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Wang S, Courreges MC, Xu L, Gurung B, Berryman M, Gu T. Revealing roles of S-layer protein (SlpA) in Clostridioides difficile pathogenicity by generating the first slpA gene deletion mutant. Microbiol Spectr 2024; 12:e0400523. [PMID: 38709045 DOI: 10.1128/spectrum.04005-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 04/16/2024] [Indexed: 05/07/2024] Open
Abstract
Clostridioides difficile infection (CDI) with high morbidity and high mortality is an urgent threat to public health, and C. difficile pathogenesis studies are eagerly required for CDI therapy. The major surface layer protein, SlpA, was supposed to play a key role in C. difficile pathogenesis; however, a lack of isogenic slpA mutants has greatly hampered analysis of SlpA functions. In this study, the whole slpA gene was successfully deleted for the first time via CRISPR-Cas9 system. Deletion of slpA in C. difficile resulted in smaller, smother-edged colonies, shorter bacterial cell size, and aggregation in suspension. For life cycle, the mutant demonstrated lower growth (changes of optical density at 600 nm, OD600) but higher cell density (colony-forming unit, CFU), decreased toxins production, and inhibited sporulation. Moreover, the mutant was more impaired in motility, more sensitive to vancomycin and Triton X-100-induced autolysis, releasing more lactate dehydrogenase. In addition, SlpA deficiency led to robust biofilm formation but weak adhesion to human host cells.IMPORTANCEClostridioides difficile infection (CDI) has been the most common hospital-acquired infection, with a high rate of antibiotic resistance and recurrence incidences, become a debilitating public health threat. It is urgently needed to study C. difficile pathogenesis for developing efficient strategies as CDI therapy. SlpA was indicated to play a key role in C. difficile pathogenesis. However, analysis of SlpA functions was hampered due to lack of isogenic slpA mutants. Surprisingly, the first slpA deletion C. difficile strain was generated in this study via CRISPR-Cas9, further negating the previous thought about slpA being essential. Results in this study will provide direct proof for roles of SlpA in C. difficile pathogenesis, which will facilitate future investigations for new targets as vaccines, new therapeutic agents, and intervention strategies in combating CDI.
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Affiliation(s)
- Shaohua Wang
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, USA
- Infectious and Tropical Disease Institute, Ohio University, Athens, Ohio, USA
| | - Maria C Courreges
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, USA
| | - Lingjun Xu
- Department of Chemical and Biomolecular Engineering, Institute for Corrosion and Multiphase Technology, Ohio University, Athens, Ohio, USA
| | - Bijay Gurung
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, USA
| | - Mark Berryman
- Department of Biomedical Sciences, Ohio University Heritage College of Osteopathic Medicine, Ohio University, Athens, Ohio, USA
| | - Tingyue Gu
- Department of Chemical and Biomolecular Engineering, Institute for Corrosion and Multiphase Technology, Ohio University, Athens, Ohio, USA
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2
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Avila Cartes J, Bonizzoni P, Ciccolella S, Della Vedova G, Denti L, Didelot X, Monti DC, Pirola Y. RecGraph: recombination-aware alignment of sequences to variation graphs. BIOINFORMATICS (OXFORD, ENGLAND) 2024; 40:btae292. [PMID: 38676570 DOI: 10.1093/bioinformatics/btae292] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Revised: 02/23/2024] [Accepted: 04/25/2024] [Indexed: 04/29/2024]
Abstract
MOTIVATION Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated. RESULTS In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination-we implement this case as RecGraph. From a modelling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events. AVAILABILITY AND IMPLEMENTATION Our implementation is open source and available at https://github.com/AlgoLab/RecGraph.
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Affiliation(s)
- Jorge Avila Cartes
- Department of Informatics, Systems and Communication, University of Milano - Bicocca. Viale Sarca 336, Milano 20126, Italy
| | - Paola Bonizzoni
- Department of Informatics, Systems and Communication, University of Milano - Bicocca. Viale Sarca 336, Milano 20126, Italy
| | - Simone Ciccolella
- Department of Informatics, Systems and Communication, University of Milano - Bicocca. Viale Sarca 336, Milano 20126, Italy
| | - Gianluca Della Vedova
- Department of Informatics, Systems and Communication, University of Milano - Bicocca. Viale Sarca 336, Milano 20126, Italy
| | - Luca Denti
- Department of Informatics, Systems and Communication, University of Milano - Bicocca. Viale Sarca 336, Milano 20126, Italy
| | - Xavier Didelot
- Department of Statistics and School of Life Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Davide Cesare Monti
- Department of Informatics, Systems and Communication, University of Milano - Bicocca. Viale Sarca 336, Milano 20126, Italy
| | - Yuri Pirola
- Department of Informatics, Systems and Communication, University of Milano - Bicocca. Viale Sarca 336, Milano 20126, Italy
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Zhang W, Zhang J, Hu F, Wang W, Du Z, Ke Y, Ma Q, Mou X, Lu J, Yang Z. Active Dual-Protein Coating Assisted by Stepwise Protein-Protein Interactions Assembly Reduces Thrombosis and Infection. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2310259. [PMID: 38424734 PMCID: PMC11077678 DOI: 10.1002/advs.202310259] [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: 12/27/2023] [Revised: 02/04/2024] [Indexed: 03/02/2024]
Abstract
Universal protein coatings have recently gained wide interest in medical applications due to their biocompatibility and ease of fabrication. However, the challenge persists in protein activity preservation, significantly complicating the functional design of these coatings. Herein, an active dual-protein surface engineering strategy assisted by a facile stepwise protein-protein interactions assembly (SPPIA) method for catheters to reduce clot formation and infection is proposed. This strategy is realized first by the partial oxidation of bovine serum albumin (BSA) and lysozyme (LZM) for creating stable nucleation platforms via hydrophobic interaction, followed by the assembly of nonoxidized BSA (pI, the isoelectric point, ≈4.7) and LZM (pI ≈11) through electrostatic interaction owing to their opposite charge under neutral conditions. The SPPIA method effectively preserves the conformation and functionality of both BSA and LZM, thus endowing the resultant coating with potent antithrombotic and bactericidal properties. Furthermore, the stable nucleation platform ensures the adhesion and durability of the coating, resisting thrombosis and bacterial proliferation even after 15 days of PBS immersion. Overall, the SPPIA approach not only provides a new strategy for the fabrication of active protein coatings but also shows promise for the surface engineering technology of catheters.
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Affiliation(s)
- Wentai Zhang
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
| | - Jiangling Zhang
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Fangkun Hu
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Wenxuan Wang
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Zeyu Du
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - You Ke
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Qing Ma
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Xiaohui Mou
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
- School of Materials Science and EngineeringKey Lab of Advanced Technology for Materials of Education MinistrySouthwest Jiaotong UniversityChengdu610031China
| | - Jing Lu
- Department of AnesthesiologySichuan Provincial People's HospitalUniversity of Electronic Science and Technology of ChinaChengduSichuan610072China
| | - Zhilu Yang
- Dongguan Key Laboratory of Smart Biomaterials and Regenerative MedicineThe Tenth Affiliated HospitalSouthern Medical UniversityDongguanGuangdong523000China
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4
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Herdman M, Isbilir B, von Kügelgen A, Schulze U, Wainman A, Bharat TAM. Cell cycle dependent coordination of surface layer biogenesis in Caulobacter crescentus. Nat Commun 2024; 15:3355. [PMID: 38637514 PMCID: PMC11026435 DOI: 10.1038/s41467-024-47529-5] [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: 06/23/2023] [Accepted: 04/04/2024] [Indexed: 04/20/2024] Open
Abstract
Surface layers (S-layers) are proteinaceous, two-dimensional paracrystalline arrays that constitute a major component of the cell envelope in many prokaryotic species. In this study, we investigated S-layer biogenesis in the bacterial model organism Caulobacter crescentus. Fluorescence microscopy revealed localised incorporation of new S-layer at the poles and mid-cell, consistent with regions of cell growth in the cell cycle. Light microscopy and electron cryotomography investigations of drug-treated bacteria revealed that localised S-layer insertion is retained when cell division is inhibited, but is disrupted upon dysregulation of MreB or lipopolysaccharide. We further uncovered that S-layer biogenesis follows new peptidoglycan synthesis and localises to regions of high cell wall turnover. Finally, correlated cryo-light microscopy and electron cryotomographic analysis of regions of S-layer insertion showed the presence of discontinuities in the hexagonal S-layer lattice, contrasting with other S-layers completed by defined symmetric defects. Our findings present insights into how C. crescentus cells form an ordered S-layer on their surface in coordination with the biogenesis of other cell envelope components.
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Affiliation(s)
- Matthew Herdman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Buse Isbilir
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Andriko von Kügelgen
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Ulrike Schulze
- Cell Biology Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK
| | - Alan Wainman
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX1 3RE, UK
| | - Tanmay A M Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge, CB2 0QH, UK.
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5
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Hu C, Garey KW. Microscopy methods for Clostridioides difficile. Anaerobe 2024; 86:102822. [PMID: 38341023 DOI: 10.1016/j.anaerobe.2024.102822] [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: 08/17/2023] [Revised: 01/25/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
Microscopic technologies including light and fluorescent, transmission electron microscopy (TEM), scanning electron microscopy (SEM), and cryo-electron microscopy have been widely utilized to visualize Clostridioides difficile at the molecular, cellular, community, and structural biology level. This comprehensive review summarizes the microscopy tools (fluorescent and reporter system) in their use to study different aspects of C. difficile life cycle and virulence (sporulation, germination) or applications (detection of C. difficile or use of antimicrobials). With these developing techniques, microscopy tools will be able to find broader applications and address more challenging questions to study C. difficile and C. difficile infection.
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Affiliation(s)
- Chenlin Hu
- University of Houston College of Pharmacy, Houston, TX, USA
| | - Kevin W Garey
- University of Houston College of Pharmacy, Houston, TX, USA.
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6
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Gambelli L, McLaren M, Conners R, Sanders K, Gaines MC, Clark L, Gold VAM, Kattnig D, Sikora M, Hanus C, Isupov MN, Daum B. Structure of the two-component S-layer of the archaeon Sulfolobus acidocaldarius. eLife 2024; 13:e84617. [PMID: 38251732 PMCID: PMC10903991 DOI: 10.7554/elife.84617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 01/19/2024] [Indexed: 01/23/2024] Open
Abstract
Surface layers (S-layers) are resilient two-dimensional protein lattices that encapsulate many bacteria and most archaea. In archaea, S-layers usually form the only structural component of the cell wall and thus act as the final frontier between the cell and its environment. Therefore, S-layers are crucial for supporting microbial life. Notwithstanding their importance, little is known about archaeal S-layers at the atomic level. Here, we combined single-particle cryo electron microscopy, cryo electron tomography, and Alphafold2 predictions to generate an atomic model of the two-component S-layer of Sulfolobus acidocaldarius. The outer component of this S-layer (SlaA) is a flexible, highly glycosylated, and stable protein. Together with the inner and membrane-bound component (SlaB), they assemble into a porous and interwoven lattice. We hypothesise that jackknife-like conformational changes in SlaA play important roles in S-layer assembly.
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Affiliation(s)
- Lavinia Gambelli
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mathew McLaren
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Rebecca Conners
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Kelly Sanders
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Matthew C Gaines
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Lewis Clark
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Vicki A M Gold
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Daniel Kattnig
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Environment, Science and Economy, University of Exeter, Exeter, United Kingdom
| | - Mateusz Sikora
- Department of Theoretical Biophysics, Max Planck Institute for Biophysics, Frankfurt, Germany
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
| | - Cyril Hanus
- Institute of Psychiatry and Neurosciences of Paris, Inserm UMR1266 - Université Paris Cité, Paris, France
- GHU Psychiatrie et Neurosciences de Paris, Paris, France
| | - Michail N Isupov
- Henry Wellcome Building for Biocatalysis, Biosciences, Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
| | - Bertram Daum
- Living Systems Institute, University of Exeter, Exeter, United Kingdom
- Faculty of Health and Life Sciences, University of Exeter, Exeter, United Kingdom
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7
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Hunault L, England P, Barbut F, Iannascoli B, Godon O, Déjardin F, Thomas C, Dupuy B, Guo C, Macdonald L, Gorochov G, Sterlin D, Bruhns P. A monoclonal antibody collection for C. difficile typing ? Gut Pathog 2024; 16:4. [PMID: 38243246 PMCID: PMC10797914 DOI: 10.1186/s13099-023-00592-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Accepted: 12/20/2023] [Indexed: 01/21/2024] Open
Abstract
Clostridioides difficile is the leading cause of antibiotic-associated diarrhea and pseudomembranous colitis in adults. Various C. difficile strains circulate currently, associated with different outcomes and antibiotic resistance profiles. However, most studies still focus on the reference strain 630 that does not circulate anymore, partly due to the lack of immunological tools to study current clinically important C. difficile PCR ribotypes. The goal of this study was to generate monoclonal antibodies recognizing various epidemic ribotypes of C. difficile. To do so, we immunized mice expressing human variable antibody genes with the Low Molecular Weight (LMW) subunit of the surface layer protein SlpA from various C. difficile strains. Monoclonal antibodies purified from hybridomas bound LMW with high-affinity and whole bacteria from current C. difficile ribotypes with different cross-specificities. This first collection of anti-C. difficile mAbs represent valuable tools for basic and clinical research.
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Affiliation(s)
- Lise Hunault
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris Cité, INSERM UMR1222, 75015, Paris, France
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM, CNRS, 75013, Paris, France
- Sorbonne Université, Collège doctoral, 75005, Paris, France
| | - Patrick England
- Plateforme de Biophysique Moléculaire, Institut Pasteur, Université Paris Cité, CNRS UMR3528, 75015, Paris, France
| | - Frédéric Barbut
- National Reference Laboratory for Clostridium difficile, 75012, Paris, France
- Université Paris Cité, INSERM UMR-1139, Paris, France
| | - Bruno Iannascoli
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris Cité, INSERM UMR1222, 75015, Paris, France
| | - Ophélie Godon
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris Cité, INSERM UMR1222, 75015, Paris, France
| | - François Déjardin
- Production and Purification of Recombinant Proteins Facility, Institut Pasteur, 75015, Paris, France
| | - Christophe Thomas
- Production and Purification of Recombinant Proteins Facility, Institut Pasteur, 75015, Paris, France
| | - Bruno Dupuy
- UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris-Cité, 75015, Paris, France
| | | | | | - Guy Gorochov
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM, CNRS, 75013, Paris, France.
| | - Delphine Sterlin
- Centre d'Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, INSERM, CNRS, 75013, Paris, France
| | - Pierre Bruhns
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris Cité, INSERM UMR1222, 75015, Paris, France.
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8
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Hunault L, Auria E, England P, Deschamps J, Briandet R, Kremer V, Iannascoli B, Vidal-Maison L, Guo C, Macdonald L, Péchiné S, Denève-Larrazet C, Dupuy B, Gorochov G, Bruhns P, Sterlin D. Anti-S-layer monoclonal antibodies impact Clostridioides difficile physiology. Gut Microbes 2024; 16:2301147. [PMID: 38289292 PMCID: PMC10829821 DOI: 10.1080/19490976.2023.2301147] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/28/2023] [Indexed: 02/01/2024] Open
Abstract
Clostridioides difficile (C. difficile), a gram-positive anaerobic and spore-forming bacterium, is the leading cause of nosocomial antibiotic-associated diarrhea in adults which is characterized by high levels of recurrence and mortality. Surface (S)-layer Protein A (SlpA), the most abundantly expressed protein on the bacterial surface, plays a crucial role in the early stages of infection although the nature of its involvement in C. difficile physiology is yet to be fully understood. Anti-S-layer antibodies have been identified in the sera of convalescent patients and have been correlated with improved outcomes of C. difficile infection (CDI). However, the precise mechanisms by which anti-S-layer antibodies confer protection to the host remain unknown. In this study, we report the first monoclonal antibodies (mAbs) targeting the S-layer of reference strain 630. Characterization of these mAbs unraveled important roles for the S-layer protein in growth, toxin secretion, and biofilm formation by C. difficile, with differential and even opposite effects of various anti-SlpA mAbs on these functions. Moreover, one anti-SlpA mAb impaired C. difficile growth and conferred sensitivity to lysozyme-induced lysis. The results of this study show that anti-S-layer antibody responses can be beneficial or harmful for the course of CDI and provide important insights for the development of adequate S-layer-targeting therapeutics.
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Affiliation(s)
- Lise Hunault
- Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, Inserm, CNRS, Paris, France
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris-Cité, Inserm UMR1222, Paris, France
- Collège doctoral, Sorbonne Université, Paris, France
| | - Emile Auria
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Patrick England
- Department of Structural Biology and Chemistry, Institut Pasteur, Université Paris Cité, CNRS UMR3528, Plateforme de Biophysique Moléculaire, Paris, France
| | - Julien Deschamps
- Institut Micalis, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Romain Briandet
- Institut Micalis, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Vanessa Kremer
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris-Cité, Inserm UMR1222, Paris, France
- Inflammation, Microbiome and Immunosurveillance, Université Paris-Saclay, Inserm, Châtenay-Malabry, France
| | - Bruno Iannascoli
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris-Cité, Inserm UMR1222, Paris, France
| | - Léo Vidal-Maison
- Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, Inserm, CNRS, Paris, France
| | | | | | - Séverine Péchiné
- Equipe Bactéries Pathogènes et Santé, Faculté de Pharmacie, Institut MICALIS (UMR 1319 Université Paris-Saclay, INRAE, AgroParisTech), Orsay, France
| | - Cécile Denève-Larrazet
- Equipe Bactéries Pathogènes et Santé, Faculté de Pharmacie, Institut MICALIS (UMR 1319 Université Paris-Saclay, INRAE, AgroParisTech), Orsay, France
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Paris, France
| | - Guy Gorochov
- Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, Inserm, CNRS, Paris, France
| | - Pierre Bruhns
- Antibodies in Therapy and Pathology, Institut Pasteur, Université Paris-Cité, Inserm UMR1222, Paris, France
| | - Delphine Sterlin
- Centre d’Immunologie et des Maladies Infectieuses (CIMI-Paris), Sorbonne Université, Inserm, CNRS, Paris, France
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9
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Buddle JE, Fagan RP. Pathogenicity and virulence of Clostridioides difficile. Virulence 2023; 14:2150452. [PMID: 36419222 DOI: 10.1080/21505594.2022.2150452] [Citation(s) in RCA: 26] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 11/02/2022] [Accepted: 11/17/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is the most common cause of nosocomial antibiotic-associated diarrhea, and is responsible for a spectrum of diseases characterized by high levels of recurrence, morbidity, and mortality. Treatment is complex, since antibiotics constitute both the main treatment and the major risk factor for infection. Worryingly, resistance to multiple antibiotics is becoming increasingly widespread, leading to the classification of this pathogen as an urgent threat to global health. As a consummate opportunist, C. difficile is well equipped for promoting disease, owing to its arsenal of virulence factors: transmission of this anaerobe is highly efficient due to the formation of robust endospores, and an array of adhesins promote gut colonization. C. difficile produces multiple toxins acting upon gut epithelia, resulting in manifestations typical of diarrheal disease, and severe inflammation in a subset of patients. This review focuses on such virulence factors, as well as the importance of antimicrobial resistance and genome plasticity in enabling pathogenesis and persistence of this important pathogen.
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Affiliation(s)
- Jessica E Buddle
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
| | - Robert P Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, UK
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10
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Bharathkar SK, Miller MJ, Stadtmueller BM. Engineered Secretory Immunoglobulin A provides insights on antibody-based effector mechanisms targeting Clostridiodes difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.08.566291. [PMID: 37986930 PMCID: PMC10659285 DOI: 10.1101/2023.11.08.566291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
Abstract
Secretory (S) Immunoglobin (Ig) A is the predominant mucosal antibody, which mediates host interactions with commensal and pathogenic microbes, including Clostridioides difficile. SIgA adopts a polymeric IgA structure that is bound by secretory component (SC). Despite significance, how SIgA supports diverse effector mechanisms is poorly characterized and SIgA-based therapies nonexistent. We engineered chimeric (c) SIgAs, in which we replaced SC domain D2 with a single domain antibody or a monomeric fluorescent protein, allowing us to investigate and enhance SIgA effector mechanisms. cSIgAs exhibited increased neutralization potency against C. difficile toxins, promoted bacterial clumping and cell rupture, and decreased cytotoxicity. cSIgA also allowed us to visualize and/or quantify C. difficile morphological changes and clumping events. Results reveal mechanisms by which SIgA combats C. difficile infection, demonstrate that cSIgA design can modulate these mechanisms, and demonstrate cSIgA's adaptability to modifications that might target a broad range of antigens and effector mechanisms.
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Affiliation(s)
- Sonya Kumar Bharathkar
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Michael J. Miller
- Carle R. Woese Institute of Genomic Biology
- Department of food science and Human Nutrition, University of Illinois Urbana-Champaign, Illinois 61801 USA
| | - Beth M. Stadtmueller
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Department of Biomedical and Translational Sciences, Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, Illinois 61801 USA
- Carle R. Woese Institute of Genomic Biology
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11
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Frost LR, Stark R, Anonye BO, MacCreath TO, Ferreira LRP, Unnikrishnan M. Dual RNA-seq identifies genes and pathways modulated during Clostridioides difficile colonization. mSystems 2023; 8:e0055523. [PMID: 37615437 PMCID: PMC10654110 DOI: 10.1128/msystems.00555-23] [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: 05/31/2023] [Accepted: 07/11/2023] [Indexed: 08/25/2023] Open
Abstract
IMPORTANCE The initial interactions between the colonic epithelium and the bacterium are likely critical in the establishment of Clostridioides difficile infection, one of the major causes of hospital-acquired diarrhea worldwide. Molecular interactions between C. difficile and human gut cells have not been well defined mainly due to the technical challenges of studying cellular host-pathogen interactions with this anaerobe. Here we have examined transcriptional changes occurring in the pathogen and host cells during the initial 24 hours of infection. Our data indicate several changes in metabolic pathways and virulence-associated factors during the initial bacterium-host cell contact and early stages of infection. We describe canonical pathways enriched based on the expression profiles of a dual RNA sequencing in the host and bacterium, and functions of bacterial factors that are modulated during infection. This study thus provides fresh insight into the early C. difficile infection process.
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Affiliation(s)
- Lucy R. Frost
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Richard Stark
- Bioinformatics Research Technology Platform, University of Warwick, Coventry, United Kingdom
| | - Blessing O. Anonye
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
| | - Thomas O. MacCreath
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
- School of Life Sciences, University of Warwick, Coventry, United Kingdom
| | - Ludmila R. P. Ferreira
- RNA Systems Biology Laboratory (RSBL), Department of Morphology, Institute of Biological Sciences, Federal University of Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, United Kingdom
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12
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Ormsby MJ, Vaz F, Kirk JA, Barwinska-Sendra A, Hallam JC, Lanzoni-Mangutchi P, Cole J, Chaudhuri RR, Salgado PS, Fagan RP, Douce GR. An intact S-layer is advantageous to Clostridioides difficile within the host. PLoS Pathog 2023; 19:e1011015. [PMID: 37384772 PMCID: PMC10310040 DOI: 10.1371/journal.ppat.1011015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Clostridioides difficile is responsible for substantial morbidity and mortality in antibiotically-treated, hospitalised, elderly patients, in which toxin production correlates with diarrhoeal disease. While the function of these toxins has been studied in detail, the contribution of other factors, including the paracrystalline surface layer (S-layer), to disease is less well understood. Here, we highlight the essentiality of the S-layer in vivo by reporting the recovery of S-layer variants, following infection with the S-layer-null strain, FM2.5. These variants carry either correction of the original point mutation, or sequence modifications which restored the reading frame, and translation of slpA. Selection of these variant clones was rapid in vivo, and independent of toxin production, with up to 90% of the recovered C. difficile population encoding modified slpA sequence within 24 h post infection. Two variants, subsequently named FM2.5varA and FM2.5varB, were selected for study in greater detail. Structural determination of SlpA from FM2.5varB indicated an alteration in the orientation of protein domains, resulting in a reorganisation of the lattice assembly, and changes in interacting interfaces, which might alter function. Interestingly, variant FM2.5varB displayed an attenuated, FM2.5-like phenotype in vivo compared to FM2.5varA, which caused disease severity more comparable to that of R20291. Comparative RNA sequencing (RNA-Seq) analysis of in vitro grown isolates revealed large changes in gene expression between R20291 and FM2.5. Downregulation of tcdA/tcdB and several genes associated with sporulation and cell wall integrity may account for the reported attenuated phenotype of FM2.5 in vivo. RNA-seq data correlated well with disease severity with the more virulent variant, FM2.5varA, showing s similar profile of gene expression to R20291 in vitro, while the attenuated FM2.5varB showed downregulation of many of the same virulence associated traits as FM2.5. Cumulatively, these data add to a growing body of evidence that the S-layer contributes to C. difficile pathogenesis and disease severity.
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Affiliation(s)
- Michael J. Ormsby
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Filipa Vaz
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Joseph A. Kirk
- Molecular Microbiology, School of Biosciences, University of Sheffield, England, United Kingdom
| | - Anna Barwinska-Sendra
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, England, United Kingdom
| | - Jennifer C. Hallam
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Paola Lanzoni-Mangutchi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, England, United Kingdom
| | - John Cole
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Roy R. Chaudhuri
- Molecular Microbiology, School of Biosciences, University of Sheffield, England, United Kingdom
| | - Paula S. Salgado
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, England, United Kingdom
| | - Robert P. Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, England, United Kingdom
| | - Gillian R Douce
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
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13
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von Kügelgen A, van Dorst S, Yamashita K, Sexton DL, Tocheva EI, Murshudov G, Alva V, Bharat TAM. Interdigitated immunoglobulin arrays form the hyperstable surface layer of the extremophilic bacterium Deinococcus radiodurans. Proc Natl Acad Sci U S A 2023; 120:e2215808120. [PMID: 37043530 PMCID: PMC10120038 DOI: 10.1073/pnas.2215808120] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 03/14/2023] [Indexed: 04/13/2023] Open
Abstract
Deinococcus radiodurans is an atypical diderm bacterium with a remarkable ability to tolerate various environmental stresses, due in part to its complex cell envelope encapsulated within a hyperstable surface layer (S-layer). Despite decades of research on this cell envelope, atomic structural details of the S-layer have remained obscure. In this study, we report the electron cryomicroscopy structure of the D. radiodurans S-layer, showing how it is formed by the Hexagonally Packed Intermediate-layer (HPI) protein arranged in a planar hexagonal lattice. The HPI protein forms an array of immunoglobulin-like folds within the S-layer, with each monomer extending into the adjacent hexamer, resulting in a highly interconnected, stable, sheet-like arrangement. Using electron cryotomography and subtomogram averaging from focused ion beam-milled D. radiodurans cells, we have obtained a structure of the cellular S-layer, showing how this HPI S-layer coats native membranes on the surface of cells. Our S-layer structure from the diderm bacterium D. radiodurans shows similarities to immunoglobulin-like domain-containing S-layers from monoderm bacteria and archaea, highlighting common features in cell surface organization across different domains of life, with connotations on the evolution of immunoglobulin-based molecular recognition systems in eukaryotes.
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Affiliation(s)
- Andriko von Kügelgen
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Sofie van Dorst
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
| | - Keitaro Yamashita
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Danielle L. Sexton
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Elitza I. Tocheva
- Department of Microbiology and Immunology, University of British Columbia, Vancouver, BCV6T 1Z3, Canada
| | - Garib Murshudov
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Vikram Alva
- Department of Protein Evolution, Max Planck Institute for Biology Tübingen, Tübingen72076, Germany
| | - Tanmay A. M. Bharat
- Structural Studies Division, MRC Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
- Sir William Dunn School of Pathology, University of Oxford, OxfordOX1 3RE, United Kingdom
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14
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Markovska R, Dimitrov G, Gergova R, Boyanova L. Clostridioides difficile, a New “Superbug”. Microorganisms 2023; 11:microorganisms11040845. [PMID: 37110267 PMCID: PMC10140992 DOI: 10.3390/microorganisms11040845] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 03/19/2023] [Accepted: 03/24/2023] [Indexed: 03/29/2023] Open
Abstract
Clostridioides difficile is a Gram-positive, spore-forming, anaerobic bacterium. The clinical features of C. difficile infections (CDIs) can vary, ranging from the asymptomatic carriage and mild self-limiting diarrhoea to severe and sometimes fatal pseudomembranous colitis. C. difficile infections (CDIs) are associated with disruption of the gut microbiota caused by antimicrobial agents. The infections are predominantly hospital-acquired, but in the last decades, the CDI patterns have changed. Their prevalence increased, and the proportion of community-acquired CDIs has also increased. This can be associated with the appearance of hypervirulent epidemic isolates of ribotype 027. The COVID-19 pandemic and the associated antibiotic overuse could additionally change the patterns of infections. Treatment of CDIs is a challenge, with only three appropriate antibiotics for use. The wide distribution of C. difficile spores in hospital environments, chronic persistence in some individuals, especially children, and the recent detection of C. difficile in domestic pets can furthermore worsen the situation. “Superbugs” are microorganisms that are both highly virulent and resistant to antibiotics. The aim of this review article is to characterise C. difficile as a new member of the “superbug” family. Due to its worldwide spread, the lack of many treatment options and the high rates of both recurrence and mortality, C. difficile has emerged as a major concern for the healthcare system.
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15
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Assandri MH, Malamud M, Trejo FM, Serradell MDLA. S-layer proteins as immune players: tales from pathogenic and non-pathogenic bacteria. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 4:100187. [PMID: 37064268 PMCID: PMC10102220 DOI: 10.1016/j.crmicr.2023.100187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023] Open
Abstract
In bacteria, as in other microorganisms, surface compounds interact with different pattern recognition receptors expressed by host cells, which usually triggers a variety of cellular responses that result in immunomodulation. The S-layer is a two-dimensional macromolecular crystalline structure formed by (glyco)-protein subunits that covers the surface of many species of Bacteria and almost all Archaea. In Bacteria, the presence of S-layer has been described in both pathogenic and non-pathogenic strains. As surface components, special attention deserves the role that S-layer proteins (SLPs) play in the interaction of bacterial cells with humoral and cellular components of the immune system. In this sense, some differences can be predicted between pathogenic and non-pathogenic bacteria. In the first group, the S-layer constitutes an important virulence factor, which in turn makes it a potential therapeutic target. For the other group, the growing interest to understand the mechanisms of action of commensal microbiota and probiotic strains has prompted the studies of the role of the S-layer in the interaction between the host immune cells and bacteria bearing this surface structure. In this review, we aim to summarize the main latest reports and the perspectives of bacterial SLPs as immune players, focusing on those from pathogenic and commensal/probiotic most studied species.
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16
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Royer ALM, Umansky AA, Allen MM, Garneau JR, Ospina-Bedoya M, Kirk JA, Govoni G, Fagan RP, Soutourina O, Fortier LC. Clostridioides difficile S-Layer Protein A (SlpA) Serves as a General Phage Receptor. Microbiol Spectr 2023; 11:e0389422. [PMID: 36790200 PMCID: PMC10100898 DOI: 10.1128/spectrum.03894-22] [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: 09/24/2022] [Accepted: 01/27/2023] [Indexed: 02/16/2023] Open
Abstract
Therapeutic bacteriophages (phages) are being considered as alternatives in the fight against Clostridioides difficile infections. To be efficient, phages should have a wide host range, buthe lack of knowledge about the cell receptor used by C. difficile phages hampers the rational design of phage cocktails. Recent reports suggested that the C. difficile surface layer protein A (SlpA) is an important phage receptor, but available data are still limited. Here, using the epidemic R20291 strain and its FM2.5 mutant derivative lacking a functional S-layer, we show that the absence of SlpA renders cells completely resistant to infection by ϕCD38-2, ϕCD111, and ϕCD146, which normally infect the parental strain. Complementation with 12 different S-layer cassette types (SLCTs) expressed from a plasmid revealed that SLCT-6 also allowed infection by ϕCD111 and SLCT-11 enabled infection by ϕCD38-2 and ϕCD146. Of note, the expression of SLCT-1, -6, -8, -9, -10, or -12 conferred susceptibility to infection by 5 myophages that normally do not infect the R20291 strain. Also, deletion of the D2 domain within the low-molecular-weight fragment of SlpA was found to abolish infection by ϕCD38-2 and ϕCD146 but not ϕCD111. Altogether, our data suggest that many phages use SlpA as their receptor and, most importantly, that both siphophages and myophages target SlpA despite major differences in their tail structures. Our study therefore represents an important step in understanding the interactions between C. difficile and its phages. IMPORTANCE Phage therapy represents an interesting alternative to treat Clostridioides difficile infections because, contrary to antibiotics, most phages are highly species specific, thereby sparing the beneficial gut microbes that protect from infection. However, currently available phages against C. difficile have a narrow host range and target members from only one or a few PCR ribotypes. Without a clear comprehension of the factors that define host specificity, and in particular the host receptor recognized by phages, it is hard to develop therapeutic cocktails in a rational manner. In our study, we provide clear and unambiguous experimental evidence that SlpA is a common receptor used by many siphophages and myophages. Although work is still needed to define how a particular phage receptor-binding protein binds to a specific SLCT, the identification of SlpA as a common receptor is a major keystone that will facilitate the rational design of therapeutic phage cocktails against clinically important strains.
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Affiliation(s)
- Alexia L. M. Royer
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Andrew A. Umansky
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Marie-Maude Allen
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Julian R. Garneau
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Maicol Ospina-Bedoya
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
| | - Joseph A. Kirk
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | | | - Robert P. Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Faculty of Medicine and Health Sciences, Université de Sherbrooke, Sherbrooke, Québec, Canada
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17
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Kikuchi K, Date K, Ueno T. Design of a Hierarchical Assembly at a Solid-Liquid Interface Using an Asymmetric Protein Needle. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2023; 39:2389-2397. [PMID: 36734675 DOI: 10.1021/acs.langmuir.2c03146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Design and control of processes for a hierarchical assembly of proteins remain challenging because it requires consideration of design principles with atomic-level accuracy. Previous studies have adopted symmetry-based strategies to minimize the complexity of protein-protein interactions and this has placed constraints on the structures of the resulting protein assemblies. In the present work, we used an anisotropic-shaped protein needle, gene product 5 (gp5) from bacteriophage T4 with a C-terminal hexahistidine-tag (His-tag) (gp5_CHis), to construct a hierarchical assembly with two distinct protein-protein interaction sites. High-speed atomic force microscopy (HS-AFM) measurements reveal that it forms unique tetrameric clusters through its N-terminal head on a mica surface. The clusters further self-assemble into a monolayer through the C-terminal His-tag. The HS-AFM images and displacement analyses show that the monolayer is a network-like structure rather than a crystalline lattice. Our results expand the toolbox for constructing hierarchical protein assemblies based on structural anisotropy.
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Affiliation(s)
- Kosuke Kikuchi
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Koki Date
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Takafumi Ueno
- School of Life Science and Technology, Tokyo Institute of Technology, 4259-B-55, Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
- Living Systems Materialogy (LiSM) Research Group, International Research Frontiers Initiative (IRFI), Tokyo Institute of Technology, Nagatsuta-cho 4259, Midori-ku, Yokohama 226-8501, Japan
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18
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Chandra H, Kovall RA, Yadav JS, Sun X. Host Immune Responses to Surface S-Layer Proteins (SLPs) of Clostridioides difficile. Microorganisms 2023; 11:380. [PMID: 36838345 PMCID: PMC9963625 DOI: 10.3390/microorganisms11020380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2023] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
Clostridioides difficile, a nosocomial pathogen, is an emerging gut pathobiont causing antibiotic-associated diarrhea. C. difficile infection involves gut colonization and disruption of the gut epithelial barrier, leading to the induction of inflammatory/immune responses. The expression of two major exotoxins, TcdA and TcdB is the major cause of C. difficile pathogenicity. Attachment of bacterial abundant cell wall proteins or surface S-layer proteins (SLPs) such as SlpA with host epithelial cells is critical for virulence. In addition to being toxins, these surface components have been shown to be highly immunogenic. Recent studies indicate that C. difficile SLPs play important roles in the adhesion of the bacteria to the intestinal epithelial cells, disruption of tight junctions, and modulation of the immune response of the host cells. These proteins might serve as new targets for vaccines and new therapeutic agents. This review summarizes our current understanding of the immunological role of SLPs in inducing host immunity and their use in the development of vaccines and novel therapeutics to combat C. difficile infection.
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Affiliation(s)
- Harish Chandra
- Department of Environmental Microbiology, School of Earth and Environmental Sciences, Babasaheb Bhimrao Ambedkar University, Lucknow 226025, UP, India
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Rhett A. Kovall
- Department of Molecular and Cellular Biosciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Jagjit S. Yadav
- Department of Environmental and Public Health Sciences, University of Cincinnati College of Medicine, Cincinnati, OH 45267, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA
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19
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Cheng JKJ, Unnikrishnan M. Clostridioides difficile infection: traversing host-pathogen interactions in the gut. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36848200 DOI: 10.1099/mic.0.001306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
C. difficile is the primary cause for nosocomial infective diarrhoea. For a successful infection, C. difficile must navigate between resident gut bacteria and the harsh host environment. The perturbation of the intestinal microbiota by broad-spectrum antibiotics alters the composition and the geography of the gut microbiota, deterring colonization resistance, and enabling C. difficile to colonize. This review will discuss how C. difficile interacts with and exploits the microbiota and the host epithelium to infect and persist. We provide an overview of C. difficile virulence factors and their interactions with the gut to aid adhesion, cause epithelial damage and mediate persistence. Finally, we document the host responses to C. difficile, describing the immune cells and host pathways that are associated and triggered during C. difficile infection.
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Affiliation(s)
- Jeffrey K J Cheng
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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20
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Phetruen T, Chanarat S, Janvilisri T, Phanchana M, Charoensutthivarakul S, Phothichaisri W, Chankhamhaengdecha S. Receptor binding protein of prophage reversibly recognizes the low-molecular weight subunit of the surface-layer protein SlpA in Clostridioides difficile. Front Microbiol 2022; 13:998215. [PMID: 36312948 PMCID: PMC9615553 DOI: 10.3389/fmicb.2022.998215] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/26/2022] [Indexed: 11/13/2022] Open
Abstract
Receptor-binding proteins (RBPs) are located at the viral tail and mediate the initial recognition of phage to a specific bacterial host. Phage RBPs have co-evolved with numerous types of host receptors resulting in the formation of a diverse assortment of cognate pairs of RBP-receptors that function during the phage attachment step. Although several Clostridioides difficile bacteriophages have been discovered, their RBPs are poorly described. Using homology analysis, putative prophage-tail structure (pts) genes were identified from the prophage genome of the C. difficile HN10 strain. Competition and enzyme-linked immunosorbent assays, using recombinant PtsHN10M, demonstrated the interaction of this Pts to C. difficile cells, suggesting a role as a phage RBP. Gel filtration and cross-linking assay revealed the native form of this protein as a homotrimer. Moreover, truncated variants indicated that the C-terminal domain of PtsHN10M was important for binding to C. difficile cells. Interaction of PtsHN10M was also observed to the low-molecular weight subunit of surface-layer protein A (SlpA), located at the outermost surface of C. difficile cells. Altogether, our study highlights the function of PtsHN10M as an RBP and potentially paves the way toward phage engineering and phage therapy against C. difficile infection.
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Affiliation(s)
- Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Sittinan Chanarat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Laboratory of Molecular Cell Biology, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Matthew Phanchana
- Department of Molecular Tropical Medicine and Genetics, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Sitthivut Charoensutthivarakul
- Faculty of Science, School of Bioinnovation and Bio-Based Product Intelligence, Mahidol University, Bangkok, Thailand
- Faculty of Science, Excellent Center for Drug Discovery (ECDD), Mahidol University, Bangkok, Thailand
| | - Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Surang Chankhamhaengdecha
- Department of Biology, Faculty of Science, Mahidol University, Bangkok, Thailand
- *Correspondence: Surang Chankhamhaengdecha,
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21
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Paria P, Chakraborty HJ, Behera BK. Identification of novel salt tolerance-associated proteins from the secretome of Enterococcus faecalis. World J Microbiol Biotechnol 2022; 38:177. [PMID: 35934729 DOI: 10.1007/s11274-022-03354-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Accepted: 07/04/2022] [Indexed: 11/30/2022]
Abstract
The ability of bacteria to adapt to the external environment is fundamental for their survival. A halotolerant microorganism Enterococcus faecalis able to grow under high salt stress conditions was isolated in the present study. The SDS-PAGE analysis of the secretome showed a protein band with a molecular weight of 28 kDa, gradually increased with an increase in salt concentration, and the highest intensity was observed at 15% salt stress condition. LC-MS/MS analysis of this particular band identified fourteen different proteins, out of which nine proteins were uncharacterized. Further, the function of uncharacterized proteins was predicted based on structure-function relationship using a reverse template search approach deciphering uncharacterized protein into type III polyketide synthases, stress-induced protein-1, Eed-h3k79me3, ba42 protein, 3-methyladenine DNA glycosylase, Atxa protein, membrane-bound respiratory hydrogenase, type-i restriction-modification system methylation subunit and ManxA. STRING network analysis further a showed strong association among the proteins. The processes predicted involvement of these proteins in signal transduction, ions transport, synthesis of the protective layer, cellular homeostasis and regulation of gene expression and different metabolic pathways. Thus, the fourteen proteins identified in the secretome play an essential role in maintaining cellular homeostasis in E. faecalis under high-salinity stress. This may represent a novel and previously unreported strategy by E. faecalis to maintain their normal growth and physiology under high salinity conditions.
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Affiliation(s)
- Prasenjit Paria
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - Hirak Jyoti Chakraborty
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India
| | - Bijay Kumar Behera
- Aquatic Environmental Biotechnology and Nanotechnology Division, ICAR-Central Inland Fisheries Research Institute, Barrackpore, Kolkata, 700120, India.
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Pfeifer K, Ehmoser EK, Rittmann SKMR, Schleper C, Pum D, Sleytr UB, Schuster B. Isolation and Characterization of Cell Envelope Fragments Comprising Archaeal S-Layer Proteins. NANOMATERIALS 2022; 12:nano12142502. [PMID: 35889727 PMCID: PMC9320373 DOI: 10.3390/nano12142502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 07/18/2022] [Accepted: 07/19/2022] [Indexed: 12/04/2022]
Abstract
The outermost component of cell envelopes of most bacteria and almost all archaea comprise a protein lattice, which is termed Surface (S-)layer. The S-layer lattice constitutes a highly porous structure with regularly arranged pores in the nm-range. Some archaea thrive in extreme milieus, thus producing highly stable S-layer protein lattices that aid in protecting the organisms. In the present study, fragments of the cell envelope from the hyperthermophilic acidophilic archaeon Saccharolobus solfataricus P2 (SSO) have been isolated by two different methods and characterized. The organization of the fragments and the molecular sieving properties have been elucidated by transmission electron microscopy and by determining the retention efficiency of proteins varying in size, respectively. The porosity of the archaeal S-layer fragments was determined to be 45%. S-layer fragments of SSO showed a retention efficiency of up to 100% for proteins having a molecular mass of ≥ 66 kDa. Moreover, the extraction costs for SSO fragments have been reduced by more than 80% compared to conventional methods, which makes the use of these archaeal S-layer material economically attractive.
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Affiliation(s)
- Kevin Pfeifer
- Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (K.P.); (E.-K.E.); (U.B.S.)
| | - Eva-Kathrin Ehmoser
- Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (K.P.); (E.-K.E.); (U.B.S.)
| | - Simon K.-M. R. Rittmann
- Archaea Physiology & Biotechnology Group, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria;
- Arkeon GmbH, 3430 Tulln an der Donau, Austria
| | - Christa Schleper
- Archaea Biology and Ecogenomics Division, Department of Functional and Evolutionary Ecology, University of Vienna, 1030 Vienna, Austria;
| | - Dietmar Pum
- Institute of Biophysics, University of Natural Resources and Life Sciences, 1190 Vienna, Austria;
| | - Uwe B. Sleytr
- Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (K.P.); (E.-K.E.); (U.B.S.)
| | - Bernhard Schuster
- Institute of Synthetic Bioarchitectures, University of Natural Resources and Life Sciences, 1190 Vienna, Austria; (K.P.); (E.-K.E.); (U.B.S.)
- Correspondence: ; Tel.: +43-1-47654-80436
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Wang S, Zhu D, Sun X. Development of an Effective Nontoxigenic Clostridioides difficile-Based Oral Vaccine against C. difficile Infection. Microbiol Spectr 2022; 10:e0026322. [PMID: 35583336 PMCID: PMC9241731 DOI: 10.1128/spectrum.00263-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/21/2022] [Indexed: 11/20/2022] Open
Abstract
The symptoms of Clostridioides difficile infection (CDI) are largely attributed to two C. difficile toxins, TcdA and TcdB. Significant efforts have been devoted to developing vaccines targeting both toxins through parenteral immunization routes. Recently, we generated a novel chimeric protein (designated Tcd169), comprised of the glucosyltransferase domain (GT), the cysteine protease domain (CPD), and the receptor binding domain (RBD) of TcdB, and the RBD of TcdA. Parenteral immunizations with Tcd169 provide mice effective protection against infection with a ribotype (RT) 027 C. difficile strain. In this study, we expressed Tcd169 in a nontoxigenic C. difficile CCUG37785 strain (designated NTCD), resulting in strain NTCD_Tcd169 to develop an oral vaccine that can target both C. difficile toxins and colonization/adhesion factors. Oral immunizations with NTCD_Tcd169 spores induced systematic and mucosal antibody responses against, not only both toxins, but also C. difficile flagellins (FliC/FliD). Intriguingly yet importantly, anti-Tcd169 sera raised against Tcd169 protein were significantly cross-reactive with FliC/FliD and two surface layer proteins (SlpA and Cwp2). Oral immunizations with NTCD_Tcd169 spores provided mice effective protection against infection with a hypervirulent RT027 C. difficile strain R20291and significantly reduced R20291spore numbers in feces compared with NTCD or PBS immunized mice. These results imply that the genetically modified, nontoxigenic C. difficile strain expressing Tcd169 may represent a novel mucosal vaccine candidate against CDI. IMPORTANCE Clostridioides difficile is an enteric pathogen, and symptoms of C. difficile infection (CDI) are mainly by two exotoxins TcdA and TcdB. Active vaccination is cost-effective approach to prevent CDI and high rates of recurrence. Ideally, vaccines should target both C. difficile toxins and cell/spore colonization. In this study, we expressed immunodominant fragments of TcdA and TcdB (i.e., Tcd169) in a nontoxigenic C. difficile CCUG37785 strain, generating a promising oral/mucosal vaccine candidate against CDI, by targeting both toxins and colonization of pathogenic C. difficile strains. Importantly, anti-Tcd169 sera raised against Tcd169 protein were significantly cross-reactive with FliC/FliD and two surface layer proteins (SlpA and Cwp2), and all of which are involved in C. difficile adhesion/colonization in vitro and in vivo.
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Affiliation(s)
- Shaohui Wang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Duolong Zhu
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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Phothichaisri W, Chankhamhaengdecha S, Janvilisri T, Nuadthaisong J, Phetruen T, Fagan RP, Chanarat S. Potential Role of the Host-Derived Cell-Wall Binding Domain of Endolysin CD16/50L as a Molecular Anchor in Preservation of Uninfected Clostridioides difficile for New Rounds of Phage Infection. Microbiol Spectr 2022; 10:e0236121. [PMID: 35377223 PMCID: PMC9045149 DOI: 10.1128/spectrum.02361-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2021] [Accepted: 03/20/2022] [Indexed: 01/21/2023] Open
Abstract
Endolysin is a phage-encoded cell-wall hydrolase which degrades the peptidoglycan layer of the bacterial cell wall. The enzyme is often expressed at the late stage of the phage lytic cycle and is required for progeny escape. Endolysins of bacteriophage that infect Gram-positive bacteria often comprises two domains: a peptidoglycan hydrolase and a cell-wall binding domain (CBD). Although the catalytic domain of endolysin is relatively well-studied, the precise role of CBD is ambiguous and remains controversial. Here, we focus on the function of endolysin CBD from a recently isolated Clostridioides difficile phage. We found that the CBD is not required for lytic activity, which is strongly prevented by the surface layer of C. difficile. Intriguingly, hidden Markov model analysis suggested that the endolysin CBD is likely derived from the CWB2 motif of C. difficile cell-wall proteins but possesses a higher binding affinity to bacterial cell-wall polysaccharides. Moreover, the CBD forms a homodimer, formation of which is necessary for interaction with the surface saccharides. Importantly, endolysin diffusion and sequential cytolytic assays showed that CBD of endolysin is required for the enzyme to be anchored to post-lytic cell-wall remnants, suggesting its physiological roles in limiting diffusion of the enzyme, preserving neighboring host cells, and thereby enabling the phage progeny to initiate new rounds of infection. Taken together, this study provides an insight into regulation of endolysin through CBD and can potentially be applied for endolysin treatment against C. difficile infection. IMPORTANCE Endolysin is a peptidoglycan hydrolase encoded in a phage genome. The enzyme is attractive due to its potential use as antibacterial treatment. To utilize endolysin for the therapeutic propose, understanding of the fundamental role of endolysin becomes important. Here, we investigate the function of cell-wall binding domain (CBD) of an endolysin from a C. difficile phage. The domain is homologous to a cell-wall associating module of bacterial cell-wall proteins, likely acquired during phage-host coevolution. The interaction of CBD to bacterial cell walls reduces enzyme diffusion and thereby limits cell lysis of the neighboring bacteria. Our findings indicate that the endolysin is trapped to the cell-wall residuals through CBD and might serve as an advantage for phage replication. Thus, employing a CBD-less endolysin might be a feasible strategy for using endolysin for the treatment of C. difficile infection.
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Affiliation(s)
- Wichuda Phothichaisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | | | - Tavan Janvilisri
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Jirayu Nuadthaisong
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Tanaporn Phetruen
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
| | - Robert P. Fagan
- School of Biosciences, Florey Institute, University of Sheffield, Sheffield, United Kingdom
| | - Sittinan Chanarat
- Department of Biochemistry, Faculty of Science, Mahidol University, Bangkok, Thailand
- Laboratory of Molecular Cell Biology, Center for Excellence in Protein and Enzyme Technology, Faculty of Science, Mahidol University, Bangkok, Thailand
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