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Naheed S, Din IU, Qamar MU, Rasool N, Ahmad M, Bilal M, Khalid A, Ahmad G, Al-Hussain SA, Zaki MEA. Synthesis, Anti-Bacterial and Molecular Docking Studies of Arylated Butyl 2-Bromoisonicotinate Against Clinical Isolates of ESBL-Producing Escherichia coli ST405 and Methicillin-Resistant Staphylococcus aureus. Infect Drug Resist 2023; 16:5295-5308. [PMID: 37601564 PMCID: PMC10438430 DOI: 10.2147/idr.s407891] [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: 04/12/2023] [Accepted: 07/12/2023] [Indexed: 08/22/2023] Open
Abstract
Introduction Global public health concerns include the emergence and spread of methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum beta-lactamase Escherichia coli (ESBL-E. coli). These pathogens cause infections that are difficult to treat, which can have fatal outcomes and require lengthy hospital stays. As a result, we created butyl 2-bromoisonicotinate and tested its antibacterial effectiveness against the ESBL-E. coli ST 405 and MRSA pathogens. Natural product discovery is complemented by synthetic compound synthesis because of the latter's potential for superior characteristics, target specificity, scalability, intellectual advantages, and chemical diversity. Because of this, the potential for discovering new medicinal compounds is increased, and the constraints placed on natural sources are overcome. Natural items are tough to obtain since they are hard to isolate and synthesize. Therefore, modern science is actively searching for small molecules as therapeutic agents by applying sustainable techniques that can be commercialized. Methods Two patients' blood samples were taken, and the BACTEC/Alert system was used to process them. On blood and MacConkey agar, the positive samples were subcultured and incubated aerobically at 37 °C. Using the VITEK 2 compact system, the isolates were subjected to isolate identification and MIC. MLST of the ESBL-E. coli was performed by PCR. Additionally, Fischer esterification was used to create butyl 2-bromoisonicotinate in excellent yields. A commercially available palladium catalyst was then used to arylate the compound, resulting in medium to good yields of arylated butyl 2-bromoisonicotinates. Using the agar well diffusion assay and the micro-broth dilution method, we assessed the in-vitro activities of the synthesized molecules (3, 5a-h) against clinically isolated ESBL-E. coli ST405, and MRSA. A molecular operating environment was used to carry out in silico validation of the synthesized compounds' binding to the active site and to evaluate the stability of their molecular interactions with the target E. coli 2Y2T protein. Results MRSA and ESBL-producing E. coli were identified as the two clinical isolates. While MRSA was also resistant to beta-lactam drugs and least resistant to vancomycin, ESBL-producing E. coli belonged to ST405 and was resistant to cephalosporins and sensitive to carbapenems. Good yields of the desired compounds were produced by our effective and economical synthesis. By using a micro-broth dilution assay, the Molecules (3, 5a, and 5d) were most effective against both resistant strains. The Molecules (3, 5a, 5b, and 5d) also displayed good binding energies. Conclusion The butyl 2-bromoisonicotinate displayed antibacterial efficacy against ESBL-producing E. coli ST405 and MRSA strains. After the in-vivo trial, this substance might offer an alternative therapeutic option.
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Affiliation(s)
- Shazia Naheed
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Irum Umar Din
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Usman Qamar
- Institute of Microbiology, Faculty of Life Sciences, Government College University, Faisalabad, 38000, Pakistan
| | - Nasir Rasool
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Matloob Ahmad
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Muhammad Bilal
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Aqsa Khalid
- School of Interdisciplinary Engineering & Science (SINES), National University of Sciences and Technology (NUST), Islamabad, 44000, Pakistan
| | - Gulraiz Ahmad
- Department of Chemistry, Government College University Faisalabad, Faisalabad, 38000, Pakistan
| | - Sami A Al-Hussain
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyad, 11623, Saudi Arabia
| | - Magdi E A Zaki
- Department of Chemistry, Faculty of Science, Imam Mohammad Ibn Saud Islamic University, Riyad, 11623, Saudi Arabia
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Rivas-Arancibia S, Miranda-Martínez A, Rodríguez-Martínez E, Hernández-Orozco E, Valdés-Fuentes M, De la Rosa-Sierra R. Ozone Environmental Pollution: Relationship between the Intestine and Neurodegenerative Diseases. Antioxidants (Basel) 2023; 12:1323. [PMID: 37507863 PMCID: PMC10376557 DOI: 10.3390/antiox12071323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 06/16/2023] [Accepted: 06/16/2023] [Indexed: 07/30/2023] Open
Abstract
Repeated exposure to environmental ozone causes a chronic state of oxidative stress. This state is present in chronic degenerative diseases and induces a loss of control of the inflammatory response. Redox system dysfunction and failures in control of inflammatory responses are involved in a vicious circle that maintains and increases the degenerative process. The intestine also responds to secondary reactive species formed by exposure to ozone doses, generating noxious stimuli that increase degenerative damage. This review aims to elucidate how environmental pollution, mainly by ozone, induces a state of chronic oxidative stress with the loss of regulation of the inflammatory response, both in the intestine and in the brain, where the functionality of both structures is altered and plays a determining role in some neurodegenerative and chronic degenerative diseases. For this purpose, we searched for information on sites such as the Cochrane Library Database, PubMed, Scopus, and Medscape. Reviewing the data published, we can conclude that environmental pollutants are a severe health problem. Ozone pollution has different pathways of action, both molecular and systemic, and participates in neurodegenerative diseases such as Parkinson's and Alzheimer's disease as well in bowel diseases as Inflammatory Bowel Disease, Crohn's Disease, and Irritable Bowel Syndrome.
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Affiliation(s)
- Selva Rivas-Arancibia
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Alfredo Miranda-Martínez
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Erika Rodríguez-Martínez
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Eduardo Hernández-Orozco
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Marlen Valdés-Fuentes
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
| | - Roberto De la Rosa-Sierra
- Departamento de Fisiología, Facultad de Medicina, Universidad Nacional Autónoma de México, Mexico City 04510, Mexico
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Buchanan JA, Varghese NR, Johnston CL, Sunde M. Functional Amyloids: Where Supramolecular Amyloid Assembly Controls Biological Activity or Generates New Functionality. J Mol Biol 2023; 435:167919. [PMID: 37330295 DOI: 10.1016/j.jmb.2022.167919] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 12/05/2022] [Accepted: 12/05/2022] [Indexed: 06/19/2023]
Abstract
Functional amyloids are a rapidly expanding class of fibrillar protein structures, with a core cross-β scaffold, where novel and advantageous biological function is generated by the assembly of the amyloid. The growing number of amyloid structures determined at high resolution reveal how this supramolecular template both accommodates a wide variety of amino acid sequences and also imposes selectivity on the assembly process. The amyloid fibril can no longer be considered a generic aggregate, even when associated with disease and loss of function. In functional amyloids the polymeric β-sheet rich structure provides multiple different examples of unique control mechanisms and structures that are finely tuned to deliver assembly or disassembly in response to physiological or environmental cues. Here we review the range of mechanisms at play in natural, functional amyloids, where tight control of amyloidogenicity is achieved by environmental triggers of conformational change, proteolytic generation of amyloidogenic fragments, or heteromeric seeding and amyloid fibril stability. In the amyloid fibril form, activity can be regulated by pH, ligand binding and higher order protofilament or fibril architectures that impact the arrangement of associated domains and amyloid stability. The growing understanding of the molecular basis for the control of structure and functionality delivered by natural amyloids in nearly all life forms should inform the development of therapies for amyloid-associated diseases and guide the design of innovative biomaterials.
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Affiliation(s)
- Jessica A Buchanan
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Nikhil R Varghese
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Caitlin L Johnston
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
| | - Margaret Sunde
- School of Medical Sciences and Sydney Nano, The University of Sydney, NSW 2006, Australia.
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Miserez A, Yu J, Mohammadi P. Protein-Based Biological Materials: Molecular Design and Artificial Production. Chem Rev 2023; 123:2049-2111. [PMID: 36692900 PMCID: PMC9999432 DOI: 10.1021/acs.chemrev.2c00621] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Polymeric materials produced from fossil fuels have been intimately linked to the development of industrial activities in the 20th century and, consequently, to the transformation of our way of living. While this has brought many benefits, the fabrication and disposal of these materials is bringing enormous sustainable challenges. Thus, materials that are produced in a more sustainable fashion and whose degradation products are harmless to the environment are urgently needed. Natural biopolymers─which can compete with and sometimes surpass the performance of synthetic polymers─provide a great source of inspiration. They are made of natural chemicals, under benign environmental conditions, and their degradation products are harmless. Before these materials can be synthetically replicated, it is essential to elucidate their chemical design and biofabrication. For protein-based materials, this means obtaining the complete sequences of the proteinaceous building blocks, a task that historically took decades of research. Thus, we start this review with a historical perspective on early efforts to obtain the primary sequences of load-bearing proteins, followed by the latest developments in sequencing and proteomic technologies that have greatly accelerated sequencing of extracellular proteins. Next, four main classes of protein materials are presented, namely fibrous materials, bioelastomers exhibiting high reversible deformability, hard bulk materials, and biological adhesives. In each class, we focus on the design at the primary and secondary structure levels and discuss their interplays with the mechanical response. We finally discuss earlier and the latest research to artificially produce protein-based materials using biotechnology and synthetic biology, including current developments by start-up companies to scale-up the production of proteinaceous materials in an economically viable manner.
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Affiliation(s)
- Ali Miserez
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,School of Biological Sciences, NTU, Singapore637551
| | - Jing Yu
- Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University (NTU), Singapore637553.,Institute for Digital Molecular Analytics and Science (IDMxS), NTU, 50 Nanyang Avenue, Singapore637553
| | - Pezhman Mohammadi
- VTT Technical Research Centre of Finland Ltd., Espoo, UusimaaFI-02044, Finland
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Facile Synthesis of Functionalized Phenoxy Quinolines: Antibacterial Activities against ESBL Producing Escherichia coli and MRSA, Docking Studies, and Structural Features Determination through Computational Approach. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27123732. [PMID: 35744858 PMCID: PMC9230019 DOI: 10.3390/molecules27123732] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Revised: 05/30/2022] [Accepted: 05/31/2022] [Indexed: 11/23/2022]
Abstract
The synthesis of new 6-Bromoquinolin-4-ol derivatives (3a–3h) by Chan–Lam coupling utilizing different types of solvents (protic, aprotic, and mixed solvents) and bases was studied in the present manuscript. Furthermore, their potential against ESBL producing Escherichia coli (ESBL E. coli) and methicillin-resistant Staphylococcusaureus (MRSA) were investigated. Commercially available 6-bromoquinolin-4-ol (3a) was reacted with different types of aryl boronic acids along with Cu(OAc)2 via Chan–Lam coupling methodology utilizing the protic and aprotic and mixed solvents. The molecules (3a–3h) exhibited very good yields with methanol, moderate yields with DMF, and low yields with ethanol solvents, while the mixed solvent CH3OH/H2O (8:1) gave more excellent results as compared to the other solvents. The in vitro antiseptic values against ESBL E. coli and MRSA were calculated at five different deliberations (10, 20, 30, 40, 50 mg/well) by agar well diffusion method. The molecule 3e depicted highest antibacterial activity while compounds 3b and 3d showed low antibacterial activity. Additionally, MIC and MBC standards were calculated against the established bacteria by broth dilution method. Furthermore, a molecular docking investigation of the derivatives (3a–3h) were performed. Compound (3e) was highly active and depicted the least binding energy of −5.4. Moreover, to investigate the essential structural and physical properties, the density functional theory (DFT) findings of the synthesized molecules were accomplished by using the basic set PBE0-D3BJ/def2-TZVP/SMD water level of the theory. The synthesized compounds showed an energy gap from 4.93 to 5.07 eV.
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6
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Reddy KA, Sahoo DK, Moi S, Gowd KH. Conformational change due to replacement of disulfide with selenosulfide and diselenide in dipeptide vicinal cysteine loop. Comput Biol Chem 2022; 97:107635. [DOI: 10.1016/j.compbiolchem.2022.107635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Revised: 12/21/2021] [Accepted: 01/17/2022] [Indexed: 11/16/2022]
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Abdali Z, Renner-Rao M, Chow A, Cai A, Harrington MJ, Dorval Courchesne NM. Extracellular Secretion and Simple Purification of Bacterial Collagen from Escherichia coli. Biomacromolecules 2022; 23:1557-1568. [PMID: 35258298 DOI: 10.1021/acs.biomac.1c01191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Because of structural similarities with type-I animal collagen, recombinant bacterial collagen-like proteins have been progressively used as a source of collagen for biomaterial applications. However, the intracellular expression combined with current costly and time-consuming chromatography methods for purification makes the large-scale production of recombinant bacterial collagen challenging. Here, we report the use of an adapted secretion pathway, used natively byEscherichia colito secrete curli fibers, for extracellular secretion of the bacterial collagen. We confirmed that a considerable fraction of expressed collagen (∼70%) is being secreted freely into the extracellular medium, with an initial purity of ∼50% in the crude culture supernatant. To simplify the purification of extracellular collagen, we avoided cell lysis and used cross-flow filtration or acid precipitation to concentrate the voluminous supernatant and separate the collagen from impurities. We confirmed that the secreted collagen forms triple helical structures, using Sirius Red staining and circular dichroism. We also detected collagen biomarkers via Raman spectroscopy, further supporting that the recombinant collagen forms a stable triple helical conformation. We further studied the effect of the isolation methods on the morphology and secondary structure, concluding that the final collagen structure is process-dependent. Overall, we show that the curli secretion system can be adapted for extracellular secretion of the bacterial collagen, eliminating the need for cell lysis, which simplifies the collagen isolation process and enables a simple cost-effective method with potential for scale-up.
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Affiliation(s)
- Zahra Abdali
- Department of Chemical Engineering, McGill University, Montreal H3A 0C5, Quebec, Canada
| | - Max Renner-Rao
- Department of Chemistry, McGill University, Montreal H3A 0C5, Quebec, Canada
| | - Amy Chow
- Department of Chemical Engineering, McGill University, Montreal H3A 0C5, Quebec, Canada
| | - Anqi Cai
- Department of Chemical Engineering, McGill University, Montreal H3A 0C5, Quebec, Canada
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8
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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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Estrella LA, Yates EA, Fears KP, Schultzhaus JN, Ryou H, Leary DH, So CR. Engineered Escherichia coli Biofilms Produce Adhesive Nanomaterials Shaped by a Patterned 43 kDa Barnacle Cement Protein. Biomacromolecules 2020; 22:365-373. [PMID: 33135878 DOI: 10.1021/acs.biomac.0c01212] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Barnacles integrate multiple protein components into distinct amyloid-like nanofibers arranged as a bulk material network for their permanent underwater attachment. The design principle for how chemistry is displayed using adhesive nanomaterials, and fragments of proteins that are responsible for their formation, remains a challenge to assess and is yet to be established. Here, we use engineered bacterial biofilms to display a library of amyloid materials outside of the cell using full-length and subdomain sequences from a major component of the barnacle adhesive. A staggered charged pattern is found throughout the full-length sequence of a 43 kDa cement protein (AACP43), establishing a conserved sequence design evolved by barnacles to make adhesive nanomaterials. AACP43 domain deletions vary in their propensity to aggregate and form fibers, as exported extracellular materials are characterized through staining, immunoblotting, scanning electron microscopy, and atomic force microscopy. Full-length AACP43 and its domains have a propensity to aggregate into nanofibers independent of all other barnacle glue components, shedding light on its function in the barnacle adhesive. Curliated Escherichia coli biofilms are a compatible system for heterologous expression and the study of foreign functional amyloid adhesive materials, used here to identify the c-terminal portion of AACP43 as critical in material formation. This approach allows us to establish a common sequence pattern between two otherwise dissimilar families of cement proteins, laying the foundation to elucidate adhesive chemistries by one of the most tenacious marine fouling organisms in the ocean.
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Affiliation(s)
- Luis A Estrella
- Chemistry Division, Code 6176, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, D.C. 20375-5342, United States
| | - Elizabeth A Yates
- US Naval Academy Faculty sited in Code 6176, US Naval Research Laboratory, Washington, D.C. 20375, United States
| | - Kenan P Fears
- Chemistry Division, Code 6176, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, D.C. 20375-5342, United States
| | - Janna N Schultzhaus
- National Research Council Research Associateship Programs Fellow sited in Code 6920, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, D.C. 20375-5342, United States
| | - Heonjune Ryou
- Materials Science and Technology Division, Code 6351, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, D.C. 20375-5342, United States
| | - Dagmar H Leary
- Center for Bio/Molecular Science and Engineering, Code 6920, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, D.C. 20375-5342, United States
| | - Christopher R So
- Chemistry Division, Code 6176, US Naval Research Laboratory, 4555 Overlook Avenue, SW, Washington, D.C. 20375-5342, United States
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Cryo-EM structure of the nonameric CsgG-CsgF complex and its implications for controlling curli biogenesis in Enterobacteriaceae. PLoS Biol 2020; 18:e3000748. [PMID: 32559189 PMCID: PMC7304575 DOI: 10.1371/journal.pbio.3000748] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Accepted: 05/20/2020] [Indexed: 01/21/2023] Open
Abstract
Curli play critical roles in biofilm formation, host cell adhesion, and colonization of inert surfaces in many Enterobacteriaceae. In Escherichia coli, curli biogenesis requires 7 curli-specific gene (csg) products—CsgA through G—working in concert. Of them, CsgG and CsgF are 2 outer membrane (OM)-localized components that consists of the core apparatus for secretion and assembly of curli structural subunits, CsgB and CsgA. Here, we report the cryogenic electron microscopy (cryo-EM) structure of CsgG in complex with CsgF from E. coli. The structure reveals that CsgF forms a stable complex with CsgG via a 1:1 stoichiometry by lining the upper lumen of the nonameric CsgG channel via its N-terminal 27 residues, forming a funnel-like entity plugged in the CsgG channel and creating a unique secretion channel with 2 constriction regions, consistent with the recently reported structure of the CsgG-CsgF complex. Functional studies indicate that export of CsgF to the cell surface requires the CsgG channel, and CsgF not only functions as an adaptor that bridges CsgB with CsgG but also may play important roles in controlling the rates of translocation and/or polymerization for curli structural subunits. Importantly, we found that a series of CsgF-derived peptides are able to efficiently inhibit curli production to E. coli when administrated exogenously, highlighting a potential strategy to interfere biofilm formation in E. coli strains. Curli are functional amyloids that play critical roles in biofilm formation and adhesion in many Enterobacteriaceae. Two outer membrane proteins, CsgG and CsgF, form the core apparatus for secretion and assembly of the curli structural subunits. The cryo-EM structure of the CsgG-CsgF complex reveals a unique amyloid secretion channel with two tandem constriction regions.
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Sewell L, Stylianou F, Xu Y, Taylor J, Sefer L, Matthews S. NMR insights into the pre-amyloid ensemble and secretion targeting of the curli subunit CsgA. Sci Rep 2020; 10:7896. [PMID: 32398666 PMCID: PMC7217966 DOI: 10.1038/s41598-020-64135-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 04/08/2020] [Indexed: 01/08/2023] Open
Abstract
The biofilms of Enterobacteriaceae are fortified by assembly of curli amyloid fibres on the cell surface. Curli not only provides structural reinforcement, but also facilitates surface adhesion. To prevent toxic intracellular accumulation of amyloid precipitate, secretion of the major curli subunit, CsgA, is tightly regulated. In this work, we have employed solution state NMR spectroscopy to characterise the structural ensemble of the pre-fibrillar state of CsgA within the bacterial periplasm, and upon recruitment to the curli pore, CsgG, and the secretion chaperone, CsgE. We show that the N-terminal targeting sequence (N) of CsgA binds specifically to CsgG and that its subsequent sequestration induces a marked transition in the conformational ensemble, which is coupled to a preference for CsgE binding. These observations lead us to suggest a sequential model for binding and structural rearrangement of CsgA at the periplasmic face of the secretion machinery.
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Affiliation(s)
- Lee Sewell
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | | | - Yingqi Xu
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Jonathan Taylor
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Lea Sefer
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Steve Matthews
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK.
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12
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Dolle A, Reddy KKA, Gunaga SS, Krishnamurthy K, Senapati DK, Rana A, Sindogi K, Biswal HS, Raghothama S, Gowd KH. Characterization of (Boc-Cys/Sec-NHMe) 2 and (Boc-Cys/Sec-OMe) 2 : Evidence of local conformational difference between disulfide and diselenide. J Pept Sci 2020; 26:e3245. [PMID: 32103604 DOI: 10.1002/psc.3245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Revised: 02/11/2020] [Accepted: 02/11/2020] [Indexed: 11/11/2022]
Abstract
Conformations of disulfide and diselenide were compared in (Boc-Cys/Sec-NHMe)2 and (Boc-Cys/Sec-OMe)2 using X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, density functional theory (DFT), and circular dichroism (CD) spectroscopy. Conformations of disulfide/diselenide in polypeptides are defined based on the sign of side chain torsion angle χ3 (-CH2 -S/Se-S/Se-CH2 -); negative indicates left-handed and positive indicates right-handed orientation. In the crystals of (Boc-Cys-OMe)2 and (Boc-Sec-OMe)2 , the disulfide exhibits a left-handed and the diselenide a right-handed orientation. Characterization of cystine and selenocystine derivatives in solution using 1 H-NMR, natural abundant 77 Se NMR, 2D-ROESY, and chemical shift analysis coupled to DMSO titration has indicated the symmetrical nature and antiparallel orientation of Cys/Sec residues about the disulfide/diselenide bridges. Structural calculations of cystine and selenocystine derivatives using DFT further support the antiparallel orientation of Cys/Sec residues about disulfide/diselenide. The far-ultraviolet (UV) region CD spectra of cystine and selenocystine derivatives have exhibited the negative Cotton effect (CE) for disulfide and positive for diselenide confirming the difference in the conformational preference of disulfide and diselenide. In the previously reported polymorphic structure of (Boc-Sec-OMe)2 , the diselenide has right-handed orientation. In the X-ray structures of disulfide and diselenide analogues of Escherichia coli protein encoded by curli specific gene C (CgsC) retrieved from Protein Databank (PDB), disulfide has left-handed and the diselenide right-handed orientation. The current report provides the evidence for the local conformational difference between a disulfide and a diselenide group under unconstrained conditions, which may be useful for the rational replacement of disulfide by diselenide in polypeptide chains.
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Affiliation(s)
- Ashwini Dolle
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - K Kasi Amarnath Reddy
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
| | - Shubha Shridhar Gunaga
- Solid State and Structural Chemistry Unit (SSCU), Indian Institute of Science, Bangalore, Karnataka, India
| | - Kiran Krishnamurthy
- NMR Research Centre, Indian Institute of Science, Bangalore, Karnataka, India
| | | | - Abhijit Rana
- School of Chemical Sciences, NISER, Bhubaneswar, Odisha, India
| | - Kishorkumar Sindogi
- Solid State and Structural Chemistry Unit (SSCU), Indian Institute of Science, Bangalore, Karnataka, India
| | | | | | - Konkallu Hanumae Gowd
- Department of Chemistry, School of Chemical Sciences, Central University of Karnataka, Kalaburagi, Karnataka, India
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13
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Yan Z, Yin M, Chen J, Li X. Assembly and substrate recognition of curli biogenesis system. Nat Commun 2020; 11:241. [PMID: 31932609 PMCID: PMC6957492 DOI: 10.1038/s41467-019-14145-7] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 11/29/2019] [Indexed: 01/22/2023] Open
Abstract
A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Understanding the curli biogenesis mechanism is critical for developing therapeutic agents for biofilm-related infections. Here we report a systematic study of the curli biogenesis system, highlighted by structural, biochemical and functional analysis of the secretion channel complexes (CsgF-CsgG) with and without the curli substrate. The dual-pore architecture of the CsgF-CsgG complex was observed and used to develop an approach to inhibit the curli secretion by physically reducing the size of the CsgF pore. We further elucidated the assembly of the CsgFG complex with curli components (CsgA and CsgB) and curli-cell association through CsgF. Importantly, the recognition of the CsgA substrate by CsgG was uncovered. Nine crevices outside of the CsgG channel provide specific and highly-conserved recognition sites for CsgA N-terminus. Together with analysis of CsgE, our study provides comprehensive insights into curli biogenesis. A major component of bacterial biofilms is curli amyloid fibrils secreted by the curli biogenesis system. Here authors use cryo-EM to visualize the secretion channel complexes (CsgF-CsgG) with and without the curli substrate and provide insights into curli biogenesis.
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Affiliation(s)
- Zhaofeng Yan
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Meng Yin
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China.,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China
| | - Jianan Chen
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China.,School of Life Sciences, Tsinghua University, Beijing, China.,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China
| | - Xueming Li
- Key Laboratory of Protein Sciences (Tsinghua University), Ministry of Education, Beijing, China. .,School of Life Sciences, Tsinghua University, Beijing, China. .,Advanced Innovation Center for Structural Biology, Tsinghua University, Beijing, China. .,Tsinghua-Peking Joint Center for Life Sciences, Beijing, China.
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14
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Olmez TT, Sahin Kehribar E, Isilak ME, Lu TK, Seker UOS. Synthetic Genetic Circuits for Self-Actuated Cellular Nanomaterial Fabrication Devices. ACS Synth Biol 2019; 8:2152-2162. [PMID: 31419103 DOI: 10.1021/acssynbio.9b00235] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Genetically controlled synthetic biosystems are being developed to create nanoscale materials. These biosystems are modeled on the natural ability of living cells to synthesize materials: many organisms have dedicated proteins that synthesize a wide range of hard tissues and solid materials, such as nanomagnets and biosilica. We designed an autonomous living material synthesizing system consisting of engineered cells with genetic circuits that synthesize nanomaterials. The circuits encode a nanomaterial precursor-sensing module (sensor) coupled with a materials synthesis module. The sensor detects the presence of cadmium, gold, or iron ions, and this detection triggers the synthesis of the related nanomaterial-nucleating extracellular matrix. We demonstrate that when engineered cells sense the availability of a precursor ion, they express the corresponding extracellular matrix to form the nanomaterials. This proof-of-concept study shows that endowing cells with synthetic genetic circuits enables nanomaterial synthesis and has the potential to be extended to the synthesis of a variety of nanomaterials and biomaterials using a green approach.
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Affiliation(s)
- Tolga Tarkan Olmez
- UNAM- Institute of Materials and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Ebru Sahin Kehribar
- UNAM- Institute of Materials and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Musa Efe Isilak
- UNAM- Institute of Materials and Nanotechnology, Bilkent University, Ankara, Turkey
| | - Timothy K. Lu
- Synthetic Biology Center, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, United States
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15
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Structural Insights into Curli CsgA Cross-β Fibril Architecture Inspire Repurposing of Anti-amyloid Compounds as Anti-biofilm Agents. PLoS Pathog 2019; 15:e1007978. [PMID: 31469892 PMCID: PMC6748439 DOI: 10.1371/journal.ppat.1007978] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 09/17/2019] [Accepted: 07/11/2019] [Indexed: 12/14/2022] Open
Abstract
Curli amyloid fibrils secreted by Enterobacteriaceae mediate host cell adhesion and contribute to biofilm formation, thereby promoting bacterial resistance to environmental stressors. Here, we present crystal structures of amyloid-forming segments from the major curli subunit, CsgA, revealing steric zipper fibrils of tightly mated β-sheets, demonstrating a structural link between curli and human pathological amyloids. D-enantiomeric peptides, originally developed to interfere with Alzheimer's disease-associated amyloid-β, inhibited CsgA fibrillation and reduced biofilm formation in Salmonella typhimurium. Moreover, as previously shown, CsgA fibrils cross-seeded fibrillation of amyloid-β, providing support for the proposed structural resemblance and potential for cross-species amyloid interactions. The presented findings provide structural insights into amyloidogenic regions important for curli formation, suggest a novel strategy for disrupting amyloid-structured biofilms, and hypothesize on the formation of self-propagating prion-like species originating from a microbial source that could influence neurodegenerative diseases.
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16
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Cytotoxic Curli Intermediates Form during Salmonella Biofilm Development. J Bacteriol 2019; 201:JB.00095-19. [PMID: 31182496 DOI: 10.1128/jb.00095-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/31/2019] [Indexed: 12/16/2022] Open
Abstract
Enterobacteriaceae produce amyloid proteins called curli that are the major proteinaceous component of biofilms. Amyloids are also produced by humans and are associated with diseases such as Alzheimer's. During the multistep process of amyloid formation, monomeric subunits form oligomers, protofibrils, and finally mature fibrils. Amyloid β oligomers are more cytotoxic to cells than the mature amyloid fibrils. Oligomeric intermediates of curli had not been previously detected. We determined that turbulence inhibited biofilm formation and that, intriguingly, curli aggregates purified from cultures grown under high-turbulence conditions were structurally smaller and contained less DNA than curli preparations from cultures grown with less turbulence. Using flow cytometry analysis, we demonstrated that CsgA was expressed in cultures exposed to higher turbulence but that these cultures had lower levels of cell death than less-turbulent cultures. Our data suggest that the DNA released during cell death drives the formation of larger fibrillar structures. Consistent with this idea, addition of exogenous genomic DNA increased the size of the curli intermediates and led to binding to thioflavin T at levels observed with mature aggregates. Similar to the intermediate oligomers of amyloid β, intermediate curli aggregates were more cytotoxic than the mature curli fibrils when incubated with bone marrow-derived macrophages. The discovery of cytotoxic curli intermediates will enable research into the roles of amyloid intermediates in the pathogenesis of Salmonella and other bacteria that cause enteric infections.IMPORTANCE Amyloid proteins are the major proteinaceous components of biofilms, which are associated with up to 65% of human bacterial infections. Amyloids produced by human cells are also associated with diseases such as Alzheimer's. The amyloid monomeric subunits self-associate to form oligomers, protofibrils, and finally mature fibrils. Amyloid β oligomers are more cytotoxic to cells than the mature amyloid fibrils. Here we detected oligomeric intermediates of curli for the first time. Like the oligomers of amyloid β, intermediate curli fibrils were more cytotoxic than the mature curli fibrillar aggregates when incubated with bone marrow-derived macrophages. The discovery of cytotoxic curli intermediates will enable research into the roles of amyloid intermediates in the pathogenesis of Salmonella and other bacteria that cause enteric infections.
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MacKenzie KD, Wang Y, Musicha P, Hansen EG, Palmer MB, Herman DJ, Feasey NA, White AP. Parallel evolution leading to impaired biofilm formation in invasive Salmonella strains. PLoS Genet 2019; 15:e1008233. [PMID: 31233504 PMCID: PMC6611641 DOI: 10.1371/journal.pgen.1008233] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Revised: 07/05/2019] [Accepted: 06/07/2019] [Indexed: 12/12/2022] Open
Abstract
Pathogenic Salmonella strains that cause gastroenteritis are able to colonize and replicate within the intestines of multiple host species. In general, these strains have retained an ability to form the rdar morphotype, a resistant biofilm physiology hypothesized to be important for Salmonella transmission. In contrast, Salmonella strains that are host-adapted or even host-restricted like Salmonella enterica serovar Typhi, tend to cause systemic infections and have lost the ability to form the rdar morphotype. Here, we investigated the rdar morphotype and CsgD-regulated biofilm formation in two non-typhoidal Salmonella (NTS) strains that caused invasive disease in Malawian children, S. Typhimurium D23580 and S. Enteritidis D7795, and compared them to a panel of NTS strains associated with gastroenteritis, as well as S. Typhi strains. Sequence comparisons combined with luciferase reporter technology identified key SNPs in the promoter region of csgD that either shut off biofilm formation completely (D7795) or reduced transcription of this key biofilm regulator (D23580). Phylogenetic analysis showed that these SNPs are conserved throughout the African clades of invasive isolates, dating as far back as 80 years ago. S. Typhi isolates were negative for the rdar morphotype due to truncation of eight amino acids from the C-terminus of CsgD. We present new evidence in support of parallel evolution between lineages of nontyphoidal Salmonella associated with invasive disease in Africa and the archetypal host-restricted invasive serovar; S. Typhi. We hypothesize that the African invasive isolates are becoming human-adapted and ‘niche specialized’ with less reliance on environmental survival, as compared to gastroenteritis-causing isolates. African clades of nontyphoidal Salmonella cause invasive disease on a daily basis and thousands of deaths each year. Although it is generally accepted that the transmission route for these organisms is fecal-oral, we know very little about their behaviour in the environment between hosts. In this paper, we have identified both a genotype and a phenotype that suggest environmental niche specialization that is distinct from lineages of Salmonella Typhimurium and Salmonella Enteritidis associated with industrialized food supply chains in resource-rich settings. We also compared with strains of Salmonella Typhi, which cause systemic typhoid fever infections exclusively in humans. In each invasive lineage, regulatory or structural gene mutations leading to loss or impairment of biofilm were identified, all associated with curli and cellulose production, the two main structures that comprise the biofilm matrix. This suggests that similar evolutionary pressures are acting on invasive Salmonella isolates. Public health strategies aimed at reducing the burden of invasive Salmonella disease must prevent transmission to vulnerable adults and children via water sanitation and hygiene practices–a process that starts with identification of environmental reservoirs. The results of our study will raise the profile of this neglected aspect of invasive salmonellosis and will challenge researchers and clinicians to search in new places for potential environmental reservoirs of these pathogens.
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Affiliation(s)
- Keith D. MacKenzie
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Yejun Wang
- Department of Cell Biology and Genetics, Shenzhen University Health Science Center, Guangdong, China
| | - Patrick Musicha
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, United Kingdom
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Elizabeth G. Hansen
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Melissa B. Palmer
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Dakoda J. Herman
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
| | - Nicholas A. Feasey
- Malawi Liverpool Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, United Kingdom
| | - Aaron P. White
- Vaccine and Infectious Disease Organization-International Vaccine Centre, Saskatoon, SK., Canada
- Department of Microbiology and Immunology, University of Saskatchewan, Saskatoon, SK., Canada
- * E-mail:
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18
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Bacterial functional amyloids: Order from disorder. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:954-960. [PMID: 31195143 DOI: 10.1016/j.bbapap.2019.05.010] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Revised: 05/24/2019] [Accepted: 05/30/2019] [Indexed: 12/15/2022]
Abstract
The discovery of intrinsic disorderness in proteins and peptide regions has given a new and useful insight into the working of biological systems. Due to enormous plasticity and heterogeneity, intrinsically disordered proteins or regions in proteins can perform myriad of functions. The flexibility in disordered proteins allows them to undergo conformation transition to form homopolymers of proteins called amyloids. Amyloids are highly structured protein aggregates associated with many neurodegenerative diseases. However, amyloids have gained much appreciation in recent years due to their functional roles. A functional amyloid fiber called curli is assembled on the bacterial cell surface as a part of the extracellular matrix during biofilm formation. The extracellular matrix that encases cells in a biofilm protects the cells and provides resistance against many environmental stresses. Several of the Csg (curli specific genes) proteins that are required for curli amyloid assembly are predicted to be intrinsically disordered. Therefore, curli amyloid formation is highly orchestrated so that these intrinsically disordered proteins do not inappropriately aggregate at the wrong time or place. The curli proteins are compartmentalized and there are chaperone-like proteins that prevent inappropriate aggregation and allow the controlled assembly of curli amyloids. Here we review the biogenesis of curli amyloids and the role that intrinsically disordered proteins play in the process.
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19
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Christensen LF, Jensen KF, Nielsen J, Vad BS, Christiansen G, Otzen DE. Reducing the Amyloidogenicity of Functional Amyloid Protein FapC Increases Its Ability To Inhibit α-Synuclein Fibrillation. ACS OMEGA 2019; 4:4029-4039. [PMID: 31459612 PMCID: PMC6647998 DOI: 10.1021/acsomega.8b03590] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 02/11/2019] [Indexed: 05/15/2023]
Abstract
Functional amyloid (FA) proteins have evolved to assemble into fibrils with a characteristic cross-β structure, which stabilizes biofilms and contributes to bacterial virulence. Some of the most studied bacterial FAs are the curli protein CsgA, expressed in a wide range of bacteria, and FapC, produced mainly by members of the Pseudomonas genus. Though unrelated, both CsgA and FapC contain imperfect repeats believed to drive the formation of amyloid fibrils. While much is known about CsgA biogenesis and fibrillation, the mechanism of FapC fibrillation remains less explored. Here, we show that removing the three imperfect repeats of FapC (FapC ΔR1R2R3) slows down the fibrillation but does not prevent it. The increased lag phase seen for FapC ΔR1R2R3 allows for disulfide bond formation, which further delays fibrillation. Remarkably, these disulfide-bonded species of FapC ΔR1R2R3 also significantly delay the fibrillation of human α-synuclein, a key protein in Parkinson's disease pathology. This attenuation of α-synuclein fibrillation was not seen for the reduced form of FapC ΔR1R2R3. The results presented here shed light on the FapC fibrillation mechanism and emphasize how unrelated fibrillation systems may share such common fibril formation mechanisms, allowing inhibitors of one fibrillating protein to affect a completely different protein.
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Affiliation(s)
- Line Friis
Bakmann Christensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Kirstine Friis Jensen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Janni Nielsen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Brian Stougaard Vad
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
| | - Gunna Christiansen
- Section
for Medical Microbiology and Immunology, Department of Biomedicine, Aarhus University, Vennelyst Boulevard 4, 8000 Aarhus C, Denmark
| | - Daniel Erik Otzen
- Interdisciplinary
Nanoscience Center (iNANO), Department of Molecular Biology and Genetics, Aarhus University, Gustav Wieds Vej 14, DK, 8000 Aarhus C, Denmark
- E-mail:
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20
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Abstract
A wide range of bacterial pathogens have been shown to form biofilms, which significantly increase their resistance to environmental stresses, such as antibiotics, and are thus of central importance in the context of bacterial diseases. One of the major structural components of these bacterial biofilms are amyloid fibrils, yet the mechanism of fibril assembly and its importance for biofilm formation are currently not fully understood. By studying fibril formation in vitro, in a model system of two common but unrelated biofilm-forming proteins, FapC from Pseudomonas fluorescens and CsgA from Escherichia coli, we found that the two proteins have a common aggregation mechanism. In both systems, fibril formation proceeds via nucleated growth of linear fibrils exhibiting similar measured rates of elongation, with negligible fibril self-replication. These similarities between two unrelated systems suggest that convergent evolution plays a key role in tuning the assembly kinetics of functional amyloid fibrils and indicates that only a narrow window of mechanisms and assembly rates allows for successful biofilm formation. Thus, the amyloid assembly reaction is likely to represent a means for controlling biofilm formation, both by the organism and by possible inhibitory drugs.IMPORTANCE Biofilms are generated by bacteria, embedded in the formed extracellular matrix. The biofilm's function is to improve the survival of a bacterial colony through, for example, increased resistance to antibiotics or other environmental stresses. Proteins secreted by the bacteria act as a major structural component of this extracellular matrix, as they self-assemble into highly stable amyloid fibrils, making the biofilm very difficult to degrade by physical and chemical means once formed. By studying the self-assembly mechanism of the fibrils from their monomeric precursors in two unrelated bacteria, our experimental and theoretical approaches shed light on the mechanism of functional amyloid assembly in the context of biofilm formation. Our results suggest that fibril formation may be a rate-limiting step in biofilm formation, which in turn has implications on the protein self-assembly reaction as a target for potential antibiotic drugs.
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Abstract
To interact with the external environments, bacteria often display long proteinaceous appendages on their cell surface, called pili or fimbriae. These non-flagellar thread-like structures are polymers composed of covalently or non-covalently interacting repeated pilin subunits. Distinct pilus classes can be identified on basis of their assembly pathways, including chaperone-usher pili, type V pili, type IV pili, curli and fap fibers, conjugative and type IV secretion pili, as well as sortase-mediated pili. Pili play versatile roles in bacterial physiology, and can be involved in adhesion and host cell invasion, DNA and protein secretion and uptake, biofilm formation, cell motility and more. Recent advances in structure determination of components involved in the various pilus systems has enabled a better molecular understanding of their mechanisms of assembly and function. In this chapter we describe the diversity in structure, biogenesis and function of the different pilus systems found in Gram-positive and Gram-negative bacteria, and review their potential as anti-microbial targets.
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Affiliation(s)
- Magdalena Lukaszczyk
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Brajabandhu Pradhan
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium
| | - Han Remaut
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050, Brussels, Belgium.
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22
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Bacterial Amyloids: Biogenesis and Biomaterials. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1174:113-159. [DOI: 10.1007/978-981-13-9791-2_4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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23
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Dorval Courchesne NM, DeBenedictis EP, Tresback J, Kim JJ, Duraj-Thatte A, Zanuy D, Keten S, Joshi NS. Biomimetic engineering of conductive curli protein films. NANOTECHNOLOGY 2018; 29:454002. [PMID: 30152795 DOI: 10.1088/1361-6528/aadd3a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Bioelectronic systems derived from peptides and proteins are of particular interest for fabricating novel flexible, biocompatible and bioactive devices. These synthetic or recombinant systems designed for mediating electron transport often mimic the proteinaceous appendages of naturally occurring electroactive bacteria. Drawing inspiration from such conductive proteins with a high content of aromatic residues, we have engineered a fibrous protein scaffold, curli fibers produced by Escherichia coli bacteria, to enable long-range electron transport. We report the genetic engineering and characterization of curli fibers containing aromatic residues of different nature, with defined spatial positioning, and with varying content on single self-assembling CsgA curli subunits. Our results demonstrate the impressive versatility of the CsgA protein for genetically engineering protein-based materials with new functions. Through a scalable purification process, we show that macroscopic gels and films can be produced, with engineered thin films exhibiting a greater conductivity compared with wild-type curli films. We anticipate that this engineered conductive scaffold, and our approach that combines computational modeling, protein engineering, and biosynthetic manufacture will contribute to the improvement of a range of useful bio-hybrid technologies.
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Affiliation(s)
- Noémie-Manuelle Dorval Courchesne
- Department of Chemical Engineering, McGill University, Montréal, QC, Canada. Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, United States of America
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Structure-Function Analysis of the Curli Accessory Protein CsgE Defines Surfaces Essential for Coordinating Amyloid Fiber Formation. mBio 2018; 9:mBio.01349-18. [PMID: 30018113 PMCID: PMC6050966 DOI: 10.1128/mbio.01349-18] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Curli amyloid fibers are produced as part of the extracellular biofilm matrix and are composed primarily of the major structural subunit CsgA. The CsgE chaperone facilitates the secretion of CsgA through CsgG by forming a cap at the base of the nonameric CsgG outer membrane pore. We elucidated a series of finely tuned nonpolar and charge-charge interactions that facilitate the oligomerization of CsgE and its ability to transport unfolded CsgA to CsgG for translocation. CsgE oligomerization in vitro is temperature dependent and is disrupted by mutations in the W48 and F79 residues. Using nuclear magnetic resonance (NMR), we identified two regions of CsgE involved in the CsgE-CsgA interaction: a head comprising a positively charged patch centered around R47 and a stem comprising a negatively charged patch containing E31 and E85. Negatively charged residues in the intrinsically disordered N- and C-terminal "tails" were not implicated in this interaction. Head and stem residues were mutated and interrogated using in vivo measurements of curli production and in vitro amyloid polymerization assays. The R47 head residue of CsgE is required for stabilization of CsgA- and CsgE-mediated curli fiber formation. Mutation of the E31 and E85 stem residues to positively charged side chains decreased CsgE-mediated curli fiber formation but increased CsgE-mediated stabilization of CsgA. No single-amino-acid substitutions in the head, stem, or tail regions affected the ability of CsgE to cap the CsgG pore as determined by a bile salt sensitivity assay. These mechanistic insights into the directed assembly of functional amyloids in extracellular biofilms elucidate possible targets for biofilm-associated bacterial infections.IMPORTANCE Curli represent a class of functional amyloid fibers produced by Escherichia coli and other Gram-negative bacteria that serve as protein scaffolds in the extracellular biofilm matrix. Despite the lack of sequence conservation among different amyloidogenic proteins, the structural and biophysical properties of functional amyloids such as curli closely resemble those of amyloids associated with several common neurodegenerative diseases. These parallels are underscored by the observation that certain proteins and chemicals can prevent amyloid formation by the major curli subunit CsgA and by alpha-synuclein, the amyloid-forming protein found in Lewy bodies during Parkinson's disease. CsgA subunits are targeted to the CsgG outer membrane pore by CsgE prior to secretion and assembly into fibers. Here, we use biophysical, biochemical, and genetic approaches to elucidate a mechanistic understanding of CsgE function in curli biogenesis.
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Amyloid by Design: Intrinsic Regulation of Microbial Amyloid Assembly. J Mol Biol 2018; 430:3631-3641. [PMID: 30017921 DOI: 10.1016/j.jmb.2018.07.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/01/2018] [Accepted: 07/09/2018] [Indexed: 12/14/2022]
Abstract
The term amyloid has historically been used to describe fibrillar aggregates formed as the result of protein misfolding and that are associated with a range of diseases broadly termed amyloidoses. The discovery of "functional amyloids" expanded the amyloid umbrella to encompass aggregates structurally similar to disease-associated amyloids but that engage in a variety of biologically useful tasks without incurring toxicity. The mechanisms by which functional amyloid systems ensure nontoxic assembly has provided insights into potential therapeutic strategies for treating amyloidoses. Some of the most-studied functional amyloids are ones produced by bacteria. Curli amyloids are extracellular fibers made by enteric bacteria that function to encase and protect bacterial communities during biofilm formation. Here we review recent studies highlighting microbial functional amyloid assembly systems that are tailored to enable the assembly of non-toxic amyloid aggregates.
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26
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Schubeis T, Spehr J, Viereck J, Köpping L, Nagaraj M, Ahmed M, Ritter C. Structural and functional characterization of the Curli adaptor protein CsgF. FEBS Lett 2018; 592:1020-1029. [DOI: 10.1002/1873-3468.13002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2017] [Revised: 12/12/2017] [Accepted: 02/03/2018] [Indexed: 11/11/2022]
Affiliation(s)
- Tobias Schubeis
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Johannes Spehr
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Janika Viereck
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Laura Köpping
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Madhu Nagaraj
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Mumdooh Ahmed
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
| | - Christiane Ritter
- Laboratory for Macromolecular Interactions; Helmholtz Centre for Infection Research; Braunschweig Germany
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27
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The Functional Amyloid Curli Protects Escherichia coli against Complement-Mediated Bactericidal Activity. Biomolecules 2018; 8:biom8010005. [PMID: 29364839 PMCID: PMC5871974 DOI: 10.3390/biom8010005] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2017] [Revised: 01/08/2018] [Accepted: 01/16/2018] [Indexed: 12/30/2022] Open
Abstract
Escherichia coli strains may be beneficial or pathogenic. Many E. coli strains that cause human disease, especially those responsible for bacteremia and sepsis, express virulence factors that impart resistance to the complement system. The bacterial amyloid curli functions in bacterial adherence and enhances the formation of biofilms. Survival of curli-producing parental and curli-deficient mutant E. coli in the context of a human complement response was evaluated using an in vivo murine model of bacteremia. Results showed that curli production enhanced E. coli survival, which suggests that curli defends against complement-mediated killing. This observation was supported by the results of in vitro assays comparing bacterial survival in human serum. Experiments in which the classical or alternative complement pathways were blocked indicated that the classical pathway is the major contributor to complement activation and that curli inhibits this activity. Our analyses indicate that curli does not appear to play a role in protecting E. coli against alternative pathway complement activation. We found that curli increases binding of E. coli cells to complement component Complement component 1q (C1q) but does not affect Complement component 3b (C3b) binding. We conclude that curli defends E. coli against complement-mediated killing via inhibition of the classical complement pathway.
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Som Chaudhury S, Das Mukhopadhyay C. Functional amyloids: interrelationship with other amyloids and therapeutic assessment to treat neurodegenerative diseases. Int J Neurosci 2017; 128:449-463. [PMID: 29076790 DOI: 10.1080/00207454.2017.1398153] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Sutapa Som Chaudhury
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, West Bengal, India
| | - Chitrangada Das Mukhopadhyay
- Centre for Healthcare Science and Technology, Indian Institute of Engineering Science and Technology, Shibpur, West Bengal, India
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The Production of Curli Amyloid Fibers Is Deeply Integrated into the Biology of Escherichia coli. Biomolecules 2017; 7:biom7040075. [PMID: 29088115 PMCID: PMC5745457 DOI: 10.3390/biom7040075] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 10/13/2017] [Accepted: 10/23/2017] [Indexed: 12/29/2022] Open
Abstract
Curli amyloid fibers are the major protein component of the extracellular matrix produced by Enterobacteriaceae during biofilm formation. Curli are required for proper biofilm development and environmental persistence by Escherichia coli. Here, we present a complete and vetted genetic analysis of functional amyloid fiber biogenesis. The Keio collection of single gene deletions was screened on Congo red indicator plates to identify E. coli mutants that had defective amyloid production. We discovered that more than three hundred gene products modulated curli production. These genes were involved in fundamental cellular processes such as regulation, environmental sensing, respiration, metabolism, cell envelope biogenesis, transport, and protein turnover. The alternative sigma factors, σS and σE, had opposing roles in curli production. Mutations that induced the σE or Cpx stress response systems had reduced curli production, while mutant strains with increased σS levels had increased curli production. Mutations in metabolic pathways, including gluconeogenesis and the biosynthesis of lipopolysaccharide (LPS), produced less curli. Regulation of the master biofilm regulator, CsgD, was diverse, and the screen revealed several proteins and small RNAs (sRNA) that regulate csgD messenger RNA (mRNA) levels. Using previously published studies, we found minimal overlap between the genes affecting curli biogenesis and genes known to impact swimming or swarming motility, underlying the distinction between motile and sessile lifestyles. Collectively, the diversity and number of elements required suggest curli production is part of a highly regulated and complex developmental pathway in E. coli.
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Rouse SL, Hawthorne WJ, Berry JL, Chorev DS, Ionescu SA, Lambert S, Stylianou F, Ewert W, Mackie U, Morgan RML, Otzen D, Herbst FA, Nielsen PH, Dueholm M, Bayley H, Robinson CV, Hare S, Matthews S. A new class of hybrid secretion system is employed in Pseudomonas amyloid biogenesis. Nat Commun 2017; 8:263. [PMID: 28811582 PMCID: PMC5557850 DOI: 10.1038/s41467-017-00361-6] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 06/23/2017] [Indexed: 11/25/2022] Open
Abstract
Gram-negative bacteria possess specialised biogenesis machineries that facilitate the export of amyloid subunits for construction of a biofilm matrix. The secretion of bacterial functional amyloid requires a bespoke outer-membrane protein channel through which unfolded amyloid substrates are translocated. Here, we combine X-ray crystallography, native mass spectrometry, single-channel electrical recording, molecular simulations and circular dichroism measurements to provide high-resolution structural insight into the functional amyloid transporter from Pseudomonas, FapF. FapF forms a trimer of gated β-barrel channels in which opening is regulated by a helical plug connected to an extended coil-coiled platform spanning the bacterial periplasm. Although FapF represents a unique type of secretion system, it shares mechanistic features with a diverse range of peptide translocation systems. Our findings highlight alternative strategies for handling and export of amyloid protein sequences. Gram-negative bacteria assemble biofilms from amyloid fibres, which translocate across the outer membrane as unfolded amyloid precursors through a secretion system. Here, the authors characterise the structural details of the amyloid transporter FapF in Pseudomonas.
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Affiliation(s)
- Sarah L Rouse
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - William J Hawthorne
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Jamie-Lee Berry
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Dror S Chorev
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sandra A Ionescu
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Sebastian Lambert
- Duke-NUS Medical School, 8 College Road, Singapore, 169857, Singapore
| | - Fisentzos Stylianou
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Wiebke Ewert
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Uma Mackie
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.,Walthamstow School for Girls, London, E17 9RZ, UK
| | - R Marc L Morgan
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Daniel Otzen
- Interdisciplinary Nanoscience Center (iNANO), Centre for Insoluble Protein Structures (inSPIN), Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Florian-Alexander Herbst
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Per H Nielsen
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Morten Dueholm
- Center for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
| | - Hagan Bayley
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Carol V Robinson
- Chemistry Research Laboratory, University of Oxford, Oxford, OX1 3TA, UK
| | - Stephen Hare
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK
| | - Stephen Matthews
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW72AZ, UK.
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Dragoš A, Kovács ÁT, Claessen D. The Role of Functional Amyloids in Multicellular Growth and Development of Gram-Positive Bacteria. Biomolecules 2017; 7:biom7030060. [PMID: 28783117 PMCID: PMC5618241 DOI: 10.3390/biom7030060] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 08/01/2017] [Accepted: 08/03/2017] [Indexed: 01/15/2023] Open
Abstract
Amyloid fibrils play pivotal roles in all domains of life. In bacteria, these fibrillar structures are often part of an extracellular matrix that surrounds the producing organism and thereby provides protection to harsh environmental conditions. Here, we discuss the role of amyloid fibrils in the two distant Gram-positive bacteria, Streptomyces coelicolor and Bacillus subtilis. We describe how amyloid fibrils contribute to a multitude of developmental processes in each of these systems, including multicellular growth and community development. Despite this variety of tasks, we know surprisingly little about how their assembly is organized to fulfill all these roles.
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Affiliation(s)
- Anna Dragoš
- Terrestrial Biofilms Group, Institute of Microbiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
| | - Ákos T Kovács
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Lyngby, Denmark.
| | - Dennis Claessen
- Institute of Biology, Leiden University, 2333BE Leiden, The Netherlands.
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Structural insights into functional amyloid inhibition in Gram -ve bacteria. Biochem Soc Trans 2017; 44:1643-1649. [PMID: 27913673 PMCID: PMC5135000 DOI: 10.1042/bst20160245] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Revised: 09/20/2016] [Accepted: 09/22/2016] [Indexed: 11/17/2022]
Abstract
Amyloids are proteinaceous aggregates known for their role in debilitating degenerative diseases involving protein dysfunction. Many forms of functional amyloid are also produced in nature and often these systems require careful control of their assembly to avoid the potentially toxic effects. The best-characterised functional amyloid system is the bacterial curli system. Three natural inhibitors of bacterial curli amyloid have been identified and recently characterised structurally. Here, we compare common structural features of CsgC, CsgE and CsgH and discuss the potential implications for general inhibition of amyloid.
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Sahlberg Bang C, Demirel I, Kruse R, Persson K. Global gene expression profiling and antibiotic susceptibility after repeated exposure to the carbon monoxide-releasing molecule-2 (CORM-2) in multidrug-resistant ESBL-producing uropathogenic Escherichia coli. PLoS One 2017; 12:e0178541. [PMID: 28591134 PMCID: PMC5462378 DOI: 10.1371/journal.pone.0178541] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 05/15/2017] [Indexed: 12/02/2022] Open
Abstract
Treatment of urinary tract infections is today a challenge due to the increasing prevalence of multidrug-resistant ESBL-producing uropathogenic Escherichia coli (UPEC). There is an urgent need for new treatment strategies for multidrug-resistant UPEC and preferably with targets that have low potential for development of resistance. Carbon monoxide-releasing molecules (CORMs) are novel and potent antibacterial agents. The present study examines the transcriptomic targets of CORM-2 in a multidrug-resistant ESBL-producing UPEC isolate in response to a single exposure to CORM-2 and after repeated exposure to CORM-2. The bacterial viability and minimal inhibitory concentration (MIC) were also examined after repeated exposure to CORM-2. Microarray analysis revealed that a wide range of processes were affected by CORM-2, including a general trend of down-regulation in energy metabolism and biosynthesis pathways and up-regulation of the SOS response and DNA repair. Several genes involved in virulence (ibpB), antibiotic resistance (marAB, mdtABC) and biofilm formation (bhsA, yfgF) were up-regulated, while some genes involved in virulence (kpsC, fepCEG, entABE), antibiotic resistance (evgA) and biofilm formation (artIP) were down-regulated. Repeated exposure to CORM-2 did not alter the gene expression patterns, the growth inhibitory response to CORM-2 or the MIC values for CORM-2, cefotaxime, ciprofloxacin and trimethoprim. This study identifies several enriched gene ontologies, modified pathways and single genes that are targeted by CORM-2 in a multidrug-resistant UPEC isolate. Repeated exposure to CORM-2 did not change the gene expression patterns or fold changes and the susceptibility to CORM-2 remained after repeated exposure.
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Affiliation(s)
- Charlotte Sahlberg Bang
- School of Medical Sciences, Faculty of Medicine and Health, iRiSC—Inflammatory Response and Infection Susceptibility Centre, Örebro University, Örebro, Sweden
- * E-mail:
| | - Isak Demirel
- School of Medical Sciences, Faculty of Medicine and Health, iRiSC—Inflammatory Response and Infection Susceptibility Centre, Örebro University, Örebro, Sweden
| | - Robert Kruse
- School of Medical Sciences, Faculty of Medicine and Health, iRiSC—Inflammatory Response and Infection Susceptibility Centre, Örebro University, Örebro, Sweden
| | - Katarina Persson
- School of Medical Sciences, Faculty of Medicine and Health, iRiSC—Inflammatory Response and Infection Susceptibility Centre, Örebro University, Örebro, Sweden
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34
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Maleki B, Tabandeh F, Soheili ZS, Morshedi D. Application of proteinous nanofibrils to culture retinal pigmented epithelium cells: A versatile biomaterial. REACT FUNCT POLYM 2017. [DOI: 10.1016/j.reactfunctpolym.2017.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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35
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Wlodawer A, Dauter Z. `Atomic resolution': a badly abused term in structural biology. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2017; 73:379-380. [PMID: 28375149 DOI: 10.1107/s205979831700225x] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2016] [Accepted: 02/09/2017] [Indexed: 02/06/2023]
Affiliation(s)
- Alexander Wlodawer
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Zbigniew Dauter
- Macromolecular Crystallography Laboratory, National Cancer Institute, Frederick, MD 21702, USA
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Seker UOS, Chen AY, Citorik RJ, Lu TK. Synthetic Biogenesis of Bacterial Amyloid Nanomaterials with Tunable Inorganic-Organic Interfaces and Electrical Conductivity. ACS Synth Biol 2017; 6:266-275. [PMID: 27794590 PMCID: PMC6422533 DOI: 10.1021/acssynbio.6b00166] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amyloids are highly ordered, hierarchal protein nanoassemblies. Functional amyloids in bacterial biofilms, such as Escherichia coli curli fibers, are formed by the polymerization of monomeric proteins secreted into the extracellular space. Curli is synthesized by living cells, is primarily composed of the major curlin subunit CsgA, and forms biological nanofibers with high aspect ratios. Here, we explore the application of curli fibers for nanotechnology by engineering curli to mediate tunable biological interfaces with inorganic materials and to controllably form gold nanoparticles and gold nanowires. Specifically, we used cell-synthesized curli fibers as templates for nucleating and growing gold nanoparticles and showed that nanoparticle size could be modulated as a function of curli fiber gold-binding affinity. Furthermore, we demonstrated that gold nanoparticles can be preseeded onto curli fibers and followed by gold enhancement to form nanowires. Using these two approaches, we created artificial cellular systems that integrate inorganic-organic materials to achieve tunable electrical conductivity. We envision that cell-synthesized amyloid nanofibers will be useful for interfacing abiotic and biotic systems to create living functional materials..
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Affiliation(s)
- Urartu Ozgur Safak Seker
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, 06800 Ankara, Turkey
| | - Allen Y. Chen
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Robert J. Citorik
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
| | - Timothy K. Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02142, United States
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- MIT Microbiology Program, 77 Massachusetts Avenue, Cambridge Massachusetts 02139, United States
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Rouse SL, Hawthorne WJ, Lambert S, Morgan ML, Hare SA, Matthews S. Purification, crystallization and characterization of the Pseudomonas outer membrane protein FapF, a functional amyloid transporter. Acta Crystallogr F Struct Biol Commun 2016; 72:892-896. [PMID: 27917837 PMCID: PMC5137466 DOI: 10.1107/s2053230x16017921] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 11/08/2016] [Indexed: 11/12/2023] Open
Abstract
Bacteria often produce extracellular amyloid fibres via a multi-component secretion system. Aggregation-prone, unstructured subunits cross the periplasm and are secreted through the outer membrane, after which they self-assemble. Here, significant progress is presented towards solving the high-resolution crystal structure of the novel amyloid transporter FapF from Pseudomonas, which facilitates the secretion of the amyloid-forming polypeptide FapC across the bacterial outer membrane. This represents the first step towards obtaining structural insight into the products of the Pseudomonas fap operon. Initial attempts at crystallizing full-length and N-terminally truncated constructs by refolding techniques were not successful; however, after preparing FapF106-430 from the membrane fraction, reproducible crystals were obtained using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.5 Å resolution. These crystals belonged to the monoclinic space group C121, with unit-cell parameters a = 143.4, b = 124.6, c = 80.4 Å, α = γ = 90, β = 96.32° and three monomers in the asymmetric unit. It was found that the switch to complete detergent exchange into C8E4 was crucial for forming well diffracting crystals, and it is suggested that this combined with limited proteolysis is a potentially useful protocol for membrane β-barrel protein crystallography. The three-dimensional structure of FapF will provide invaluable information on the mechanistic differences of biogenesis between the curli and Fap functional amyloid systems.
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Affiliation(s)
- Sarah L. Rouse
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Wlliam J. Hawthorne
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Sebastian Lambert
- Biological Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117543, Singapore
| | - Marc L. Morgan
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Stephen A. Hare
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
| | - Stephen Matthews
- Life Sciences, Imperial College London, South Kensington, London SW7 2AZ, England
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Amigo N, Zhang Q, Amadio A, Zhang Q, Silva WM, Cui B, Chen Z, Larzabal M, Bei J, Cataldi A. Overexpressed Proteins in Hypervirulent Clade 8 and Clade 6 Strains of Escherichia coli O157:H7 Compared to E. coli O157:H7 EDL933 Clade 3 Strain. PLoS One 2016; 11:e0166883. [PMID: 27880834 PMCID: PMC5120812 DOI: 10.1371/journal.pone.0166883] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2016] [Accepted: 11/04/2016] [Indexed: 11/19/2022] Open
Abstract
Escherichia coli O157:H7 is responsible for severe diarrhea and hemolytic uremic syndrome (HUS), and predominantly affects children under 5 years. The major virulence traits are Shiga toxins, necessary to develop HUS and the Type III Secretion System (T3SS) through which bacteria translocate effector proteins directly into the host cell. By SNPs typing, E. coli O157:H7 was separated into nine different clades. Clade 8 and clade 6 strains were more frequently associated with severe disease and HUS. In this study, we aimed to identify differentially expressed proteins in two strains of E. coli O157:H7 (clade 8 and clade 6), obtained from cattle and compared them with the well characterized reference EDL933 strain (clade 3). Clade 8 and clade 6 strains show enhanced pathogenicity in a mouse model and virulence-related properties. Proteins were extracted and analyzed using the TMT-6plex labeling strategy associated with two dimensional liquid chromatography and mass spectrometry in tandem. We detected 2241 proteins in the cell extract and 1787 proteins in the culture supernatants. Attention was focused on the proteins related to virulence, overexpressed in clade 6 and 8 strains compared to EDL933 strain. The proteins relevant overexpressed in clade 8 strain were the curli protein CsgC, a transcriptional activator (PchE), phage proteins, Stx2, FlgM and FlgD, a dienelactone hydrolase, CheW and CheY, and the SPATE protease EspP. For clade 6 strain, a high overexpression of phage proteins was detected, mostly from Stx2 encoding phage, including Stx2, flagellin and the protease TagA, EDL933_p0016, dienelactone hydrolase, and Haemolysin A, amongst others with unknown function. Some of these proteins were analyzed by RT-qPCR to corroborate the proteomic data. Clade 6 and clade 8 strains showed enhanced transcription of 10 out of 12 genes compared to EDL933. These results may provide new insights in E. coli O157:H7 mechanisms of pathogenesis.
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Affiliation(s)
- Natalia Amigo
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
| | - Qi Zhang
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Ariel Amadio
- Rafaela Experimental Station, National Institute of Agricultural Technology. Rafaela, Santa Fe, Argentina
| | - Qunjie Zhang
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Wanderson M. Silva
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
| | - Baiyuan Cui
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Zhongjian Chen
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
| | - Mariano Larzabal
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
| | - Jinlong Bei
- AGRO-Biological Gene Research Center, Guangdong `Academy of Agricultural Sciences (GDAAS), Guangzhou, China
- * E-mail:
| | - Angel Cataldi
- Institute of Biotechnology, CICVyA, National Institute of Agricultural Technology. Hurlingham, Buenos Aires, Argentina
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Abstract
Recent insights into bacterial biofilm matrix structures have induced a paradigm shift toward the recognition of amyloid fibers as common building block structures that confer stability to the exopolysaccharide matrix. Here we describe the functional amyloid systems related to biofilm matrix formation in both Gram-negative and Gram-positive bacteria and recent knowledge regarding the interaction of amyloids with other biofilm matrix components such as extracellular DNA (eDNA) and the host immune system. In addition, we summarize the efforts to identify compounds that target amyloid fibers for therapeutic purposes and recent developments that take advantage of the amyloid structure to engineer amyloid fibers of bacterial biofilm matrices for biotechnological applications.
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40
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Liu G, Zhang S, Yang K, Zhu L, Lin D. Toxicity of perfluorooctane sulfonate and perfluorooctanoic acid to Escherichia coli: Membrane disruption, oxidative stress, and DNA damage induced cell inactivation and/or death. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2016; 214:806-815. [PMID: 27155098 DOI: 10.1016/j.envpol.2016.04.089] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Revised: 04/19/2016] [Accepted: 04/25/2016] [Indexed: 06/05/2023]
Abstract
Perfluorooctane sulfonate (PFOS) and perfluorooctanoic acid (PFOA) are two widely used polyfluorinated compounds (PFCs) and are persistent in the environment. This study for the first time systematically investigated their toxicities and the underlying mechanisms to Escherichia coli. Much higher toxicity was observed for PFOA than PFOS, with the 3 h half growth inhibition concentrations (IC50) determined to be 10.6 ± 1.0 and 374 ± 3 mg L(-1), respectively, while the bacterial accumulation of PFOS was much greater than that of PFOA. The PFC exposures disrupted cell membranes as evidenced by the dose-dependent variations of cell structures (by transmission electron microscopy observations), surface properties (electronegativity, hydrophobicity, and membrane fluidity), and membrane compositions (by gas chromatogram and Fourier transform infrared spectroscopy analyses). The increases in the contents of intracellular reactive oxygen species (ROS) and malondialdehyde and the activity of superoxide dismutase indicated the increment of oxidative stress induced by the PFCs in the bacterial cells. The fact that the cell growth inhibition was mitigated by the addition of ROS scavenger (N-acetyl cysteine) further evidenced the important role of oxidative damage in the toxicities of PFOS and PFOA. Eighteen genes involved in cell division, membrane instability, oxidative stress, and DNA damage of the exposed cells were up or down expressed, indicating the DNA damage by the PFCs. The toxicities of PFOS and PFOA to E. coli were therefore ascribed to the membrane disruption, oxidative stress, and DNA damage induced cell inactivation and/or death. The difference in the bactericidal effect between PFOS and PFOA was supposed to be related to their different dominating toxicity mechanisms, i.e., membrane disruption and oxidative damage, respectively. The outcomes will shed new light on the assessment of ecological effects of PFCs.
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Affiliation(s)
- Gesheng Liu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Shuai Zhang
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China
| | - Kun Yang
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Lizhong Zhu
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China
| | - Daohui Lin
- Department of Environmental Science, Zhejiang University, Hangzhou 310058, China; Zhejiang Provincial Key Laboratory of Organic Pollution Process and Control, Zhejiang University, Hangzhou 310058, China.
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41
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Taylor JD, Hawthorne WJ, Lo J, Dear A, Jain N, Meisl G, Andreasen M, Fletcher C, Koch M, Darvill N, Scull N, Escalera-Maurer A, Sefer L, Wenman R, Lambert S, Jean J, Xu Y, Turner B, Kazarian SG, Chapman MR, Bubeck D, de Simone A, Knowles TPJ, Matthews SJ. Electrostatically-guided inhibition of Curli amyloid nucleation by the CsgC-like family of chaperones. Sci Rep 2016; 6:24656. [PMID: 27098162 PMCID: PMC4838910 DOI: 10.1038/srep24656] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 03/29/2016] [Indexed: 11/16/2022] Open
Abstract
Polypeptide aggregation into amyloid is linked with several debilitating human diseases. Despite the inherent risk of aggregation-induced cytotoxicity, bacteria control the export of amyloid-prone subunits and assemble adhesive amyloid fibres during biofilm formation. An Escherichia protein, CsgC potently inhibits amyloid formation of curli amyloid proteins. Here we unlock its mechanism of action, and show that CsgC strongly inhibits primary nucleation via electrostatically-guided molecular encounters, which expands the conformational distribution of disordered curli subunits. This delays the formation of higher order intermediates and maintains amyloidogenic subunits in a secretion-competent form. New structural insight also reveal that CsgC is part of diverse family of bacterial amyloid inhibitors. Curli assembly is therefore not only arrested in the periplasm, but the preservation of conformational flexibility also enables efficient secretion to the cell surface. Understanding how bacteria safely handle amyloidogenic polypeptides contribute towards efforts to control aggregation in disease-causing amyloids and amyloid-based biotechnological applications.
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Affiliation(s)
- Jonathan D Taylor
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | | | - Joanne Lo
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Alexander Dear
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Neha Jain
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Georg Meisl
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Maria Andreasen
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Catherine Fletcher
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Marion Koch
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Nicholas Darvill
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Nicola Scull
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | | | - Lea Sefer
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Rosemary Wenman
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Sebastian Lambert
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Jisoo Jean
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Yingqi Xu
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Benjamin Turner
- Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Sergei G Kazarian
- Department of Chemical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Matthew R Chapman
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Doryen Bubeck
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Alfonso de Simone
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK
| | - Steve J Matthews
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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42
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Green A, Pham N, Osby K, Aram A, Claudius R, Patray S, Jayasinghe SA. Are the curli proteins CsgE and CsgF intrinsically disordered? INTRINSICALLY DISORDERED PROTEINS 2016; 4:e1130675. [PMID: 28232894 DOI: 10.1080/21690707.2015.1130675] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 12/05/2015] [Indexed: 10/22/2022]
Abstract
Curli are a type of proteinaceous cell surface filament produced by enteric bacteria such as Escherichia and Salmonella that facilitate cell adhesion and invasion, bio-film formation, and environmental persistence. Curli assembly involves 6 proteins encoded by the curli specific genes A, B, C, E, F, and G. Although CsgA is the major structural component of curli, CsgE, and CsgF, are thought to play important chaperone like functions in the assembly of CsgA into curli. Given that some proteins with chaperone like function have been observed to contain disordered regions, sequence analysis and circular dichroism spectroscopy was used to investigate the possibility that structures of CsgE and CsgF were also disordered. Sequence analysis based on charge and hydrophobicity, as well as using the disorder prediction software PONDR, indicates that both proteins have significant regions of disorder. The secondary structure and unfolding, of CsgE and CsgF, analyzed using circular dichroism spectroscopy suggests that both proteins lack a well defined and stable structure. These observations support the hypothesis that the curli assembly proteins CsgE and CsgF are disordered proteins containing intrinsically disordered regions.
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Affiliation(s)
- Amanda Green
- Department of Chemistry and Biochemistry, California State University San Marcos , San Marcos, CA, USA
| | - Nguyen Pham
- Department of Chemistry and Biochemistry, California State University San Marcos , San Marcos, CA, USA
| | - Krystle Osby
- Department of Chemistry and Biochemistry, California State University San Marcos , San Marcos, CA, USA
| | - Alexander Aram
- Department of Chemistry and Biochemistry, California State University San Marcos , San Marcos, CA, USA
| | - Rochelle Claudius
- Department of Chemistry and Biochemistry, California State University San Marcos , San Marcos, CA, USA
| | - Sharon Patray
- Department of Chemistry and Biochemistry, California State University San Marcos , San Marcos, CA, USA
| | - Sajith A Jayasinghe
- Department of Chemistry and Biochemistry, California State University San Marcos , San Marcos, CA, USA
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43
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Akbari M, Bakhshi B, Najar Peerayeh S, Behmanesh M. Detection of Curli Biogenesis Genes Among Enterobacter cloacae Isolated From Blood Cultures. INTERNATIONAL JOURNAL OF ENTERIC PATHOGENS 2015. [DOI: 10.17795/ijep28413] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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44
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Chorell E, Andersson E, Evans ML, Jain N, Götheson A, Åden J, Chapman MR, Almqvist F, Wittung-Stafshede P. Bacterial Chaperones CsgE and CsgC Differentially Modulate Human α-Synuclein Amyloid Formation via Transient Contacts. PLoS One 2015; 10:e0140194. [PMID: 26465894 PMCID: PMC4605646 DOI: 10.1371/journal.pone.0140194] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2015] [Accepted: 09/22/2015] [Indexed: 11/20/2022] Open
Abstract
Amyloid formation is historically associated with cytotoxicity, but many organisms produce functional amyloid fibers (e.g., curli) as a normal part of cell biology. Two E. coli genes in the curli operon encode the chaperone-like proteins CsgC and CsgE that both can reduce in vitro amyloid formation by CsgA. CsgC was also found to arrest amyloid formation of the human amyloidogenic protein α-synuclein, which is involved in Parkinson's disease. Here, we report that the inhibitory effects of CsgC arise due to transient interactions that promote the formation of spherical α-synuclein oligomers. We find that CsgE also modulates α-synuclein amyloid formation through transient contacts but, in contrast to CsgC, CsgE accelerates α-synuclein amyloid formation. Our results demonstrate the significance of transient protein interactions in amyloid regulation and emphasize that the same protein may inhibit one type of amyloid while accelerating another.
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Affiliation(s)
- Erik Chorell
- Department of Chemistry, Umeå University, Umeå, Sweden
| | | | - Margery L. Evans
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Neha Jain
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Anna Götheson
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Jörgen Åden
- Department of Chemistry, Umeå University, Umeå, Sweden
| | - Matthew R. Chapman
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, Michigan, United States of America
| | - Fredrik Almqvist
- Department of Chemistry, Umeå University, Umeå, Sweden
- Umeå Centre for Microbial Research, Umeå University, Umeå, Sweden
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45
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Van Gerven N, Klein RD, Hultgren SJ, Remaut H. Bacterial amyloid formation: structural insights into curli biogensis. Trends Microbiol 2015; 23:693-706. [PMID: 26439293 DOI: 10.1016/j.tim.2015.07.010] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Revised: 07/06/2015] [Accepted: 07/22/2015] [Indexed: 01/20/2023]
Abstract
Curli are functional amyloid fibers assembled by many Gram-negative bacteria as part of an extracellular matrix that encapsulates the bacteria within a biofilm. A multicomponent secretion system ensures the safe transport of the aggregation-prone curli subunits across the periplasm and outer membrane, and coordinates subunit self-assembly into surface-attached fibers. To avoid the build-up of potentially toxic intracellular protein aggregates, the timing and location of the interactions of the different curli proteins are of paramount importance. Here we review the structural and molecular biology of curli biogenesis, with a focus on the recent breakthroughs in our understanding of subunit chaperoning and secretion. The mechanistic insight into the curli assembly pathway will provide tools for new biotechnological applications and inform the design of targeted inhibitors of amyloid polymerization and biofilm formation.
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Affiliation(s)
- Nani Van Gerven
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Roger D Klein
- Department of Molecular Microbiology and Microbial Pathogenesis, Washington University in Saint Louis School of Medicine, St Louis, MO 63110-1010, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology and Microbial Pathogenesis, Washington University in Saint Louis School of Medicine, St Louis, MO 63110-1010, USA
| | - Han Remaut
- Structural and Molecular Microbiology, Structural Biology Research Center, VIB, Pleinlaan 2, 1050 Brussels, Belgium; Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium.
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46
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Chahales P, Thanassi DG. Structure, Function, and Assembly of Adhesive Organelles by Uropathogenic Bacteria. Microbiol Spectr 2015; 3:10.1128/microbiolspec.UTI-0018-2013. [PMID: 26542038 PMCID: PMC4638162 DOI: 10.1128/microbiolspec.uti-0018-2013] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Indexed: 01/02/2023] Open
Abstract
Bacteria assemble a wide range of adhesive proteins, termed adhesins, to mediate binding to receptors and colonization of surfaces. For pathogenic bacteria, adhesins are critical for early stages of infection, allowing the bacteria to initiate contact with host cells, colonize different tissues, and establish a foothold within the host. The adhesins expressed by a pathogen are also critical for bacterial-bacterial interactions and the formation of bacterial communities, including biofilms. The ability to adhere to host tissues is particularly important for bacteria that colonize sites such as the urinary tract, where the flow of urine functions to maintain sterility by washing away non-adherent pathogens. Adhesins vary from monomeric proteins that are directly anchored to the bacterial surface to polymeric, hair-like fibers that extend out from the cell surface. These latter fibers are termed pili or fimbriae, and were among the first identified virulence factors of uropathogenic Escherichia coli. Studies since then have identified a range of both pilus and non-pilus adhesins that contribute to bacterial colonization of the urinary tract, and have revealed molecular details of the structures, assembly pathways, and functions of these adhesive organelles. In this review, we describe the different types of adhesins expressed by both Gram-negative and Gram-positive uropathogens, what is known about their structures, how they are assembled on the bacterial surface, and the functions of specific adhesins in the pathogenesis of urinary tract infections.
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Affiliation(s)
- Peter Chahales
- Center for Infectious Diseases and Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794
| | - David G Thanassi
- Center for Infectious Diseases and Department of Molecular Genetics and Microbiology, Stony Brook University, Stony Brook, NY 11794
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Landreh M, Rising A, Presto J, Jörnvall H, Johansson J. Specific chaperones and regulatory domains in control of amyloid formation. J Biol Chem 2015; 290:26430-6. [PMID: 26354437 DOI: 10.1074/jbc.r115.653097] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Many proteins can form amyloid-like fibrils in vitro, but only about 30 amyloids are linked to disease, whereas some proteins form physiological amyloid-like assemblies. This raises questions of how the formation of toxic protein species during amyloidogenesis is prevented or contained in vivo. Intrinsic chaperoning or regulatory factors can control the aggregation in different protein systems, thereby preventing unwanted aggregation and enabling the biological use of amyloidogenic proteins. The molecular actions of these chaperones and regulators provide clues to the prevention of amyloid disease, as well as to the harnessing of amyloidogenic proteins in medicine and biotechnology.
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Affiliation(s)
- Michael Landreh
- From the Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 5QY, United Kingdom
| | - Anna Rising
- the Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet - Novum, 141 57 Huddinge, Sweden, the Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, Box 575, 751 23 Uppsala, Sweden
| | - Jenny Presto
- the Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet - Novum, 141 57 Huddinge, Sweden
| | - Hans Jörnvall
- the Department of Medical Biochemistry and Biophysics (MBB), Karolinska Institutet, SE-171 77 Stockholm, Sweden, and
| | - Jan Johansson
- the Department of Neurobiology, Care Sciences and Society (NVS), Center for Alzheimer Research, Karolinska Institutet - Novum, 141 57 Huddinge, Sweden, the Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, The Biomedical Centre, Box 575, 751 23 Uppsala, Sweden, the Institute of Mathematics and Natural Sciences, Tallinn University, Narva mnt 25, 101 20 Tallinn, Estonia
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48
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Ramsugit S, Pillay M. Pili of Mycobacterium tuberculosis: current knowledge and future prospects. Arch Microbiol 2015; 197:737-44. [PMID: 25975850 DOI: 10.1007/s00203-015-1117-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2014] [Revised: 05/02/2015] [Accepted: 05/05/2015] [Indexed: 11/29/2022]
Abstract
Many pathogenic bacteria express filamentous appendages, termed pili, on their surface. These organelles function in several important bacterial processes, including mediating bacterial interaction with, and colonization of the host, signalling events, locomotion, DNA uptake, electric conductance, and biofilm formation. In the last decade, it has been established that the tuberculosis-causing bacterium, Mycobacterium tuberculosis, produces two pili types: curli and type IV pili. In this paper, we review studies on M. tuberculosis pili, highlighting their structure and biological significance to M. tuberculosis pathogenesis, and discuss their potential as targets for therapeutic intervention and diagnostic test development.
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Affiliation(s)
- Saiyur Ramsugit
- Medical Microbiology and Infection Control, School of Laboratory Medicine and Medical Sciences, College of Health Sciences, University of KwaZulu-Natal, 1st Floor Doris Duke Medical Research Institute, Private Bag 7, Congella, Durban, 4013, South Africa
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49
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Hobley L, Harkins C, MacPhee CE, Stanley-Wall NR. Giving structure to the biofilm matrix: an overview of individual strategies and emerging common themes. FEMS Microbiol Rev 2015; 39:649-69. [PMID: 25907113 PMCID: PMC4551309 DOI: 10.1093/femsre/fuv015] [Citation(s) in RCA: 319] [Impact Index Per Article: 35.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/09/2015] [Indexed: 01/24/2023] Open
Abstract
Biofilms are communities of microbial cells that underpin diverse processes including sewage bioremediation, plant growth promotion, chronic infections and industrial biofouling. The cells resident in the biofilm are encased within a self-produced exopolymeric matrix that commonly comprises lipids, proteins that frequently exhibit amyloid-like properties, eDNA and exopolysaccharides. This matrix fulfils a variety of functions for the community, from providing structural rigidity and protection from the external environment to controlling gene regulation and nutrient adsorption. Critical to the development of novel strategies to control biofilm infections, or the capability to capitalize on the power of biofilm formation for industrial and biotechnological uses, is an in-depth knowledge of the biofilm matrix. This is with respect to the structure of the individual components, the nature of the interactions between the molecules and the three-dimensional spatial organization. We highlight recent advances in the understanding of the structural and functional role that carbohydrates and proteins play within the biofilm matrix to provide three-dimensional architectural integrity and functionality to the biofilm community. We highlight, where relevant, experimental techniques that are allowing the boundaries of our understanding of the biofilm matrix to be extended using Escherichia coli, Staphylococcus aureus, Vibrio cholerae, and Bacillus subtilis as exemplars. Examining the structure and function of the biofilm extracellular matrix.
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Affiliation(s)
- Laura Hobley
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Catriona Harkins
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
| | - Cait E MacPhee
- James Clerk Maxwell Building, School of Physics, University of Edinburgh, Edinburgh EH9 3JZ, UK
| | - Nicola R Stanley-Wall
- Division of Molecular Microbiology, College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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50
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Abstract
In this issue of Molecular Cell, Evans et al. (2015) report that the hitherto largely unstudied CsgC protein is responsible for the suppression of premature amyloidogenesis within the cellular periplasm, preventing early aggregation and cellular toxicity.
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Affiliation(s)
- Roger D Klein
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA
| | - Scott J Hultgren
- Department of Molecular Microbiology, Washington University School of Medicine, Saint Louis, MO 63110, USA; Center for Women's Infectious Disease Research, Washington University School of Medicine, Saint Louis, MO 63110, USA.
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