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Afonso AC, Botting J, Gomes IB, Saavedra MJ, Simões LC, Liu J, Simões M. Elucidating bacterial coaggregation through a physicochemical and imaging surface characterization. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 948:174872. [PMID: 39032752 DOI: 10.1016/j.scitotenv.2024.174872] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Revised: 07/10/2024] [Accepted: 07/16/2024] [Indexed: 07/23/2024]
Abstract
Bacterial coaggregation is a highly specific type of cell-cell interaction, well-documented among oral bacteria, and involves specific characteristics of the cell surface of the coaggregating strains. However, the understanding of the mechanisms promoting coaggregation in aquatic systems remains limited. This gap is critical to address, given the broad implications of coaggregation for multispecies biofilm formation, water quality, the performance of engineered systems, and diverse biotechnological applications. Therefore, this study aims to comprehensively characterize the cell surface of the coaggregating strain Delftia acidovorans 005P, isolated from drinking water, alongside a non-coaggregating strain, D. acidovorans 009P. By analyzing two strains of the same species, we aim to identify the factors contributing to the coaggregation ability of strain 005P. To achieve this, we employed a combination of physicochemical characterization, Fourier-transform infrared spectroscopy (FTIR), and advancing imaging techniques [transmission electron microscopy and cryo-electron tomography (cryo-ET)]. The coaggregating strain (005P) exhibited higher surface hydrophobicity, negative surface charge, and cell surface and co-adhesion energies than the non-coaggregating strain (009P). The chemical characterization of bacterial surfaces through FTIR revealed subtle differences, particularly in spectral regions linked to carbohydrates and phosphodiesters/amide III of proteins (860-930 cm-1 and 1212-1240 cm-1, respectively). Cryo-ET highlighted significant differences in pili structures between the strains, such as variations in length, frequency, and arrangement. The pili in the 005P strain, identified as pili-like adhesins, serve as key mediators of coaggregation. By integrating physicochemical analyses and high-resolution imaging techniques, this study conclusively links the coaggregation ability of D. acidovorans 005P to its unique pili characteristics, emphasizing their crucial role in microbial coaggregation in aquatic environments.
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Affiliation(s)
- Ana C Afonso
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; CITAB, Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal; CEB-LABBELS, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jack Botting
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, United States; New Haven Microbial Sciences Institute, Yale University, West Haven, CT 06516, United States
| | - Inês B Gomes
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal
| | - Maria J Saavedra
- CITAB, Department of Veterinary Sciences, University of Trás-os-Montes e Alto Douro, 5000-801 Vila Real, Portugal
| | - Lúcia C Simões
- CEB-LABBELS, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal
| | - Jun Liu
- Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06536, United States; New Haven Microbial Sciences Institute, Yale University, West Haven, CT 06516, United States
| | - Manuel Simões
- LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr Roberto Frias, 4200-465 Porto, Portugal.
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Liu X, Ishak MI, Ma H, Su B, Nobbs AH. Bacterial Surface Appendages Modulate the Antimicrobial Activity Induced by Nanoflake Surfaces on Titanium. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024; 20:e2310149. [PMID: 38233200 DOI: 10.1002/smll.202310149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 01/06/2024] [Indexed: 01/19/2024]
Abstract
Bioinspired nanotopography is a promising approach to generate antimicrobial surfaces to combat implant-associated infection. Despite efforts to develop bactericidal 1D structures, the antibacterial capacity of 2D structures and their mechanism of action remains uncertain. Here, hydrothermal synthesis is utilized to generate two 2D nanoflake surfaces on titanium (Ti) substrates and investigate the physiological effects of nanoflakes on bacteria. The nanoflakes impair the attachment and growth of Escherichia coli and trigger the accumulation of intracellular reactive oxygen species (ROS), potentially contributing to the killing of adherent bacteria. E. coli surface appendages type-1 fimbriae and flagella are not implicated in the nanoflake-mediated modulation of bacterial attachment but do influence the bactericidal effects of nanoflakes. An E. coli ΔfimA mutant lacking type-1 fimbriae is more susceptible to the bactericidal effects of nanoflakes than the parent strain, while E. coli cells lacking flagella (ΔfliC) are more resistant. The results suggest that type-1 fimbriae confer a cushioning effect that protects bacteria upon initial contact with the nanoflake surface, while flagella-mediated motility can lead to elevated membrane abrasion. This finding offers a better understanding of the antibacterial properties of nanoflake structures that can be applied to the design of antimicrobial surfaces for future medical applications.
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Affiliation(s)
- Xiayi Liu
- Bristol Dental School Research Laboratories, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1, 3NY, UK
| | - Mohd I Ishak
- Bristol Dental School Research Laboratories, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1, 3NY, UK
| | - Huan Ma
- School of Chemistry, Centre for Organized Matter Chemistry and Centre for Protolife Research, University of Bristol, Bristol, BS8 1TS, UK
| | - Bo Su
- Bristol Dental School Research Laboratories, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1, 3NY, UK
| | - Angela H Nobbs
- Bristol Dental School Research Laboratories, University of Bristol, Dorothy Hodgkin Building, Whitson Street, Bristol, BS1, 3NY, UK
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Long J, Yang C, Liu J, Ma C, Jiao M, Hu H, Xiong J, Zhang Y, Wei W, Yang H, He Y, Zhu M, Yu Y, Fu L, Chen H. Tannic acid inhibits Escherichia coli biofilm formation and underlying molecular mechanisms: Biofilm regulator CsgD. Biomed Pharmacother 2024; 175:116716. [PMID: 38735084 DOI: 10.1016/j.biopha.2024.116716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Revised: 04/27/2024] [Accepted: 05/06/2024] [Indexed: 05/14/2024] Open
Abstract
Biofilms often engender persistent infections, heightened antibiotic resistance, and the recurrence of infections. Therefor, infections related to bacterial biofilms are often chronic and pose challenges in terms of treatment. The main transcription regulatory factor, CsgD, activates csgABC-encoded curli to participate in the composition of extracellular matrix, which is an important skeleton for biofilm development in enterobacteriaceae. In our previous study, a wide range of natural bioactive compounds that exhibit strong affinity to CsgD were screened and identified via molecular docking. Tannic acid (TA) was subsequently chosen, based on its potent biofilm inhibition effect as observed in crystal violet staining. Therefore, the aim of this study was to investigate the specific effects of TA on the biofilm formation of clinically isolated Escherichia coli (E. coli). Results demonstrated a significant inhibition of E. coli Ec032 biofilm formation by TA, while not substantially affecting the biofilm of the ΔcsgD strain. Moreover, deletion of the csgD gene led to a reduction in Ec032 biofilm formation, alongside diminished bacterial motility and curli synthesis inhibition. Transcriptomic analysis and RT-qPCR revealed that TA repressed genes associated with the csg operon and other biofilm-related genes. In conclusion, our results suggest that CsgD is one of the key targets for TA to inhibit E. coli biofilm formation. This work preliminarily elucidates the molecular mechanisms of TA inhibiting E. coli biofilm formation, which could provide a lead structure for the development of future antibiofilm drugs.
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Affiliation(s)
- Jinying Long
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China
| | - Can Yang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China
| | - JingJing Liu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Chengjun Ma
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Min Jiao
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China
| | - Huiming Hu
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China
| | - Jing Xiong
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Yang Zhang
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Wei Wei
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Traditional Chinese Veterinary Research Institute, Southwest University, Chongqing 402460, China
| | - Hongzao Yang
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Traditional Chinese Veterinary Research Institute, Southwest University, Chongqing 402460, China
| | - Yuzhang He
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China
| | - Maixun Zhu
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Yuandi Yu
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China
| | - Lizhi Fu
- National Center of Technology Innovation for Pigs, Chongqing 402460, China; Chongqing Academy of Animal Sciences, Chongqing 402460, China.
| | - Hongwei Chen
- College of Veterinary Medicine, Southwest University, Chongqing 402460, China; National Center of Technology Innovation for Pigs, Chongqing 402460, China; Immunology Research Center, Medical Research Institute, Southwest University, Chongqing 402460, China; Traditional Chinese Veterinary Research Institute, Southwest University, Chongqing 402460, China.
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Philipp LA, Bühler K, Ulber R, Gescher J. Beneficial applications of biofilms. Nat Rev Microbiol 2024; 22:276-290. [PMID: 37957398 DOI: 10.1038/s41579-023-00985-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/05/2023] [Indexed: 11/15/2023]
Abstract
Many microorganisms live in the form of a biofilm. Although they are feared in the medical sector, biofilms that are composed of non-pathogenic organisms can be highly beneficial in many applications, including the production of bulk and fine chemicals. Biofilm systems are natural retentostats in which the biocatalysts can adapt and optimize their metabolism to different conditions over time. The adherent nature of biofilms allows them to be used in continuous systems in which the hydraulic retention time is much shorter than the doubling time of the biocatalysts. Moreover, the resilience of organisms growing in biofilms, together with the potential of uncoupling growth from catalytic activity, offers a wide range of opportunities. The ability to work with continuous systems using a potentially self-advancing whole-cell biocatalyst is attracting interest from a range of disciplines, from applied microbiology to materials science and from bioengineering to process engineering. The field of beneficial biofilms is rapidly evolving, with an increasing number of applications being explored, and the surge in demand for sustainable and biobased solutions and processes is accelerating advances in the field. This Review provides an overview of the research topics, challenges, applications and future directions in beneficial and applied biofilm research.
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Affiliation(s)
- Laura-Alina Philipp
- Hamburg University of Technology, Institute of Technical Microbiology, Hamburg, Germany
| | - Katja Bühler
- Department of Environmental Microbiology, Helmholtz-Centre for Environmental Research, Leipzig, Germany
| | - Roland Ulber
- RPTU Kaiserslautern-Landau, Institute of Bioprocess Engineering, Kaiserslautern, Germany
| | - Johannes Gescher
- Hamburg University of Technology, Institute of Technical Microbiology, Hamburg, Germany.
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Mirza Agha M, Tavili E, Dabirmanesh B. Functional amyloids. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:389-434. [PMID: 38811086 DOI: 10.1016/bs.pmbts.2024.03.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
While amyloid has traditionally been viewed as a harmful formation, emerging evidence suggests that amyloids may also play a functional role in cell biology, contributing to normal physiological processes that have been conserved throughout evolution. Functional amyloids have been discovered in several creatures, spanning from bacteria to mammals. These amyloids serve a multitude of purposes, including but not limited to, forming biofilms, melanin synthesis, storage, information transfer, and memory. The functional role of amyloids has been consistently validated by the discovery of more functional amyloids, indicating a conceptual convergence. The biology of amyloids is well-represented by non-pathogenic amyloids, given the numerous ones already identified and the ongoing rate of new discoveries. In this chapter, functional amyloids in microorganisms, animals, and plants are described.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elaheh Tavili
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Bahareh Dabirmanesh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran.
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Ellis JR, Rowley PA. An apparent lack of synergy between degradative enzymes against Staphylococcus aureus biofilms. MICROPUBLICATION BIOLOGY 2024; 2024:10.17912/micropub.biology.001119. [PMID: 38596361 PMCID: PMC11002645 DOI: 10.17912/micropub.biology.001119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 01/25/2024] [Accepted: 03/12/2024] [Indexed: 04/11/2024]
Abstract
Enzymes combat bacterial infections by degrading biomolecules to disperse Staphylococcus aureus biofilms. Commercial enzyme mixtures, like cellulase and pepsin, show concentration-dependent dispersion, but low concentrations lack synergy. Only the sequential addition of pepsin followed by Arthrobacter luteus zymolyase 20T displays synergy, effectively dispersing biofilms. Purified zymolyase 100T outperforms zymolyase 20T but lacks synergy with pepsin. This study underscores the complexity of enzymatic biofilm dispersal, highlighting the need for tailored approaches based on enzyme properties and biofilm composition.
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Affiliation(s)
- Jeremy R. Ellis
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States
- The Johns Hopkins University School of Medicine, Johns Hopkins University, Baltimore, Maryland, United States
| | - Paul A. Rowley
- Department of Biological Sciences, University of Idaho, Moscow, Idaho, United States
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Fu C, Wang Z, Zhou X, Hu B, Li C, Yang P. Protein-based bioactive coatings: from nanoarchitectonics to applications. Chem Soc Rev 2024; 53:1514-1551. [PMID: 38167899 DOI: 10.1039/d3cs00786c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Protein-based bioactive coatings have emerged as a versatile and promising strategy for enhancing the performance and biocompatibility of diverse biomedical materials and devices. Through surface modification, these coatings confer novel biofunctional attributes, rendering the material highly bioactive. Their widespread adoption across various domains in recent years underscores their importance. This review systematically elucidates the behavior of protein-based bioactive coatings in organisms and expounds on their underlying mechanisms. Furthermore, it highlights notable advancements in artificial synthesis methodologies and their functional applications in vitro. A focal point is the delineation of assembly strategies employed in crafting protein-based bioactive coatings, which provides a guide for their expansion and sustained implementation. Finally, the current trends, challenges, and future directions of protein-based bioactive coatings are discussed.
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Affiliation(s)
- Chengyu Fu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Zhengge Wang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Xingyu Zhou
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Bowen Hu
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
| | - Chen Li
- School of Chemistry and Chemical Engineering, Henan Institute of Science and Technology, Eastern HuaLan Avenue, Xinxiang, Henan 453003, China
| | - Peng Yang
- Key Laboratory of Applied Surface and Colloid Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China.
- Xi'an Key Laboratory of Polymeric Soft Matter, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
- International Joint Research Center on Functional Fiber and Soft Smart Textile, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710119, China
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Bondarev SA, Uspenskaya MV, Leclercq J, Falgarone T, Zhouravleva GA, Kajava AV. AmyloComp: A Bioinformatic Tool for Prediction of Amyloid Co-aggregation. J Mol Biol 2024:168437. [PMID: 38185324 DOI: 10.1016/j.jmb.2024.168437] [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: 11/17/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
Typically, amyloid fibrils consist of multiple copies of the same protein. In these fibrils, each polypeptide chain adopts the same β-arc-containing conformation and these chains are stacked in a parallel and in-register manner. In the last few years, however, a considerable body of data has been accumulated about co-aggregation of different amyloid-forming proteins. Among known examples of the co-aggregation are heteroaggregates of different yeast prions and human proteins Rip1 and Rip3. Since the co-aggregation is linked to such important phenomena as infectivity of amyloids and molecular mechanisms of functional amyloids, we analyzed its structural aspects in more details. An axial stacking of different proteins within the same amyloid fibril is one of the most common type of co-aggregation. By using an approach based on structural similarity of the growing tips of amyloids, we developed a computational method to predict amyloidogenic β-arch structures that are able to interact with each other by the axial stacking. Furthermore, we compiled a dataset consisting of 26 experimentally known pairs of proteins capable or incapable to co-aggregate. We utilized this dataset to test and refine our algorithm. The developed method opens a way for a number of applications, including the identification of microbial proteins capable triggering amyloidosis in humans. AmyloComp is available on the website: https://bioinfo.crbm.cnrs.fr/index.php?route=tools&tool=30.
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Affiliation(s)
- Stanislav A Bondarev
- Department of Genetics and Biotechnology and Laboratory of Amyloid Biology, St. Petersburg State University, Saint Petersburg 199034, Russian Federation.
| | - Mayya V Uspenskaya
- Institute of Bioengineering, ITMO University, St. Petersburg 197101, Russian Federation
| | - Jérémy Leclercq
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France
| | - Théo Falgarone
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France
| | - Galina A Zhouravleva
- Department of Genetics and Biotechnology and Laboratory of Amyloid Biology, St. Petersburg State University, Saint Petersburg 199034, Russian Federation
| | - Andrey V Kajava
- Centre de Recherche en Biologie Cellulaire de Montpellier, CNRS, Université Montpellier, Montpellier 34293, France.
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Sampson T. Microbial amyloids in neurodegenerative amyloid diseases. FEBS J 2023:10.1111/febs.17023. [PMID: 38041542 PMCID: PMC11144261 DOI: 10.1111/febs.17023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/13/2023] [Accepted: 11/30/2023] [Indexed: 12/03/2023]
Abstract
Human-disease associated amyloidogenic proteins are not unique in their ability to form amyloid fibrillar structures. Numerous microbes produce amyloidogenic proteins that have distinct functions for their physiology in their amyloid form, rather than solely detrimental. Emerging data indicate associations between various microbial organisms, including those which produce functional amyloids, with neurodegenerative diseases. Here, we review some of the evidence suggesting that microbial amyloids impact amyloid disease in host organisms. Experimental data are building a foundation for continued lines of enquiry and suggest that that direct or indirect interactions between microbial and host amyloids may be a contributor to amyloid pathologies. Inhibiting microbial amyloids or their interactions with the host may therefore represent a tangible target to limit various amyloid pathologies.
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Affiliation(s)
- Timothy Sampson
- Department of Cell Biology, Emory University School of Medicine, Atlanta, GA, USA
- Aligning Science Across Parkinson's (ASAP) Collaborative Research Network, Chevy Chase, MD, USA
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Ellis JR, Rowley PA. An apparent lack of synergy between degradative enzymes against Staphylococcus aureus biofilms. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.05.561034. [PMID: 37873330 PMCID: PMC10592981 DOI: 10.1101/2023.10.05.561034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
The use of enzymes represents an approach to combat bacterial infections by degrading extracellular biomolecules to disperse Staphylococcus aureus biofilms. Commercial enzyme preparations, including cellulase, amylase, pectinase, zymolyase, and pepsin, exhibit concentration-dependent dispersion of S. aureus biofilms. Here, we report that low concentrations of these enzymes generally lack synergy when combined or added together sequentially to biofilms. Only the addition of a protease (pepsin) followed by a commercial mixture of degradative enzymes from Arthrobacter luteus (zymolyase 20T), demonstrated synergy and was effective at dispersing S. aureus biofilms. A more purified mixture of Arthrobacter luteus enzymes (zymolyase 100T) showed improved dispersal of S. aureus biofilms compared to zymolyase 20T but lacked synergy with pepsin. This study emphasizes the complexity of enzymatic biofilm dispersal and the need for tailored approaches based on the properties of degradative enzymes and biofilm composition.
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Affiliation(s)
- Jeremy R Ellis
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
- Johns Hopkins University, The Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Paul A Rowley
- University of Idaho, Department of Biological Sciences, Moscow, ID 83844, USA
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11
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Cámara-Almirón J, Domínguez-García L, El Mammeri N, Lends A, Habenstein B, de Vicente A, Loquet A, Romero D. Molecular characterization of the N-terminal half of TasA during amyloid-like assembly and its contribution to Bacillus subtilis biofilm formation. NPJ Biofilms Microbiomes 2023; 9:68. [PMID: 37739955 PMCID: PMC10516879 DOI: 10.1038/s41522-023-00437-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 09/12/2023] [Indexed: 09/24/2023] Open
Abstract
Biofilms are bacterial communities that result from a cell differentiation process leading to the secretion of an extracellular matrix (ECM) by part of the population. In Bacillus subtilis, the main protein component of the ECM is TasA, which forms a fiber-based scaffold that confers structure to the ECM. The N-terminal half of TasA is strongly conserved among Bacillus species and contains a protein domain, the rigid core (RcTasA), which is critical for the structural and functional properties of the recombinant protein. In this study, we demonstrate that recombinantly purified RcTasA in vitro retains biochemical properties previously observed for the entire protein. Further analysis of the RcTasA amino acid sequence revealed two aggregation-prone stretches and a region of imperfect amino acid repeats, which are known to contribute to functional amyloid assembly. Biochemical characterization of these stretches found in RcTasA revealed their amyloid-like capacity in vitro, contributing to the amyloid nature of RcTasA. Moreover, the study of the imperfect amino acid repeats revealed the critical role of residues D64, K68 and D69 in the structural function of TasA. Experiments with versions of TasA carrying the substitutions D64A and K68AD69A demonstrated a partial loss of function of the protein either in the assembly of the ECM or in the stability of the core and amyloid-like properties. Taken together, our findings allow us to better understand the polymerization process of TasA during biofilm formation and provide knowledge into the sequence determinants that promote the molecular behavior of protein filaments in bacteria.
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Affiliation(s)
- Jesús Cámara-Almirón
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
- Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, Lausanne, Switzerland
| | - Laura Domínguez-García
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Nadia El Mammeri
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Department of Chemistry, Massachusetts Institute of Technology, 170 Albany Street, Cambridge, MA, 02139, USA
| | - Alons Lends
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
- Latvian Institute of Organic Synthesis, Aizkraukles 21, Riga LV, 1006, Latvia
| | - Birgit Habenstein
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Antonio de Vicente
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain
| | - Antoine Loquet
- CNRS, Chemistry and Biology of Membranes and Nanoobjects (CBMN), Institut Europeen de Chimie et Biologie (IECB), University of Bordeaux, Pessac, France
| | - Diego Romero
- Departamento de Microbiología, Instituto de Hortofruticultura Subtropical y Mediterránea "La Mayora", Universidad de Málaga, (Campus Universitario de Teatinos), Málaga, Spain.
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12
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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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13
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Nakahara K, Nakane S, Ishii K, Ikeda T, Ando Y. Gut microbiota of Parkinson's disease in an appendectomy cohort: a preliminary study. Sci Rep 2023; 13:2210. [PMID: 36750613 PMCID: PMC9905566 DOI: 10.1038/s41598-023-29219-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 01/31/2023] [Indexed: 02/09/2023] Open
Abstract
In patients with Parkinson's disease (PD), α-synuclein pathology is thought to spread to the brain via the dorsal motor nucleus of the vagus nerve. The link between the gut microbiome and PD has been explored in various studies. The appendix might play an important role in immunity by maintaining the microbiota as a reservoir. In recent times, appendectomy has been linked to a lower risk of PD, possibly owing to the role of the appendix in altering the gut microbiome. We aimed to elucidate whether the gut microbiota affects PD development in the appendectomy cohort. We analyzed the fecal microbial composition in patients with PD and healthy controls with and without a history of appendectomy. The abundance of microbes from the family Enterobacteriaceae was higher in feces samples from patients with Parkinson's disease compared to that in samples collected from healthy controls. Furthermore, there was a significant phylogenetic difference between patients with PD and healthy controls who had undergone appendectomy. There was a significant phylogenetic difference between patients with PD and HCs who had undergone APP. These results suggest the correlation between gut microbiota and PD in patients who have undergone APP.
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Affiliation(s)
- Keiichi Nakahara
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Shunya Nakane
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan. .,Department of Neurology, Nippon Medical School Hospital, 1-1-5 Sendagi, Bunkyo-Ku, Tokyo, 113-8603, Japan.
| | - Kazuo Ishii
- Biostatistics Center, Kurume University, 67 Asahi-Machi, Kurume, Fukuoka, 830-0011, Japan
| | - Tokunori Ikeda
- Department of Clinical Investigation, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
| | - Yukio Ando
- Department of Neurology, Graduate School of Medical Sciences, Kumamoto University, 1-1-1 Honjo, Chuo-Ku, Kumamoto, 860-8556, Japan
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14
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 53] [Impact Index Per Article: 53.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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15
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Wong LL, Mugunthan S, Kundukad B, Ho JCS, Rice SA, Hinks J, Seviour T, Parikh AN, Kjelleberg S. Microbial biofilms are shaped by the constant dialogue between biological and physical forces in the extracellular matrix. Environ Microbiol 2023; 25:199-208. [PMID: 36502515 DOI: 10.1111/1462-2920.16306] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Accepted: 12/07/2022] [Indexed: 12/14/2022]
Affiliation(s)
- Lan Li Wong
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Sudarsan Mugunthan
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Binu Kundukad
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - James Chin Shing Ho
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore
| | - Scott A Rice
- CSIRO, Agriculture and Food, Microbiomes for One Systems Health, Canberra, Australia
| | - Jamie Hinks
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore
| | - Thomas Seviour
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,WATEC Aarhus University Centre for Water Technology, Aarhus, Denmark
| | - Atul N Parikh
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, Singapore.,Department of Biomedical Engineering, University of California, Davis, California, USA
| | - Staffan Kjelleberg
- Singapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
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16
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Antibiofilm Action of Plant Terpenes in Salmonella Strains: Potential Inhibitors of the Synthesis of Extracellular Polymeric Substances. Pathogens 2022; 12:pathogens12010035. [PMID: 36678383 PMCID: PMC9864247 DOI: 10.3390/pathogens12010035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Revised: 12/08/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Salmonella can form biofilms that contribute to its resistance in food processing environments. Biofilms are a dense population of cells that adhere to the surface, creating a matrix composed of extracellular polymeric substances (EPS) consisting mainly of polysaccharides, proteins, and eDNA. Remarkably, the secreted substances, including cellulose, curli, and colanic acid, act as protective barriers for Salmonella and contribute to its resistance and persistence when exposed to disinfectants. Conventional treatments are mostly ineffective in controlling this problem; therefore, exploring anti-biofilm molecules that minimize and eradicate Salmonella biofilms is required. The evidence indicated that terpenes effectively reduce biofilms and affect their three-dimensional structure due to the decrease in the content of EPS. Specifically, in the case of Salmonella, cellulose is an essential component in their biofilms, and its control could be through the inhibition of glycosyltransferase, the enzyme that synthesizes this polymer. The inhibition of polymeric substances secreted by Salmonella during biofilm development could be considered a target to reduce its resistance to disinfectants, and terpenes can be regarded as inhibitors of this process. However, more studies are needed to evaluate the effectiveness of these compounds against Salmonella enzymes that produce extracellular polymeric substances.
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17
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Shanmugasundarasamy T, Karaiyagowder Govindarajan D, Kandaswamy K. A review on pilus assembly mechanisms in Gram-positive and Gram-negative bacteria. Cell Surf 2022; 8:100077. [PMID: 35493982 PMCID: PMC9046445 DOI: 10.1016/j.tcsw.2022.100077] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Revised: 04/08/2022] [Accepted: 04/18/2022] [Indexed: 12/17/2022] Open
Abstract
The surface of Gram-positive and Gram-negative bacteria contains long hair-like proteinaceous protrusion known as pili or fimbriae. Historically, pilin proteins were considered to play a major role in the transfer of genetic material during bacterial conjugation. Recent findings however elucidate their importance in virulence, biofilm formation, phage transduction, and motility. Therefore, it is crucial to gain mechanistic insights on the subcellular assembly of pili and the localization patterns of their subunit proteins (major and minor pilins) that aid the macromolecular pilus assembly at the bacterial surface. In this article, we review the current knowledge of pilus assembly mechanisms in a wide range of Gram-positive and Gram-negative bacteria, including subcellular localization patterns of a few pilin subunit proteins and their role in virulence and pathogenesis.
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18
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Rathi B, Gupta S, Kumar P, Kesarwani V, Dhanda RS, Kushwaha SK, Yadav M. Anti-biofilm activity of caffeine against uropathogenic E. coli is mediated by curli biogenesis. Sci Rep 2022; 12:18903. [PMID: 36344808 PMCID: PMC9640630 DOI: 10.1038/s41598-022-23647-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/03/2022] [Indexed: 11/09/2022] Open
Abstract
Biofilms are assemblages of sessile microorganisms that form an extracellular matrix around themselves and mediate attachment to surfaces. The major component of the extracellular matrix of Uropathogenic E. coli and other Enterobacteriaceae are curli fibers, making biofilms robust and resistant to antimicrobials. It is therefore imperative to screen antibiofilm compounds that can impair biofilm formation. In the present study, we investigated the curli-dependent antibiofilm activity of caffeine against UPEC strain CFT073 and commensal strain E. coli K-12MG1655.Caffeine significantly reduced the biofilm formation of both UPEC and E. coli K-12 by 86.58% and 91.80% respectively at 48 mM caffeine as determined by Crystal Violet assay. These results were further confirmed by fluorescence microscopy and Scanning Electron Microscope (SEM). Caffeine significantly reduced the cytotoxicity and survivability of UPEC. Molecular docking analysis revealed a strong interaction between caffeine and curli regulator protein (Csg D) of E. coli. The qRT-PCR data also showed significant downregulation in the expression of CsgBA and the CsgDEFG operon at both 24 mM and 48 mM caffeine. The findings revealed that caffeine could inhibit E. coli biofilm formation by regulating curli assembly and thus may be used as an alternative therapeutic strategy for the treatment of chronic E. coli biofilm-related infections.
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Affiliation(s)
- Bhawna Rathi
- grid.8195.50000 0001 2109 4999Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007 India
| | - Surbhi Gupta
- grid.8195.50000 0001 2109 4999Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007 India
| | - Parveen Kumar
- grid.265892.20000000106344187Department of Urology, University of Alabama at Birmingham, Birmingham, AL USA
| | | | | | - Sandeep Kumar Kushwaha
- grid.508105.90000 0004 1798 2821DBT-National Institute of Animal Biotechnology (NIAB), Hyderabad, India
| | - Manisha Yadav
- grid.8195.50000 0001 2109 4999Dr. B. R. Ambedkar Center for Biomedical Research, University of Delhi (North Campus), New Delhi, 110007 India ,grid.4514.40000 0001 0930 2361Department of Clinical Sciences, Lund University, Malmö, Sweden
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19
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Qiao L, Du K. Magnetic field-induced self-assembly of urchin-like polymeric particles: mechanism, dispersity, and application in wastewater treatment. Sep Purif Technol 2022. [DOI: 10.1016/j.seppur.2022.121742] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
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20
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Özkul G, Kehribar EŞ, Ahan RE, Köksaldı İÇ, Özkul A, Dinç B, Aydoğan S, Şeker UÖŞ. A Genetically Engineered Biofilm Material for SARS-CoV-2 Capturing and Isolation. ADVANCED MATERIALS INTERFACES 2022; 9:2201126. [PMID: 36248312 PMCID: PMC9538133 DOI: 10.1002/admi.202201126] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 08/10/2022] [Indexed: 06/16/2023]
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is continuously infecting people all around the world since its outbreak in 2019. Studies for numerous infection detection strategies are continuing. The sensitivity of detection methods is crucial to separate people with mild infections from people who are asymptomatic. In this sense, a strategy that would help to capture and isolate the SARS-CoV-2 virus prior to tests can be effective and beneficial. To this extent, genetically engineered biomaterials grounding from the biofilm protein of Escherichia coli are beneficial due to their robustness and adaptability to various application areas. Through functionalizing the E. coli biofilm protein, diverse properties can be attained such as enzyme display, nanoparticle production, and medical implant structures. Here, E. coli species are employed to express major curli protein CsgA and Griffithsin (GRFT) as fusion proteins, through a complex formation using SpyTag and SpyCatcher domains. In this study, a complex system with a CsgA scaffold harboring the affinity of GRFT against Spike protein to capture and isolate SARS-CoV-2 virus is successfully developed. It is shown that the hybrid recombinant protein can dramatically increase the sensitivity of currently available lateral flow assays for Sars-CoV-2 diagnostics.
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Affiliation(s)
- Gökçe Özkul
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Ebru Şahin Kehribar
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Recep Erdem Ahan
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - İlkay Çisil Köksaldı
- UNAM ‐ Institute of Materials Science and NanotechnologyBilkent UniversityAnkara06800Turkey
| | - Aykut Özkul
- Department of VirologyFaculty of Veterinary MedicineAnkara UniversityDışkapıAnkara06110Turkey
| | - Bedia Dinç
- Medical Microbiology Laboratory and Department of Clinical Microbiology and Infectious DiseasesAnkara Bilkent City HospitalHealth Sciences UniversityAnkara06800Turkey
| | - Sibel Aydoğan
- Medical Microbiology Laboratory and Department of Clinical Microbiology and Infectious DiseasesAnkara Bilkent City HospitalHealth Sciences UniversityAnkara06800Turkey
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21
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Gelfat I, Aqeel Y, Tremblay JM, Jaskiewicz JJ, Shrestha A, Lee JN, Hu S, Qian X, Magoun L, Sheoran A, Bedenice D, Giem C, Manjula-Basavanna A, Pulsifer AR, Tu HX, Li X, Minus ML, Osburne MS, Tzipori S, Shoemaker CB, Leong JM, Joshi NS. Single domain antibodies against enteric pathogen virulence factors are active as curli fiber fusions on probiotic E. coli Nissle 1917. PLoS Pathog 2022; 18:e1010713. [PMID: 36107831 PMCID: PMC9477280 DOI: 10.1371/journal.ppat.1010713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 06/29/2022] [Indexed: 11/18/2022] Open
Abstract
Enteric microbial pathogens, including Escherichia coli, Shigella and Cryptosporidium species, take a particularly heavy toll in low-income countries and are highly associated with infant mortality. We describe here a means to display anti-infective agents on the surface of a probiotic bacterium. Because of their stability and versatility, VHHs, the variable domains of camelid heavy-chain-only antibodies, have potential as components of novel agents to treat or prevent enteric infectious disease. We isolated and characterized VHHs targeting several enteropathogenic E. coli (EPEC) virulence factors: flagellin (Fla), which is required for bacterial motility and promotes colonization; both intimin and the translocated intimin receptor (Tir), which together play key roles in attachment to enterocytes; and E. coli secreted protein A (EspA), an essential component of the type III secretion system (T3SS) that is required for virulence. Several VHHs that recognize Fla, intimin, or Tir blocked function in vitro. The probiotic strain E. coli Nissle 1917 (EcN) produces on the bacterial surface curli fibers, which are the major proteinaceous component of E. coli biofilms. A subset of Fla-, intimin-, or Tir-binding VHHs, as well as VHHs that recognize either a T3SS of another important bacterial pathogen (Shigella flexneri), a soluble bacterial toxin (Shiga toxin or Clostridioides difficile toxin TcdA), or a major surface antigen of an important eukaryotic pathogen (Cryptosporidium parvum) were fused to CsgA, the major curli fiber subunit. Scanning electron micrographs indicated CsgA-VHH fusions were assembled into curli fibers on the EcN surface, and Congo Red binding indicated that these recombinant curli fibers were produced at high levels. Ectopic production of these VHHs conferred on EcN the cognate binding activity and, in the case of anti-Shiga toxin, was neutralizing. Taken together, these results demonstrate the potential of the curli-based pathogen sequestration strategy described herein and contribute to the development of novel VHH-based gut therapeutics.
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Affiliation(s)
- Ilia Gelfat
- John A. Paulson School of Engineering and Applied Sciences, Harvard University, Allston, Massachusetts, United States of America
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Yousuf Aqeel
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Jacqueline M. Tremblay
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Justyna J. Jaskiewicz
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Anishma Shrestha
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - James N. Lee
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Shenglan Hu
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Xi Qian
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Loranne Magoun
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Abhineet Sheoran
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Daniela Bedenice
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Colter Giem
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Avinash Manjula-Basavanna
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Amanda R. Pulsifer
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Hann X. Tu
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
| | - Xiaoli Li
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Marilyn L. Minus
- Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts, United States of America
| | - Marcia S. Osburne
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
| | - Saul Tzipori
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - Charles B. Shoemaker
- Department of Infectious Disease and Global Health, Cummings School of Veterinary Medicine, Tufts University, North Grafton, Massachusetts, United States of America
| | - John M. Leong
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, Massachusetts, United States of America
- Stuart B. Levy Center for Integrated Management of Antimicrobial Resistance, Tufts University, Medford, Massachusetts, United States of America
| | - Neel S. Joshi
- Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts, United States of America
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22
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Nicastro LK, de Anda J, Jain N, Grando KCM, Miller AL, Bessho S, Gallucci S, Wong GCL, Tükel Ç. Assembly of ordered DNA-curli fibril complexes during Salmonella biofilm formation correlates with strengths of the type I interferon and autoimmune responses. PLoS Pathog 2022; 18:e1010742. [PMID: 35972973 PMCID: PMC9380926 DOI: 10.1371/journal.ppat.1010742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/14/2022] [Indexed: 11/23/2022] Open
Abstract
Deposition of human amyloids is associated with complex human diseases such as Alzheimer's and Parkinson's. Amyloid proteins are also produced by bacteria. The bacterial amyloid curli, found in the extracellular matrix of both commensal and pathogenic enteric bacterial biofilms, forms complexes with extracellular DNA, and recognition of these complexes by the host immune system may initiate an autoimmune response. Here, we isolated early intermediate, intermediate, and mature curli fibrils that form throughout the biofilm development and investigated the structural and pathogenic properties of each. Early intermediate aggregates were smaller than intermediate and mature curli fibrils, and circular dichroism, tryptophan, and thioflavin T analyses confirmed the establishment of a beta-sheet secondary structure as the curli conformations matured. Intermediate and mature curli fibrils were more immune stimulatory than early intermediate fibrils in vitro. The intermediate curli was cytotoxic to macrophages independent of Toll-like receptor 2. Mature curli fibrils had the highest DNA content and induced the highest levels of Isg15 expression and TNFα production in macrophages. In mice, mature curli fibrils induced the highest levels of anti-double-stranded DNA autoantibodies. The levels of autoantibodies were higher in autoimmune-prone NZBWxF/1 mice than wild-type C57BL/6 mice. Chronic exposure to all curli forms led to significant histopathological changes and synovial proliferation in the joints of autoimmune-prone mice; mature curli was the most detrimental. In conclusion, curli fibrils, generated during biofilm formation, cause pathogenic autoimmune responses that are stronger when curli complexes contain higher levels of DNA and in mice predisposed to autoimmunity.
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Affiliation(s)
- Lauren K. Nicastro
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Jaime de Anda
- Department of Bioengineering, California Nano Systems Institute, University of California, Los Angeles, California, United States of America
| | - Neha Jain
- Department of Bioscience and Bioengineering, Indian Institute of Technology, Jodhpur, India
| | - Kaitlyn C. M. Grando
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Amanda L. Miller
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Shingo Bessho
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Stefania Gallucci
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
| | - Gerard C. L. Wong
- Department of Bioengineering, California Nano Systems Institute, University of California, Los Angeles, California, United States of America
| | - Çagla Tükel
- Center for Microbiology and Immunology, Lewis Katz School of Medicine, Temple University, Philadelphia, Pennsylvania, United States of America
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23
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Matilla-Cuenca L, Taglialegna A, Gil C, Toledo-Arana A, Lasa I, Valle J. Bacterial biofilm functionalization through Bap amyloid engineering. NPJ Biofilms Microbiomes 2022; 8:62. [PMID: 35909185 PMCID: PMC9339546 DOI: 10.1038/s41522-022-00324-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/01/2022] [Indexed: 11/09/2022] Open
Abstract
Biofilm engineering has emerged as a controllable way to fabricate living structures with programmable functionalities. The amyloidogenic proteins comprising the biofilms can be engineered to create self-assembling extracellular functionalized surfaces. In this regard, facultative amyloids, which play a dual role in biofilm formation by acting as adhesins in their native conformation and as matrix scaffolds when they polymerize into amyloid-like fibrillar structures, are interesting candidates. Here, we report the use of the facultative amyloid-like Bap protein of Staphylococcus aureus as a tool to decorate the extracellular biofilm matrix or the bacterial cell surface with a battery of functional domains or proteins. We demonstrate that the localization of the functional tags can be change by simply modulating the pH of the medium. Using Bap features, we build a tool for trapping and covalent immobilizing molecules at bacterial cell surface or at the biofilm matrix based on the SpyTag/SpyCatcher system. Finally, we show that the cell wall of several Gram-positive bacteria could be functionalized through the external addition of the recombinant engineered Bap-amyloid domain. Overall, this work shows a simple and modulable system for biofilm functionalization based on the facultative protein Bap.
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Affiliation(s)
| | - Agustina Taglialegna
- Instituto de Agrobiotecnología (IDAB). CSIC- Gobierno de Navarra, Mutilva, Spain.,The Campus 4 Crinan Street London N1, London, UK
| | - Carmen Gil
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | | | - Iñigo Lasa
- Laboratory of Microbial Pathogenesis, Navarrabiomed, Hospital Universitario de Navarra (HUN), Universidad Pública de Navarra (UPNA), IdiSNA, Pamplona, Spain
| | - Jaione Valle
- Instituto de Agrobiotecnología (IDAB). CSIC- Gobierno de Navarra, Mutilva, Spain.
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Chen YY, Yang FQ, Xu N, Wang XQ, Xie PC, Wang YZ, Fang Z, Yong YC. Engineered cytochrome fused extracellular matrix enabled efficient extracellular electron transfer and improved performance of microbial fuel cell. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 830:154806. [PMID: 35341857 DOI: 10.1016/j.scitotenv.2022.154806] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/20/2022] [Accepted: 03/20/2022] [Indexed: 06/14/2023]
Abstract
Microbial fuel cell (MFC) was a promising technology for energy harvesting from wastewater. However, inefficient bacterial extracellular electron transfer (EET) limited the performance as well as the applications of MFC. Here, a new strategy to reinforce the EET by engineering synthetic extracellular matrix (ECM) with cytochrome fused curli was developed. By genetically fusing a minimal cytochrome domain (MCD) with the curli protein CsgA and heterogeneously expressing in model exoelectrogen of Shewanella oneidensis MR-1, the cytochrome fused electroactive curli network was successfully constructed and assembled. Interestingly, the strain with the MCD fused synthetic ECM delivered about 2.4 times and 2.0 times higher voltage and power density output than these of wild type MR-1 in MFC. More impressively, electrochemical analysis suggested that this synthetic ECM not only introduced cytochrome of MCD, but also attracted more self-secreted electrochemically active substances, which might facilitate the EET and improve the MFC performance. This work demonstrated the possibility to manipulation the EET with ECM engineering, which opened up new path for exoelectrogen design and engineering.
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Affiliation(s)
- Yuan-Yuan Chen
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Fu-Qiao Yang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Nuo Xu
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Xing-Qiang Wang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Peng-Cheng Xie
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yan-Zhai Wang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Zhen Fang
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China
| | - Yang-Chun Yong
- Biofuels Institute, School of Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China.
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25
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Shahryarimorad K, Alipour A, Honar YS, Abtahi B, Shokrgozar MA, Shahsavarani H. In silico prediction and in vitro validation of the effect of pH on adhesive behaviour of the fused CsgA-MFP3 protein. AMB Express 2022; 12:94. [PMID: 35838851 PMCID: PMC9287526 DOI: 10.1186/s13568-022-01435-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
Recombinant production of mussel foot proteins among marine-inspired proteinaceous adhesive materials has been attracted high attention for medical applications, due to their exceptional versatility potential of hierarchically arranged nanostructures. Various biochemical and proteinous factors such as amyloid CsgA curli protein have been used as a synergistic factor to enhance the constancy of obtained bio-adhesion but their mechanistic interactions have not yet been deeply investigated widely in different pH conditions. To this end, the present study has first sought to assess molecular simulation and prediction by using RosettaFold to predict the 3-dimensional structure of the fused CsgA subunit and the MFP3 protein followed by in vitro verification. It was developed an ensemble of quantitative structure-activity relationship models relying on simulations according to the surface area and molecular weight values of the fused proteins in acidic to basic situations using PlayMolecule (protein preparation app for MD simulations) online databases followed by molecular dynamic simulation at different pHs. It was found that acidic conditions positively affect adhesive strength throughout the chimeric structure based on comparative structure-based analyses along with those obtained in prevailing literature. Atomic force microscopy analysis was confirmed obtained in silico data which showed enhanced adhesive properties of fused protein after self-assembly in low pH conditions. In conclusion, the augmented model for reactivity predictions not only unravels the performance and explain ability of the adhesive proteins but in turn paves the way for the decision-making process for chimeric subunits modifications needed for future industrial production.
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Affiliation(s)
- Keyvan Shahryarimorad
- Laboratory of Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Atefeh Alipour
- Department of Nanobiotechnology, Pasteur Institute of Iran, Tehran, 1316943551, Iran.
| | - Yousof Saeedi Honar
- Department of Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran
| | - Behrouz Abtahi
- Department of Animal, Marine and Aquatic Biology and Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran
| | - Mohammad Ali Shokrgozar
- Department of National Cell Bank of Iran, Pasteur Institute of Iran, Tehran, 1316943551, Iran
| | - Hosein Shahsavarani
- Laboratory of Regenerative Medicine and Biomedical Innovations, Pasteur Institute of Iran, Tehran, 1316943551, Iran. .,Department of Cell and Molecular Sciences, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, 1983963113, Iran.
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Shi Y, Chen T, Shaw P, Wang PY. Manipulating Bacterial Biofilms Using Materiobiology and Synthetic Biology Approaches. Front Microbiol 2022; 13:844997. [PMID: 35875573 PMCID: PMC9301480 DOI: 10.3389/fmicb.2022.844997] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 06/13/2022] [Indexed: 11/25/2022] Open
Abstract
Bacteria form biofilms on material surfaces within hours. Biofilms are often considered problematic substances in the fields such as biomedical devices and the food industry; however, they are beneficial in other fields such as fermentation, water remediation, and civil engineering. Biofilm properties depend on their genome and the extracellular environment, including pH, shear stress, and matrices topography, stiffness, wettability, and charges during biofilm formation. These surface properties have feedback effects on biofilm formation at different stages. Due to emerging technology such as synthetic biology and genome editing, many studies have focused on functionalizing biofilm for specific applications. Nevertheless, few studies combine these two approaches to produce or modify biofilms. This review summarizes up-to-date materials science and synthetic biology approaches to controlling biofilms. The review proposed a potential research direction in the future that can gain better control of bacteria and biofilms.
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Affiliation(s)
- Yue Shi
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
| | - Tingli Chen
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
- College of Life Science, University of Chinese Academy of Sciences, Beijing, China
| | - Peter Shaw
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
| | - Peng-Yuan Wang
- Oujiang Laboratory, Key Laboratory of Alzheimer’s Disease of Zhejiang Province, Institute of Aging, Wenzhou Medical University, Wenzhou, China
- Shenzhen Key Laboratory of Biomimetic Materials and Cellular Immunomodulation, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, China
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27
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Di Muccio G, Morozzo della Rocca B, Chinappi M. Geometrically Induced Selectivity and Unidirectional Electroosmosis in Uncharged Nanopores. ACS NANO 2022; 16:8716-8728. [PMID: 35587777 PMCID: PMC9245180 DOI: 10.1021/acsnano.1c03017] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
Selectivity toward positive and negative ions in nanopores is often associated with electroosmotic flow, the control of which is pivotal in several micro-nanofluidic technologies. Selectivity is traditionally understood to be a consequence of surface charges that alter the ion distribution in the pore lumen. Here we present a purely geometrical mechanism to induce ionic selectivity and electroosmotic flow in uncharged nanopores, and we tested it via molecular dynamics simulations. Our approach exploits the accumulation of charges, driven by an external electric field, in a coaxial cavity that decorates the membrane close to the pore entrance. The selectivity was shown to depend on the applied voltage and becomes completely inverted when reversing the voltage. The simultaneous inversion of ionic selectivity and electric field direction causes a unidirectional electroosmotic flow. We developed a quantitatively accurate theoretical model for designing pore geometry to achieve the desired electroosmotic velocity. Finally, we show that unidirectional electroosmosis also occurs in much more complex scenarios, such as a biological pore whose structure presents a coaxial cavity surrounding the pore constriction as well as a complex surface charge pattern. The capability to induce ion selectivity without altering the pore lumen shape or the surface charge may be useful for a more flexible design of selective membranes.
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Affiliation(s)
- Giovanni Di Muccio
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
| | - Blasco Morozzo della Rocca
- Dipartimento
di Biologia, Università di Roma Tor
Vergata, Via della Ricerca Scientifica 1, 00133, Rome, Italy
| | - Mauro Chinappi
- Dipartimento
di Ingegneria Industriale, Università
di Roma Tor Vergata, Via del Politecnico 1, 00133, Rome, Italy
- E-mail:
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28
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Filloux A. Bacterial protein secretion systems: Game of types. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35536734 DOI: 10.1099/mic.0.001193] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Protein trafficking across the bacterial envelope is a process that contributes to the organisation and integrity of the cell. It is the foundation for establishing contact and exchange between the environment and the cytosol. It helps cells to communicate with one another, whether they establish symbiotic or competitive behaviours. It is instrumental for pathogenesis and for bacteria to subvert the host immune response. Understanding the formation of envelope conduits and the manifold strategies employed for moving macromolecules across these channels is a fascinating playground. The diversity of the nanomachines involved in this process logically resulted in an attempt to classify them, which is where the protein secretion system types emerged. As our knowledge grew, so did the number of types, and their rightful nomenclature started to be questioned. While this may seem a semantic or philosophical issue, it also reflects scientific rigour when it comes to assimilating findings into textbooks and science history. Here I give an overview on bacterial protein secretion systems, their history, their nomenclature and why it can be misleading for newcomers in the field. Note that I do not try to suggest a new nomenclature. Instead, I explore the reasons why naming could have escaped our control and I try to reiterate basic concepts that underlie protein trafficking cross membranes.
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Affiliation(s)
- Alain Filloux
- MRC Centre for Molecular Bacteriology and Infection, Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK
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29
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Trivedi A, Gosai J, Nakane D, Shrivastava A. Design Principles of the Rotary Type 9 Secretion System. Front Microbiol 2022; 13:845563. [PMID: 35620107 PMCID: PMC9127263 DOI: 10.3389/fmicb.2022.845563] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Accepted: 01/17/2022] [Indexed: 01/05/2023] Open
Abstract
The Fo ATP synthase, the bacterial flagellar motor, and the bacterial type 9 secretion system (T9SS) are the three known proton motive force driven biological rotary motors. In this review, we summarize the current information on the nuts and bolts of T9SS. Torque generation by T9SS, its role in gliding motility of bacteria, and the mechanism via which a T9SS-driven swarm shapes the microbiota are discussed. The knowledge gaps in our current understanding of the T9SS machinery are outlined.
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Affiliation(s)
- Abhishek Trivedi
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- Center for Biological Physics, Arizona State University, Tempe, AZ, United States
| | - Jitendrapuri Gosai
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- Center for Biological Physics, Arizona State University, Tempe, AZ, United States
| | - Daisuke Nakane
- Department of Engineering Science, The University of Electro-Communications, Tokyo, Japan
| | - Abhishek Shrivastava
- School of Life Sciences, Arizona State University, Tempe, AZ, United States
- Biodesign Center for Fundamental and Applied Microbiomics, Arizona State University, Tempe, AZ, United States
- Center for Biological Physics, Arizona State University, Tempe, AZ, United States
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30
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Hassan MN, Nabi F, Khan AN, Hussain M, Siddiqui WA, Uversky VN, Khan RH. The amyloid state of proteins: A boon or bane? Int J Biol Macromol 2022; 200:593-617. [PMID: 35074333 DOI: 10.1016/j.ijbiomac.2022.01.115] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 11/05/2022]
Abstract
Proteins and their aggregation is significant field of research due to their association with various conformational maladies including well-known neurodegenerative diseases like Alzheimer's (AD), Parkinson's (PD), and Huntington's (HD) diseases. Amyloids despite being given negative role for decades are also believed to play a functional role in bacteria to humans. In this review, we discuss both facets of amyloid. We have shed light on AD, which is one of the most common age-related neurodegenerative disease caused by accumulation of Aβ fibrils as extracellular senile plagues. We also discuss PD caused by the aggregation and deposition of α-synuclein in form of Lewy bodies and neurites. Other amyloid-associated diseases such as HD and amyotrophic lateral sclerosis (ALS) are also discussed. We have also reviewed functional amyloids that have various biological roles in both prokaryotes and eukaryotes that includes formation of biofilm and cell attachment in bacteria to hormone storage in humans, We discuss in detail the role of Curli fibrils' in biofilm formation, chaplins in cell attachment to peptide hormones, and Pre-Melansomal Protein (PMEL) roles. The disease-related and functional amyloids are compared with regard to their structural integrity, variation in regulation, and speed of forming aggregates and elucidate how amyloids have turned from foe to friend.
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Affiliation(s)
- Md Nadir Hassan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Faisal Nabi
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Asra Nasir Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Murtaza Hussain
- Department of Biochemistry, Aligarh Muslim University, Aligarh 202002, India
| | - Waseem A Siddiqui
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India
| | - Vladimir N Uversky
- Protein Research Group, Institute for Biological Instrumentation of the Russian Academy of Sciences, 10 Federal Research Center "Pushchino Scientific Center for Biological Research of the Russian Academy 11 of Sciences", Pushchino, Moscow Region 142290, Russia; Department of Molecular Medicine, USF Health Byrd Alzheimer's Research Institute, Morsani College 13 of Medicine, University of South Florida, Tampa, FL 33612, United States
| | - Rizwan Hasan Khan
- Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh 202002, India.
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31
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Dey A, Maiti S. Determining the Stoichiometry of Amyloid Oligomers by Single-Molecule Photobleaching. Methods Mol Biol 2022; 2538:55-74. [PMID: 35951293 DOI: 10.1007/978-1-0716-2529-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Small oligomers are the initial intermediates in the pathway to amyloid fibril formation. They have a distinct identity from the monomers as well as from the protofibrils and the fibrils, both in their structure and in their properties. In many cases, they play a crucial biological role. However, due to their transient nature, they are difficult to characterize. "Oligomer" is a diffuse definition, encompassing aggregates of many different sizes, and this lack of precise definition causes much confusion and disagreement between different research groups. Here, we define the small oligomers as "n"-mers with n < 10, which is the size range in which the amyloid proteins typically exist at the initial phase of the aggregation process. Since the oligomers dynamically interconvert into each other, a solution of aggregating amyloid proteins will contain a distribution of sizes. A precise characterization of an oligomeric solution will, therefore, require quantification of the relative population of each size. Size-based separation methods, such as size-exclusion chromatography, are typically used to characterize this distribution. However, if the interconversion between oligomers of different sizes is fast, this would not yield reliable results. Single-molecule photobleaching (smPB) is a direct method to evaluate this size distribution in a heterogeneous solution without separation. In addition, understanding the mechanism of action of amyloid oligomers requires knowing the affinity of each oligomer type to different cellular components, such as the cell membrane. These measurements are also amenable to smPB. Here we show how to perform smPB, both for oligomers in solution and for oligomers attached to the membrane.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India.
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32
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Yuca E, Şeker UÖŞ. Monitoring Molecular Assembly of Biofilms Using Quartz Crystal Microbalance with Dissipation (QCM-D). Methods Mol Biol 2022; 2538:25-33. [PMID: 35951291 DOI: 10.1007/978-1-0716-2529-3_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The structure and the functionality of biofilm proteins, the main components of the extracellular matrix, can be tuned by protein engineering. The use of binding kinetics data has been demonstrated in the characterization of recombinantly produced biofilm proteins to control their behavior on certain surfaces or under certain conditions. Quartz crystal microbalance with dissipation monitoring (QCM-D) allows measuring the change in resonance frequency and the energy loss and distribution upon the interaction of molecules with the surface. The characterization of the molecular assembly of curli biofilm proteins on different surfaces using QCM-D is presented here as a detailed protocol. The experimental procedure detailed in this chapter can be applied and modified for other biofilm proteins or subunits to determine their surface adsorption and kinetic binding characteristics.
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Affiliation(s)
- Esra Yuca
- Molecular Biology and Genetics Department, Yildiz Technical University, İstanbul, Turkey
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33
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Kubiak K, Gaffke L, Pierzynowska K, Cyske Z, Grabowski Ł, Kosznik-Kwaśnicka K, Jaroszewicz W, Węgrzyn A, Węgrzyn G. Determination of Effects and Mechanisms of Action of Bacterial Amyloids on Antibiotic Resistance. Methods Mol Biol 2022; 2538:189-205. [PMID: 35951301 DOI: 10.1007/978-1-0716-2529-3_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Bacterial functional amyloids, apart from their many other functions, can influence the resistance of bacteria to antibiotics and other antibacterial agents. Mechanisms of modulation of susceptibility of bacterial cells to antimicrobials can be either indirect or direct. The former mechanisms are exemplified by the contribution of functional amyloids to biofilm formation, which may effectively prevent the penetration of various compounds into bacterial cells. The direct mechanisms include the effects of bacterial proteins revealing amyloid-like structures, like the C-terminal region of the Escherichia coli Hfq protein, on the expression of genes involved in antibiotic resistance. Therefore, in this paper, we describe methods by which effects and mechanisms of action of bacterial amyloids on antibiotic resistance can be studied. Assessment of formation of biofilms, determination of the efficiency of antibiotic resistance in solid and liquid media, and determination of the effects on gene expression at levels of mRNA abundance and stability and protein abundance are described.
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Affiliation(s)
- Krzysztof Kubiak
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Lidia Gaffke
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | | | - Zuzanna Cyske
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland
| | - Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdansk, Poland
| | - Katarzyna Kosznik-Kwaśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdansk, Poland
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Gdansk, Gdansk, Poland
| | | | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Gdansk, Poland
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Gdansk, Poland.
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Lekchand Dasriya V, Samtiya M, Dhewa T, Puniya M, Kumar S, Ranveer S, Chaudhary V, Vij S, Behare P, Singh N, Aluko RE, Puniya AK. Etiology and management of Alzheimer's disease: Potential role of gut microbiota modulation with probiotics supplementation. J Food Biochem 2021; 46:e14043. [PMID: 34927261 DOI: 10.1111/jfbc.14043] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 11/11/2021] [Accepted: 12/13/2021] [Indexed: 12/15/2022]
Abstract
Alzheimer's disease (AD) is the leading type of dementia in aging people and is a progressive condition that causes neurodegeneration, resulting in confusion, memory loss, and deterioration of mental functions. AD happens because of abnormal twisting of the microtubule tau protein in neurons into a tangled neurofibrillary structure. Different factors responsible for AD pathogenesis include heavy metals, aging, cardiovascular disease, and environmental and genetic factors. Market available drugs for AD have several side effects that include hepato-toxicity, accelerated cognitive decline, worsened neuropsychiatric symptoms, and triggered suicidal ideation. Therefore, an emerging alternative therapeutic approach is probiotics, which can improve AD by modulating the gut-brain axis. Probiotics modulate different neurochemical pathways by regulating the signalling pathways associated with inflammation, histone deacetylation, and microglial cell activation and maturation. In addition, probiotics-derived metabolites (i.e., short-chain fatty acid, neurotransmitters, and antioxidants) have shown ameliorative effects against AD. Probiotics also modulate gut microbiota, with a beneficial impact on neural signalling and cognitive activity, which can attenuate AD progression. Therefore, the current review describes the etiology and mechanism of AD progression as well as various treatment options with a focus on the use of probiotics. PRACTICAL APPLICATIONS: In an aging population, dementia concerns are quite prevalent globally. AD is one of the most commonly occurring cognition disorders, which is linked to diminished brain functions. Scientific evidence supports the findings that probiotics and gut microbiota can regulate/modulate brain functions, one of the finest strategies to alleviate such disorders through the gut-brain axis. Thus, gut microbiota modulation, especially through probiotic supplementation, could become an effective solution to ameliorate AD.
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Affiliation(s)
| | - Mrinal Samtiya
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, India
| | - Tejpal Dhewa
- Department of Nutrition Biology, Central University of Haryana, Mahendergarh, India
| | - Monica Puniya
- Food Safety and Standards Authority of India, FDA Bhawan, New Delhi, India
| | - Sanjeev Kumar
- Department of Life Science and Bioinformatics, Assam University, Silchar, India
| | - Soniya Ranveer
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Vishu Chaudhary
- Department of Microbiology, Punjab Agriculture University, Ludhiana, India
| | - Shilpa Vij
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Pradip Behare
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
| | - Namita Singh
- Department of Bio and Nano Technology, Guru Jambheshwar University of Science and Technology, Hisar, India
| | - Rotimi E Aluko
- Department of Food and Human Nutritional Sciences, University of Manitoba, Winnipeg, Manitoba, Canada
| | - Anil Kumar Puniya
- Dairy Microbiology Division, ICAR-National Dairy Research Institute, Karnal, India
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35
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Goosens VJ, Walker KT, Aragon SM, Singh A, Senthivel VR, Dekker L, Caro-Astorga J, Buat MLA, Song W, Lee KY, Ellis T. Komagataeibacter Tool Kit (KTK): A Modular Cloning System for Multigene Constructs and Programmed Protein Secretion from Cellulose Producing Bacteria. ACS Synth Biol 2021; 10:3422-3434. [PMID: 34767345 DOI: 10.1021/acssynbio.1c00358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteria proficient at producing cellulose are an attractive synthetic biology host for the emerging field of Engineered Living Materials (ELMs). Species from the Komagataeibacter genus produce high yields of pure cellulose materials in a short time with minimal resources, and pioneering work has shown that genetic engineering in these strains is possible and can be used to modify the material and its production. To accelerate synthetic biology progress in these bacteria, we introduce here the Komagataeibacter tool kit (KTK), a standardized modular cloning system based on Golden Gate DNA assembly that allows DNA parts to be combined to build complex multigene constructs expressed in bacteria from plasmids. Working in Komagataeibacter rhaeticus, we describe basic parts for this system, including promoters, fusion tags, and reporter proteins, before showcasing how the assembly system enables more complex designs. Specifically, we use KTK cloning to reformat the Escherichia coli curli amyloid fiber system for functional expression in K. rhaeticus, and go on to modify it as a system for programming protein secretion from the cellulose producing bacteria. With this toolkit, we aim to accelerate modular synthetic biology in these bacteria, and enable more rapid progress in the emerging ELMs community.
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Affiliation(s)
- Vivianne J. Goosens
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Kenneth T. Walker
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Silvia M. Aragon
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Amritpal Singh
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Vivek R. Senthivel
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Linda Dekker
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Joaquin Caro-Astorga
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | | | - Wenzhe Song
- Department of Aeronautics, Imperial College London, London SW7 2AZ, U.K
| | - Koon-Yang Lee
- Department of Aeronautics, Imperial College London, London SW7 2AZ, U.K
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
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de Oliveira AL, Barbieri NL, Newman DM, Young MM, Nolan LK, Logue CM. Characterizing the Type 6 Secretion System (T6SS) and its role in the virulence of avian pathogenic Escherichia coli strain APECO18. PeerJ 2021; 9:e12631. [PMID: 35003930 PMCID: PMC8686734 DOI: 10.7717/peerj.12631] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Accepted: 11/22/2021] [Indexed: 11/22/2022] Open
Abstract
Avian pathogenic E. coli is the causative agent of extra-intestinal infections in birds known as colibacillosis, which can manifest as localized or systemic infections. The disease affects all stages of poultry production, resulting in economic losses that occur due to morbidity, carcass condemnation and increased mortality of the birds. APEC strains have a diverse virulence trait repertoire, which includes virulence factors involved in adherence to and invasion of the host cells, serum resistance factors, and toxins. However, the pathogenesis of APEC infections remains to be fully elucidated. The Type 6 secretion (T6SS) system has recently gained attention due to its role in the infection process and protection of bacteria from host defenses in human and animal pathogens. Previous work has shown that T6SS components are involved in the adherence to and invasion of host cells, as well as in the formation of biofilm, and intramacrophage bacterial replication. Here, we analyzed the frequency of T6SS genes hcp, impK, evpB, vasK and icmF in a collection of APEC strains and their potential role in virulence-associated phenotypes of APECO18. The T6SS genes were found to be significantly more prevalent in APEC than in fecal E. coli isolates from healthy birds. Expression of T6SS genes was analyzed in culture media and upon contact with host cells. Mutants were generated for hcp, impK, evpB, and icmF and characterized for their impact on virulence-associated phenotypes, including adherence to and invasion of host model cells, and resistance to predation by Dictyostelium discoideum. Deletion of the aforementioned genes did not significantly affect adherence and invasion capabilities of APECO18. Deletion of hcp reduced resistance of APECO18 to predation by D. discoideum, suggesting that T6SS is involved in the virulence of APECO18.
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Affiliation(s)
- Aline L. de Oliveira
- Department of Population Health, University of Georgia, Athens, GA, United States of America
- Department of Microbiology, University of Georgia, Athens, GA, United States of America
| | - Nicolle L. Barbieri
- Department of Population Health, University of Georgia, Athens, GA, United States of America
| | - Darby M. Newman
- Department of Population Health, University of Georgia, Athens, GA, United States of America
| | - Meaghan M. Young
- Department of Population Health, University of Georgia, Athens, GA, United States of America
| | - Lisa K. Nolan
- Department of Infectious Diseases, University of Georgia, Athens, GA, United States of America
| | - Catherine M. Logue
- Department of Population Health, University of Georgia, Athens, GA, United States of America
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Kim HS, Kim S, Shin SJ, Park YH, Nam Y, Kim CW, Lee KW, Kim SM, Jung ID, Yang HD, Park YM, Moon M. Gram-negative bacteria and their lipopolysaccharides in Alzheimer's disease: pathologic roles and therapeutic implications. Transl Neurodegener 2021; 10:49. [PMID: 34876226 PMCID: PMC8650380 DOI: 10.1186/s40035-021-00273-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 11/09/2021] [Indexed: 02/07/2023] Open
Abstract
Alzheimer's disease (AD) is the most serious age-related neurodegenerative disease and causes destructive and irreversible cognitive decline. Failures in the development of therapeutics targeting amyloid-β (Aβ) and tau, principal proteins inducing pathology in AD, suggest a paradigm shift towards the development of new therapeutic targets. The gram-negative bacteria and lipopolysaccharides (LPS) are attractive new targets for AD treatment. Surprisingly, an altered distribution of gram-negative bacteria and their LPS has been reported in AD patients. Moreover, gram-negative bacteria and their LPS have been shown to affect a variety of AD-related pathologies, such as Aβ homeostasis, tau pathology, neuroinflammation, and neurodegeneration. Moreover, therapeutic approaches targeting gram-negative bacteria or gram-negative bacterial molecules have significantly alleviated AD-related pathology and cognitive dysfunction. Despite multiple evidence showing that the gram-negative bacteria and their LPS play a crucial role in AD pathogenesis, the pathogenic mechanisms of gram-negative bacteria and their LPS have not been clarified. Here, we summarize the roles and pathomechanisms of gram-negative bacteria and LPS in AD. Furthermore, we discuss the possibility of using gram-negative bacteria and gram-negative bacterial molecules as novel therapeutic targets and new pathological characteristics for AD.
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Affiliation(s)
- Hyeon Soo Kim
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Sujin Kim
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
- Research Institute for Dementia Science, Konyang University, Daejeon, 35365, Republic of Korea
| | - Soo Jung Shin
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Yong Ho Park
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Yunkwon Nam
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Chae Won Kim
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Kang Won Lee
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea
| | - Sung-Min Kim
- Dandi Bioscience Inc, 6th Floor of Real Company Building, 66, Achasan-ro, Sungdong-gu, Seoul, Republic of Korea
| | - In Duk Jung
- Dandi Bioscience Inc, 6th Floor of Real Company Building, 66, Achasan-ro, Sungdong-gu, Seoul, Republic of Korea
| | - Hyun Duk Yang
- Harvard Neurology Clinic, 294 Gwanggyojungang-ro, Suji-gu, Yongin, 16943, Republic of Korea.
| | - Yeong-Min Park
- Dandi Bioscience Inc, 6th Floor of Real Company Building, 66, Achasan-ro, Sungdong-gu, Seoul, Republic of Korea.
- Department of Immunology, School of Medicine, Konkuk University, 268, Chungwondaero, Chungju-si, Chungcheongbuk-do, Republic of Korea.
| | - Minho Moon
- Department of Biochemistry, College of Medicine, Konyang University, Daejeon, 35365, Republic of Korea.
- Research Institute for Dementia Science, Konyang University, Daejeon, 35365, Republic of Korea.
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Alabresm A, Chandler SL, Benicewicz BC, Decho AW. Nanotargeting of Resistant Infections with a Special Emphasis on the Biofilm Landscape. Bioconjug Chem 2021; 32:1411-1430. [PMID: 34319073 PMCID: PMC8527872 DOI: 10.1021/acs.bioconjchem.1c00116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Bacterial resistance to antimicrobial compounds is a growing concern in medical and public health circles. Overcoming the adaptable and duplicative resistance mechanisms of bacteria requires chemistry-based approaches. Engineered nanoparticles (NPs) now offer unique advantages toward this effort. However, most in situ infections (in humans) occur as attached biofilms enveloped in a protective surrounding matrix of extracellular polymers, where survival of microbial cells is enhanced. This presents special considerations in the design and deployment of antimicrobials. Here, we review recent efforts to combat resistant bacterial strains using NPs and, then, explore how NP surfaces may be specifically engineered to enhance the potency and delivery of antimicrobial compounds. Special NP-engineering challenges in the design of NPs must be overcome to penetrate the inherent protective barriers of the biofilm and to successfully deliver antimicrobials to bacterial cells. Future challenges are discussed in the development of new antibiotics and their mechanisms of action and targeted delivery via NPs.
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Affiliation(s)
- Amjed Alabresm
- Department of Environmental Health Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
- Department of Biological Development of Shatt Al-Arab & N. Arabian Gulf, Marine Science Centre, University of Basrah, Basrah, Iraq
| | - Savannah L Chandler
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Brian C Benicewicz
- Department of Chemistry and Biochemistry, University of South Carolina, Columbia, South Carolina 29208, United States
- USC NanoCenter, University of South Carolina, Columbia, South Carolina 29208, United States
| | - Alan W Decho
- Department of Environmental Health Sciences, University of South Carolina, Columbia, South Carolina 29208, United States
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40
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Plasmid-encoded H-NS controls extracellular matrix composition in a modern Acinetobacter baumannii urinary isolate. J Bacteriol 2021; 203:e0027721. [PMID: 34398664 DOI: 10.1128/jb.00277-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Acinetobacter baumannii is emerging as a multidrug-resistant (MDR) nosocomial pathogen of increasing threat to human health worldwide. The recent MDR urinary isolate UPAB1 carries the plasmid pAB5, a member of a family of large conjugative plasmids (LCP). LCP encode several antibiotic resistance genes and repress the type VI secretion system (T6SS) to enable their dissemination, employing two TetR transcriptional regulators. Furthermore, pAB5 controls the expression of additional chromosomally encoded genes, impacting UPAB1 virulence. Here we show that a pAB5-encoded H-NS transcriptional regulator represses the synthesis of the exopolysaccharide PNAG and the expression of a previously uncharacterized three-gene cluster that encodes a protein belonging to the CsgG/HfaB family. Members of this protein family are involved in amyloid or polysaccharide formation in other species. Deletion of the CsgG homolog abrogated PNAG production and CUP pili formation, resulting in a subsequent reduction in biofilm formation. Although this gene cluster is widely distributed in Gram-negative bacteria, it remains largely uninvestigated. Our results illustrate the complex cross-talks that take place between plasmids and the chromosomes of their bacterial host, which in this case can contribute to the pathogenesis of Acinetobacter. IMPORTANCE The opportunistic human pathogen Acinetobacter baumannii displays the highest reported rates of multidrug resistance among Gram-negative pathogens. Many A. baumannii strains carry large conjugative plasmids like pAB5. In recent years, we have witnessed an increase in knowledge about the regulatory cross-talks between plasmids and bacterial chromosomes. Here we show that pAB5 controls the composition of the bacterial extracellular matrix, resulting in a drastic reduction in biofilm formation. The association between biofilm formation, virulence, and antibiotic resistance is well-documented. Therefore, understanding the factors involved in the regulation of biofilm formation in Acinetobacter has remarkable therapeutic potential.
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Matilla-Cuenca L, Toledo-Arana A, Valle J. Anti-Biofilm Molecules Targeting Functional Amyloids. Antibiotics (Basel) 2021; 10:antibiotics10070795. [PMID: 34210036 PMCID: PMC8300730 DOI: 10.3390/antibiotics10070795] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/18/2022] Open
Abstract
The choice of an effective therapeutic strategy in the treatment of biofilm-related infections is a significant issue. Amyloids, which have been historically related to human diseases, are now considered to be prevailing structural components of the biofilm matrix in a wide range of bacteria. This assumption creates the potential for an exciting research area, in which functional amyloids are considered to be attractive targets for drug development to dissemble biofilm structures. The present review describes the best-characterized bacterial functional amyloids and focuses on anti-biofilm agents that target intrinsic and facultative amyloids. This study provides a better understanding of the different modes of actions of the anti-amyloid molecules to inhibit biofilm formation. This information can be further exploited to improve the therapeutic strategies to combat biofilm-related infections.
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Khodaparast L, Wu G, Khodaparast L, Schmidt BZ, Rousseau F, Schymkowitz J. Bacterial Protein Homeostasis Disruption as a Therapeutic Intervention. Front Mol Biosci 2021; 8:681855. [PMID: 34150852 PMCID: PMC8206779 DOI: 10.3389/fmolb.2021.681855] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 05/04/2021] [Indexed: 12/15/2022] Open
Abstract
Cells have evolved a complex molecular network, collectively called the protein homeostasis (proteostasis) network, to produce and maintain proteins in the appropriate conformation, concentration and subcellular localization. Loss of proteostasis leads to a reduction in cell viability, which occurs to some degree during healthy ageing, but is also the root cause of a group of diverse human pathologies. The accumulation of proteins in aberrant conformations and their aggregation into specific beta-rich assemblies are particularly detrimental to cell viability and challenging to the protein homeostasis network. This is especially true for bacteria; it can be argued that the need to adapt to their changing environments and their high protein turnover rates render bacteria particularly vulnerable to the disruption of protein homeostasis in general, as well as protein misfolding and aggregation. Targeting bacterial proteostasis could therefore be an attractive strategy for the development of novel antibacterial therapeutics. This review highlights advances with an antibacterial strategy that is based on deliberately inducing aggregation of target proteins in bacterial cells aiming to induce a lethal collapse of protein homeostasis. The approach exploits the intrinsic aggregation propensity of regions residing in the hydrophobic core regions of the polypeptide sequence of proteins, which are genetically conserved because of their essential role in protein folding and stability. Moreover, the molecules were designed to target multiple proteins, to slow down the build-up of resistance. Although more research is required, results thus far allow the hope that this strategy may one day contribute to the arsenal to combat multidrug-resistant bacterial infections.
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Affiliation(s)
- Laleh Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Ladan Khodaparast
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Béla Z Schmidt
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, Leuven, Belgium
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Szulc N, Gąsior-Głogowska M, Wojciechowski JW, Szefczyk M, Żak AM, Burdukiewicz M, Kotulska M. Variability of Amyloid Propensity in Imperfect Repeats of CsgA Protein of Salmonella enterica and Escherichia coli. Int J Mol Sci 2021; 22:ijms22105127. [PMID: 34066237 PMCID: PMC8151669 DOI: 10.3390/ijms22105127] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 04/22/2021] [Accepted: 05/07/2021] [Indexed: 11/18/2022] Open
Abstract
CsgA is an aggregating protein from bacterial biofilms, representing a class of functional amyloids. Its amyloid propensity is defined by five fragments (R1–R5) of the sequence, representing non-perfect repeats. Gate-keeper amino acid residues, specific to each fragment, define the fragment’s propensity for self-aggregation and aggregating characteristics of the whole protein. We study the self-aggregation and secondary structures of the repeat fragments of Salmonella enterica and Escherichia coli and comparatively analyze their potential effects on these proteins in a bacterial biofilm. Using bioinformatics predictors, ATR-FTIR and FT-Raman spectroscopy techniques, circular dichroism, and transmission electron microscopy, we confirmed self-aggregation of R1, R3, R5 fragments, as previously reported for Escherichia coli, however, with different temporal characteristics for each species. We also observed aggregation propensities of R4 fragment of Salmonella enterica that is different than that of Escherichia coli. Our studies showed that amyloid structures of CsgA repeats are more easily formed and more durable in Salmonella enterica than those in Escherichia coli.
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Affiliation(s)
- Natalia Szulc
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; (N.S.); (M.G.-G.); (J.W.W.)
- LPCT, CNRS, Université de Lorraine, F-54000 Nancy, France
| | - Marlena Gąsior-Głogowska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; (N.S.); (M.G.-G.); (J.W.W.)
| | - Jakub W. Wojciechowski
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; (N.S.); (M.G.-G.); (J.W.W.)
| | - Monika Szefczyk
- Department of Bioorganic Chemistry, Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
| | - Andrzej M. Żak
- Electron Microscopy Laboratory, Faculty of Mechanical Engineering, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland;
| | - Michał Burdukiewicz
- Clinical Research Centre, Medical University of Białystok, Jana Kilińskiego 1, 15-089 Białystok, Poland
- Institute of Biochemistry and Biophysics, Polish Academy Sciences, 02-106 Warsaw, Poland
- Faculty of Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
- Correspondence: (M.B.); (M.K.)
| | - Malgorzata Kotulska
- Department of Biomedical Engineering, Faculty of Fundamental Problems of Technology, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland; (N.S.); (M.G.-G.); (J.W.W.)
- Correspondence: (M.B.); (M.K.)
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Computational prediction of secreted proteins in gram-negative bacteria. Comput Struct Biotechnol J 2021; 19:1806-1828. [PMID: 33897982 PMCID: PMC8047123 DOI: 10.1016/j.csbj.2021.03.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Revised: 03/18/2021] [Accepted: 03/18/2021] [Indexed: 12/29/2022] Open
Abstract
Gram-negative bacteria harness multiple protein secretion systems and secrete a large proportion of the proteome. Proteins can be exported to periplasmic space, integrated into membrane, transported into extracellular milieu, or translocated into cytoplasm of contacting cells. It is important for accurate, genome-wide annotation of the secreted proteins and their secretion pathways. In this review, we systematically classified the secreted proteins according to the types of secretion systems in Gram-negative bacteria, summarized the known features of these proteins, and reviewed the algorithms and tools for their prediction.
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Ageorges V, Monteiro R, Leroy S, Burgess CM, Pizza M, Chaucheyras-Durand F, Desvaux M. Molecular determinants of surface colonisation in diarrhoeagenic Escherichia coli (DEC): from bacterial adhesion to biofilm formation. FEMS Microbiol Rev 2021; 44:314-350. [PMID: 32239203 DOI: 10.1093/femsre/fuaa008] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 03/31/2020] [Indexed: 12/11/2022] Open
Abstract
Escherichia coli is primarily known as a commensal colonising the gastrointestinal tract of infants very early in life but some strains being responsible for diarrhoea, which can be especially severe in young children. Intestinal pathogenic E. coli include six pathotypes of diarrhoeagenic E. coli (DEC), namely, the (i) enterotoxigenic E. coli, (ii) enteroaggregative E. coli, (iii) enteropathogenic E. coli, (iv) enterohemorragic E. coli, (v) enteroinvasive E. coli and (vi) diffusely adherent E. coli. Prior to human infection, DEC can be found in natural environments, animal reservoirs, food processing environments and contaminated food matrices. From an ecophysiological point of view, DEC thus deal with very different biotopes and biocoenoses all along the food chain. In this context, this review focuses on the wide range of surface molecular determinants acting as surface colonisation factors (SCFs) in DEC. In the first instance, SCFs can be broadly discriminated into (i) extracellular polysaccharides, (ii) extracellular DNA and (iii) surface proteins. Surface proteins constitute the most diverse group of SCFs broadly discriminated into (i) monomeric SCFs, such as autotransporter (AT) adhesins, inverted ATs, heat-resistant agglutinins or some moonlighting proteins, (ii) oligomeric SCFs, namely, the trimeric ATs and (iii) supramolecular SCFs, including flagella and numerous pili, e.g. the injectisome, type 4 pili, curli chaperone-usher pili or conjugative pili. This review also details the gene regulatory network of these numerous SCFs at the various stages as it occurs from pre-transcriptional to post-translocational levels, which remains to be fully elucidated in many cases.
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Affiliation(s)
- Valentin Ageorges
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Ricardo Monteiro
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,GSK, Via Fiorentina 1, 53100 Siena, Italy
| | - Sabine Leroy
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
| | - Catherine M Burgess
- Food Safety Department, Teagasc Food Research Centre, Ashtown, Dublin 15, Ireland
| | | | - Frédérique Chaucheyras-Durand
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France.,Lallemand Animal Nutrition SAS, F-31702 Blagnac Cedex, France
| | - Mickaël Desvaux
- Université Clermont Auvergne, INRAE, MEDiS, F-63000 Clermont-Ferrand, France
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Pellicle formation by Escherichia coli K-12: Role of adhesins and motility. J Biosci Bioeng 2021; 131:381-389. [PMID: 33495047 DOI: 10.1016/j.jbiosc.2020.12.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 11/24/2020] [Accepted: 12/05/2020] [Indexed: 01/01/2023]
Abstract
Initial work to generate physically robust biofilms for biocatalytic applications revealed that Escherichia coli K-12 can form a floating biofilm at the air-liquid interface, commonly referred to as a pellicle. Unlike other species where pellicle formation is well-characterised, such as Bacillus subtilis, there are few reports of E. coli K-12 pellicles in the literature. In order to study pellicle formation, a growth model was developed and pellicle formation was monitored over time. Mechanical forces, both motility and shaking, were shown to have effects on pellicle formation and development. The role and regulation of curli, an amyloid protein adhesin critical in E. coli K-12 biofilm formation, was studied by using promoter-green fluorescent protein reporters; flow cytometry and confocal laser scanning microscopy were used to monitor curli expression over time and in different locations. Curli were found to be not only crucial for pellicle formation, but also heterogeneously expressed within the pellicle. The components of the extracellular polymeric substances (EPS) in pellicles were analysed by confocal microscopy using lectins, revealing distinct pellicle morphology on the air-facing and medium-facing sides, and spatially- and temporally-regulated generation of the EPS components poly-N-acetyl glucosamine and colanic acid. We discuss the difference between pellicles formed by E. coli K-12, pathogenic E. coli strains and other species, and the relationship between E. coli K-12 pellicles and solid surface-attached biofilms.
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47
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Karan S, Choudhury D, Dixit A. Immunogenic characterization and protective efficacy of recombinant CsgA, major subunit of curli fibers, against Vibrio parahaemolyticus. Appl Microbiol Biotechnol 2021; 105:599-616. [PMID: 33404830 DOI: 10.1007/s00253-020-11038-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 11/22/2020] [Accepted: 11/27/2020] [Indexed: 12/17/2022]
Abstract
Vibrio parahaemolyticus is one of the major pathogens responsible for vibriosis and zoonotic infections in teleosts, marine invertebrates, and also humans through consumption of contaminated or unprocessed seafood. Emergence of resistance against current accessible antibiotics and spread to the food chain and environment necessitate the development of safe and effective subunit vaccine against this bacterium. Many bacteria including V. parahaemolyticus produce extracellular curli fibrils, heteropolymeric filaments of major and minor subunit, which have been implicated in adhesion, biofilm formation, and virulence. Adhesins are the primary contact points with the host which help in establishing infection and colonization. CsgA, an adhesin, is the major structural component of the curli fiber that forms homopolymers of several hundred units. Due to their exposure on the cell surface, the curli fibers are recognized by the host's immune system, would generate high immune response, and therefore can serve as effective vaccine candidate. In the present study, we describe characterization of the csgA gene, and preparation of recombinant soluble CsgA of V. parahaemolyticus (rVpCsgA), and evaluation of its vaccine potential. Immunization of BALB/c mice with the rVpCsgA mounted a strong immune response. Cellular immune assays such as antibody isotyping, in vitro splenocyte proliferation analysis, and cytokine profiling revealed mixed T-helper cell immune response. The anti-rVpCsgA antiserum was agglutination positive and specifically cross-reacted with the curli CsgA present on the outer membrane of V. parahaemolyticus cells, thus demonstrating its neutralization potential. One hundred percent survival of the immunized mice upon challenge with the lethal dosage of the bacterium established that the rVpCsgA could serve as an effective vaccine against the bacterium. KEY POINTS: • Recombinant histidine-tagged CsgA of V. parahaemolyticus, rVpCsgA, was purified. • The rVpCsgA immunization produced mixed immune response and agglutinating antibodies. • Immunization with the rVpCsgA protected mice against V. parahaemolyticus challenge.
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Affiliation(s)
- Sweta Karan
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru Universitys, New Delhi, 110067, India
| | - Devapriya Choudhury
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru Universitys, New Delhi, 110067, India.
| | - Aparna Dixit
- Gene Regulation Laboratory, School of Biotechnology, Jawaharlal Nehru Universitys, New Delhi, 110067, India.
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Yuca E, Şahin Kehribar E, Şeker UÖŞ. Interaction of microbial functional amyloids with solid surfaces. Colloids Surf B Biointerfaces 2021; 199:111547. [PMID: 33385820 DOI: 10.1016/j.colsurfb.2020.111547] [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: 10/21/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 10/22/2022]
Abstract
HYPOTHESIS Self-assembling protein subunits hold great potential as biomaterials with improved functions. Among the self-assembled protein structures functional amyloids are promising unique properties such as resistance to harsh physical and chemical conditions their mechanical strength, and ease of functionalization. Curli proteins, which are functional amyloids of bacterial biofilms can be programmed as intelligent biomaterials. EXPERIMENTS In order to obtain controllable curli based biomaterials for biomedical applications, and to understand role of each of the curli forming monomeric proteins (namely CsgA and CsgB from Escherichia coli) we characterized their binding kinetics to gold, hydroxyapatite, and silica surfaces. FINDINGS We demonstrated that CsgA, CsgB, and their equimolar mixture have different binding strengths for different surfaces. On hydroxyapatite and silica surfaces, CsgB is the crucial element that determines the final adhesiveness of the CsgA-CsgB mixture. On the gold surface, on the other hand, CsgA controls the behavior of the mixture. Those findings uncover the binding behavior of curli proteins CsgA and CsgB on different biomedically valuable surfaces to obtain a more precise control on their adhesion to a targeted surface.
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Affiliation(s)
- Esra Yuca
- Molecular Biology and Genetics Department, Yildiz Technical University, 34210 Istanbul, Turkey
| | - Ebru Şahin Kehribar
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, TR-06800 Ankara, Turkey
| | - Urartu Özgür Şafak Şeker
- UNAM-Institute of Materials Science and Nanotechnology, Bilkent University, TR-06800 Ankara, Turkey.
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Multifunctional Amyloids in the Biology of Gram-Positive Bacteria. Microorganisms 2020; 8:microorganisms8122020. [PMID: 33348645 PMCID: PMC7766987 DOI: 10.3390/microorganisms8122020] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/18/2023] Open
Abstract
Since they were discovered, amyloids have proven to be versatile proteins able to participate in a variety of cellular functions across all kingdoms of life. This multitask trait seems to reside in their ability to coexist as monomers, aggregates or fibrillar entities, with morphological and biochemical peculiarities. It is precisely this common molecular behaviour that allows amyloids to cross react with one another, triggering heterologous aggregation. In bacteria, many of these functional amyloids are devoted to the assembly of biofilms by organizing the matrix scaffold that keeps cells together. However, consistent with their notion of multifunctional proteins, functional amyloids participate in other biological roles within the same organisms, and emerging unprecedented functions are being discovered. In this review, we focus on functional amyloids reported in gram-positive bacteria, which are diverse in their assembly mechanisms and remarkably specific in their biological functions that they perform. Finally, we consider cross-seeding between functional amyloids as an emerging theme in interspecies interactions that contributes to the diversification of bacterial biology.
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50
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Humenik M, Winkler A, Scheibel T. Patterning of protein-based materials. Biopolymers 2020; 112:e23412. [PMID: 33283876 DOI: 10.1002/bip.23412] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 11/23/2020] [Accepted: 11/25/2020] [Indexed: 01/03/2023]
Abstract
Micro- and nanopatterning of proteins on surfaces allows to develop for example high-throughput biosensors in biomedical diagnostics and in general advances the understanding of cell-material interactions in tissue engineering. Today, many techniques are available to generate protein pattern, ranging from technically simple ones, such as micro-contact printing, to highly tunable optical lithography or even technically sophisticated scanning probe lithography. Here, one focus is on the progress made in the development of protein-based materials as positive or negative photoresists allowing micro- to nanostructured scaffolds for biocompatible photonic, electronic and tissue engineering applications. The second one is on approaches, which allow a controlled spatiotemporal positioning of a single protein on surfaces, enabled by the recent developments in immobilization techniques coherent with the sensitive nature of proteins, defined protein orientation and maintenance of the protein activity at interfaces. The third one is on progress in photolithography-based methods, which allow to control the formation of protein-repellant/adhesive polymer brushes.
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Affiliation(s)
- Martin Humenik
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany
| | - Anika Winkler
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany
| | - Thomas Scheibel
- Department of Biomaterials, Faculty of Engineering Science, Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Colloids and Interfaces (BZKG), Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Molecular Biosciences (BZMB), Universität Bayreuth, Bayreuth, Germany.,Bayreuth Center for Material Science (BayMAT), Universität Bayreuth, Bayreuth, Germany.,Bavarian Polymer Institute (BPI), Universität Bayreuth, Bayreuth, Germany
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