51
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Antonova NP, Vasina DV, Lendel AM, Usachev EV, Makarov VV, Gintsburg AL, Tkachuk AP, Gushchin VA. Broad Bactericidal Activity of the Myoviridae Bacteriophage Lysins LysAm24, LysECD7, and LysSi3 against Gram-Negative ESKAPE Pathogens. Viruses 2019; 11:v11030284. [PMID: 30901901 PMCID: PMC6466606 DOI: 10.3390/v11030284] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/18/2019] [Accepted: 03/19/2019] [Indexed: 11/30/2022] Open
Abstract
The extremely rapid spread of multiple-antibiotic resistance among Gram-negative pathogens threatens to move humankind into the so-called “post-antibiotic era” in which the most efficient and safe antibiotics will not work. Bacteriophage lysins represent promising alternatives to antibiotics, as they are capable of digesting bacterial cell wall peptidoglycans to promote their osmotic lysis. However, relatively little is known regarding the spectrum of lysin bactericidal activity against Gram-negative bacteria. In this study, we present the results of in vitro activity assays of three putative and newly cloned Myoviridae bacteriophage endolysins (LysAm24, LysECD7, and LysSi3). The chosen proteins represent lysins with diverse domain organization (single-domain vs. two-domain) and different predicted mechanisms of action (lysozyme vs. peptidase). The enzymes were purified, and their properties were characterized. The enzymes were tested against a panel of Gram-negative clinical bacterial isolates comprising all Gram-negative representatives of the ESKAPE group. Despite exhibiting different structural organizations, all of the assayed lysins were shown to be capable of lysing Pseudomonas aeruginosa, Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, and Salmonella typhi strains. Less than 50 μg/mL was enough to eradicate growing cells over more than five orders of magnitude. Thus, LysAm24, LysECD7, and LysSi3 represent promising therapeutic agents for drug development.
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Affiliation(s)
- Nataliia P Antonova
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
- Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Daria V Vasina
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | | | - Evgeny V Usachev
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | - Valentine V Makarov
- Center for Strategic Planning of the Ministry of Health of the Russian Federation, 119435 Moscow, Russia.
| | - Alexander L Gintsburg
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | - Artem P Tkachuk
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
| | - Vladimir A Gushchin
- N.F. Gamaleya Federal Research Centre for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, 123098 Moscow, Russia.
- Lomonosov Moscow State University, 119991 Moscow, Russia.
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52
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Broendum SS, Buckle AM, McGowan S. Catalytic diversity and cell wall binding repeats in the phage-encoded endolysins. Mol Microbiol 2018; 110:879-896. [DOI: 10.1111/mmi.14134] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/14/2018] [Indexed: 01/21/2023]
Affiliation(s)
- Sebastian S. Broendum
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology; Monash University; Victoria 3800 Australia
- Biomedicine Discovery Institute, Department of Microbiology; Monash University; Victoria 3800 Australia
| | - Ashley M. Buckle
- Biomedicine Discovery Institute, Department of Biochemistry and Molecular Biology; Monash University; Victoria 3800 Australia
| | - Sheena McGowan
- Biomedicine Discovery Institute, Department of Microbiology; Monash University; Victoria 3800 Australia
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53
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Baktash A, Terveer EM, Zwittink RD, Hornung BVH, Corver J, Kuijper EJ, Smits WK. Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections. Front Microbiol 2018; 9:1242. [PMID: 29946308 PMCID: PMC6005852 DOI: 10.3389/fmicb.2018.01242] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Fecal microbiota transplantation has proven to be an effective treatment for infections with the gram-positive enteropathogen Clostridium difficile. Despite its effectiveness, the exact mechanisms that underlie its success are largely unclear. In this review, we highlight the pleiotropic effectors that are transferred during fecal microbiota transfer and relate this to the C. difficile lifecycle. In doing so, we show that it is likely that multiple factors contribute to the elimination of symptoms of C. difficile infections after fecal microbiota transplantation.
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Affiliation(s)
- Amoe Baktash
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Netherlands Donor Feces Bank, Leiden, Netherlands
| | - Romy D Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Bastian V H Hornung
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Jeroen Corver
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ed J Kuijper
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Netherlands Donor Feces Bank, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Wiep Klaas Smits
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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54
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Phage-Derived Peptidoglycan Degrading Enzymes: Challenges and Future Prospects for In Vivo Therapy. Viruses 2018; 10:v10060292. [PMID: 29844287 PMCID: PMC6024856 DOI: 10.3390/v10060292] [Citation(s) in RCA: 79] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 05/23/2018] [Accepted: 05/24/2018] [Indexed: 01/17/2023] Open
Abstract
Peptidoglycan degrading enzymes are of increasing interest as antibacterial agents, especially against multi-drug resistant pathogens. Herein we present a review about the biological features of virion-associated lysins and endolysins, phage-derived enzymes that have naturally evolved to compromise the bacterial peptidoglycan from without and from within, respectively. These natural features may determine the adaptability of the enzymes to kill bacteria in different environments. Endolysins are by far the most studied group of peptidoglycan-degrading enzymes, with several studies showing that they can exhibit potent antibacterial activity under specific conditions. However, the lytic activity of most endolysins seems to be significantly reduced when tested against actively growing bacteria, something that may be related to fact that these enzymes are naturally designed to degrade the peptidoglycan from within dead cells. This may negatively impact the efficacy of the endolysin in treating some infections in vivo. Here, we present a critical view of the methods commonly used to evaluate in vitro and in vivo the antibacterial performance of PG-degrading enzymes, focusing on the major hurdles concerning in vitro-to-in vivo translation.
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55
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Discovery and Biochemical Characterization of PlyP56, PlyN74, and PlyTB40- Bacillus Specific Endolysins. Viruses 2018; 10:v10050276. [PMID: 29883383 PMCID: PMC5977269 DOI: 10.3390/v10050276] [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] [Subscribe] [Scholar Register] [Received: 04/30/2018] [Revised: 05/15/2018] [Accepted: 05/17/2018] [Indexed: 12/27/2022] Open
Abstract
Three Bacillus bacteriophage-derived endolysins, designated PlyP56, PlyN74, and PlyTB40, were identified, cloned, purified, and characterized for their antimicrobial properties. Sequence alignment reveals these endolysins have an N-terminal enzymatically active domain (EAD) linked to a C-terminal cell wall binding domain (CBD). PlyP56 has a Peptidase_M15_4/VanY superfamily EAD with a conserved metal binding motif and displays biological dependence on divalent ions for activity. In contrast, PlyN74 and PlyTB40 have T7 lysozyme-type Amidase_2 and carboxypeptidase T-type Amidase_3 EADs, respectively, which are members of the MurNAc-LAA superfamily, but are not homologs and thus do not have a shared protein fold. All three endolysins contain similar SH3-family CBDs. Although minor host range differences were noted, all three endolysins show relatively broad antimicrobial activity against members of the Bacillus cereus sensu lato group with the highest lytic activity against B. cereus ATCC 4342. Characterization studies determined the optimal lytic activity for these enzymes was at physiological pH (pH 7.0–8.0), over a broad temperature range (4–55 °C), and at low concentrations of NaCl (<50 mM). Direct comparison of lytic activity shows the PlyP56 enzyme to be twice as effective at lysing the cell wall peptidoglycan as PlyN74 or PlyTB40, suggesting PlyP56 is a good candidate for further antimicrobial development as well as bioengineering studies.
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56
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Gerstmans H, Criel B, Briers Y. Synthetic biology of modular endolysins. Biotechnol Adv 2018; 36:624-640. [DOI: 10.1016/j.biotechadv.2017.12.009] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/08/2017] [Accepted: 12/13/2017] [Indexed: 01/15/2023]
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57
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Engineering of Phage-Derived Lytic Enzymes: Improving Their Potential as Antimicrobials. Antibiotics (Basel) 2018; 7:antibiotics7020029. [PMID: 29565804 PMCID: PMC6023083 DOI: 10.3390/antibiotics7020029] [Citation(s) in RCA: 81] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Revised: 03/16/2018] [Accepted: 03/20/2018] [Indexed: 12/31/2022] Open
Abstract
Lytic enzymes encoded by bacteriophages have been intensively explored as alternative agents for combating bacterial pathogens in different contexts. The antibacterial character of these enzymes (enzybiotics) results from their degrading activity towards peptidoglycan, an essential component of the bacterial cell wall. In fact, phage lytic products have the capacity to kill target bacteria when added exogenously in the form of recombinant proteins. However, there is also growing recognition that the natural bactericidal activity of these agents can, and sometimes needs to be, substantially improved through manipulation of their functional domains or by equipping them with new functions. In addition, often, native lytic proteins exhibit features that restrict their applicability as effective antibacterials, such as poor solubility or reduced stability. Here, I present an overview of the engineering approaches that can be followed not only to overcome these and other restrictions, but also to generate completely new antibacterial agents with significantly enhanced characteristics. As conventional antibiotics are running short, the remarkable progress in this field opens up the possibility of tailoring efficient enzybiotics to tackle the most menacing bacterial infections.
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58
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Gómez‐Torres N, Dunne M, Garde S, Meijers R, Narbad A, Ávila M, Mayer MJ. Development of a specific fluorescent phage endolysin for in situ detection of Clostridium species associated with cheese spoilage. Microb Biotechnol 2018; 11:332-345. [PMID: 29160025 PMCID: PMC5812242 DOI: 10.1111/1751-7915.12883] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/21/2017] [Accepted: 09/25/2017] [Indexed: 11/29/2022] Open
Abstract
Late blowing defect (LBD) is a major cause of spoilage in cheeses, caused by the growth of Clostridium spp. in the cheese matrix. We investigated the application of CTP1L, a bacteriophage endolysin active against Clostridium tyrobutyricum, and its enzymatically active and cell wall-binding domains (EAD and CBD) attached to green fluorescent protein (GFP) to detect dairy-related Clostridium species by fluorescence microscopy. GFP-CTP1L and GFP-CBD demonstrated specificity for Clostridium spp. by labelling 15 and 17 of 20 Clostridium strains, respectively, but neither bound to other members of the cheese microbiota. However, GFP-EAD did not label any Clostridium strain tested. Unexpectedly, GFP-CTP1L and GFP-CBD were also able to bind to clostridial spores. In addition, GFP-CBD allowed us to visualize the vegetative cells of C. tyrobutyricum directly in the matrix of a LBD cheese. Site-directed mutants of GFP-CTP1L and GFP-CBD were made to examine the amino acids involved in binding and oligomer formation. Oligomerization was not essential for binding, but specific mutations in the CBD which affected oligomer formation also affected binding and lytic activity. We conclude that GFP-CTP1L and GFP-CBD could be good biomarkers for rapid detection of Clostridium spores in milk, so measures can be taken for the prevention of LBD in cheese, and also provide effective tools to study the development of Clostridium populations during cheese ripening.
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Affiliation(s)
- Natalia Gómez‐Torres
- Departamento de Tecnología de AlimentosInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Carretera de La Coruña km 728040MadridSpain
| | - Matthew Dunne
- European Molecular Biology Laboratory (EMBL) Hamburg OutstationNotkestrasse 8522607HamburgGermany
- Present address:
Institute of Food, Nutrition and HealthETH ZurichLFV B36, Schmelzbergstr. 78092ZurichSwitzerland
| | - Sonia Garde
- Departamento de Tecnología de AlimentosInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Carretera de La Coruña km 728040MadridSpain
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL) Hamburg OutstationNotkestrasse 8522607HamburgGermany
| | - Arjan Narbad
- Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceColneyNorwichNR4 7UAUK
| | - Marta Ávila
- Departamento de Tecnología de AlimentosInstituto Nacional de Investigación y Tecnología Agraria y Alimentaria (INIA)Carretera de La Coruña km 728040MadridSpain
| | - Melinda J. Mayer
- Gut Health and Food Safety Institute Strategic ProgrammeQuadram Institute BioscienceColneyNorwichNR4 7UAUK
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59
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Love MJ, Bhandari D, Dobson RCJ, Billington C. Potential for Bacteriophage Endolysins to Supplement or Replace Antibiotics in Food Production and Clinical Care. Antibiotics (Basel) 2018; 7:E17. [PMID: 29495476 PMCID: PMC5872128 DOI: 10.3390/antibiotics7010017] [Citation(s) in RCA: 85] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 02/06/2018] [Accepted: 02/23/2018] [Indexed: 01/21/2023] Open
Abstract
There is growing concern about the emergence of bacterial strains showing resistance to all classes of antibiotics commonly used in human medicine. Despite the broad range of available antibiotics, bacterial resistance has been identified for every antimicrobial drug developed to date. Alarmingly, there is also an increasing prevalence of multidrug-resistant bacterial strains, rendering some patients effectively untreatable. Therefore, there is an urgent need to develop alternatives to conventional antibiotics for use in the treatment of both humans and food-producing animals. Bacteriophage-encoded lytic enzymes (endolysins), which degrade the cell wall of the bacterial host to release progeny virions, are potential alternatives to antibiotics. Preliminary studies show that endolysins can disrupt the cell wall when applied exogenously, though this has so far proven more effective in Gram-positive bacteria compared with Gram-negative bacteria. Their potential for development is furthered by the prospect of bioengineering, and aided by the modular domain structure of many endolysins, which separates the binding and catalytic activities into distinct subunits. These subunits can be rearranged to create novel, chimeric enzymes with optimized functionality. Furthermore, there is evidence that the development of resistance to these enzymes may be more difficult compared with conventional antibiotics due to their targeting of highly conserved bonds.
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Affiliation(s)
- Michael J Love
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand.
| | - Dinesh Bhandari
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand.
- Institute of Environmental Science and Research, Christchurch 8041, New Zealand.
| | - Renwick C J Dobson
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand.
- Department of Biochemistry and Molecular Biology, University of Melbourne, Melbourne 3052, Australia.
| | - Craig Billington
- Biomolecular Interaction Centre and School of Biological Sciences, University of Canterbury, Christchurch 8041, New Zealand.
- Institute of Environmental Science and Research, Christchurch 8041, New Zealand.
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60
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Mordaka PM, Heap JT. Stringency of Synthetic Promoter Sequences in Clostridium Revealed and Circumvented by Tuning Promoter Library Mutation Rates. ACS Synth Biol 2018; 7:672-681. [PMID: 29320851 DOI: 10.1021/acssynbio.7b00398] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Collections of characterized promoters of different strengths are key resources for synthetic biology, but are not well established for many important organisms, including industrially relevant Clostridium spp. When generating promoters, reporter constructs are used to measure expression, but classical fluorescent reporter proteins are oxygen-dependent and hence inactive in anaerobic bacteria like Clostridium. We directly compared oxygen-independent reporters of different types in Clostridium acetobutylicum and found that glucuronidase (GusA) from E. coli performed best. Using GusA, a library of synthetic promoters was first generated by a typical approach entailing complete randomization of a constitutive thiolase gene promoter (Pthl) except for the consensus -35 and -10 elements. In each synthetic promoter, the chance of each degenerate position matching Pthl was 25%. Surprisingly, none of the tested synthetic promoters from this library were functional in C. acetobutylicum, even though they functioned as expected in E. coli. Next, instead of complete randomization, we specified lower promoter mutation rates using oligonucleotide primers synthesized using custom mixtures of nucleotides. Using these primers, two promoter libraries were constructed in which the chance of each degenerate position matching Pthl was 79% or 58%, instead of 25% as before. Synthetic promoters from these "stringent" libraries functioned well in C. acetobutylicum, covering a wide range of strengths. The promoters functioned similarly in the distantly related species Clostridium sporogenes, and allowed predictable metabolic engineering of C. acetobutylicum for acetoin production. Besides generating the desired promoters and demonstrating their useful properties, this work indicates an unexpected "stringency" of promoter sequences in Clostridium, not reported previously.
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Affiliation(s)
- Paweł M. Mordaka
- Imperial College Centre for
Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
| | - John T. Heap
- Imperial College Centre for
Synthetic Biology, Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom
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61
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Haddad Kashani H, Schmelcher M, Sabzalipoor H, Seyed Hosseini E, Moniri R. Recombinant Endolysins as Potential Therapeutics against Antibiotic-Resistant Staphylococcus aureus: Current Status of Research and Novel Delivery Strategies. Clin Microbiol Rev 2018; 31:e00071-17. [PMID: 29187396 PMCID: PMC5740972 DOI: 10.1128/cmr.00071-17] [Citation(s) in RCA: 112] [Impact Index Per Article: 18.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Staphylococcus aureus is one of the most common pathogens of humans and animals, where it frequently colonizes skin and mucosal membranes. It is of major clinical importance as a nosocomial pathogen and causative agent of a wide array of diseases. Multidrug-resistant strains have become increasingly prevalent and represent a leading cause of morbidity and mortality. For this reason, novel strategies to combat multidrug-resistant pathogens are urgently needed. Bacteriophage-derived enzymes, so-called endolysins, and other peptidoglycan hydrolases with the ability to disrupt cell walls represent possible alternatives to conventional antibiotics. These lytic enzymes confer a high degree of host specificity and could potentially replace or be utilized in combination with antibiotics, with the aim to specifically treat infections caused by Gram-positive drug-resistant bacterial pathogens such as methicillin-resistant S. aureus. LysK is one of the best-characterized endolysins with activity against multiple staphylococcal species. Various approaches to further enhance the antibacterial efficacy and applicability of endolysins have been demonstrated. These approaches include the construction of recombinant endolysin derivatives and the development of novel delivery strategies for various applications, such as the production of endolysins in lactic acid bacteria and their conjugation to nanoparticles. These novel strategies are a major focus of this review.
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Affiliation(s)
- Hamed Haddad Kashani
- Anatomical Sciences Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Mathias Schmelcher
- Institute of Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
| | - Hamed Sabzalipoor
- Department of Nanobiotechnology, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Elahe Seyed Hosseini
- Anatomical Sciences Research Center, Kashan University of Medical Sciences, Kashan, Iran
| | - Rezvan Moniri
- Anatomical Sciences Research Center, Kashan University of Medical Sciences, Kashan, Iran
- Department of Immunology and Microbiology, Kashan University of Medical Sciences, Kashan, Iran
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62
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Disparate subcellular location of putative sortase substrates in Clostridium difficile. Sci Rep 2017; 7:9204. [PMID: 28835650 PMCID: PMC5569036 DOI: 10.1038/s41598-017-08322-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Accepted: 07/07/2017] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile is a gastrointestinal pathogen but how the bacterium colonises this niche is still little understood. Sortase enzymes covalently attach specific bacterial proteins to the peptidoglycan cell wall and are often involved in colonisation by pathogens. Here we show C. difficile proteins CD2537 and CD3392 are functional substrates of sortase SrtB. Through manipulation of the C-terminal regions of these proteins we show the SPKTG motif is essential for covalent attachment to the cell wall. Two additional putative substrates, CD0183 which contains an SPSTG motif, and CD2768 which contains an SPQTG motif, are not cleaved or anchored to the cell wall by sortase. Finally, using an in vivo asymmetric cleavage assay, we show that despite containing a conserved SPKTG motif, in the absence of SrtB these proteins are localised to disparate cellular compartments.
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63
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Wu X, Kwon SJ, Kim J, Kane RS, Dordick JS. Biocatalytic Nanocomposites for Combating Bacterial Pathogens. Annu Rev Chem Biomol Eng 2017; 8:87-113. [DOI: 10.1146/annurev-chembioeng-060816-101612] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Xia Wu
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Seok-Joon Kwon
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
| | - Jungbae Kim
- Department of Chemical and Biological Engineering, Korea University, Seoul 02841, Republic of Korea
| | - Ravi S. Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332
| | - Jonathan S. Dordick
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Biomedical Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180
- Department of Materials Science and Engineering, Rensselaer Polytechnic Institute, Troy, New York 12180
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64
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Mehta KK, Paskaleva EE, Wu X, Grover N, Mundra RV, Chen K, Zhang Y, Yang Z, Feng H, Dordick JS, Kane RS. Newly identified bacteriolytic enzymes that target a wide range of clinical isolates of Clostridium difficile. Biotechnol Bioeng 2016; 113:2568-2576. [PMID: 27260850 PMCID: PMC5367918 DOI: 10.1002/bit.26029] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 05/23/2016] [Accepted: 05/29/2016] [Indexed: 12/18/2022]
Abstract
Clostridium difficile has emerged as a major cause of infectious diarrhea in hospitalized patients, with increasing mortality rate and annual healthcare costs exceeding $3 billion. Since C. difficile infections are associated with the use of antibiotics, there is an urgent need to develop treatments that can inactivate the bacterium selectively without affecting commensal microflora. Lytic enzymes from bacteria and bacteriophages show promise as highly selective and effective antimicrobial agents. These enzymes often have a modular structure, consisting of a catalytic domain and a binding domain. In the current work, using consensus catalytic domain and cell-wall binding domain sequences as probes, we analyzed in silico the genome of C. difficile, as well as phages infecting C. difficile. We identified two genes encoding cell lytic enzymes with possible activity against C. difficile. We cloned the genes in a suitable expression vector, expressed and purified the protein products, and tested enzyme activity in vitro. These newly identified enzymes were found to be active against C. difficile cells in a dose-dependent manner. We achieved a more than 4-log reduction in the number of viable bacteria within 5 h of application. Moreover, we found that the enzymes were active against a wide range of C. difficile clinical isolates. We also characterized the biocatalytic mechanism by identifying the specific bonds cleaved by these enzymes within the cell wall peptidoglycan. These results suggest a new approach to combating the growing healthcare problem associated with C. difficile infections. Biotechnol. Bioeng. 2016;113: 2568-2576. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Krunal K Mehta
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180, New York
| | - Elena E Paskaleva
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180, New York
| | - Xia Wu
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180, New York
| | - Navdeep Grover
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180, New York
| | - Ruchir V Mundra
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180, New York
| | - Kevin Chen
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland
| | - Yongrong Zhang
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland
| | - Zhiyong Yang
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland
| | - Hanping Feng
- Department of Microbial Pathogenesis, University of Maryland Dental School, Baltimore, Maryland
| | - Jonathan S Dordick
- Howard P. Isermann Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, New York.
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, 110 8th Street, Troy, 12180, New York.
| | - Ravi S Kane
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology, 950 Atlantic Drive, Atlanta, 30332, Georgia.
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65
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Moelling K, Broecker F. Fecal microbiota transplantation to fight Clostridium difficile infections and other intestinal diseases. BACTERIOPHAGE 2016; 6:e1251380. [PMID: 28090385 DOI: 10.1080/21597081.2016.1251380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 10/13/2016] [Accepted: 10/18/2016] [Indexed: 12/16/2022]
Abstract
We have analyzed fecal bacterial and viral communities of a patient with recurrent C. difficile infection (rCDI) who was cured by fecal microbiota transplantation (FMT). The "Zürich Patient" experienced immediate cure and has remained free of symptoms for now over 5 y. Donor-similar bacterial compositions after 4.5 y post-FMT demonstrated sustainable engraftment of donor microbiota predominated by Bacteroidetes and Firmicutes bacteria. Appearance of beneficial species Faecalibacterium prausnitzii and Akkermansia municiphila was detected while disease-related Proteobacteria decreased. Stabilization of the microbiota took longer than expected from the rapidly improving clinical symptoms, suggesting the need for longer-lasting patient observation. The virome was mainly composed of Caudovirales bacteriophages but surprisingly also contained sequences related to a Chlorella giant virus that normally infects green algae not known to inhabitate the human intestine. FMT is highly effective against rCDI and is presently broadening its application to other conditions including inflammatory bowel disease (IBD). Here, we discuss the prospects and challenges of FMT against rCDI and other indications including a focus on bacteriophages.
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Affiliation(s)
- Karin Moelling
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical Microbiology, Unversity of Zürich, Zürich, Switzerland
| | - Felix Broecker
- Max Planck Institute for Molecular Genetics, Berlin, Germany; Institute for Medical Microbiology, Unversity of Zürich, Zürich, Switzerland; Max Planck Institute of Colloids and Interfaces, Potsdam, Germany; Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA
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66
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Wu X, Paskaleva EE, Mehta KK, Dordick JS, Kane RS. Wall Teichoic Acids Are Involved in the Medium-Induced Loss of Function of the Autolysin CD11 against Clostridium difficile. Sci Rep 2016; 6:35616. [PMID: 27759081 PMCID: PMC5069495 DOI: 10.1038/srep35616] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 09/23/2016] [Indexed: 01/05/2023] Open
Abstract
Bacterial lysins are potent antibacterial enzymes with potential applications in the treatment of bacterial infections. Some lysins lose activity in the growth media of target bacteria, and the underlying mechanism remains unclear. Here we use CD11, an autolysin of Clostridium difficile, as a model lysin to demonstrate that the inability of this enzyme to kill C. difficile in growth medium is not associated with inhibition of the enzyme activity by medium, or the modification of the cell wall peptidoglycan. Rather, wall teichoic acids (WTAs) appear to prevent the enzyme from binding to the cells and cleaving the cell wall peptidoglycan. By partially blocking the biosynthetic pathway of WTAs with tunicamycin, cell binding improved and the lytic efficacy of CD11 was significantly enhanced. This is the first report of the mechanism of lysin inactivation in growth medium, and provides insights into understanding the behavior of lysins in complex environments, including the gastrointestinal tract.
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Affiliation(s)
- Xia Wu
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, US.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, US
| | - Elena E Paskaleva
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, US
| | - Krunal K Mehta
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, US.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, US
| | - Jonathan S Dordick
- Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, NY, US.,Department of Chemical and Biological Engineering, Rensselaer Polytechnic Institute, Troy, NY, US
| | - Ravi S Kane
- School of Chemical &Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA, US
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67
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Kirk JA, Banerji O, Fagan RP. Characteristics of the Clostridium difficile cell envelope and its importance in therapeutics. Microb Biotechnol 2016; 10:76-90. [PMID: 27311697 PMCID: PMC5270738 DOI: 10.1111/1751-7915.12372] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Revised: 05/26/2016] [Accepted: 05/30/2016] [Indexed: 01/08/2023] Open
Abstract
Clostridium difficile infection (CDI) is a challenging threat to human health. Infections occur after disruption of the normal microbiota, most commonly through the use of antibiotics. Current treatment for CDI largely relies on the broad‐spectrum antibiotics vancomycin and metronidazole that further disrupt the microbiota resulting in frequent recurrence, highlighting the need for C. difficile‐specific antimicrobials. The cell surface of C. difficile represents a promising target for the development of new drugs. C. difficile possesses a highly deacetylated peptidoglycan cell wall containing unique secondary cell wall polymers. Bound to the cell wall is an essential S‐layer, formed of SlpA and decorated with an additional 28 related proteins. In addition to the S‐layer, many other cell surface proteins have been identified, including several with roles in host colonization. This review aims to summarize our current understanding of these different C. difficile cell surface components and their viability as therapeutic targets.
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Affiliation(s)
- Joseph A Kirk
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Oishik Banerji
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert P Fagan
- Krebs Institute, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, S10 2TN, UK
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68
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Dunne M, Leicht S, Krichel B, Mertens HDT, Thompson A, Krijgsveld J, Svergun DI, Gómez-Torres N, Garde S, Uetrecht C, Narbad A, Mayer MJ, Meijers R. Crystal Structure of the CTP1L Endolysin Reveals How Its Activity Is Regulated by a Secondary Translation Product. J Biol Chem 2016; 291:4882-93. [PMID: 26683375 PMCID: PMC4777826 DOI: 10.1074/jbc.m115.671172] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 12/16/2015] [Indexed: 11/18/2022] Open
Abstract
Bacteriophages produce endolysins, which lyse the bacterial host cell to release newly produced virions. The timing of lysis is regulated and is thought to involve the activation of a molecular switch. We present a crystal structure of the activated endolysin CTP1L that targets Clostridium tyrobutyricum, consisting of a complex between the full-length protein and an N-terminally truncated C-terminal cell wall binding domain (CBD). The truncated CBD is produced through an internal translation start site within the endolysin gene. Mutants affecting the internal translation site change the oligomeric state of the endolysin and reduce lytic activity. The activity can be modulated by reconstitution of the full-length endolysin-CBD complex with free CBD. The same oligomerization mechanism applies to the CD27L endolysin that targets Clostridium difficile and the CS74L endolysin that targets Clostridium sporogenes. When the CTP1L endolysin gene is introduced into the commensal bacterium Lactococcus lactis, the truncated CBD is also produced, showing that the alternative start codon can be used in other bacterial species. The identification of a translational switch affecting oligomerization presented here has implications for the design of effective endolysins for the treatment of bacterial infections.
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Affiliation(s)
- Matthew Dunne
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Stefan Leicht
- the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Boris Krichel
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany
| | - Haydyn D T Mertens
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Andrew Thompson
- the Synchrotron Soleil, L'Orme des Merisiers, BP 48, Saint Aubin, 91192 Gif sur Yvette, France
| | - Jeroen Krijgsveld
- the European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - Dmitri I Svergun
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany
| | - Natalia Gómez-Torres
- the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Departamento de Tecnología de Alimentos, Carretera de La Coruña km 7, 28040 Madrid, Spain
| | - Sonia Garde
- the Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Departamento de Tecnología de Alimentos, Carretera de La Coruña km 7, 28040 Madrid, Spain
| | - Charlotte Uetrecht
- the Heinrich Pette Institute, Leibniz Institute for Experimental Virology, Martinistrasse 52, 20251 Hamburg, Germany, the European XFEL GmbH, Notkestrasse 85, 22607 Hamburg, Germany, and
| | - Arjan Narbad
- the Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - Melinda J Mayer
- the Institute of Food Research, Colney, Norwich NR4 7UA, United Kingdom
| | - Rob Meijers
- From the European Molecular Biology Laboratory, Notkestrasse 85, 22607 Hamburg, Germany,
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69
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Büttner FM, Faulhaber K, Forchhammer K, Maldener I, Stehle T. Enabling cell-cell communication via nanopore formation: structure, function and localization of the unique cell wall amidase AmiC2 of Nostoc punctiforme. FEBS J 2016; 283:1336-50. [PMID: 26833702 DOI: 10.1111/febs.13673] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 01/07/2016] [Accepted: 01/27/2016] [Indexed: 01/14/2023]
Abstract
UNLABELLED To orchestrate a complex life style in changing environments, the filamentous cyanobacterium Nostoc punctiforme facilitates communication between neighboring cells through septal junction complexes. This is achieved by nanopores that perforate the peptidoglycan (PGN) layer and traverse the cell septa. The N-acetylmuramoyl-l-alanine amidase AmiC2 (Npun_F1846; EC 3.5.1.28) in N. punctiforme generates arrays of such nanopores in the septal PGN, in contrast to homologous amidases that mediate daughter cell separation after cell division in unicellular bacteria. Nanopore formation is therefore a novel property of AmiC homologs. Immunofluorescence shows that native AmiC2 localizes to the maturing septum. The high-resolution crystal structure (1.12 Å) of its catalytic domain (AmiC2-cat) differs significantly from known structures of cell splitting and PGN recycling amidases. A wide and shallow binding cavity allows easy access of the substrate to the active site, which harbors an essential zinc ion. AmiC2-cat exhibits strong hydrolytic activity in vitro. A single point mutation of a conserved glutamate near the zinc ion results in total loss of activity, whereas zinc removal leads to instability of AmiC2-cat. An inhibitory α-helix, as found in the Escherichia coli AmiC(E. coli) structure, is absent. Taken together, our data provide insight into the cell-biological, biochemical and structural properties of an unusual cell wall lytic enzyme that generates nanopores for cell-cell communication in multicellular cyanobacteria. The novel structural features of the catalytic domain and the unique biological function of AmiC2 hint at mechanisms of action and regulation that are distinct from other amidases. DATABASE The AmiC2-cat structure has been deposited in the Protein Data Bank under accession number 5EMI.
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Affiliation(s)
- Felix M Büttner
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany
| | - Katharina Faulhaber
- Interfaculty Institute for Microbiology and Infection Medicine, Department of Organismic Interactions, University of Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute for Microbiology and Infection Medicine, Department of Organismic Interactions, University of Tübingen, Germany
| | - Iris Maldener
- Interfaculty Institute for Microbiology and Infection Medicine, Department of Organismic Interactions, University of Tübingen, Germany
| | - Thilo Stehle
- Interfaculty Institute of Biochemistry, University of Tübingen, Germany.,Department of Pediatrics, Vanderbilt University School of Medicine, Nashville, TN, USA
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70
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Van Tassell ML, Angela Daum M, Kim JS, Miller MJ. Creative lysins: Listeria and the engineering of antimicrobial enzymes. Curr Opin Biotechnol 2015; 37:88-96. [PMID: 26710271 DOI: 10.1016/j.copbio.2015.10.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Revised: 10/13/2015] [Accepted: 10/30/2015] [Indexed: 01/31/2023]
Abstract
Cell wall lytic enzymes have been of increasing interest as antimicrobials for targeting Gram-positive spoilage and pathogenic bacteria, largely due to the development of strains resistant to antibiotics and bacteriophage therapy. Such lysins show considerable promise against Listeria monocytogenes, a primary concern in food-processing environments, but there is room for improvement via protein engineering. Advances in antilisterial applications could benefit from recent developments in lysin biotechnology that have largely targeted other organisms. Herein we present various considerations for the future development of lysins, including environmental factors, cell physiology concerns, and dynamics of protein architecture. Our goal is to review key developments in lysin biotechnology to provide a contextual framework for the current models of lysin-cell interactions and highlight key considerations for the characterization and design of novel lytic enzymes.
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Affiliation(s)
- Maxwell L Van Tassell
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL 61801, USA
| | - M Angela Daum
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL 61801, USA
| | - Jun-Seob Kim
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL 61801, USA
| | - Michael J Miller
- Department of Food Science & Human Nutrition, University of Illinois, Urbana, IL 61801, USA.
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71
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Using a Novel Lysin To Help Control Clostridium difficile Infections. Antimicrob Agents Chemother 2015; 59:7447-57. [PMID: 26392484 DOI: 10.1128/aac.01357-15] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 09/11/2015] [Indexed: 02/06/2023] Open
Abstract
As a consequence of excessive antibiotic therapies in hospitalized patients, Clostridium difficile, a Gram-positive anaerobic spore-forming intestinal pathogen, is the leading cause of hospital-acquired diarrhea and colitis. Drug treatments for these diseases are often complicated by antibiotic-resistant strains and a high frequency of treatment failures and relapse; therefore, novel nonantibiotic approaches may prove to be more effective. In this study, we recombinantly expressed a prophage lysin identified from a C. difficile strain, CD630, which we named PlyCD. PlyCD was found to have lytic activity against specific C. difficile strains. However, the recombinantly expressed catalytic domain of this protein, PlyCD1-174, displayed significantly greater lytic activity (>4-log kill) and a broader lytic spectrum against C. difficile strains while still retaining a high degree of specificity toward C. difficile versus commensal clostridia and other bacterial species. Our data also indicated that noneffective doses of vancomycin and PlyCD1-174 when combined in vitro could be significantly more bactericidal against C. difficile. In an ex vivo treatment model of mouse colon infection, we found that PlyCD1-174 functioned in the presence of intestinal contents, significantly decreasing colonizing C. difficile compared to controls. Together, these data suggest that PlyCD1-174 has potential as a novel therapeutic for clinical application against C. difficile infection, either alone or in combination with other preexisting treatments to improve their efficacy.
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72
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Peltier J, Shaw HA, Couchman EC, Dawson LF, Yu L, Choudhary JS, Kaever V, Wren BW, Fairweather NF. Cyclic diGMP regulates production of sortase substrates of Clostridium difficile and their surface exposure through ZmpI protease-mediated cleavage. J Biol Chem 2015; 290:24453-69. [PMID: 26283789 PMCID: PMC4591827 DOI: 10.1074/jbc.m115.665091] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2015] [Indexed: 01/12/2023] Open
Abstract
In Gram-positive pathogens, surface proteins may be covalently anchored to the bacterial peptidoglycan by sortase, a cysteine transpeptidase enzyme. In contrast to other Gram-positive bacteria, only one single sortase enzyme, SrtB, is conserved between strains of Clostridium difficile. Sortase-mediated peptidase activity has been reported in vitro, and seven potential substrates have been identified. Here, we demonstrate the functionality of sortase in C. difficile. We identify two sortase-anchored proteins, the putative adhesins CD2831 and CD3246, and determine the cell wall anchor structure of CD2831. The C-terminal PPKTG sorting motif of CD2831 is cleaved between the threonine and glycine residues, and the carboxyl group of threonine is amide-linked to the side chain amino group of diaminopimelic acid within the peptidoglycan peptide stem. We show that CD2831 protein levels are elevated in the presence of high intracellular cyclic diGMP (c-diGMP) concentrations, in agreement with the control of CD2831 expression by a c-diGMP-dependent type II riboswitch. Low c-diGMP levels induce the release of CD2831 and presumably CD3246 from the surface of cells. This regulation is mediated by proteolytic cleavage of CD2831 and CD3246 by the zinc metalloprotease ZmpI, whose expression is controlled by a type I c-diGMP riboswitch. These data reveal a novel regulatory mechanism for expression of two sortase substrates by the secondary messenger c-diGMP, on which surface anchoring is dependent.
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Affiliation(s)
- Johann Peltier
- From the Department of Life Sciences, Center for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Helen A Shaw
- From the Department of Life Sciences, Center for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Edward C Couchman
- From the Department of Life Sciences, Center for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom
| | - Lisa F Dawson
- the Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Lu Yu
- the Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom, and
| | - Jyoti S Choudhary
- the Wellcome Trust Sanger Institute, Hinxton CB10 1SA, United Kingdom, and
| | - Volkhard Kaever
- the Research Core Unit Metabolomics, Hannover Medical School, Hannover D-30625, Germany
| | - Brendan W Wren
- the Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Neil F Fairweather
- From the Department of Life Sciences, Center for Molecular Bacteriology and Infection, Imperial College London, London SW7 2AZ, United Kingdom,
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73
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Nakonieczna A, Cooper CJ, Gryko R. Bacteriophages and bacteriophage-derived endolysins as potential therapeutics to combat Gram-positive spore forming bacteria. J Appl Microbiol 2015; 119:620-31. [PMID: 26109320 DOI: 10.1111/jam.12881] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 05/28/2015] [Accepted: 06/11/2015] [Indexed: 01/21/2023]
Abstract
Since their discovery in 1915, bacteriophages have been routinely used within Eastern Europe to treat a variety of bacterial infections. Although initially ignored by the West due to the success of antibiotics, increasing levels and diversity of antibiotic resistance is driving a renaissance for bacteriophage-derived therapy, which is in part due to the highly specific nature of bacteriophages as well as their relative abundance. This review focuses on the bacteriophages and derived lysins of relevant Gram-positive spore formers within the Bacillus cereus group and Clostridium genus that could have applications within the medical, food and environmental sectors.
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Affiliation(s)
- A Nakonieczna
- Biological Threats Identification and Countermeasure Center of the Military Institute of Hygiene and Epidemiology, Pulawy, Poland
| | - C J Cooper
- Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Stockholm, Sweden
| | - R Gryko
- Biological Threats Identification and Countermeasure Center of the Military Institute of Hygiene and Epidemiology, Pulawy, Poland
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74
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Roach DR, Donovan DM. Antimicrobial bacteriophage-derived proteins and therapeutic applications. BACTERIOPHAGE 2015; 5:e1062590. [PMID: 26442196 DOI: 10.1080/21597081.2015.1062590] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/08/2015] [Accepted: 06/11/2015] [Indexed: 02/07/2023]
Abstract
Antibiotics have the remarkable power to control bacterial infections. Unfortunately, widespread use, whether regarded as prudent or not, has favored the emergence and persistence of antibiotic resistant strains of human pathogenic bacteria, resulting in a global health threat. Bacteriophages (phages) are parasites that invade the cells of virtually all known bacteria. Phages reproduce by utilizing the host cell's machinery to replicate viral proteins and genomic material, generally damaging and killing the cell in the process. Thus, phage can be exploited therapeutically as bacteriolytic agents against bacteria. Furthermore, understanding of the molecular processes involved in the viral life cycle, particularly the entry and cell lysis steps, has led to the development of viral proteins as antibacterial agents. Here we review the current preclinical state of using phage-derived endolysins, virion-associated peptidoglycan hydrolases, polysaccharide depolymerases, and holins for the treatment of bacterial infection. The scope of this review is a focus on the viral proteins that have been assessed for protective effects against human pathogenic bacteria in animal models of infection and disease.
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Affiliation(s)
- Dwayne R Roach
- Molecular Biology of the Genes in Extremophiles; Department of Microbiology; Institute Pasteur ; Paris, France
| | - David M Donovan
- Animal Biosciences and Biotechnology Laboratory; NEA; Agricultural Research Service; US Department of Agriculture ; Beltsville, MD USA
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75
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Ugorcakova J, Medzova L, Solteszova B, Bukovska G. Characterization of a phiBP endolysin encoded by the Paenibacillus polymyxa CCM 7400 phage. FEMS Microbiol Lett 2015; 362:fnv098. [PMID: 26085488 DOI: 10.1093/femsle/fnv098] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Accepted: 06/09/2015] [Indexed: 01/22/2023] Open
Abstract
Endolysin (gp1.2) from the Paenibacillus polymyxa CCM 7400 temperate phage phiBP has a modular structure consisting of an N-terminal region with a catalytic glycosyl hydrolase 25 domain and a C-terminal cell wall-binding domain. The entire gene of this endolysin and fragments containing its catalytic and binding domains separately were cloned into expression vectors and the corresponding recombinant proteins were expressed in Escherichia coli and purified by affinity chromatography. The lytic activities of endolysin and its catalytic domain were tested on cell wall substrates from paenibacilli, bacilli, corynebacteria and E. coli. The presence of a cell wall-binding domain was found to be essential, as the phiBP endolysin was fully active only as a full-length protein. The binding ability of the cell wall-binding domain alone and in fusion with green fluorescent protein was demonstrated by specific binding assays to the cell surface of P. polymyxa CCM 7400 and to those of other Paenibacillus strains. Thus the ability of phiBP endolysin to hydrolyze the paenibacilli cell wall was confirmed.
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Affiliation(s)
- Jana Ugorcakova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravská cesta 21, 845 51 Bratislava, Slovakia
| | - Livia Medzova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravská cesta 21, 845 51 Bratislava, Slovakia
| | - Barbora Solteszova
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravská cesta 21, 845 51 Bratislava, Slovakia
| | - Gabriela Bukovska
- Department of Genomics and Biotechnology, Institute of Molecular Biology, Slovak Academy of Sciences, Dubravská cesta 21, 845 51 Bratislava, Slovakia
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76
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Hargreaves KR, Clokie MRJ. A Taxonomic Review of Clostridium difficile Phages and Proposal of a Novel Genus, "Phimmp04likevirus". Viruses 2015; 7:2534-41. [PMID: 26008700 PMCID: PMC4452919 DOI: 10.3390/v7052534] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2015] [Accepted: 05/13/2015] [Indexed: 02/03/2023] Open
Abstract
Currently, only three phages that infect the medically important bacterium Clostridium difficile have been discussed by the International Committee of Viral Taxonomy (ICTV). They are all myoviruses, and have been assigned to the genus “phicd119likevirus”. An additional nine phages have since been described in the literature with their genome data available. The Phicd119likevirus is named after the type species: the myovirus ΦCD119 which was the first C. difficile phage to be sequenced. The two additional myoviruses, ϕCD27 and φC2, also fall into this genus based on the similarity of their genome and morphological characteristics. The other nine phages have not been assigned to this genus, and four of them do not fit the criteria for the current taxonomic grouping. We have applied protein clustering analysis to determine their phylogenetic relationships. From these results we propose an additional myoviridae genus, that we term “phiMMP04likevirus”.
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Affiliation(s)
- Katherine R Hargreaves
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicestershire LE1 9HN, UK.
- Department of Ecology and Evolutionary Biology, University of Arizona, AZ 85721, USA.
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicestershire LE1 9HN, UK.
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77
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Wu X, Grover N, Paskaleva EE, Mundra RV, Page MA, Kane RS, Dordick JS. Characterization of the activity of the spore cortex lytic enzyme CwlJ1. Biotechnol Bioeng 2015; 112:1365-75. [DOI: 10.1002/bit.25565] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2014] [Revised: 01/27/2015] [Accepted: 02/02/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Xia Wu
- Howard P. Isermann Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; 110 8th Street, Troy New York 12180
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York 12180
| | - Navdeep Grover
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York 12180
| | - Elena E. Paskaleva
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York 12180
| | - Ruchir V. Mundra
- Howard P. Isermann Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; 110 8th Street, Troy New York 12180
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York 12180
| | - Martin A. Page
- U.S. Army Engineer Research and Development Center; Construction Engineering Research Laboratory; Champaign Illinois
| | - Ravi S. Kane
- Howard P. Isermann Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; 110 8th Street, Troy New York 12180
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York 12180
| | - Jonathan S. Dordick
- Howard P. Isermann Department of Chemical and Biological Engineering; Rensselaer Polytechnic Institute; 110 8th Street, Troy New York 12180
- Center for Biotechnology and Interdisciplinary Studies; Rensselaer Polytechnic Institute; Troy New York 12180
- Department of Materials Science and Engineering; Department of Biology; Department of Biomedical Engineering; Rensselaer Polytechnic Institute; Troy New York 12180
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78
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Rodríguez-Rubio L, Gutiérrez D, Donovan DM, Martínez B, Rodríguez A, García P. Phage lytic proteins: biotechnological applications beyond clinical antimicrobials. Crit Rev Biotechnol 2015; 36:542-52. [PMID: 25603721 DOI: 10.3109/07388551.2014.993587] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Most bacteriophages encode two types of cell wall lytic proteins: endolysins (lysins) and virion-associated peptidoglycan hydrolases. Both enzymes have the ability to degrade the peptidoglycan of Gram-positive bacteria resulting in cell lysis when they are applied externally. Bacteriophage lytic proteins have a demonstrated potential in treating animal models of infectious diseases. There has also been an increase in the study of these lytic proteins for their application in areas such as food safety, pathogen detection/diagnosis, surfaces disinfection, vaccine development and nanotechnology. This review summarizes the more recent developments, outlines the full potential of these proteins to develop new biotechnological tools and discusses the feasibility of these proposals.
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Affiliation(s)
- Lorena Rodríguez-Rubio
- a DairySafe Group, Department of Technology and Biotechnology of Dairy Products , Instituto de Productos Lácteos de Asturias (IPLA-CSIC) , Villaviciosa , Asturias , Spain and
| | - Diana Gutiérrez
- a DairySafe Group, Department of Technology and Biotechnology of Dairy Products , Instituto de Productos Lácteos de Asturias (IPLA-CSIC) , Villaviciosa , Asturias , Spain and
| | - David M Donovan
- b Animal Biosciences and Biotechnology Laboratory , BARC, ARS, USDA , Beltsville , MD , USA
| | - Beatriz Martínez
- a DairySafe Group, Department of Technology and Biotechnology of Dairy Products , Instituto de Productos Lácteos de Asturias (IPLA-CSIC) , Villaviciosa , Asturias , Spain and
| | - Ana Rodríguez
- a DairySafe Group, Department of Technology and Biotechnology of Dairy Products , Instituto de Productos Lácteos de Asturias (IPLA-CSIC) , Villaviciosa , Asturias , Spain and
| | - Pilar García
- a DairySafe Group, Department of Technology and Biotechnology of Dairy Products , Instituto de Productos Lácteos de Asturias (IPLA-CSIC) , Villaviciosa , Asturias , Spain and
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79
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Bacteriophage PBC1 and its endolysin as an antimicrobial agent against Bacillus cereus. Appl Environ Microbiol 2015; 81:2274-83. [PMID: 25595773 DOI: 10.1128/aem.03485-14] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bacillus cereus is an opportunistic human pathogen responsible for food poisoning and other, nongastrointestinal infections. Due to the emergence of multidrug-resistant B. cereus strains, the demand for alternative therapeutic options is increasing. To address these problems, we isolated and characterized a Siphoviridae virulent phage, PBC1, and its lytic enzymes. PBC1 showed a very narrow host range, infecting only 1 of 22 B. cereus strains. Phylogenetic analysis based on the major capsid protein revealed that PBC1 is more closely related to the Bacillus clarkii phage BCJA1c and phages of lactic acid bacteria than to the phages infecting B. cereus. Whole-genome comparison showed that the late-gene region, including the terminase gene, structural genes, and holin gene of PBC1, is similar to that from B. cereus temperate phage 250, whereas their endolysins are different. Compared to the extreme host specificity of PBC1, its endolysin, LysPBC1, showed a much broader lytic spectrum, albeit limited to the genus Bacillus. The catalytic domain of LysPBC1 when expressed alone also showed Bacillus-specific lytic activity, which was lower against the B. cereus group but higher against the Bacillus subtilis group than the full-length protein. Taken together, these results suggest that the virulent phage PBC1 is a useful component of a phage cocktail to control B. cereus, even with its exceptionally narrow host range, as it can kill a strain of B. cereus that is not killed by other phages, and that LysPBC1 is an alternative biocontrol agent against B. cereus.
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80
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Hargreaves KR, Flores CO, Lawley TD, Clokie MRJ. Abundant and diverse clustered regularly interspaced short palindromic repeat spacers in Clostridium difficile strains and prophages target multiple phage types within this pathogen. mBio 2014; 5:e01045-13. [PMID: 25161187 PMCID: PMC4173771 DOI: 10.1128/mbio.01045-13] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 07/01/2014] [Indexed: 01/04/2023] Open
Abstract
UNLABELLED Clostridium difficile is an important human-pathogenic bacterium causing antibiotic-associated nosocomial infections worldwide. Mobile genetic elements and bacteriophages have helped shape C. difficile genome evolution. In many bacteria, phage infection may be controlled by a form of bacterial immunity called the clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) system. This uses acquired short nucleotide sequences (spacers) to target homologous sequences (protospacers) in phage genomes. C. difficile carries multiple CRISPR arrays, and in this paper we examine the relationships between the host- and phage-carried elements of the system. We detected multiple matches between spacers and regions in 31 C. difficile phage and prophage genomes. A subset of the spacers was located in prophage-carried CRISPR arrays. The CRISPR spacer profiles generated suggest that related phages would have similar host ranges. Furthermore, we show that C. difficile strains of the same ribotype could either have similar or divergent CRISPR contents. Both synonymous and nonsynonymous mutations in the protospacer sequences were identified, as well as differences in the protospacer adjacent motif (PAM), which could explain how phages escape this system. This paper illustrates how the distribution and diversity of CRISPR spacers in C. difficile, and its prophages, could modulate phage predation for this pathogen and impact upon its evolution and pathogenicity. IMPORTANCE Clostridium difficile is a significant bacterial human pathogen which undergoes continual genome evolution, resulting in the emergence of new virulent strains. Phages are major facilitators of genome evolution in other bacterial species, and we use sequence analysis-based approaches in order to examine whether the CRISPR/Cas system could control these interactions across divergent C. difficile strains. The presence of spacer sequences in prophages that are homologous to phage genomes raises an extra level of complexity in this predator-prey microbial system. Our results demonstrate that the impact of phage infection in this system is widespread and that the CRISPR/Cas system is likely to be an important aspect of the evolutionary dynamics in C. difficile.
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Affiliation(s)
- Katherine R Hargreaves
- Department of Infection, Inflammation and Immunity, University of Leicester, Leicester, United Kingdom
| | - Cesar O Flores
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia, USA
| | - Trevor D Lawley
- Microbial Pathogenesis Laboratory, Wellcome Trust Sanger Institute, Hinxton, United Kingdom
| | - Martha R J Clokie
- Department of Infection, Inflammation and Immunity, University of Leicester, Leicester, United Kingdom
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81
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Dunne M, Mertens HDT, Garefalaki V, Jeffries CM, Thompson A, Lemke EA, Svergun DI, Mayer MJ, Narbad A, Meijers R. The CD27L and CTP1L endolysins targeting Clostridia contain a built-in trigger and release factor. PLoS Pathog 2014; 10:e1004228. [PMID: 25058163 PMCID: PMC4110038 DOI: 10.1371/journal.ppat.1004228] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2013] [Accepted: 05/19/2014] [Indexed: 02/04/2023] Open
Abstract
The bacteriophage ΦCD27 is capable of lysing Clostridium difficile, a pathogenic bacterium that is a major cause for nosocomial infection. A recombinant CD27L endolysin lyses C. difficile in vitro, and represents a promising alternative as a bactericide. To better understand the lysis mechanism, we have determined the crystal structure of an autoproteolytic fragment of the CD27L endolysin. The structure covers the C-terminal domain of the endolysin, and represents a novel fold that is identified in a number of lysins that target Clostridia bacteria. The structure indicates endolysin cleavage occurs at the stem of the linker connecting the catalytic domain with the C-terminal domain. We also solved the crystal structure of the C-terminal domain of a slow cleaving mutant of the CTP1L endolysin that targets C. tyrobutyricum. Two distinct dimerization modes are observed in the crystal structures for both endolysins, despite a sequence identity of only 22% between the domains. The dimers are validated to be present for the full length protein in solution by right angle light scattering, small angle X-ray scattering and cross-linking experiments using the cross-linking amino acid p-benzoyl-L-phenylalanine (pBpa). Mutagenesis on residues contributing to the dimer interfaces indicates that there is a link between the dimerization modes and the autocleavage mechanism. We show that for the CTP1L endolysin, there is a reduction in lysis efficiency that is proportional to the cleavage efficiency. We propose a model for endolysin triggering, where the extended dimer presents the inactive state, and a switch to the side-by-side dimer triggers the cleavage of the C-terminal domain. This leads to the release of the catalytic portion of the endolysin, enabling the efficient digestion of the bacterial cell wall. Clostridium difficile infection is a common cause of hospital-acquired diarrhea, following broad-spectrum antibiotic treatment particularly in elderly patients. Bacteriophage therapy could provide an alternative treatment, but a better understanding of the viral components that lyse the bacterial cell is necessary. Here, we report on the activation of two endolysins from bacteriophages that lyse Clostridia. The structures of autoproteolytic fragments of two endolysins were determined by X-ray crystallography. Based on the structures, we introduced mutations that affect the autolytic cleavage of the enzymatic portion of the endolysins, and we show that two oligomeric states have an effect on the cleavage mechanism. Moreover, the lysis activity is affected when autocleavage is inhibited for one endolysin. We propose that the cleavage and oligomerization are linked, and they provide the endolysin with a trigger and release mechanism that leads to activation. The identification of a trigger and release factor may not only be relevant to Clostridia endolysins, but could be an important factor in the triggering of many bacteriophage endolysins. A fuller understanding of this activation mechanism will help in the design of recombinant endolysins or bacteriophages with a more efficient therapeutic potential.
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Affiliation(s)
- Matthew Dunne
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | | | | | - Cy M. Jeffries
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
| | - Andrew Thompson
- Synchrotron Soleil, L'Orme des Merisiers, Saint Aubin, Gif sur Yvette, France
| | - Edward A. Lemke
- European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Melinda J. Mayer
- Institute of Food Research, Colney, Norwich, United Kingdom
- * E-mail: (MJM); (RM)
| | - Arjan Narbad
- Institute of Food Research, Colney, Norwich, United Kingdom
| | - Rob Meijers
- European Molecular Biology Laboratory (EMBL), Hamburg, Germany
- * E-mail: (MJM); (RM)
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82
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Hargreaves KR, Clokie MRJ. Clostridium difficile phages: still difficult? Front Microbiol 2014; 5:184. [PMID: 24808893 PMCID: PMC4009436 DOI: 10.3389/fmicb.2014.00184] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/03/2014] [Indexed: 12/18/2022] Open
Abstract
Phages that infect Clostridium difficile were first isolated for typing purposes in the 1980s, but their use was short lived. However, the rise of C. difficile epidemics over the last decade has triggered a resurgence of interest in using phages to combat this pathogen. Phage therapy is an attractive treatment option for C. difficile infection, however, developing suitable phages is challenging. In this review we summarize the difficulties faced by researchers in this field, and we discuss the solutions and strategies used for the development of C. difficile phages for use as novel therapeutics. Epidemiological data has highlighted the diversity and distribution of C. difficile, and shown that novel strains continue to emerge in clinical settings. In parallel with epidemiological studies, advances in molecular biology have bolstered our understanding of C. difficile biology, and our knowledge of phage–host interactions in other bacterial species. These three fields of biology have therefore paved the way for future work on C. difficile phages to progress and develop. Benefits of using C. difficile phages as therapeutic agents include the fact that they have highly specific interactions with their bacterial hosts. Studies also show that they can reduce bacterial numbers in both in vitro and in vivo systems. Genetic analysis has revealed the genomic diversity among these phages and provided an insight into their taxonomy and evolution. No strictly virulent C. difficile phages have been reported and this contributes to the difficulties with their therapeutic exploitation. Although treatment approaches using the phage-encoded endolysin protein have been explored, the benefits of using “whole-phages” are such that they remain a major research focus. Whilst we don’t envisage working with C. difficile phages will be problem-free, sufficient study should inform future strategies to facilitate their development to combat this problematic pathogen.
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Affiliation(s)
- Katherine R Hargreaves
- Department of Infection, Immunity and Inflammation, University of Leicester Leicester, UK
| | - Martha R J Clokie
- Department of Infection, Immunity and Inflammation, University of Leicester Leicester, UK
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83
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Tišáková L, Vidová B, Farkašovská J, Godány A. Bacteriophage endolysin Lyt μ1/6: characterization of the C-terminal binding domain. FEMS Microbiol Lett 2013; 350:199-208. [DOI: 10.1111/1574-6968.12338] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Revised: 11/14/2013] [Accepted: 11/14/2013] [Indexed: 11/29/2022] Open
Affiliation(s)
- Lenka Tišáková
- Department of Genomics and Biotechnology; Laboratory of Prokaryotic Biology; Institute of Molecular Biology Slovak Academy of Sciences (IMB SAS); Bratislava Slovakia
| | - Barbora Vidová
- Department of Genomics and Biotechnology; Laboratory of Prokaryotic Biology; Institute of Molecular Biology Slovak Academy of Sciences (IMB SAS); Bratislava Slovakia
| | - Jarmila Farkašovská
- Department of Genomics and Biotechnology; Laboratory of Prokaryotic Biology; Institute of Molecular Biology Slovak Academy of Sciences (IMB SAS); Bratislava Slovakia
| | - Andrej Godány
- Department of Genomics and Biotechnology; Laboratory of Prokaryotic Biology; Institute of Molecular Biology Slovak Academy of Sciences (IMB SAS); Bratislava Slovakia
- Faculty of Natural Sciences; Department of Biotechnology; University of Ss. Cyril and Methodius in Trnava; Trnava Slovakia
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84
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Kumar A, Kumar S, Kumar D, Mishra A, Dewangan RP, Shrivastava P, Ramachandran S, Taneja B. The structure of Rv3717 reveals a novel amidase from Mycobacterium tuberculosis. ACTA CRYSTALLOGRAPHICA. SECTION D, BIOLOGICAL CRYSTALLOGRAPHY 2013; 69:2543-54. [PMID: 24311595 PMCID: PMC3852659 DOI: 10.1107/s0907444913026371] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2013] [Accepted: 09/24/2013] [Indexed: 11/16/2022]
Abstract
Bacterial N-acetylmuramoyl-L-alanine amidases are cell-wall hydrolases that hydrolyze the bond between N-acetylmuramic acid and L-alanine in cell-wall glycopeptides. Rv3717 of Mycobacterium tuberculosis has been identified as a unique autolysin that lacks a cell-wall-binding domain (CBD) and its structure has been determined to 1.7 Å resolution by the Pt-SAD phasing method. Rv3717 possesses an α/β-fold and is a zinc-dependent hydrolase. The structure reveals a short flexible hairpin turn that partially occludes the active site and may be involved in autoregulation. This type of autoregulation of activity of PG hydrolases has been observed in Bartonella henselae amidase (AmiB) and may be a general mechanism used by some of the redundant amidases to regulate cell-wall hydrolase activity in bacteria. Rv3717 utilizes its net positive charge for substrate binding and exhibits activity towards a broad spectrum of substrate cell walls. The enzymatic activity of Rv3717 was confirmed by isolation and identification of its enzymatic products by LC/MS. These studies indicate that Rv3717, an N-acetylmuramoyl-L-alanine amidase from M. tuberculosis, represents a new family of lytic amidases that do not have a separate CBD and are regulated conformationally.
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Affiliation(s)
- Atul Kumar
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Sanjiv Kumar
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Dilip Kumar
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Arpit Mishra
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Rikeshwer P. Dewangan
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | - Priyanka Shrivastava
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
| | | | - Bhupesh Taneja
- Structural Biology Unit, CSIR–IGIB, South Campus, Mathura Road, New Delhi 110 025, India
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85
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Prigozhin DM, Mavrici D, Huizar JP, Vansell HJ, Alber T. Structural and biochemical analyses of Mycobacterium tuberculosis N-acetylmuramyl-L-alanine amidase Rv3717 point to a role in peptidoglycan fragment recycling. J Biol Chem 2013; 288:31549-55. [PMID: 24019530 DOI: 10.1074/jbc.m113.510792] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Peptidoglycan hydrolases are key enzymes in bacterial cell wall homeostasis. Understanding the substrate specificity and biochemical activity of peptidoglycan hydrolases in Mycobacterium tuberculosis is of special interest as it can aid in the development of new cell wall targeting therapeutics. In this study, we report biochemical and structural characterization of the mycobacterial N-acetylmuramyl-L-alanine amidase, Rv3717. The crystal structure of Rv3717 in complex with a dipeptide product shows that, compared with previously characterized peptidoglycan amidases, the enzyme contains an extra disulfide-bonded β-hairpin adjacent to the active site. The structure of two intermediates in assembly reveal that Zn(2+) binding rearranges active site residues, and disulfide formation promotes folding of the β-hairpin. Although Zn(2+) is required for hydrolysis of muramyl dipeptide, disulfide oxidation is not required for activity on this substrate. The orientation of the product in the active site suggests a role for a conserved glutamate (Glu-200) in catalysis; mutation of this residue abolishes activity. The product binds at the head of a closed tunnel, and the enzyme showed no activity on polymerized peptidoglycan. These results point to a potential role for Rv3717 in peptidoglycan fragment recycling.
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Affiliation(s)
- Daniil M Prigozhin
- From the Department of Molecular and Cell Biology, University of California, Berkeley, California 94720-3220
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86
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Rocaboy M, Herman R, Sauvage E, Remaut H, Moonens K, Terrak M, Charlier P, Kerff F. The crystal structure of the cell division amidase AmiC reveals the fold of the AMIN domain, a new peptidoglycan binding domain. Mol Microbiol 2013; 90:267-77. [PMID: 23927005 DOI: 10.1111/mmi.12361] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2013] [Indexed: 11/29/2022]
Abstract
Binary fission is the ultimate step of the prokaryotic cell cycle. In Gram-negative bacteria like Escherichia coli, this step implies the invagination of three biological layers (cytoplasmic membrane, peptidoglycan and outer membrane), biosynthesis of the new poles and eventually, daughter cells separation. The latter requires the coordinated action of the N-acetylmuramyl-L-alanine amidases AmiA/B/C and their LytM activators EnvC and NlpD to cleave the septal peptidoglycan. We present here the 2.5 Å crystal structure of AmiC which includes the first report of an AMIN domain structure, a β-sandwich of two symmetrical four-stranded β-sheets exposing highly conserved motifs on the two outer faces. We show that this N-terminal domain, involved in the localization of AmiC at the division site, is a new peptidoglycan-binding domain. The C-terminal catalytic domain shows an auto-inhibitory alpha helix obstructing the active site. AmiC lacking this helix exhibits by itself an activity comparable to that of the wild type AmiC activated by NlpD. We also demonstrate the interaction between AmiC and NlpD by microscale thermophoresis and confirm the importance of the active site blocking alpha helix in the regulation of the amidase activity.
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Affiliation(s)
- Mathieu Rocaboy
- Centre d'Ingénierie des Protéines, University of Liège, Liège, Belgium
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87
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Peters NT, Morlot C, Yang DC, Uehara T, Vernet T, Bernhardt TG. Structure-function analysis of the LytM domain of EnvC, an activator of cell wall remodelling at the Escherichia coli division site. Mol Microbiol 2013; 89:690-701. [PMID: 23796240 DOI: 10.1111/mmi.12304] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/19/2013] [Indexed: 12/19/2022]
Abstract
Proteins with LytM (Peptidase_M23) domains are broadly distributed in bacteria and have been implicated in a variety of important processes, including cell division and cell-shape determination. Most LytM-like proteins that have been structurally and/or biochemically characterized are metallo-endopeptidases that cleave cross-links in the peptidoglycan (PG) cell wall matrix. Notable exceptions are the Escherichia coli cell division proteins EnvC and NlpD. These LytM factors are not hydrolases themselves, but instead serve as activators that stimulate PG cleavage by target enzymes called amidases to promote cell separation. Here we report the structure of the LytM domain from EnvC, the first structure of a LytM factor implicated in the regulation of PG hydrolysis. As expected, the fold is highly similar to that of other LytM proteins. However, consistent with its role as a regulator, the active-site region is degenerate and lacks a catalytic metal ion. Importantly, genetic analysis indicates that residues in and around this degenerate active site are critical for amidase activation in vivo and in vitro. Thus, in the regulatory LytM factors, the apparent substrate binding pocket conserved in active metallo-endopeptidases has been adapted to control PG hydrolysis by another set of enzymes.
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Affiliation(s)
- Nick T Peters
- Department of Microbiology and Immunobiology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
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88
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Characterization of AmiBA2446, a novel bacteriolytic enzyme active against Bacillus species. Appl Environ Microbiol 2013; 79:5899-906. [PMID: 23872558 DOI: 10.1128/aem.02235-13] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
There continues to be a need for developing efficient and environmentally friendly treatments for Bacillus anthracis, the causative agent of anthrax. One emerging approach for inactivation of vegetative B. anthracis is the use of bacteriophage endolysins or lytic enzymes encoded by bacterial genomes (autolysins) with highly evolved specificity toward bacterium-specific peptidoglycan cell walls. In this work, we performed in silico analysis of the genome of Bacillus anthracis strain Ames, using a consensus binding domain amino acid sequence as a probe, and identified a novel lytic enzyme that we termed AmiBA2446. This enzyme exists as a homodimer, as determined by size exclusion studies. It possesses N-acetylmuramoyl-l-alanine amidase activity, as determined from liquid chromatography-mass spectrometry (LC-MS) analysis of muropeptides released due to the enzymatic digestion of peptidoglycan. Phylogenetic analysis suggested that AmiBA2446 was an autolysin of bacterial origin. We characterized the effects of enzyme concentration and phase of bacterial growth on bactericidal activity and observed close to a 5-log reduction in the viability of cells of Bacillus cereus 4342, a surrogate for B. anthracis. We further tested the bactericidal activity of AmiBA2446 against various Bacillus species and demonstrated significant activity against B. anthracis and B. cereus strains. We also demonstrated activity against B. anthracis spores after pretreatment with germinants. AmiBA2446 enzyme was also stable in solution, retaining its activity after 4 months of storage at room temperature.
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89
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Rea MC, Alemayehu D, Ross RP, Hill C. Gut solutions to a gut problem: bacteriocins, probiotics and bacteriophage for control of Clostridium difficile infection. J Med Microbiol 2013; 62:1369-1378. [PMID: 23699066 DOI: 10.1099/jmm.0.058933-0] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Clostridium difficile infection (CDI) is a major cause of morbidity and mortality among hospitalized patients and imposes a considerable financial burden on health service providers in both Europe and the USA. The incidence of CDI has dramatically increased in recent years, partly due to the emergence of a number of hypervirulent strains. The most commonly documented risk factors associated with CDIs are antibiotic usage leading to alterations of the gut microbiota, age >65 years and long-term hospital stay. Since standard therapies for antibiotic-associated diarrhoea and CDI have limited efficacy, there is now an urgent need for alternative therapeutics. In this review, we outline the current state of play with regard to the potential of gut-derived bacteriocins, probiotics and phage to act as antimicrobial agents against CDI in the human gut.
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Affiliation(s)
- Mary C Rea
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Debebe Alemayehu
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - R Paul Ross
- Alimentary Pharmabiotic Centre, University College, Cork, Ireland.,Teagasc Food Research Centre, Moorepark, Fermoy, County Cork, Ireland
| | - Colin Hill
- Department of Microbiology, University College, Cork, Ireland.,Alimentary Pharmabiotic Centre, University College, Cork, Ireland
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90
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Schmelcher M, Donovan DM, Loessner MJ. Bacteriophage endolysins as novel antimicrobials. Future Microbiol 2013; 7:1147-71. [PMID: 23030422 DOI: 10.2217/fmb.12.97] [Citation(s) in RCA: 490] [Impact Index Per Article: 44.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endolysins are enzymes used by bacteriophages at the end of their replication cycle to degrade the peptidoglycan of the bacterial host from within, resulting in cell lysis and release of progeny virions. Due to the absence of an outer membrane in the Gram-positive bacterial cell wall, endolysins can access the peptidoglycan and destroy these organisms when applied externally, making them interesting antimicrobial candidates, particularly in light of increasing bacterial drug resistance. This article reviews the modular structure of these enzymes, in which cell wall binding and catalytic functions are separated, as well as their mechanism of action, lytic activity and potential as antimicrobials. It particularly focuses on molecular engineering as a means of optimizing endolysins for specific applications, highlights new developments that may render these proteins active against Gram-negative and intracellular pathogens and summarizes the most recent applications of endolysins in the fields of medicine, food safety, agriculture and biotechnology.
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Affiliation(s)
- Mathias Schmelcher
- Institute of Food, Nutrition & Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
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Zucca M, Scutera S, Savoia D. Novel avenues forClostridium difficileinfection drug discovery. Expert Opin Drug Discov 2013; 8:459-77. [DOI: 10.1517/17460441.2013.770466] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mario Zucca
- University of Torino, at S. Luigi Gonzaga Hospital, Department of Clinical and Biological Sciences, Regione Gonzole 10, Orbassano (To) 10043, Italy ;
| | - Sara Scutera
- University of Torino, Department of Public Health and Paediatric Sciences, V. Santena 9, Torino 10126, Italy
| | - Dianella Savoia
- University of Torino, at S. Luigi Gonzaga Hospital, Department of Clinical and Biological Sciences, Regione Gonzole 10, Orbassano (To) 10043, Italy ;
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92
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Yang DC, Tan K, Joachimiak A, Bernhardt TG. A conformational switch controls cell wall-remodelling enzymes required for bacterial cell division. Mol Microbiol 2012; 85:768-81. [PMID: 22715947 DOI: 10.1111/j.1365-2958.2012.08138.x] [Citation(s) in RCA: 89] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Remodelling of the peptidoglycan (PG) exoskeleton is intimately tied to the growth and division of bacteria. Enzymes that hydrolyse PG are critical for these processes, but their activities must be tightly regulated to prevent the generation of lethal breaches in the PG matrix. Despite their importance, the mechanisms regulating PG hydrolase activity have remained elusive. Here we investigate the control of cell division hydrolases called amidases (AmiA, AmiB and AmiC) required for Escherichia coli cell division. Poorly regulated amiB mutants were isolated encoding lytic AmiB variants with elevated basal PG hydrolase activities in vitro. The structure of an AmiB orthologue was also solved, revealing that the active site of AmiB is occluded by a conserved alpha helix. Strikingly, most of the amino acid substitutions in the lytic AmiB variants mapped to this domain and are predicted to disrupt its interaction with the active site. Our results therefore support a model in which cell separation is stimulated by the reversible relief of amidase autoinhibition governed by conserved subcomplexes within the cytokinetic ring. Analogous conformational control mechanisms are likely to be part of a general strategy used to control PG hydrolases present within multienzyme PG-remodelling machines.
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Affiliation(s)
- Desirée C Yang
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
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93
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Genomic sequence of bacteriophage ATCC 8074-B1 and activity of its endolysin and engineered variants against Clostridium sporogenes. Appl Environ Microbiol 2012; 78:3685-92. [PMID: 22427494 DOI: 10.1128/aem.07884-11] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Lytic bacteriophage ATCC 8074-B1 produces large plaques on its host Clostridium sporogenes. Sequencing of the 47,595-bp genome allowed the identification of 82 putative open reading frames, including those encoding proteins for head and tail morphogenesis and lysis. However, sequences commonly associated with lysogeny were absent. ORF 22 encodes an endolysin, CS74L, that shows homology to N-acetylmuramoyl-L-alanine amidases, and when expressed in Escherichia coli, the protein causes effective lysis of C. sporogenes cells when added externally. CS74L was also active on Clostridium tyrobutyricum and Clostridium acetobutylicum. The catalytic domain expressed alone (CS74L(1-177)) exhibited a similar activity and the same host range as the full-length endolysin. A chimeric endolysin consisting of the CS74L catalytic domain fused to the C-terminal domain of endolysin CD27L, derived from Clostridium difficile bacteriophage ΦCD27, was produced. This chimera (CSCD) lysed C. sporogenes cells with an activity equivalent to that of the catalytic domain alone. In contrast, the CD27L C-terminal domain reduced the efficacy of the CS74L catalytic domain when tested against C. tyrobutyricum. The addition of the CD27L C-terminal domain did not enable the lysin to target C. difficile or other CD27L-sensitive bacteria.
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