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Wang S, Zhao Y, Breslawec AP, Liang T, Deng Z, Kuperman LL, Yu Q. Strategy to combat biofilms: a focus on biofilm dispersal enzymes. NPJ Biofilms Microbiomes 2023; 9:63. [PMID: 37679355 PMCID: PMC10485009 DOI: 10.1038/s41522-023-00427-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 08/15/2023] [Indexed: 09/09/2023] Open
Abstract
Bacterial biofilms, which consist of three-dimensional extracellular polymeric substance (EPS), not only function as signaling networks, provide nutritional support, and facilitate surface adhesion, but also serve as a protective shield for the residing bacterial inhabitants against external stress, such as antibiotics, antimicrobials, and host immune responses. Biofilm-associated infections account for 65-80% of all human microbial infections that lead to serious mortality and morbidity. Tremendous effort has been spent to address the problem by developing biofilm-dispersing agents to discharge colonized microbial cells to a more vulnerable planktonic state. Here, we discuss the recent progress of enzymatic eradicating strategies against medical biofilms, with a focus on dispersal mechanisms. Particularly, we review three enzyme classes that have been extensively investigated, namely glycoside hydrolases, proteases, and deoxyribonucleases.
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Affiliation(s)
- Shaochi Wang
- Otorhinolaryngology Hospital, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Yanteng Zhao
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Alexandra P Breslawec
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20740, USA
| | - Tingting Liang
- Key Laboratory of Natural Medicine and Immune-Engineering of Henan Province, Henan University Jinming Campus, 475004, Kaifeng, Henan, China
| | - Zhifen Deng
- Translational Medicine Center, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China
| | - Laura L Kuperman
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, 20740, USA.
- Mirimus Inc., 760 Parkside Avenue, Brooklyn, NY, 11226, USA.
| | - Qiuning Yu
- Otorhinolaryngology Hospital, The First Affiliated Hospital of Zhengzhou University, 450052, Zhengzhou, China.
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2
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Choi V, Rohn JL, Stoodley P, Carugo D, Stride E. Drug delivery strategies for antibiofilm therapy. Nat Rev Microbiol 2023; 21:555-572. [PMID: 37258686 DOI: 10.1038/s41579-023-00905-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2023] [Indexed: 06/02/2023]
Abstract
Although new antibiofilm agents have been developed to prevent and eliminate pathogenic biofilms, their widespread clinical use is hindered by poor biocompatibility and bioavailability, unspecific interactions and insufficient local concentrations. The development of innovative drug delivery strategies can facilitate penetration of antimicrobials through biofilms, promote drug dispersal and synergistic bactericidal effects, and provide novel paradigms for clinical application. In this Review, we discuss the potential benefits of such emerging techniques for improving the clinical efficacy of antibiofilm agents, as well as highlighting the existing limitations and future prospects for these therapies in the clinic.
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Affiliation(s)
- Victor Choi
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK
| | - Jennifer L Rohn
- Department of Renal Medicine, Centre for Urological Biology, Division of Medicine, University College London, London, UK
| | - Paul Stoodley
- Departments of Microbial Infection and Immunity, Microbiology and Orthopaedics, The Ohio State University, Columbus, OH, USA
- Department of Mechanical Engineering, National Centre for Advanced Tribology at Southampton (nCATS) and National Biofilm Innovation Centre (NBIC), University of Southampton, Southampton, UK
| | - Dario Carugo
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK
| | - Eleanor Stride
- Department of Engineering Science, Institute of Biomedical Engineering, University of Oxford, Oxford, UK.
- Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford, UK.
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3
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Silicone Oil Decreases Biofilm Formation in a Capacitance-Based Automatic Urine Measurement System. SENSORS 2021; 21:s21020445. [PMID: 33435177 PMCID: PMC7826702 DOI: 10.3390/s21020445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Revised: 01/02/2021] [Accepted: 01/07/2021] [Indexed: 11/17/2022]
Abstract
Capacitance-based automatic urine measurement is a validated technique already implemented in clinical practice. However, albuminuria and free hemoglobinuria cause progressive biofilm buildup on the capacitance sensors of the urinometers. The aim of this experimental study is to investigate the influence of albumin and free hemoglobin on the capacitance signal of an automatic urinometer with and without the addition of silicone oil. A solution of Ringer’s acetate mixed with either albumin or free hemoglobin was run through an automatic urinometer containing either a water-soluble capsule with silicone oil or not. In total, around 500 capacitance measurements were retrieved from the albumin and free hemoglobin group, respectively. The mean increase in capacitance in the albumin 3 g/L group was 257 ± 100 pF without and 105 ± 30 pF with silicone oil, respectively, during 24 h. After ten hours of recording, differences between the two albumin groups reached statistical significance. For the free hemoglobin groups (0.01 g/L), the mean increase in capacitance was 190 ± 170 pF with silicone oil, and 324 ± 80 pF without, with a significant difference between the groups after 20 h and onwards. Coating of the capacitance measurement membrane of the automatic urinometer by albumin or free hemoglobin was significantly decreased by silicone oil, prolonging the functionality of the device.
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4
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Structural insights of the enzymes from the chitin utilization locus of Flavobacterium johnsoniae. Sci Rep 2020; 10:13775. [PMID: 32792608 PMCID: PMC7426924 DOI: 10.1038/s41598-020-70749-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 07/22/2020] [Indexed: 12/17/2022] Open
Abstract
Chitin is one of the most abundant renewable organic materials found on earth. The chitin utilization locus in Flavobacterium johnsoniae, which encodes necessary proteins for complete enzymatic depolymerization of crystalline chitin, has recently been characterized but no detailed structural information on the enzymes was provided. Here we present protein structures of the F. johnsoniae chitobiase (FjGH20) and chitinase B (FjChiB). FjGH20 is a multi-domain enzyme with a helical domain not before observed in other chitobiases and a domain organization reminiscent of GH84 (β-N-acetylglucosaminidase) family members. The structure of FjChiB reveals that the protein lacks loops and regions associated with exo-acting activity in other chitinases and instead has a more solvent accessible substrate binding cleft, which is consistent with its endo-chitinase activity. Additionally, small angle X-ray scattering data were collected for the internal 70 kDa region that connects the N- and C-terminal chitinase domains of the unique 158 kDa multi-domain chitinase A (FjChiA). The resulting model of the molecular envelope supports bioinformatic predictions of the region comprising six domains, each with similarities to either Fn3-like or Ig-like domains. Taken together, the results provide insights into chitin utilization by F. johnsoniae and reveal structural diversity in bacterial chitin metabolism.
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Abstract
Despite efforts to develop new antibiotics, antibacterial resistance still develops too fast for drug discovery to keep pace. Often, resistance against a new drug develops even before it reaches the market. This continued resistance crisis has demonstrated that resistance to antibiotics with single protein targets develops too rapidly to be sustainable. Most successful long-established antibiotics target more than one molecule or possess targets, which are encoded by multiple genes. This realization has motivated a change in antibiotic development toward drug candidates with multiple targets. Some mechanisms of action presuppose multiple targets or at least multiple effects, such as targeting the cytoplasmic membrane or the carrier molecule bactoprenol phosphate and are therefore particularly promising. Moreover, combination therapy approaches are being developed to break antibiotic resistance or to sensitize bacteria to antibiotic action. In this Review, we provide an overview of antibacterial multitarget approaches and the mechanisms behind them.
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Affiliation(s)
- Declan Alan Gray
- Newcastle University
Biosciences Institute, Newcastle University, NE2 4HH Newcastle
upon Tyne, United Kingdom
| | - Michaela Wenzel
- Division of Chemical
Biology, Department of Biology and Biological Engineering, Chalmers University of Technology, 412 96 Gothenburg, Sweden
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6
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Eddenden A, Kitova EN, Klassen JS, Nitz M. An Inactive Dispersin B Probe for Monitoring PNAG Production in Biofilm Formation. ACS Chem Biol 2020; 15:1204-1211. [PMID: 31917539 DOI: 10.1021/acschembio.9b00907] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial exopolysaccharide poly-β-1,6-N-acetylglucosamine is a major extracellular matrix component in biofilms of both Gram-positive and Gram-negative organisms. We have leveraged the specificity of the biofilm-dispersing glycoside hydrolase Dispersin B (DspB) to generate a probe (Dispersin B PNAG probe, DiPP) for monitoring PNAG production and localization during biofilm formation. Mutation of the active site of Dispersin B gave DiPP, which was an effective probe despite its low affinity for PNAG oligosaccharides (KD ∼ 1-10 mM). Imaging of PNAG-dependent and -independent biofilms stained with a fluorescent-protein fusion of DiPP (GFP-DiPP) demonstrated the specificity of the probe for the structure of PNAG on both single-cell and biofilm levels, indicating a high local concentration of PNAG at the bacterial cell surface. Through quantitative bacterial cell binding assays and confocal microscopy analysis using GFP-DiPP, discrete areas of local high concentrations of PNAG were detected on the surface of early log phase cells. These distinct areas were seen to grow, slough from cells, and accumulate in interbacterial regions over the course of several cell divisions, showing the development of a PNAG-dependent biofilm. A potential helical distribution of staining was also noted, suggesting some degree of organization of PNAG production at the cell surface prior to cell aggregation. Together, these experiments shed light on the early stages of PNAG-dependent biofilm formation and demonstrate the value of a low-affinity-high-specificity probe for monitoring the production of bacterial exopolysaccharides.
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Affiliation(s)
- Alexander Eddenden
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario, Canada M5S 3H6
| | - Elena N. Kitova
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. Edmonton, Alberta, Canada T6G 2G2
| | - John S. Klassen
- Alberta Glycomics Centre and Department of Chemistry, University of Alberta, 11227 Saskatchewan Dr. Edmonton, Alberta, Canada T6G 2G2
| | - Mark Nitz
- Department of Chemistry, University of Toronto, 80 St. George St, Toronto, Ontario, Canada M5S 3H6
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Forman A, Pfoh R, Eddenden A, Howell PL, Nitz M. Synthesis of defined mono-de-N-acetylated β-(1→6)-N-acetyl-d-glucosamine oligosaccharides to characterize PgaB hydrolase activity. Org Biomol Chem 2019; 17:9456-9466. [PMID: 31642455 DOI: 10.1039/c9ob02079a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many clinically-relevant biofilm-forming bacterial strains produce partially de-N-acetylated poly-β-(1→6)-N-acetyl-d-glucosamine (dPNAG) as an exopolysaccharide. In Gram-negative bacteria, the periplasmic protein PgaB is responsible for partial de-N-acetylation of PNAG prior to its export to the extracellular space. In addition to de-N-acetylase activity found in the N-terminal domain, PgaB contains a C-terminal hydrolase domain that can disrupt dPNAG-dependent biofilms and hydrolyzes dPNAG but not fully acetylated PNAG. The role of this C-terminal domain in biofilm formation has yet to be determined in vivo. Further characterization of the enzyme's hydrolase activity has been hampered by a lack of specific dPNAG oligosaccharides. Here, we report the synthesis of a defined mono de-N-acetylated dPNAG penta- and hepta-saccharide. Using mass spectrometry analysis and a fluorescence-based thin-layer chromatography (TLC) assay, we found that our defined dPNAG oligosaccharides are hydrolase substrates. In addition to the expected cleavage site, two residues to the reducing side of the de-N-acetylated residue, minor cleavage products on the non-reducing side of the de-N-acetylation site were observed. These findings provide quantitative data to support how PNAG is processed in Gram-negative bacteria.
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Affiliation(s)
- Adam Forman
- Department of Chemistry, University of Toronto, 80 St. George Street, Toronto, ON, Canada M5S 3H6.
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8
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Černáková L, Light C, Salehi B, Rogel-Castillo C, Victoriano M, Martorell M, Sharifi-Rad J, Martins N, Rodrigues CF. Novel Therapies for Biofilm-Based Candida spp. Infections. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1214:93-123. [DOI: 10.1007/5584_2019_400] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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9
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Cywes-Bentley C, Rocha JN, Bordin AI, Vinacur M, Rehman S, Zaidi TS, Meyer M, Anthony S, Lambert M, Vlock DR, Giguère S, Cohen ND, Pier GB. Antibody to Poly-N-acetyl glucosamine provides protection against intracellular pathogens: Mechanism of action and validation in horse foals challenged with Rhodococcus equi. PLoS Pathog 2018; 14:e1007160. [PMID: 30024986 PMCID: PMC6053243 DOI: 10.1371/journal.ppat.1007160] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Accepted: 06/15/2018] [Indexed: 12/16/2022] Open
Abstract
Immune correlates of protection against intracellular bacterial pathogens are largely thought to be cell-mediated, although a reasonable amount of data supports a role for antibody-mediated protection. To define a role for antibody-mediated immunity against an intracellular pathogen, Rhodococcus equi, that causes granulomatous pneumonia in horse foals, we devised and tested an experimental system relying solely on antibody-mediated protection against this host-specific etiologic agent. Immunity was induced by vaccinating pregnant mares 6 and 3 weeks prior to predicted parturition with a conjugate vaccine targeting the highly conserved microbial surface polysaccharide, poly-N-acetyl glucosamine (PNAG). We ascertained antibody was transferred to foals via colostrum, the only means for foals to acquire maternal antibody. Horses lack transplacental antibody transfer. Next, a randomized, controlled, blinded challenge was conducted by inoculating at ~4 weeks of age ~106 cfu of R. equi via intrabronchial challenge. Eleven of 12 (91%) foals born to immune mares did not develop clinical R. equi pneumonia, whereas 6 of 7 (86%) foals born to unvaccinated controls developed pneumonia (P = 0.0017). In a confirmatory passive immunization study, infusion of PNAG-hyperimmune plasma protected 100% of 5 foals against R. equi pneumonia whereas all 4 recipients of normal horse plasma developed clinical disease (P = 0.0079). Antibodies to PNAG mediated killing of extracellular and intracellular R. equi and other intracellular pathogens. Killing of intracellular organisms depended on antibody recognition of surface expression of PNAG on infected cells, along with complement deposition and PMN-assisted lysis of infected macrophages. Peripheral blood mononuclear cells from immune and protected foals released higher levels of interferon-γ in response to PNAG compared to controls, indicating vaccination also induced an antibody-dependent cellular release of this critical immune cytokine. Overall, antibody-mediated opsonic killing and interferon-γ release in response to PNAG may protect against diseases caused by intracellular bacterial pathogens. Development of effective vaccines for diseases such as tuberculosis, brucellosis and others caused by intracellular pathogens has proved challenging, as data exist supporting both antibody and cellular immune effectors as mediators of protection. To address this problem against an important, and representative, equine intracellular pathogen, we chose to test a vaccine candidate for the ability to protect horse foals challenged at 4 weeks of age with Rhodococcus equi. To make these foals immune, their pregnant mares were immunized with a vaccine targeting the conserved surface antigen found on many microbes, termed PNAG. Antibody in the pregnant mares was transferred to their foals and, after the foals were challenged, 91% of those born to vaccinated mares were protected against R. equi pneumonia. Meanwhile, 86% of the non-vaccinated controls developed pneumonia. We also showed antibody to PNAG could kill various bacteria that produce this antigen when residing inside of human macrophage cells, a new mechanism for antibody-mediated immunity to intracellular bacteria. These results support the development of PNAG as a vaccine for intracellular bacterial pathogens.
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Affiliation(s)
- Colette Cywes-Bentley
- Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, United States of America
| | - Joana N. Rocha
- College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States of America
| | - Angela I. Bordin
- College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States of America
| | - Mariana Vinacur
- Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, United States of America
| | - Safia Rehman
- Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, United States of America
| | - Tanweer S. Zaidi
- Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, United States of America
| | - Mark Meyer
- Mg Biologics, Ames, IA, United States of America
| | | | | | | | - Steeve Giguère
- College of Veterinary Medicine, University of Georgia, Athens, GA, United States of America
| | - Noah D. Cohen
- College of Veterinary Medicine & Biomedical Sciences, Texas A&M University, College Station, TX, United States of America
- * E-mail: (NDC); (GBP)
| | - Gerald B. Pier
- Harvard Medical School, Brigham & Women’s Hospital, Boston, MA, United States of America
- * E-mail: (NDC); (GBP)
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10
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Blanchette KA, Wenke JC. Current therapies in treatment and prevention of fracture wound biofilms: why a multifaceted approach is essential for resolving persistent infections. J Bone Jt Infect 2018; 3:50-67. [PMID: 29761067 PMCID: PMC5949568 DOI: 10.7150/jbji.23423] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 01/16/2018] [Indexed: 12/13/2022] Open
Abstract
Traumatic orthopedic injuries, particularly extremity wounds, are a significant cause of morbidity. Despite prophylactic antibiotic treatment and surgical intervention, persistent infectious complications can and do occur. Persistent bacterial infections are often caused by biofilms, communities of antibiotic tolerant bacteria encased within a matrix. The structural and metabolic differences in this mode of growth make treatment difficult. Herein, we describe both established and novel, experimental treatments targeted at various stages of wound healing that are specifically aimed at reducing and eliminating biofilm bacteria. Importantly, the highly tolerant nature of these bacterial communities suggests that most singular approaches could be circumvented and a multifaceted, combinatorial approach will be the most effective strategy for treating these complicated infections.
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Affiliation(s)
| | - Joseph C Wenke
- US Army Institute of Surgical Research, Ft Sam Houston, TX
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11
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Tremblay YD, Hathroubi S, Jacques M. [Bacterial biofilms: their importance in animal health and public health]. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2014; 78:110-116. [PMID: 24688172 PMCID: PMC3962273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Bacterial biofilms are structured communities of bacterial cells enclosed in a self-produced polymer matrix that is attached to a surface. Biofilms protect and allow bacteria to survive and thrive in hostile environments. Bacteria within biofilms can withstand host immune responses, and are much less susceptible to antibiotics and disinfectants when compared to their planktonic counterparts. The ability to form biofilms is now considered an attribute of many microorganisms. Diseases associated with biofilms require novel methods for their prevention, diagnosis and treatment; this is largely due to the properties of biofilms. Furthermore, the presence of biofilms on surfaces found at farms, slaughterhouses or food processing plants will have an impact on the efficacy of disinfection protocols. Surprisingly, biofilm formation by bacterial pathogens of veterinary or zoonotic importance has received relatively little attention. The objective of this brief Review article is to bring awareness about the importance of biofilms to animal health stakeholders.(Translated by the authors).
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Affiliation(s)
| | | | - Mario Jacques
- Adresser toute correspondance à Docteur Mario Jacques; téléphone : 450-773-8521 (poste 8348); fax : 450-778-8108; e-mail :
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12
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Thi NN, Offen WA, Shareck F, Davies GJ, Doucet N. Structure and Activity of the Streptomyces coelicolor A3(2) β-N-Acetylhexosaminidase Provides Further Insight into GH20 Family Catalysis and Inhibition. Biochemistry 2014; 53:1789-800. [DOI: 10.1021/bi401697j] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Nhung Nguyen Thi
- INRS-Institut
Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
- PROTEO,
the Québec Network for Research on Protein Function, Structure,
and Engineering, 1045
Avenue de la Médecine, Université Laval, Québec, Québec G1V 0A6, Canada
- GRASP,
the Groupe de Recherche Axé sur la Structure des Protéines,
3649 Promenade Sir William Osler, McGill University, Montréal, Québec H3G 0B1, Canada
- Military
Institute of Science and Technology, 17 Hoang Sam, Hanoi, Vietnam
- Vietnam
Academy of Science and Technology, 18 Hoang Quoc Viet, Hanoi, Vietnam
| | - Wendy A. Offen
- Structural
Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - François Shareck
- INRS-Institut
Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
| | - Gideon J. Davies
- Structural
Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Nicolas Doucet
- INRS-Institut
Armand-Frappier, Université du Québec, 531 Boul. des Prairies, Laval, Québec H7V 1B7, Canada
- PROTEO,
the Québec Network for Research on Protein Function, Structure,
and Engineering, 1045
Avenue de la Médecine, Université Laval, Québec, Québec G1V 0A6, Canada
- GRASP,
the Groupe de Recherche Axé sur la Structure des Protéines,
3649 Promenade Sir William Osler, McGill University, Montréal, Québec H3G 0B1, Canada
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13
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Gökçen A, Vilcinskas A, Wiesner J. Methods to identify enzymes that degrade the main extracellular polysaccharide component of Staphylococcus epidermidis biofilms. Virulence 2013; 4:260-70. [PMID: 23357872 PMCID: PMC3711985 DOI: 10.4161/viru.23560] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
The production of extracellular poly-β-1,6-N-acetyl-d-glucosamine (PNAG) by Staphylococcus epidermidis is the principal determinant of biofilm formation on indwelling medical devices. Enzymes that degrade PNAG therefore provide an attractive strategy for biofilm removal and for the manufacture of biofilm-resistant coatings. Here we present methods that allow the identification of PNAG-degrading enzymes with the ability to detach biofilms. Our protocol includes the preparation of soluble PNAG from S. epidermidis cultures, the incubation of soluble PNAG with candidate enzymes and assays that detect the release of N-acetyl-d-glucosamine using high-pH anion-exchange chromatography (HPAEC) followed in parallel by pulsed amperometric detection (PAD) and online electrospray ionization mass spectrometry (ESI-MS). We validated our procedures using dispersin B, which is currently the only known PNAG-degrading enzyme.
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Affiliation(s)
- Anke Gökçen
- Fraunhofer Institute for Molecular Biology and Applied Ecology IME, Gießen, Germany
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14
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Fazekas E, Kandra L, Gyémánt G. Model for β-1,6-N-acetylglucosamine oligomer hydrolysis catalysed by DispersinB, a biofilm degrading enzyme. Carbohydr Res 2012; 363:7-13. [DOI: 10.1016/j.carres.2012.09.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2012] [Revised: 09/15/2012] [Accepted: 09/20/2012] [Indexed: 11/29/2022]
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15
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Kortagere S, Lill M, Kerrigan J. Role of computational methods in pharmaceutical sciences. Methods Mol Biol 2012; 929:21-48. [PMID: 23007425 DOI: 10.1007/978-1-62703-050-2_3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
Abstract
Over the past two decades computational methods have eased up the financial and experimental burden of early drug discovery process. The in silico methods have provided support in terms of databases, data mining of large genomes, network analysis, systems biology on the bioinformatics front and structure-activity relationship, similarity analysis, docking, and pharmacophore methods for lead design and optimization. This review highlights some of the applications of bioinformatics and chemoinformatics methods that have enriched the field of drug discovery. In addition, the review also provided insights into the use of free energy perturbation methods for efficiently computing binding energy. These in silico methods are complementary and can be easily integrated into the traditional in vitro and in vivo methods to test pharmacological hypothesis.
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Affiliation(s)
- Sandhya Kortagere
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, PA, USA.
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16
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Chibba A, Dasgupta S, Yakandawala N, Madhyastha S, Nitz M. Chromogenic Carbamate and Acetal Substrates for Glycosaminidases. J Carbohydr Chem 2011. [DOI: 10.1080/07328303.2011.610543] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
Affiliation(s)
- Anthony Chibba
- a Department of Chemistry, 80 St. George Street , University of Toronto , Toronto , ON , M5S 3H6
| | - Somnath Dasgupta
- a Department of Chemistry, 80 St. George Street , University of Toronto , Toronto , ON , M5S 3H6
| | | | | | - Mark Nitz
- a Department of Chemistry, 80 St. George Street , University of Toronto , Toronto , ON , M5S 3H6
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17
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Fekete A, Borbás A, Gyémánt G, Kandra L, Fazekas E, Ramasubbu N, Antus S. Synthesis of β-(1→6)-linked N-acetyl-D-glucosamine oligosaccharide substrates and their hydrolysis by Dispersin B. Carbohydr Res 2011; 346:1445-53. [PMID: 21482420 DOI: 10.1016/j.carres.2011.03.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2011] [Revised: 03/06/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
Abstract
Dispersin B (DspB) from Aggregatibacter actinomycetemcomitans is a β-hexosaminidase exhibiting biofilm detachment activity. A series of β-(1→6)-linked N-acetyl-D-glucosamine thiophenyl glycosides with degree of polymerisation (DP) of 2, 3, 4 and 5 were synthesized, and substrate specificity of DspB was studied on the obtained oligosaccharides. For oligomer synthesis a 1+2, 2+2, 1+4 coupling strategy was applied, using bromo-sugars as glycosyl donors. The formation of 1,2-trans interglycosidic bond has been ensured by 2-phtalimido protecting group; chloroacetyl group was installed to mask temporarily the 6-hydroxyl and acetate esters were applied as permanent protecting groups. Enzymatic studies revealed that DP of the GlcNAc oligomers strongly affected the hydrolysis rate, and the hydrolytic activity of DspB on the tetramer and pentamer have been found to be approximately 10-fold higher than that of the dimer. This fact indicates that four units are required for a strong binding at the active centre of DspB. The role of aromatic amino acids W237, Y187 and Y278 in substrate specificity and catalysis was also examined using mutant enzymes.
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Affiliation(s)
- Anikó Fekete
- Research Group for Carbohydrates of Hungarian Academy of Sciences, PO Box 94, H-4010 Debrecen, Hungary
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Abstract
Bacterial biofilms are structured communities of bacterial cells enclosed in a self-produced polymer matrix that is attached to a surface. Biofilms protect and allow bacteria to survive and thrive in hostile environments. Bacteria within biofilms can withstand host immune responses, and are much less susceptible to antibiotics and disinfectants when compared with their planktonic counterparts. The ability to form biofilms is now considered a universal attribute of micro-organisms. Diseases associated with biofilms require novel methods for their prevention, diagnosis and treatment; this is largely due to the properties of biofilms. Surprisingly, biofilm formation by bacterial pathogens of veterinary importance has received relatively little attention. Here, we review the current knowledge of bacterial biofilms as well as studies performed on animal pathogens.
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Labrie J, Pelletier-Jacques G, Deslandes V, Ramjeet M, Auger E, Nash JHE, Jacques M. Effects of growth conditions on biofilm formation by Actinobacillus pleuropneumoniae. Vet Res 2009; 41:3. [PMID: 19737507 PMCID: PMC2762130 DOI: 10.1051/vetres/2009051] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2009] [Accepted: 09/08/2009] [Indexed: 11/26/2022] Open
Abstract
Biofilm formation is an important virulence trait of many bacterial pathogens. It has been reported in the literature that only two of the reference strains of the swine pathogen Actinobacillus pleuropneumoniae, representing serotypes 5b and 11, were able to form biofilm in vitro. In this study, we compared biofilm formation by the serotype 1 reference strain S4074 of A. pleuropneumoniae grown in five different culture media. We observed that strain S4074 of A. pleuropneumoniae is able to form biofilms after growth in one of the culture conditions tested brain heart infusion (BHI medium, supplier B). Confocal laser scanning microscopy using a fluorescent probe specific to the poly-N-acetylglucosamine (PGA) polysaccharide further confirmed biofilm formation. In accordance, biofilm formation was susceptible to dispersin B, a PGA hydrolase. Transcriptional profiles of A. pleuropneumoniae S4074 following growth in BHI-B, which allowed a robust biofilm formation, and in BHI-A, in which only a slight biofilm formation was observed, were compared. Genes such as tadC, tadD, genes with homology to autotransporter adhesins as well as genes pgaABC involved in PGA biosynthesis and genes involved in zinc transport were up-regulated after growth in BHI-B. Interestingly, biofilm formation was inhibited by zinc, which was found to be more present in BHI-A (no or slight biofilm) than in BHI-B. We also observed biofilm formation in reference strains representing serotypes 3, 4, 5a, 12 and 14 as well as in 20 of the 37 fresh field isolates tested. Our data indicate that A. pleuropneumoniae has the ability to form biofilms under appropriate growth conditions and transition from a biofilm-positive to a biofilm-negative phenotype was reversible.
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Affiliation(s)
- Josée Labrie
- Groupe de recherche sur les maladies infectieuses du porc et Centre de recherche en infectiologie porcine, Faculté de médecine vétérinaire, Université de Montréal, 3200 Sicotte, St-Hyacinthe, Québec, Canada
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