of Fap reproduced the CF pathotype. The molecular basis of Fap-mediated pulmonary adaptation was explored through surface-associated proteomics in vitro. Differential proteomics positively associated Fap expression with activation of known proteins related to pulmonary pathoadaptation, attachment, and biofilm fitness. The aggregative bacterial phenotype in the pulmonary niche correlated with Fap-influenced activation of biofilm sustainability regulators and stress response regulators that favored persistence-mediated establishment of pulmonary infection. Fap overexpression upregulated proteins that are abundant in the proteome of P. aeruginosa in colonizing CF lungs. Planktonic lifestyle, defects in anaerobic pathway, and neutrophilic evasion were key factors in the absence of Fap that impaired establishment of infection. We concluded that Fap is essential for cellular equilibration to establish pulmonary infection. Amyloid-induced bacterial aggregation subverted the immune response, leading to chronic infection by collaterally damaging tissue and reinforcing bacterial persistence. IMPORTANCE Pseudomonas aeruginosa is inextricably linked with chronic lung infections. In this study, the well-conserved Fap operon was found to be essential for pathoadaptation in pulmonary infection in a rat lung model. Moreover, the presence of Fap increased pathogenesis and biofilm sustainability by modulating bacterial physiology. Hence, a pathoadaptive role of Fap in pulmonary infections can be exploited for clinical application by targeting amyloids. Furthermore, genetic conservation and extracellular exposure of Fap make it a commendable target for such interventions.
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Affiliation(s)
- Ayesha Z. Beg
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | | | - Absar Talat
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Mohd Azam Haseen
- Department of Cardiothoracic Surgery, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Nadeem Raza
- Department of Anaesthesiology, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Kafil Akhtar
- Pathology Department, Jawaharlal Nehru Medical College, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
| | - Morten Kam Dahl Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Asad U. Khan
- Medical Microbiology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, Uttar Pradesh, India
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16
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Rasmussen HØ, Kumar A, Shin B, Stylianou F, Sewell L, Xu Y, Otzen DE, Pedersen JS, Matthews SJ. FapA is an Intrinsically Disordered Chaperone for Pseudomonas Functional Amyloid FapC. J Mol Biol 2023; 435:167878. [PMID: 36368411 DOI: 10.1016/j.jmb.2022.167878] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/18/2022] [Accepted: 11/01/2022] [Indexed: 11/09/2022]
Abstract
Bacterial functional amyloids contribute to biofilm development by bacteria and provide protection from the immune system and prevent antibiotic treatment. Strategies to target amyloid formation and interrupt biofilm formation have attracted recent interest due to their antimicrobial potential. Functional amyloid in Pseudomonas (Fap) includes FapC as the major component of the fibril while FapB is a minor component suggested to function as a nucleator of FapC. The system also includes the small periplasmic protein FapA, which has been shown to regulate fibril composition and morphology. The interplay between these three components is central in Fap fibril biogenesis. Here we present a comprehensive biophysical and spectroscopy analysis of FapA, FapB and FapC and provide insight into their molecular interactions. We show that all three proteins are primarily disordered with some regions with structural propensities for α-helix and β-sheet. FapA inhibits FapC fibrillation by targeting the nucleation step, whereas for FapB the elongation step is modulated. Furthermore, FapA alters the morphology of FapC (more than FapB) fibrils. Complex formation is observed between FapA and FapC, but not between FapA and FapB, and likely involves the N-terminus of FapA. We conclude that FapA is an intrinsically disordered chaperone for FapC that guards against fibrillation within the periplasm. This new understanding of a natural protective mechanism of Pseudomonas against amyloid formations can serve as inspiration for strategies blocking biofilm formation in infections.
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Affiliation(s)
- Helena Ø Rasmussen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Amit Kumar
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Ben Shin
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Lee Sewell
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Jan Skov Pedersen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Chemistry, Aarhus University, Gustav Wieds Vej 14, 8000 Aarhus C, Denmark
| | - Steve J Matthews
- Department of Life Sciences, Imperial College London, Exhibition Road, South Kensington, London, United Kingdom.
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17
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Moshynets OV, Pokholenko I, Iungin O, Potters G, Spiers AJ. eDNA, Amyloid Fibers and Membrane Vesicles Identified in Pseudomonas fluorescens SBW25 Biofilms. Int J Mol Sci 2022; 23:ijms232315096. [PMID: 36499433 PMCID: PMC9738004 DOI: 10.3390/ijms232315096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 11/25/2022] [Accepted: 11/26/2022] [Indexed: 12/03/2022] Open
Abstract
Pseudomonas fluorescens SBW25 is a model soil- and plant-associated bacterium capable of forming a variety of air-liquid interface biofilms in experimental microcosms and on plant surfaces. Previous investigations have shown that cellulose is the primary structural matrix component in the robust and well-attached Wrinkly Spreader biofilm, as well as in the fragile Viscous Mass biofilm. Here, we demonstrate that both biofilms include extracellular DNA (eDNA) which can be visualized using confocal laser scanning microscopy (CLSM), quantified by absorbance measurements, and degraded by DNase I treatment. This eDNA plays an important role in cell attachment and biofilm development. However, exogenous high-molecular-weight DNA appears to decrease the strength and attachment levels of mature Wrinkly Spreader biofilms, whereas low-molecular-weight DNA appears to have little effect. Further investigation with CLSM using an amyloid-specific fluorophore suggests that the Wrinkly Spreader biofilm might also include Fap fibers, which might be involved in attachment and contribute to biofilm strength. The robust nature of the Wrinkly Spreader biofilm also allowed us, using MALDI-TOF mass spectrometry, to identify matrix-associated proteins unable to diffuse out of the structure, as well as membrane vesicles which had a different protein profile compared to the matrix-associated proteins. CLSM and DNase I treatment suggest that some vesicles were also associated with eDNA. These findings add to our understanding of the matrix components in this model pseudomonad, and, as found in other biofilms, biofilm-specific products and material from lysed cells contribute to these structures through a range of complex interactions.
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Affiliation(s)
- Olena V. Moshynets
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Ianina Pokholenko
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
| | - Olga Iungin
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03143 Kyiv, Ukraine
- Department of Biotechnology, Leather and Fur, Kyiv National University of Technologies and Design, 01011 Kyiv, Ukraine
| | - Geert Potters
- Antwerp Maritime Academy, 2030 Antwerp, Belgium
- Department of Bioscience Engineering, University of Antwerp, 2000 Antwerp, Belgium
- Correspondence:
| | - Andrew J. Spiers
- School of Applied Sciences, Abertay University, Dundee DD1 1HG, UK
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18
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Functional amyloid in a lipid-like environment: a merry dance of many steps. Essays Biochem 2022; 66:1035-1046. [PMID: 36205438 DOI: 10.1042/ebc20220062] [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: 08/08/2022] [Revised: 09/18/2022] [Accepted: 09/21/2022] [Indexed: 11/17/2022]
Abstract
Functional amyloid, which unlike its pathological counterpart serves a biological purpose, is produced in a carefully orchestrated sequence of events. In bacteria, the major amyloid component is transported over the periplasm and through the outer membrane to assemble on the bacterial cell surface. During its life time, the amyloid protein may be exposed to both membrane lipids and extracellular surfactant, making it relevant to study its interactions with these components in vitro. Particularly for charged surfactants, the interaction is quite complex and highly dependent on the surfactant:protein molar ratio. Low ratios typically promote aggregation, likely by binding the proteins to micelles and thus increasing the local concentration of proteins, while higher concentrations see an inhibition of the same process as the protein is diluted out and immobilized on individual micelles. This is particularly pronounced for strongly anionic surfactants like SDS; the naturally occurring biosurfactant rhamnolipid interacts more weakly with the protein, which still not only allows aggregation but also leads to less detrimental effects at higher ratios. Similarly, anionic vesicle-forming lipids largely stimulate aggregation likely because of weaker interactions. Anionic lysolipids, thanks to their micelle-forming properties, resemble SDS in their impact on fibrillation. There are also examples of systems where membrane binding sequesters an otherwise amyloidogenic sequence and prevents fibrillation or-quite the opposite- liberates another part of the protein to engage in self-assembly. Thus, membranes and surfactants have very varied roles to play in the biogenesis and function of bacterial amyloid.
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19
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Wang Y, Bian Z, Wang Y. Biofilm formation and inhibition mediated by bacterial quorum sensing. Appl Microbiol Biotechnol 2022; 106:6365-6381. [DOI: 10.1007/s00253-022-12150-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Revised: 08/23/2022] [Accepted: 08/24/2022] [Indexed: 11/25/2022]
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20
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Functional Bacterial Amyloids: Understanding Fibrillation, Regulating Biofilm Fibril Formation and Organizing Surface Assemblies. Molecules 2022; 27:molecules27134080. [PMID: 35807329 PMCID: PMC9268375 DOI: 10.3390/molecules27134080] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 06/21/2022] [Accepted: 06/22/2022] [Indexed: 02/01/2023] Open
Abstract
Functional amyloid is produced by many organisms but is particularly well understood in bacteria, where proteins such as CsgA (E. coli) and FapC (Pseudomonas) are assembled as functional bacterial amyloid (FuBA) on the cell surface in a carefully optimized process. Besides a host of helper proteins, FuBA formation is aided by multiple imperfect repeats which stabilize amyloid and streamline the aggregation mechanism to a fast-track assembly dominated by primary nucleation. These repeats, which are found in variable numbers in Pseudomonas, are most likely the structural core of the fibrils, though we still lack experimental data to determine whether the repeats give rise to β-helix structures via stacked β-hairpins (highly likely for CsgA) or more complicated arrangements (possibly the case for FapC). The response of FuBA fibrillation to denaturants suggests that nucleation and elongation involve equal amounts of folding, but protein chaperones preferentially target nucleation for effective inhibition. Smart peptides can be designed based on these imperfect repeats and modified with various flanking sequences to divert aggregation to less stable structures, leading to a reduction in biofilm formation. Small molecules such as EGCG can also divert FuBA to less organized structures, such as partially-folded oligomeric species, with the same detrimental effect on biofilm. Finally, the strong tendency of FuBA to self-assemble can lead to the formation of very regular two-dimensional amyloid films on structured surfaces such as graphite, which strongly implies future use in biosensors or other nanobiomaterials. In summary, the properties of functional amyloid are a much-needed corrective to the unfortunate association of amyloid with neurodegenerative disease and a testimony to nature’s ability to get the best out of a protein fold.
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21
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Akbey Ü, Andreasen M. Functional amyloids from bacterial biofilms - structural properties and interaction partners. Chem Sci 2022; 13:6457-6477. [PMID: 35756505 PMCID: PMC9172111 DOI: 10.1039/d2sc00645f] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/05/2022] [Indexed: 12/26/2022] Open
Abstract
Protein aggregation and amyloid formation have historically been linked with various diseases such as Alzheimer's and Parkinson's disease, but recently functional amyloids have gained a great deal of interest in not causing a disease and having a distinct function in vivo. Functional bacterial amyloids form the structural scaffold in bacterial biofilms and provide a survival strategy for the bacteria along with antibiotic resistance. The formation of functional amyloids happens extracellularly which differs from most disease related amyloids. Studies of functional amyloids have revealed several distinctions compared to disease related amyloids including primary structures designed to optimize amyloid formation while still retaining a controlled assembly of the individual subunits into classical cross-β-sheet structures, along with a unique cross-α-sheet amyloid fold. Studies have revealed that functional amyloids interact with components found in the extracellular matrix space such as lipids from membranes and polymers from the biofilm. Intriguingly, a level of complexity is added as functional amyloids also interact with several disease related amyloids and a causative link has even been established between functional amyloids and neurodegenerative diseases. It is hence becoming increasingly clear that functional amyloids are not inert protein structures found in bacterial biofilms but interact with many different components including human proteins related to pathology. Gaining a clear understanding of the factors governing the interactions will lead to improved strategies to combat biofilm associated infections and the correlated antibiotic resistance. In the current review we summarize the current state of the art knowledge on this exciting and fast growing research field of biofilm forming bacterial functional amyloids, their structural features and interaction partners.
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Affiliation(s)
- Ümit Akbey
- Department of Structural Biology, School of Medicine, University of Pittsburgh Pittsburgh PA 15261 USA
| | - Maria Andreasen
- Department of Biomedicine, Aarhus University Wilhelm Meyers Allé 3 8000 Aarhus Denmark
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22
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Guo M, Tan S, Zhu J, Sun A, Du P, Liu X. Genes Involved in Biofilm Matrix Formation of the Food Spoiler Pseudomonas fluorescens PF07. Front Microbiol 2022; 13:881043. [PMID: 35733961 PMCID: PMC9207406 DOI: 10.3389/fmicb.2022.881043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/17/2022] [Indexed: 11/13/2022] Open
Abstract
The extracellular matrix is essential for the biofilm formation of food spoilers. Pseudomonas fluorescens PF07 is a previous isolate from spoiled marine fish; however, the genes involved in the extracellular matrix formation of PF07 biofilms remain poorly defined. In this study, PF07 formed a wrinkled macrocolony biofilm through the high production of extracellular matrix. The genes involved in biofilm matrix formation and regulation were screened and identified by RNA-seq-dependent transcriptomic analysis and gene knock-out analysis. The macrocolony biofilms of PF07 grown for 5 days (PF07_5d) were compared with those grown for 1 day (PF07_1d). A total of 1,403 genes were significantly differentially expressed during biofilm formation. These mainly include the genes related to biofilm matrix proteins, polysaccharides, rhamnolipids, secretion system, biofilm regulation, and metabolism. Among them, functional amyloid genes fapABCDE were highly upregulated in the mature biofilm, and the operon fapA-E had a –24/–12 promoter dependent on the sigma factor RpoN. Moreover, the RNA-seq analyses of the rpoN mutant, compared with PF07, revealed 159 genes were differentially expressed in the macrocolony biofilms, and fapA-E genes were positively regulated by RpoN. In addition, the deletion mutants of fapC, rpoN, and brfA (a novel gene coding for an RpoN-dependent transcriptional regulator) were defective in forming mature macrocolony biofilms, solid surface-associated (SSA) biofilms, and pellicles, and they showed significantly reduced biofilm matrices. The fap genes were significantly downregulated in ΔbrfA, as in ΔrpoN. These findings suggest that the functional amyloid Fap is the main component of PF07 biofilm matrices, and RpoN may directly regulate the transcription of fap genes, in conjunction with BrfA. These genes may serve as potential molecular targets for screening new anti-biofilm agents or for biofilm detection in food environments.
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Affiliation(s)
- Miao Guo
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Siqi Tan
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- School of Public Health, Hangzhou Medical College, Hangzhou, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Aihua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Peng Du
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Xiaoxiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
- *Correspondence: Xiaoxiang Liu,
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23
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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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24
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Interaction of membrane vesicles with the Pseudomonas functional amyloid protein FapC facilitates amyloid formation. BBA ADVANCES 2022; 2:100055. [PMID: 37082589 PMCID: PMC10074931 DOI: 10.1016/j.bbadva.2022.100055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 09/13/2022] [Accepted: 09/16/2022] [Indexed: 11/20/2022] Open
Abstract
Functional amyloids (FA) are proteins which are evolutionarily optimized to form highly stable fibrillar structures that strengthen the bacterial biofilm matrix. FA such as CsgA (E. coli) and FapC (Pseudomonas) are secreted to the bacterial surface where they integrate into growing fibril structures projecting from the outer membrane. FA are exposed to membrane surfaces in this process, but it remains unclear how membranes can interact with FA and potentially affect the self-assembly. Here we report the effect of different vesicles (DOPG, DMPG, DOPS, DOPC and DMPC) on the kinetics and structural endpoints of FapC fibrillation using various biophysical techniques. Particularly anionic lipids such as DMPG trigger FapC fibrillation, and the protein's second repeat sequence (R2) appears to be important for this interaction. Vesicles formed from phospholipids extracted from three different Pseudomonas strains (Δfap, ΔFapC and pfap) induce FapC fibrillation by accelerating nucleation. The general aggregation inhibitor epigallocatechin gallate (EGCG) inhibits FapC fibrillation by blocking interactions between FapC and vesicles and redirecting FapC monomers to oligomer structures. Our work indicates that biological membranes can contribute significantly to the fibrillation of functional amyloid.
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25
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Nagaraj M, Najarzadeh Z, Pansieri J, Biverstål H, Musteikyte G, Smirnovas V, Matthews S, Emanuelsson C, Johansson J, Buxbaum JN, Morozova-Roche L, Otzen DE. Chaperones mainly suppress primary nucleation during formation of functional amyloid required for bacterial biofilm formation. Chem Sci 2022; 13:536-553. [PMID: 35126986 PMCID: PMC8729806 DOI: 10.1039/d1sc05790a] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 12/11/2021] [Indexed: 11/21/2022] Open
Abstract
Unlike misfolding in neurodegenerative diseases, aggregation of functional amyloids involved in bacterial biofilm, e.g. CsgA (E. coli) and FapC (Pseudomonas), is carefully regulated.
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Affiliation(s)
- Madhu Nagaraj
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Zahra Najarzadeh
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
| | - Jonathan Pansieri
- Department of Medical Biochemistry and Biophysics, Umeå University, 90187, Umeå, Sweden
| | - Henrik Biverstål
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, S – 141 83 Huddinge, Sweden
| | - Greta Musteikyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Cecilia Emanuelsson
- Department of Biochemistry and Structural Biology, Center for Molecular Protein Science, Lund University, PO Box 124, SE-22100 Lund, Sweden
| | - Janne Johansson
- Department of Biosciences and Nutrition, Neo, Karolinska Institutet, S – 141 83 Huddinge, Sweden
| | - Joel N. Buxbaum
- The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA 92037, USA
| | | | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Gustav Wieds Vej 14, DK – 8000 Aarhus C, Denmark
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26
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Siri M, Herrera M, Moyano AJ, Celej MS. Influence of the macromolecular crowder alginate in the fibrillar organization of the functional amyloid FapC from Pseudomonas aeruginosa. Arch Biochem Biophys 2021; 713:109062. [PMID: 34688606 DOI: 10.1016/j.abb.2021.109062] [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: 06/24/2021] [Revised: 10/03/2021] [Accepted: 10/15/2021] [Indexed: 11/28/2022]
Abstract
Bacterial biofilms are an alternative lifestyle in which communities of bacteria are embedded in an extracellular matrix manly composed by polysaccharides, nucleic acids and proteins, being the hallmark of bacterial survival in a variety of ecological niches. Amyloid fibrils are one of the proteinaceous components of such extracellular crowded environments. FapC is the main component of the functional amyloid recently discovered in Pseudomonas species, including the opportunistic pathogen P. aeruginosa, which is a major cause of nosocomial infections and contamination of medical devices. Considering that several functional roles have been attributed to this bacterial amyloid, FapC emerged as a novel target to control Pseudomonas biofilm formation and to design new treatments against chronic infections. In this study, we used complementary biophysical techniques to evaluate conformational signatures of FapC amyloids formed in the presence of alginate, the major exopolysaccharide associated with the mucoid phenotype of P. aeruginosa strains isolated from cystic fibrosis patients. We found that the this naturally occurring macromolecular crowder leads to morphological similar yet polymorphic FapC fibrils, highlighting the importance of considering the complexity of the extracellular matrix in order to improve our understanding of microbial functional amyloids.
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Affiliation(s)
- Macarena Siri
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Melisa Herrera
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - Alejandro J Moyano
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina
| | - M Soledad Celej
- Departamento de Química Biológica Ranwel Caputto, Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC, CONICET), Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Haya de La Torre y Medina Allende, Ciudad Universitaria, X5000HUA, Córdoba, Argentina.
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27
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Folding Steps in the Fibrillation of Functional Amyloid: Denaturant Sensitivity Reveals Common Features in Nucleation and Elongation. J Mol Biol 2021; 434:167337. [PMID: 34748745 DOI: 10.1016/j.jmb.2021.167337] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 10/22/2021] [Accepted: 10/27/2021] [Indexed: 01/09/2023]
Abstract
Functional bacterial amyloids (FuBA) are intrinsically disordered proteins (IDPs) which rapidly and efficiently aggregate, forming extremely stable fibrils. The conversion from IDP to amyloid is evolutionarily optimized and likely couples folding to association. Many FuBA contain several imperfect repeat sequences which contribute to the stability of mature FuBA fibrils. Aggregation can be considered an intermolecular extension of the process of intramolecular protein folding which has traditionally been studied using chemical denaturants. Here we employ denaturants to investigate folding steps during fibrillation of CsgA and FapC. We quantify protein compactification (i.e. the extent of burial of otherwise exposed surface area upon association of proteins) during different stages of fibrillation based on the dependence of fibrillation rate constants on the denaturant concentration (m-values) determined from fibrillation curves. For both proteins, urea mainly affects nucleation and elongation (not fragmentation), consistent with the fact that these steps involve both intra- and intermolecular association. The two steps have similar m-values, indicating that activation steps in nucleation and elongation involve the same level of folding. Surprisingly, deletion of two or three repeats from FapC leads to larger m-values (i.e. higher compactification) during the activation step of fibril growth. This observation is extended by SAXS analysis of the fibrils which indicates that weakening of the amyloidogenic core caused by repeat deletions causes a larger portion of normally unstructured regions of the protein to be included into the amyloid backbone. We conclude that the sensitivity of fibrillation to denaturants can provide useful insight into molecular mechanisms of aggregation.
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28
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Patil A, Banerji R, Kanojiya P, Saroj SD. Foodborne ESKAPE Biofilms and Antimicrobial Resistance: lessons Learned from Clinical Isolates. Pathog Glob Health 2021; 115:339-356. [PMID: 33851566 PMCID: PMC8592604 DOI: 10.1080/20477724.2021.1916158] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The ESKAPE pathogens (Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) are identified to be multidrug-resistant (MDR), extensively drug-resistant (XDR), and pan drug-resistant (PDR); thereby, imposing severe challenges in the treatment of associated infections. ESKAPE pathogens colonize on various biotic and abiotic surfaces; biofilms formed by these pathogens are a potential source for food contamination. Moreover, biofilms play a pivotal role in the development of antimicrobial-resistant (AMR) strains. Hence, the frequent isolation of antimicrobial-resistant ESKAPE pathogens from food products across the globe imposes a threat to public health. A comprehensive understanding of the adhesion signaling involved in the polymicrobial and single-species biofilm will assist in developing alternative preservation techniques and novel therapeutic strategies to combat ESKAPE pathogens. The review provides a comprehensive overview of the signaling mechanisms that prevail in the ESKAPE pathogens for adhesion to abiotic and biotic surfaces and molecular mechanisms associated with poly-microbial biofilm-assisted AMR in ESKAPE.
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Affiliation(s)
- Amrita Patil
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
| | - Rajashri Banerji
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
| | - Poonam Kanojiya
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
| | - Sunil D. Saroj
- Symbiosis School of Biological Sciences, Symbiosis International (Deemed University), Symbiosis Knowledge Village, PuneMaharashtra, India
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29
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Alabresm A, Chandler SL, Benicewicz BC, Decho AW. Nanotargeting of Resistant Infections with a Special Emphasis on the Biofilm Landscape. Bioconjug Chem 2021; 32:1411-1430. [PMID: 34319073 PMCID: PMC8527872 DOI: 10.1021/acs.bioconjchem.1c00116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bacterial resistance to antimicrobial compounds is a growing concern in medical and public health circles. Overcoming the adaptable and duplicative resistance mechanisms of bacteria requires chemistry-based approaches. Engineered nanoparticles (NPs) now offer unique advantages toward this effort. However, most in situ infections (in humans) occur as attached biofilms enveloped in a protective surrounding matrix of extracellular polymers, where survival of microbial cells is enhanced. This presents special considerations in the design and deployment of antimicrobials. Here, we review recent efforts to combat resistant bacterial strains using NPs and, then, explore how NP surfaces may be specifically engineered to enhance the potency and delivery of antimicrobial compounds. Special NP-engineering challenges in the design of NPs must be overcome to penetrate the inherent protective barriers of the biofilm and to successfully deliver antimicrobials to bacterial cells. Future challenges are discussed in the development of new antibiotics and their mechanisms of action and targeted delivery via NPs.
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Affiliation(s)
- Amjed Alabresm
- Department of Environmental Health Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Biological Development of Shatt Al-Arab & N. Arabian Gulf, Marine Science Centre, University of Basrah, Basrah, Iraq
| | - Savannah L Chandler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Brian C Benicewicz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- USC NanoCenter, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Alan W Decho
- Department of Environmental Health Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
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30
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Daskalov A, El Mammeri N, Lends A, Shenoy J, Lamon G, Fichou Y, Saad A, Martinez D, Morvan E, Berbon M, Grélard A, Kauffmann B, Ferber M, Bardiaux B, Habenstein B, Saupe SJ, Loquet A. Structures of Pathological and Functional Amyloids and Prions, a Solid-State NMR Perspective. Front Mol Neurosci 2021; 14:670513. [PMID: 34276304 PMCID: PMC8280340 DOI: 10.3389/fnmol.2021.670513] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 05/26/2021] [Indexed: 12/20/2022] Open
Abstract
Infectious proteins or prions are a remarkable class of pathogens, where pathogenicity and infectious state correspond to conformational transition of a protein fold. The conformational change translates into the formation by the protein of insoluble amyloid aggregates, associated in humans with various neurodegenerative disorders and systemic protein-deposition diseases. The prion principle, however, is not limited to pathogenicity. While pathological amyloids (and prions) emerge from protein misfolding, a class of functional amyloids has been defined, consisting of amyloid-forming domains under natural selection and with diverse biological roles. Although of great importance, prion amyloid structures remain challenging for conventional structural biology techniques. Solid-state nuclear magnetic resonance (SSNMR) has been preferentially used to investigate these insoluble, morphologically heterogeneous aggregates with poor crystallinity. SSNMR methods have yielded a wealth of knowledge regarding the fundamentals of prion biology and have helped to solve the structures of several prion and prion-like fibrils. Here, we will review pathological and functional amyloid structures and will discuss some of the obtained structural models. We will finish the review with a perspective on integrative approaches combining solid-state NMR, electron paramagnetic resonance and cryo-electron microscopy, which can complement and extend our toolkit to structurally explore various facets of prion biology.
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Affiliation(s)
- Asen Daskalov
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Nadia El Mammeri
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Alons Lends
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | | | - Gaelle Lamon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Yann Fichou
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Ahmad Saad
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Denis Martinez
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Estelle Morvan
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | - Melanie Berbon
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Axelle Grélard
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
| | - Brice Kauffmann
- CNRS, INSERM, IECB, UMS 3033, University of Bordeaux, Pessac, France
| | | | | | | | - Sven J. Saupe
- CNRS, IBGC UMR 5095, University of Bordeaux, Bordeaux, France
| | - Antoine Loquet
- CNRS, CBMN UMR 5348, IECB, University of Bordeaux, Pessac, France
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31
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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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32
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Beg AZ, Farhat N, Khan AU. Designing multi-epitope vaccine candidates against functional amyloids in Pseudomonas aeruginosa through immunoinformatic and structural bioinformatics approach. INFECTION GENETICS AND EVOLUTION 2021; 93:104982. [PMID: 34186254 DOI: 10.1016/j.meegid.2021.104982] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/09/2021] [Accepted: 06/24/2021] [Indexed: 10/21/2022]
Abstract
Pseudomonas aeruginosa (P. aeruginosa) displays high drug resistance and biofilm-mediated adaptability, which makes its infections difficult to treat. Alternative intervention methods and targets have made such infections treatment manageable. One of the biofilm components, functional amyloids of Pseudomonas (Fap) is correlated positively with virulence and mucoidy phenotype found in infection in cystic fibrosis (CF) patients. Extracellular accessibility, conservation across P. aeruginosa isolates and linkage with lung infections phenotype in CF patients, makes Fap a promising intervention target. Furthermore, the reported effect of bacterial amyloid on neuronal function and immune response makes it a targetable candidate. In the current study, Fap C protein and its immediate interactions were explored to extract antigenic T-cell and B-cell epitopes. A combination of epitopes and peptide adjuvants has been linked to derive vaccine candidate structures. The vaccine candidates were validated for antigenicity, allergenicity, physiochemical properties, stability and interactions with TLRs and MHC alleles. Immunosimulation studies have demonstrated that vaccines elicit Th1 dominated response, which can assist in good prognosis of infection in CF patients.
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Affiliation(s)
- Ayesha Z Beg
- Medical Microbiology and Molecular Biology Lab., Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, India
| | - Nabeela Farhat
- 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; Centre for Bioinformatic on Antimicrobial Resistance, IBU, Aligarh Muslim University, Aligarh, India.
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33
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Christensen LFB, Alijanvand SH, Burdukiewicz M, Herbst FA, Kjeldal H, Dueholm MS, Otzen DE. Identification of amyloidogenic proteins in the microbiomes of a rat Parkinson's disease model and wild-type rats. Protein Sci 2021; 30:1854-1870. [PMID: 34075639 DOI: 10.1002/pro.4137] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/24/2021] [Accepted: 05/25/2021] [Indexed: 12/18/2022]
Abstract
Cross seeding between amyloidogenic proteins in the gut is receiving increasing attention as a possible mechanism for initiation or acceleration of amyloid formation by aggregation-prone proteins such as αSN, which is central in the development of Parkinson's disease (PD). This is particularly pertinent in view of the growing number of functional (i.e., benign and useful) amyloid proteins discovered in bacteria. Here we identify two amyloidogenic proteins, Pr12 and Pr17, in fecal matter from PD transgenic rats and their wild type counterparts, based on their stability against dissolution by formic acid (FA). Both proteins show robust aggregation into ThT-positive aggregates that contain higher-order β-sheets and have a fibrillar morphology, indicative of amyloid proteins. In addition, Pr17 aggregates formed in vitro showed significant resistance against FA, suggesting an ability to form highly stable amyloid. Treatment with proteinase K revealed a protected core of approx. 9 kDa. Neither Pr12 nor Pr17, however, affected αSN aggregation in vitro. Thus, amyloidogenicity does not per se lead to an ability to cross-seed fibrillation of αSN. Our results support the use of proteomics and FA to identify amyloidogenic protein in complex mixtures and suggests that there may be numerous functional amyloid proteins in microbiomes.
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Affiliation(s)
- Line Friis Bakmann Christensen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Saeid Hadi Alijanvand
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.,Institute of Biochemistry and Biophysics (IBB), Department of Biophysics, University of Tehran, Tehran, Iran
| | - Michał Burdukiewicz
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland.,Centre for Clinical Research, Medical University of Białystok, Białystok, Poland
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Henrik Kjeldal
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Simonsen Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
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34
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Gómez-Pérez D, Chaudhry V, Kemen A, Kemen E. Amyloid Proteins in Plant-Associated Microbial Communities. Microb Physiol 2021; 31:88-98. [PMID: 34107493 DOI: 10.1159/000516014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 03/17/2021] [Indexed: 11/19/2022]
Abstract
Amyloids have proven to be a widespread phenomenon rather than an exception. Many proteins presenting the hallmarks of this characteristic beta sheet-rich folding have been described to date. Particularly common are functional amyloids that play an important role in the promotion of survival and pathogenicity in prokaryotes. Here, we describe important developments in amyloid protein research that relate to microbe-microbe and microbe-host interactions in the plant microbiome. Starting with biofilms, which are a broad strategy for bacterial persistence that is extremely important for plant colonization. Microbes rely on amyloid-based mechanisms to adhere and create a protective coating that shelters them from external stresses and promotes cooperation. Another strategy generally carried out by amyloids is the formation of hydrophobic surface layers. Known as hydrophobins, these proteins coat the aerial hyphae and spores of plant pathogenic fungi, as well as certain bacterial biofilms. They contribute to plant virulence through promoting dissemination and infectivity. Furthermore, antimicrobial activity is an interesting outcome of the amyloid structure that has potential application in medicine and agriculture. There are many known antimicrobial amyloids released by animals and plants; however, those produced by bacteria or fungi remain still largely unknown. Finally, we discuss amyloid proteins with a more indirect mode of action in their host interactions. These include virulence-promoting harpins, signaling transduction that functions through amyloid templating, and root nodule bacteria proteins that promote plant-microbe symbiosis. In summary, amyloids are an interesting paradigm for their many functional mechanisms linked to bacterial survival in plant-associated microbial communities.
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Affiliation(s)
| | | | - Ariane Kemen
- ZMBP/IMIT, University of Tübingen, Tübingen, Germany
| | - Eric Kemen
- ZMBP/IMIT, University of Tübingen, Tübingen, Germany
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35
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Liu X, Ye Y, Zhu Y, Wang L, Yuan L, Zhu J, Sun A. Involvement of RpoN in Regulating Motility, Biofilm, Resistance, and Spoilage Potential of Pseudomonas fluorescens. Front Microbiol 2021; 12:641844. [PMID: 34135871 PMCID: PMC8202526 DOI: 10.3389/fmicb.2021.641844] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/30/2021] [Indexed: 11/17/2022] Open
Abstract
Pseudomonas fluorescens is a typical spoiler of proteinaceous foods, and it is characterized by high spoilage activity. The sigma factor RpoN is a well-known regulator controlling nitrogen assimilation and virulence in many pathogens. However, its exact role in regulating the spoilage caused by P. fluorescens is unknown. Here, an in-frame deletion mutation of rpoN was constructed to investigate its global regulatory function through phenotypic and RNA-seq analysis. The results of phenotypic assays showed that the rpoN mutant was deficient in swimming motility, biofilm formation, and resistance to heat and nine antibiotics, while the mutant increased the resistance to H2O2. Moreover, the rpoN mutant markedly reduced extracellular protease and total volatile basic nitrogen (TVB-N) production in sterilized fish juice at 4°C; meanwhile, the juice with the rpoN mutant showed significantly higher sensory scores than that with the wild-type strain. To identify RpoN-controlled genes, RNA-seq-dependent transcriptomics analysis of the wild-type strain and the rpoN mutant was performed. A total of 1224 genes were significantly downregulated, and 474 genes were significantly upregulated by at least two folds at the RNA level in the rpoN mutant compared with the wild-type strain, revealing the involvement of RpoN in several cellular processes, mainly flagellar mobility, adhesion, polysaccharide metabolism, resistance, and amino acid transport and metabolism; this may contribute to the swimming motility, biofilm formation, stress and antibiotic resistance, and spoilage activities of P. fluorescens. Our results provide insights into the regulatory role of RpoN of P. fluorescens in food spoilage, which can be valuable to ensure food quality and safety.
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Affiliation(s)
- Xiaoxiang Liu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Yifan Ye
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Yin Zhu
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Lifang Wang
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
| | - Leyang Yuan
- Zhejiang Museum of Natural History, Hangzhou, China
| | - Junli Zhu
- College of Food Science and Biotechnology, Zhejiang Gongshang University, Hangzhou, China
| | - Aihua Sun
- School of Basic Medical Sciences and Forensic Medicine, Hangzhou Medical College, Hangzhou, China
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36
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Renzetti A, Betts JW, Fukumoto K, Rutherford RN. Antibacterial green tea catechins from a molecular perspective: mechanisms of action and structure-activity relationships. Food Funct 2021; 11:9370-9396. [PMID: 33094767 DOI: 10.1039/d0fo02054k] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
This review summarizes the mechanisms of antibacterial action of green tea catechins, discussing the structure-activity relationship (SAR) studies for each mechanism. The antibacterial activity of green tea catechins results from a variety of mechanisms that can be broadly classified into the following groups: (1) inhibition of virulence factors (toxins and extracellular matrix); (2) cell wall and cell membrane disruption; (3) inhibition of intracellular enzymes; (4) oxidative stress; (5) DNA damage; and (6) iron chelation. These mechanisms operate simultaneously with relative importance differing among bacterial strains. In all SAR studies, the highest antibacterial activity is observed for galloylated compounds (EGCG, ECG, and theaflavin digallate). This observation, combined with numerous experimental and theoretical evidence, suggests that catechins share a common binding mode, characterized by the formation of hydrogen bonds and hydrophobic interactions with their target.
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Affiliation(s)
- Andrea Renzetti
- Global Education Institute, University of the Ryukyus, Nishihara, Okinawa 903-0213, Japan.
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37
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Antibiofilm activity of Fmoc-phenylalanine against Gram-positive and Gram-negative bacterial biofilms. J Antibiot (Tokyo) 2021; 74:407-416. [PMID: 33637856 DOI: 10.1038/s41429-021-00409-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 11/08/2022]
Abstract
Biofilm associated infections are the major contributor of mortality, morbidity and financial burden in patients with a bacterial infection. About 65% of all bacterial infections are associated with the information of bacterial biofilms. Bacterial biofilms not only reduce the efficacy of antibacterial treatment but also increases the threat of developing antibacterial resistance. Recently, our group has discovered the antibacterial activity of Fmoc-phenylalanine (Fmoc-F) and other Fmoc-amino acids (Fmoc-AA). Fmoc-F and other Fmoc-AA showed antibacterial activity due to their surfactant properties. Surfactants are known to eradicate biofilm and enhance antimicrobial activity in biofilm. Thus, in the present study, we evaluated the anti-biofilm activity of Fmoc-F against clinically relevant bacteria. We found that Fmoc-F not only inhibits the biofilm formation in Staphylococcus aureus and Pseudomonas aeruginosa, but also eradicates the already formed biofilms over the surface. Further, Fmoc-F coated glass surface resists S. aureus and P. aeruginosa biofilm formation and attachment, when biofilm is grown over the surface. The mechanistic investigation suggests that Fmoc-F reduces the extracellular matrix (ECM) components such as proteins, carbohydrates and eDNA in the biofilm and affect its stability via direct interactions with ECM components and/ or indirectly through reducing bacterial cell population. Finally, we showed that Fmoc-F treatment in combination with vancomycin and ampicillin synergistically inhibit biofilm formation. Overall, the study demonstrates the potential application of Fmoc-F and other Fmoc-AA molecules individually as well as in combination as anti-biofilm coating material for treating biofilm associated infections.
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38
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Moser C, Jensen PØ, Thomsen K, Kolpen M, Rybtke M, Lauland AS, Trøstrup H, Tolker-Nielsen T. Immune Responses to Pseudomonas aeruginosa Biofilm Infections. Front Immunol 2021; 12:625597. [PMID: 33692800 PMCID: PMC7937708 DOI: 10.3389/fimmu.2021.625597] [Citation(s) in RCA: 62] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Accepted: 01/20/2021] [Indexed: 12/17/2022] Open
Abstract
Pseudomonas aeruginosa is a key pathogen of chronic infections in the lungs of cystic fibrosis patients and in patients suffering from chronic wounds of diverse etiology. In these infections the bacteria congregate in biofilms and cannot be eradicated by standard antibiotic treatment or host immune responses. The persistent biofilms induce a hyper inflammatory state that results in collateral damage of the adjacent host tissue. The host fails to eradicate the biofilm infection, resulting in hindered remodeling and healing. In the present review we describe our current understanding of innate and adaptive immune responses elicited by P. aeruginosa biofilms in cystic fibrosis lung infections and chronic wounds. This includes the mechanisms that are involved in the activation of the immune responses, as well as the effector functions, the antimicrobial components and the associated tissue destruction. The mechanisms by which the biofilms evade immune responses, and potential treatment targets of the immune response are also discussed.
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Affiliation(s)
- Claus Moser
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Peter Østrup Jensen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kim Thomsen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Mette Kolpen
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten Rybtke
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Anne Sofie Lauland
- Department of Clinical Microbiology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Hannah Trøstrup
- Department of Plastic Surgery and Breast Surgery, Zealand University Hospital, Roskilde, Denmark
| | - Tim Tolker-Nielsen
- Costerton Biofilm Center, Department of Immunology and Microbiology, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
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Hansen SH, Nierychlo M, Christensen ML, Nielsen PH, Jørgensen MK. Fouling of membranes in membrane bioreactors for wastewater treatment: Planktonic bacteria can have a significant contribution. WATER ENVIRONMENT RESEARCH : A RESEARCH PUBLICATION OF THE WATER ENVIRONMENT FEDERATION 2021; 93:207-216. [PMID: 32645226 DOI: 10.1002/wer.1392] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/17/2020] [Accepted: 06/30/2020] [Indexed: 06/11/2023]
Abstract
Membrane bioreactors (MBRs) for wastewater treatment show great potentials in the sustainable development of urban environments. However, fouling of membranes remains the largest challenge of MBR technology. Dissolved extracellular polymeric substances (EPS) are often assumed be the main foulant in MBRs. However, single bacterial cells are often erroneously measured as EPS in traditional spectrophotometric analysis of EPS in activated sludge, so we hypothesized that single cells in many cases could be the true foulants in MBRs for wastewater treatment. To study this, raw MBR sludge and sludge supernatant with varying concentrations of planktonic cells were filtered on microfiltration (MF) membranes, and we found a direct correlation between the cell count and rate of flux decline. Addition of planktonic cells to fresh MBR sludge dramatically increased the flux decline. The identity of the most abundant planktonic cells in a full-scale MBR water resource recovery facility was determined by DNA fingerprinting. Many of these genera are known to be abundant in influent wastewater suggesting that the influent bacterial cells may have a direct effect on the fouling propensity in MBR systems. This new knowledge may lead to new anti-fouling strategies targeting incoming planktonic bacteria from the wastewater feed. PRACTITIONER POINTS: Planktonic cells constituted up to 60% of the total protein content of "soluble extracellular polymeric substances" in membrane bioreactor sludge. Planktonic cells are hidden under a surrogate concentration of extracellular polymeric substances which is often associated with fouling. Membrane fouling rate is directly proportional to amount of free planktonic cells suspended in sludge. Several influent bacterial genera are enriched in the water phase of membrane bioreactor sludge. Removing these may mitigate fouling.
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Affiliation(s)
- Susan Hove Hansen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Marta Nierychlo
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Morten L Christensen
- Department of Chemistry and Bioscience, Center for Membrane Technology, Aalborg University, Aalborg, Denmark
| | - Per Halkjaer Nielsen
- Department of Chemistry and Bioscience, Center for Microbial Communities, Aalborg University, Aalborg, Denmark
| | - Mads Koustrup Jørgensen
- Department of Chemistry and Bioscience, Center for Membrane Technology, Aalborg University, Aalborg, Denmark
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Konstantoulea K, Louros N, Rousseau F, Schymkowitz J. Heterotypic interactions in amyloid function and disease. FEBS J 2021; 289:2025-2046. [PMID: 33460517 DOI: 10.1111/febs.15719] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 01/07/2021] [Accepted: 01/15/2021] [Indexed: 11/27/2022]
Abstract
Amyloid aggregation results from the self-assembly of identical aggregation-prone sequences into cross-beta-sheet structures. The process is best known for its association with a wide range of human pathologies but also as a functional mechanism in all kingdoms of life. Less well elucidated is the role of heterotypic interactions between amyloids and other proteins and macromolecules and how this contributes to disease. We here review current data with a focus on neurodegenerative amyloid-associated diseases. Evidence indicates that heterotypic interactions occur in a wide range of amyloid processes and that these interactions modify fundamental aspects of amyloid aggregation including seeding, aggregation rates and toxicity. More work is required to understand the mechanistic origin of these interactions, but current understanding suggests that both supersaturation and sequence-specific binding can contribute to heterotypic amyloid interactions. Further unravelling these mechanisms may help to answer outstanding questions in the field including the selective vulnerability of cells types and tissues and the stereotypical spreading patterns of amyloids in disease.
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Affiliation(s)
- Katerina Konstantoulea
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Nikolaos Louros
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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Heredia-Ponce Z, Gutiérrez-Barranquero JA, Purtschert-Montenegro G, Eberl L, de Vicente A, Cazorla FM. Role of extracellular matrix components in the formation of biofilms and their contribution to the biocontrol activity of Pseudomonas chlororaphis PCL1606. Environ Microbiol 2020; 23:2086-2101. [PMID: 33314481 DOI: 10.1111/1462-2920.15355] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 12/09/2020] [Accepted: 12/10/2020] [Indexed: 12/15/2022]
Abstract
Pseudomonas chlororaphis PCL1606 (PcPCL1606) displays plant-colonizing features and exhibits antagonistic traits against soil-borne phytopathogenic fungi. Biofilm formation could be relevant for the PcPCL1606 lifestyle, and in this study the role of some putative extracellular matrix components (EMC; Fap-like fibre, alginate and Psl-like polysaccharides) in the biofilm architecture and biocontrol activity of this bacterium were determined. EMC such as the Fap-like fibre and alginate polysaccharide play secondary roles in biofilm formation in PcPCL1606, because they are not fundamental to its biofilm architecture in flow cell chamber, but synergistically they have shown to favour bacterial competition during biofilm formation. Conversely, studies on Psl-like polysaccharide have revealed that it may contain mannose, and that it is strongly involved in the PcPCL1606 biofilm architecture and niche competition. Furthermore, the Fap-like fibre and Psl-like exopolysaccharide play roles in early surface attachment and contribute to biocontrol activity against the white root rot disease caused by Rosellinia necatrix in avocado plants. These results constitute the first report regarding the study of the extracellular matrix of the PcPCL1606 strain and highlight the importance of a putative Fap-like fibre and Psl-like exopolysaccharide produced by PcPCL1606 in the biofilm formation process and interactions with the host plant root.
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Affiliation(s)
- Zaira Heredia-Ponce
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - José Antonio Gutiérrez-Barranquero
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | | | - Leo Eberl
- Department of Plant and Microbial Biology, University of Zurich, Zollikerstrasse 107, Zurich, CH-8008, Switzerland
| | - Antonio de Vicente
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
| | - Francisco M Cazorla
- Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora" (IHSM-UMA-CSIC) - Departamento de Microbiología, Universidad de Málaga, Bulevar Louis Pasteur, 31 (Campus Universitario de Teatinos), Málaga, 29071, Spain
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Functional Amyloids Are the Rule Rather Than the Exception in Cellular Biology. Microorganisms 2020; 8:microorganisms8121951. [PMID: 33316961 PMCID: PMC7764130 DOI: 10.3390/microorganisms8121951] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Revised: 11/28/2020] [Accepted: 12/04/2020] [Indexed: 12/15/2022] Open
Abstract
Amyloids are a class of protein aggregates that have been historically characterized by their relationship with human disease. Indeed, amyloids can be the result of misfolded proteins that self-associate to form insoluble, extracellular plaques in diseased tissue. For the first 150 years of their study, the pathogen-first definition of amyloids was sufficient. However, new observations of amyloids foster an appreciation for non-pathological roles for amyloids in cellular systems. There is now evidence from all domains of life that amyloids can be non-pathogenic and functional, and that their formation can be the result of purposeful and controlled cellular processes. So-called functional amyloids fulfill an assortment of biological functions including acting as structural scaffolds, regulatory mechanisms, and storage mechanisms. The conceptual convergence of amyloids serving a functional role has been repeatedly confirmed by discoveries of additional functional amyloids. With dozens already known, and with the vigorous rate of discovery, the biology of amyloids is robustly represented by non-pathogenic amyloids.
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Blanco-Romero E, Garrido-Sanz D, Rivilla R, Redondo-Nieto M, Martín M. In Silico Characterization and Phylogenetic Distribution of Extracellular Matrix Components in the Model Rhizobacteria Pseudomonas fluorescens F113 and Other Pseudomonads. Microorganisms 2020; 8:E1740. [PMID: 33171989 PMCID: PMC7716237 DOI: 10.3390/microorganisms8111740] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 11/01/2020] [Accepted: 11/04/2020] [Indexed: 12/23/2022] Open
Abstract
Biofilms are complex structures that are crucial during host-bacteria interaction and colonization. Bacteria within biofilms are surrounded by an extracellular matrix (ECM) typically composed of proteins, polysaccharides, lipids, and DNA. Pseudomonads contain a variety of ECM components, some of which have been extensively characterized. However, neither the ECM composition of plant-associated pseudomonads nor their phylogenetic distribution within the genus has been so thoroughly studied. In this work, we use in silico methods to describe the ECM composition of Pseudomonas fluorescens F113, a plant growth-promoting rhizobacteria and model for rhizosphere colonization. These components include the polysaccharides alginate, poly-N-acetyl-glucosamine (PNAG) and levan; the adhesins LapA, MapA and PsmE; and the functional amyloids in Pseudomonas. Interestingly, we identified novel components: the Pseudomonas acidic polysaccharide (Pap), whose presence is limited within the genus; and a novel type of Flp/Tad pilus, partially different from the one described in P. aeruginosa. Furthermore, we explored the phylogenetic distribution of the most relevant ECM components in nearly 600 complete Pseudomonas genomes. Our analyses show that Pseudomonas populations contain a diverse set of gene/gene clusters potentially involved in the formation of their ECMs, showing certain commensal versus pathogen lifestyle specialization.
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Affiliation(s)
| | | | | | | | - Marta Martín
- Departamento de Biología, Facultad de Ciencias, Universidad Autónoma de Madrid, c/Darwin 2, 28049 Madrid, Spain; (E.B.-R.); (D.G.-S.); (R.R.); (M.R.-N.)
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Eskandari H, Ghanadian M, Noleto-Dias C, Lomax C, Tawfike A, Christiansen G, Sutherland DS, Ward JL, Mohammad-Beigi H, Otzen DE. Inhibitors of α-Synuclein Fibrillation and Oligomer Toxicity in Rosa damascena: The All-Pervading Powers of Flavonoids and Phenolic Glycosides. ACS Chem Neurosci 2020; 11:3161-3173. [PMID: 32886481 DOI: 10.1021/acschemneuro.0c00528] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
There is an intense search for natural compounds that can inhibit the oligomerization and fibrillation of α-synuclein (α-Syn), whose aggregation is key to the development of Parkinson's disease (PD). Rosa damascena is a medicinal herb widely used in Middle Eastern food, ceremonies, and perfumes. The herb is known to contain many different polyphenols. Here we investigated the existence of α-Syn fibrillation inhibitors in R. damascena extract. Different HPLC fractions of the extract were assessed in α-Syn fibrillation and toxicity assays. The most active fractions led to the formation of more α-Syn oligomers but with less toxicity to SH-SY5Y cells, according to MTT and LDH assays. LC-MS analysis identified gallic acid, kaempferol 3-glucoside, kaempferol-3-O-β-rutinoside, and quercetin which were subsequently shown to be strong α-Syn fibrillation inhibitors. Our results highlight the benefits of R. damascena extract to combat PD at the population level.
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Affiliation(s)
- Hoda Eskandari
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, DK− 8000 Aarhus C, Denmark
| | - Mustafa Ghanadian
- Department of Pharmacognosy, Isfahan Faculty of Pharmacy, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Clarice Noleto-Dias
- Computational and Analytical Sciences Department, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, U.K
| | - Charlotte Lomax
- Computational and Analytical Sciences Department, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, U.K
| | - Ahmed Tawfike
- Computational and Analytical Sciences Department, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, U.K
| | - Gunna Christiansen
- Department of Biomedicine-Medical Microbiology and Immunology, Aarhus University, 8000 Aarhus C, Denmark
| | - Duncan S. Sutherland
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, DK− 8000 Aarhus C, Denmark
| | - Jane L. Ward
- Computational and Analytical Sciences Department, Rothamsted Research, West Common, Harpenden, Herts AL5 2JQ, U.K
| | - Hossein Mohammad-Beigi
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, DK− 8000 Aarhus C, Denmark
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Centre (iNANO), Aarhus University, Gustav Wieds Vej 14, DK− 8000 Aarhus C, Denmark
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Kosolapova AO, Antonets KS, Belousov MV, Nizhnikov AA. Biological Functions of Prokaryotic Amyloids in Interspecies Interactions: Facts and Assumptions. Int J Mol Sci 2020; 21:E7240. [PMID: 33008049 PMCID: PMC7582709 DOI: 10.3390/ijms21197240] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 09/25/2020] [Accepted: 09/28/2020] [Indexed: 02/07/2023] Open
Abstract
Amyloids are fibrillar protein aggregates with an ordered spatial structure called "cross-β". While some amyloids are associated with development of approximately 50 incurable diseases of humans and animals, the others perform various crucial physiological functions. The greatest diversity of amyloids functions is identified within prokaryotic species where they, being the components of the biofilm matrix, function as adhesins, regulate the activity of toxins and virulence factors, and compose extracellular protein layers. Amyloid state is widely used by different pathogenic bacterial species in their interactions with eukaryotic organisms. These amyloids, being functional for bacteria that produce them, are associated with various bacterial infections in humans and animals. Thus, the repertoire of the disease-associated amyloids includes not only dozens of pathological amyloids of mammalian origin but also numerous microbial amyloids. Although the ability of symbiotic microorganisms to produce amyloids has recently been demonstrated, functional roles of prokaryotic amyloids in host-symbiont interactions as well as in the interspecies interactions within the prokaryotic communities remain poorly studied. Here, we summarize the current findings in the field of prokaryotic amyloids, classify different interspecies interactions where these amyloids are involved, and hypothesize about their real occurrence in nature as well as their roles in pathogenesis and symbiosis.
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Affiliation(s)
- Anastasiia O. Kosolapova
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Kirill S. Antonets
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Mikhail V. Belousov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
| | - Anton A. Nizhnikov
- Laboratory for Proteomics of Supra-Organismal Systems, All-Russia Research Institute for Agricultural Microbiology (ARRIAM), 196608 St. Petersburg, Russia (K.S.A.); (M.V.B.)
- Faculty of Biology, St. Petersburg State University (SPbSU), 199034 St. Petersburg, Russia
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Christensen LFB, Nowak JS, Sønderby TV, Frank SA, Otzen DE. Quantitating denaturation by formic acid: imperfect repeats are essential to the stability of the functional amyloid protein FapC. J Biol Chem 2020; 295:13031-13046. [PMID: 32719003 PMCID: PMC7489911 DOI: 10.1074/jbc.ra120.013396] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 07/11/2020] [Indexed: 12/27/2022] Open
Abstract
Bacterial functional amyloids are evolutionarily optimized to aggregate, so much so that the extreme robustness of functional amyloid makes it very difficult to examine their structure-function relationships in a detailed manner. Previous work has shown that functional amyloids are resistant to conventional chemical denaturants, but they dissolve in formic acid (FA) at high concentrations. However, systematic investigation requires a quantitative analysis of FA's ability to denature proteins. Amyloid formed by Pseudomonas sp. protein FapC provides an excellent model to investigate FA denaturation. It contains three imperfect repeats, and stepwise removal of these repeats slows fibrillation and increases fragmentation during aggregation. However, the link to stability is unclear. We first calibrated FA denaturation using three small, globular, and acid-resistant proteins. This revealed a linear relationship between the concentration of FA and the free energy of unfolding with a slope of mFA+pH (the combined contribution of FA and FA-induced lowering of pH), as well as a robust correlation between protein size and mFA+pH We then measured the solubilization of fibrils formed from different FapC variants with varying numbers of repeats as a function of the concentration of FA. This revealed a decline in the number of residues driving amyloid formation upon deleting at least two repeats. The midpoint of denaturation declined with the removal of repeats. Complete removal of all repeats led to fibrils that were solubilized at FA concentrations 2-3 orders of magnitude lower than the repeat-containing variants, showing that at least one repeat is required for the stability of functional amyloid.
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Affiliation(s)
| | - Jan Stanislaw Nowak
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | | | - Signe Andrea Frank
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Center (iNANO), Aarhus University, Aarhus C, Denmark.
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Phase Transitions by an Abundant Protein in the Anammox Extracellular Matrix Mediate Cell-to-Cell Aggregation and Biofilm Formation. mBio 2020; 11:mBio.02052-20. [PMID: 32900808 PMCID: PMC7482068 DOI: 10.1128/mbio.02052-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
By employing biophysical and liquid-liquid phase separation concepts, this study revealed how a highly abundant extracellular protein enhances the key environmental and industrial bioprocess of anaerobic ammonium oxidation (anammox). Extracellular proteins of environmental biofilms are understudied and poorly annotated in public databases. Understanding the function of extracellular proteins is also increasingly important for improving bioprocesses and resource recovery. Here, protein functions were assessed based on theoretical predictions of intrinsically disordered domains, known to promote adhesion and liquid-liquid phase separation, and available surface layer protein properties. A model is thus proposed to explain how the protein promotes aggregation and biofilm formation by extracellular matrix remodeling and phase transitions. This work provides a strong foundation for functional investigations of extracellular proteins involved in biofilm development. This study describes the first direct functional assignment of a highly abundant extracellular protein from a key environmental and biotechnological biofilm performing an anaerobic ammonium oxidation (anammox) process. Expression levels of Brosi_A1236, belonging to a class of proteins previously suggested to be cell surface associated, were in the top one percentile of all genes in the “Candidatus Brocadia sinica”-enriched biofilm. The Brosi_A1236 structure was computationally predicted to consist of immunoglobulin-like anti-parallel β-strands, and circular dichroism conducted on the isolated surface protein indicated that β-strands are the dominant higher-order structure. The isolated protein was stained positively by the β-sheet-specific stain thioflavin T, along with cell surface- and matrix-associated regions of the biofilm. The surface protein has a large unstructured content, including two highly disordered domains at its C terminus. The disordered domains bound to the substratum and thereby facilitated the adhesion of negatively charged latex microspheres, which were used as a proxy for cells. The disordered domains and isolated whole surface protein also underwent liquid-liquid phase separation to form liquid droplets in suspension. Liquid droplets of disordered protein wet the surfaces of microspheres and bacterial cells and facilitated their coalescence. Furthermore, the surface layer protein formed gels as well as ordered crystalline structures. These observations suggest that biophysical remodeling through phase transitions promotes aggregation and biofilm formation.
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Javed I, Zhang Z, Adamcik J, Andrikopoulos N, Li Y, Otzen DE, Lin S, Mezzenga R, Davis TP, Ding F, Ke PC. Accelerated Amyloid Beta Pathogenesis by Bacterial Amyloid FapC. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2020; 7:2001299. [PMID: 32999841 PMCID: PMC7509637 DOI: 10.1002/advs.202001299] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 06/10/2020] [Indexed: 05/03/2023]
Abstract
The gut-brain axis has attracted increasing attention in recent years, fueled by accumulating symptomatic, physiological, and pathological findings. In this study, the aggregation and toxicity of amyloid beta (Aβ), the pathogenic peptide associated with Alzheimer's disease (AD), seeded by FapC amyloid fragments (FapCS) of Pseudomonas aeruginosa that colonizes the gut microbiome through infections are examined. FapCS display favorable binding with Aβ and a catalytic capacity in seeding the peptide amyloidosis. Upon seeding, twisted Aβ fibrils assume a much-shortened periodicity approximating that of FapC fibrils, accompanied by a 37% sharp rise in the fibrillar diameter, compared with the control. The robust seeding capacity for Aβ by FapCS and the biofilm fragments derived from P. aeruginosa entail abnormal behavior pathology and immunohistology, as well as impaired cognitive function of zebrafish. Together, the data offer the first concrete evidence of structural integration and inheritance in peptide cross-seeding, a crucial knowledge gap in understanding the pathological correlations between different amyloid diseases. The catalytic role of infectious bacteria in promoting Aβ amyloidosis may be exploited as a potential therapeutic target, while the altered mesoscopic signatures of Aβ fibrils may serve as a prototype for molecular assembly and a biomarker for screening bacterial infections in AD.
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Affiliation(s)
- Ibrahim Javed
- Australian Institute for Bioengineering and NanotechnologyUniversity of QueenslandBrisbaneQLD4072Australia
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Zhenzhen Zhang
- Department of Physics and AstronomyClemson UniversityClemsonSC29634USA
| | - Jozef Adamcik
- Food & Soft MaterialsDepartment of Health Science & TechnologyETH ZurichSchmelzbergstrasse 9, LFO, E23Zurich8092Switzerland
| | - Nicholas Andrikopoulos
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Yuhuan Li
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Daniel E. Otzen
- Interdisciplinary Nanoscience Center (iNANO)University of AarhusAarhus CAarhus8000Denmark
| | - Sijie Lin
- College of Environmental Science and EngineeringBiomedical Multidisciplinary Innovation Research InstituteShanghai East HospitalShanghai Institute of Pollution Control and Ecological SecurityTongji University1239 Siping RoadShanghai200092China
| | - Raffaele Mezzenga
- Food & Soft MaterialsDepartment of Health Science & TechnologyETH ZurichSchmelzbergstrasse 9, LFO, E23Zurich8092Switzerland
| | - Thomas P. Davis
- Australian Institute for Bioengineering and NanotechnologyUniversity of QueenslandBrisbaneQLD4072Australia
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
| | - Feng Ding
- Department of Physics and AstronomyClemson UniversityClemsonSC29634USA
| | - Pu Chun Ke
- ARC Centre of Excellence in Convergent Bio‐Nano Science and TechnologyMonash Institute of Pharmaceutical SciencesMonash University381 Royal ParadeParkvilleVIC3052Australia
- Zhongshan HospitalFudan University111 Yixueyuan Rd, Xuhui DistrictShanghai200032China
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Moshynets O, Chernii S, Chernii V, Losytskyy M, Karakhim S, Czerwieniec R, Pekhnyo V, Yarmoluk S, Kovalska V. Fluorescent β-ketoenole AmyGreen dye for visualization of amyloid components of bacterial biofilms. Methods Appl Fluoresc 2020; 8:035006. [PMID: 32375137 DOI: 10.1088/2050-6120/ab90e0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Green-emitting water-soluble amino-ketoenole dye AmyGreen is proposed as an efficient fluorescent stain for visualization of bacterial amyloids in biofilms and the detection of pathological amyloids in vitro. This dye is almost non-fluorescent in solution, displays strong green emission in the presence of amyloid fibril of proteins. AmyGreen is also weakly fluorescent in presence to biomolecules that are components of cells, extracellular matrix or medium: nucleic acids, polysaccharides, lipids, and proteins. Thus, the luminescence turn-on behavior of AmyGreen can be utilized for visualization of amyloid components of bacterial biofilm extracellular matrix. Herein we report the application of AmyGreen for fluorescent staining of a number of amyloid-contained bacteria biofilms produced by Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Bordetella avium, and Staphylococcus aureus. The effectiveness of AmyGreen was compared to traditional amyloid sensitive dye Thioflavine T. The main advantage of AmyGreen (concentration 10-5 M) is a higher sensitivity in the visualization of amyloid biofilm components over Thioflavine T (10-4 M) as it was revealed when staining E. coli and K. pneumoniae bacterial biofilms. Besides, AmyGreen displays lower cross-selectivity to nucleic acids as demonstrated both in in-solution experiments and upon staining of eukaryotic human mesenchymal stem cells used as amyloid-free negative control over amyloid-rich bacterial biofilms. The results point to a lower risk of false-positive response upon determination of amyloid components of bacterial biofilm using AmyGreen. Co-staining of biofilm by AmyGreen and cellulose sensitive dye Calcofluor White show difference in their staining patterns and localization, indicating separation of polysaccharide-rich and amyloid-rich regions of investigated biofilms. Thus, we suggest the new AmyGreen stain for visualization and differentiation of amyloid fibrils in bacterial biofilms to be used solely and in combination with other stains for confocal and fluorescence microscopy analysis.
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Affiliation(s)
- Olena Moshynets
- Institute of Molecular Biology and Genetics NASU, 150 Zabolotnogo St., 03143 Kyiv, Ukraine
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Voth S, Gwin M, Francis CM, Balczon R, Frank DW, Pittet JF, Wagener BM, Moser SA, Alexeyev M, Housley N, Audia JP, Piechocki S, Madera K, Simmons A, Crawford M, Stevens T. Virulent Pseudomonas aeruginosa infection converts antimicrobial amyloids into cytotoxic prions. FASEB J 2020; 34:9156-9179. [PMID: 32413239 PMCID: PMC7383673 DOI: 10.1096/fj.202000051rrr] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2020] [Revised: 04/19/2020] [Accepted: 04/21/2020] [Indexed: 01/05/2023]
Abstract
Pseudomonas aeruginosa infection elicits the production of cytotoxic amyloids from lung endothelium, yet molecular mechanisms of host‐pathogen interaction that underlie the amyloid production are not well understood. We examined the importance of type III secretion system (T3SS) effectors in the production of cytotoxic amyloids. P aeruginosa possessing a functional T3SS and effectors induced the production and release of cytotoxic amyloids from lung endothelium, including beta amyloid, and tau. T3SS effector intoxication was sufficient to generate cytotoxic amyloid release, yet intoxication with exoenzyme Y (ExoY) alone or together with exoenzymes S and T (ExoS/T/Y) generated the most virulent amyloids. Infection with lab and clinical strains engendered cytotoxic amyloids that were capable of being propagated in endothelial cell culture and passed to naïve cells, indicative of a prion strain. Conversely, T3SS‐incompetent P aeruginosa infection produced non‐cytotoxic amyloids with antimicrobial properties. These findings provide evidence that (1) endothelial intoxication with ExoY is sufficient to elicit self‐propagating amyloid cytotoxins during infection, (2) pulmonary endothelium contributes to innate immunity by generating antimicrobial amyloids in response to bacterial infection, and (3) ExoY contributes to the virulence arsenal of P aeruginosa through the subversion of endothelial amyloid host‐defense to promote a lung endothelial‐derived cytotoxic proteinopathy.
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Affiliation(s)
- Sarah Voth
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Meredith Gwin
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Christopher Michael Francis
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Ron Balczon
- Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Department of Biochemistry and Molecular Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Dara W Frank
- Department of Microbiology and Molecular Genetics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Jean-Francois Pittet
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Brant M Wagener
- Department of Anesthesiology and Perioperative Medicine, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Stephen A Moser
- Department of Pathology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
| | - Mikhail Alexeyev
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Nicole Housley
- Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Jonathon P Audia
- Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Department of Microbiology and Immunology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Scott Piechocki
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Kayla Madera
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Autumn Simmons
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Michaela Crawford
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA
| | - Troy Stevens
- Department of Physiology and Cell Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Center for Lung Biology, College of Medicine, University of South Alabama, Mobile, AL, USA.,Department of Internal Medicine, College of Medicine, University of South Alabama, Mobile, AL, USA
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