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Boeckaerts D, Stock M, Ferriol-González C, Oteo-Iglesias J, Sanjuán R, Domingo-Calap P, De Baets B, Briers Y. Prediction of Klebsiella phage-host specificity at the strain level. Nat Commun 2024; 15:4355. [PMID: 38778023 PMCID: PMC11111740 DOI: 10.1038/s41467-024-48675-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 05/08/2024] [Indexed: 05/25/2024] Open
Abstract
Phages are increasingly considered promising alternatives to target drug-resistant bacterial pathogens. However, their often-narrow host range can make it challenging to find matching phages against bacteria of interest. Current computational tools do not accurately predict interactions at the strain level in a way that is relevant and properly evaluated for practical use. We present PhageHostLearn, a machine learning system that predicts strain-level interactions between receptor-binding proteins and bacterial receptors for Klebsiella phage-bacteria pairs. We evaluate this system both in silico and in the laboratory, in the clinically relevant setting of finding matching phages against bacterial strains. PhageHostLearn reaches a cross-validated ROC AUC of up to 81.8% in silico and maintains this performance in laboratory validation. Our approach provides a framework for developing and evaluating phage-host prediction methods that are useful in practice, which we believe to be a meaningful contribution to the machine-learning-guided development of phage therapeutics and diagnostics.
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Affiliation(s)
- Dimitri Boeckaerts
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Michiel Stock
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Celia Ferriol-González
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Madrid, Spain
- CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Rafael Sanjuán
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I2SysBio), Universitat de Valencia-CSIC, Paterna, Spain
| | - Bernard De Baets
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, Ghent, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Ghent University, Ghent, Belgium.
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2
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Huang T, Zhang Z, Tao X, Shi X, Lin P, Liao D, Ma C, Cai X, Lin W, Jiang X, Luo P, Wu S, Xie Y. Structural and functional basis of bacteriophage K64-ORF41 depolymerase for capsular polysaccharide degradation of Klebsiella pneumoniae K64. Int J Biol Macromol 2024; 265:130917. [PMID: 38513899 DOI: 10.1016/j.ijbiomac.2024.130917] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/04/2024] [Accepted: 03/14/2024] [Indexed: 03/23/2024]
Abstract
Capsule polysaccharide is an important virulence factor of Klebsiella pneumoniae (K. pneumoniae), which protects bacteria against the host immune response. A promising therapeutic approach is using phage-derived depolymerases to degrade the capsular polysaccharide and expose and sensitize the bacteria to the host immune system. Here we determined the cryo-electron microscopy (cryo-EM) structures of a bacteriophage tail-spike protein against K. pneumoniae K64, ORF41 (K64-ORF41) and ORF41 in EDTA condition (K64-ORF41EDTA), at 2.37 Å and 2.50 Å resolution, respectively, for the first time. K64-ORF41 exists as a trimer and each protomer contains a β-helix domain including a right-handed parallel β-sheet helix fold capped at both ends, an insertion domain, and one β-sheet jellyroll domain. Moreover, our structural comparison with other depolymerases of K. pneumoniae suggests that the catalytic residues (Tyr528, His574 and Arg628) are highly conserved although the substrate of capsule polysaccharide is variable. Besides that, we figured out the important residues involved in the substrate binding pocket including Arg405, Tyr526, Trp550 and Phe669. This study establishes the structural and functional basis for the promising phage-derived broad-spectrum activity depolymerase therapeutics and effective CPS-degrading agents for the treatment of carbapenem-resistant K. pneumoniae K64 infections.
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Affiliation(s)
- Tianyun Huang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; Department of Pharmacy, Xi'an No.3 Hospital, the Affiliated Hospital of Northwest University, Xi'an, Shaanxi 710021, China; School of Pharmacy, Health Science Center, Xi'an Jiaotong University, Xi'an, Shaanxi 710061, China
| | - Zhuoyuan Zhang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China; College of Life Sciences, Northwest University, Xi'an 710069, China
| | - Xin Tao
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China
| | - Xinyu Shi
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Peng Lin
- National Translational Science Center for Molecular Medicine & Department of Cell Biology, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Dan Liao
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Chenyu Ma
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xinle Cai
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Wei Lin
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China
| | - Xiaofan Jiang
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Peng Luo
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
| | - Shan Wu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Hubei Collaborative Innovation Center for Green Transformation of Bio-Resources, Hubei Key Laboratory of Industrial Biotechnology, School of Life Sciences, Hubei University, Wuhan, Hubei 430062, China.
| | - Yuan Xie
- Department of Neurosurgery, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi 710032, China.
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3
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Ye TJ, Fung KM, Lee IM, Ko TP, Lin CY, Wong CL, Tu IF, Huang TY, Yang FL, Chang YP, Wang JT, Lin TL, Huang KF, Wu SH. Klebsiella pneumoniae K2 capsular polysaccharide degradation by a bacteriophage depolymerase does not require trimer formation. mBio 2024; 15:e0351923. [PMID: 38349137 PMCID: PMC10936425 DOI: 10.1128/mbio.03519-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 01/22/2024] [Indexed: 03/14/2024] Open
Abstract
K2-capsular Klebsiella pneumoniae is a hypervirulent pathogen that causes fatal infections. Here, we describe a phage tailspike protein, named K2-2, that specifically depolymerizes the K2 capsular polysaccharide (CPS) of K. pneumoniae into tetrasaccharide repeating units. Nearly half of the products contained O-acetylation, which was thought crucial to the immunogenicity of CPS. The product-bound structures of this trimeric enzyme revealed intersubunit carbohydrate-binding grooves, each accommodating three tetrasaccharide units of K2 CPS. The catalytic residues and the key interactions responsible for K2 CPS recognition were identified and verified by site-directed mutagenesis. Further biophysical and functional characterization, along with the structure of a tetrameric form of K2-2, demonstrated that the formation of intersubunit catalytic center does not require trimerization, which could be nearly completely disrupted by a single-residue mutation in the C-terminal domain. Our findings regarding the assembly and catalysis of K2-2 provide cues for the development of glycoconjugate vaccines against K. pneumoniae infection. IMPORTANCE Generating fragments of capsular polysaccharides from pathogenic bacteria with crucial antigenic determinants for vaccine development continues to pose challenges. The significance of the C-terminal region of phage tailspike protein (TSP) in relation to its folding and trimer formation remains largely unexplored. The polysaccharide depolymerase described here demonstrates the ability to depolymerize the K2 CPS of K. pneumoniae into tetrasaccharide fragments while retaining the vital O-acetylation modification crucial for immunogenicity. By carefully characterizing the enzyme, elucidating its three-dimensional structures, conducting site-directed mutagenesis, and assessing the antimicrobial efficacy of the mutant enzymes against K2 K. pneumoniae, we offer valuable insights into the mechanism by which this enzyme recognizes and depolymerizes the K2 CPS. Our findings, particularly the discovery that trimer formation is not required for depolymerizing activity, challenge the current understanding of trimer-dependent TSP activity and highlight the catalytic mechanism of the TSP with an intersubunit catalytic center.
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Affiliation(s)
- Ting-Juan Ye
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Kit-Man Fung
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - I-Ming Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Yi Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chia-Ling Wong
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Tzu-Yin Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Yu-Pei Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, Taiwan
| | - Tzu-Lung Lin
- Department of Microbiology, National Taiwan University College of Medicine, Taipei, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
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4
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R S, Kumar SN, M MR, Pattar J, B V DR. Investigating the effect of acidic and basic precipitation on the antibacterial activity of ZnO nanoparticles against Gram-negative and Gram-positive bacteria. J Mater Chem B 2024; 12:2180-2196. [PMID: 38323518 DOI: 10.1039/d3tb02119j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2024]
Abstract
In the present work, acidic (direct) and basic precipitation (indirect) methods were used to demonstrate the influence of the mode of precipitation on the structural properties of ZnO nanoparticles (NPs). Four samples of ZnO nanoparticles were prepared, two samples via each mode of precipitation. DZOa and IZOa were the aged samples prepared via acidic and basic precipitation methods, and DZOwa and IZOwa were processed without aging. Both precipitation processes were carried out without using any surfactant reagents. Zinc hydroxide precipitate, which was formed during the basic precipitation method, could be critical in deciding the properties of ZnO NPs, unlike zinc hydroxide formed during acidic precipitation. Aging of zinc hydroxide, synthesised by basic precipitation method for 48 hours was found to be an added advantage in controlling the properties of ZnO NPs. The influence of the mode of precipitation on the structural properties and antibacterial activity of ZnO NPs against Gram-positive and Gram-negative bacterial strains was tested. The antibacterial activity of all four ZnO NPs was analysed via zone of inhibition measurements at a concentration dose of 200 μg ml-1. IZOa nanoparticles prepared using the basic precipitation method showed a higher antibacterial activity against three Gram-negative and one Gram-positive strains, namely, Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Escherichia coli. DZOa nanoparticles synthesized through acidic precipitation showed relatively high antibacterial activity against Salmonella typhimurium, a Gram-negative strain. ZnO NPs prepared without aging, IZOwa and DZOwa, showed a higher antibacterial activity against E. coli and Bacillus sp. strains, respectively. All ZnO NPs were characterized via UV-visible, FTIR, XRD, and HRSEM techniques.
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Affiliation(s)
- Sreekanth R
- Department of Chemistry, REVA University, Bengaluru, Karnataka, India.
| | - S Naveen Kumar
- Department of Chemistry, REVA University, Bengaluru, Karnataka, India.
| | | | - Jayadev Pattar
- Department of Physics, REVA University, Bengaluru, Karnataka, India
| | - Damodar Reddy B V
- Department of Biotechnology, REVA University, Bengaluru, Karnataka, India
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5
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Ostenfeld LJ, Sørensen AN, Neve H, Vitt A, Klumpp J, Sørensen MCH. A hybrid receptor binding protein enables phage F341 infection of Campylobacter by binding to flagella and lipooligosaccharides. Front Microbiol 2024; 15:1358909. [PMID: 38380094 PMCID: PMC10877375 DOI: 10.3389/fmicb.2024.1358909] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 01/18/2024] [Indexed: 02/22/2024] Open
Abstract
Flagellotropic bacteriophages are interesting candidates as therapeutics against pathogenic bacteria dependent on flagellar motility for colonization and causing disease. Yet, phage resistance other than loss of motility has been scarcely studied. Here we developed a soft agar assay to study flagellotropic phage F341 resistance in motile Campylobacter jejuni. We found that phage adsorption was prevented by diverse genetic mutations in the lipooligosaccharides forming the secondary receptor of phage F341. Genome sequencing showed phage F341 belongs to the Fletchervirus genus otherwise comprising capsular-dependent C. jejuni phages. Interestingly, phage F341 encodes a hybrid receptor binding protein (RBP) predicted as a short tail fiber showing partial similarity to RBP1 encoded by capsular-dependent Fletchervirus, but with a receptor binding domain similar to tail fiber protein H of C. jejuni CJIE1 prophages. Thus, C. jejuni prophages may represent a genetic pool from where lytic Fletchervirus phages can acquire new traits like recognition of new receptors.
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Affiliation(s)
- Line Jensen Ostenfeld
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | | | - Horst Neve
- Department of Microbiology and Biotechnology, Max-Rubner Institut, Kiel, Germany
| | - Amira Vitt
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jochen Klumpp
- Institute for Food, Nutrition and Health, ETH Zurich, Zurich, Switzerland
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6
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Łubkowska B, Sobolewski I, Adamowicz K, Zylicz-Stachula A, Skowron PM. Recombinant TP-84 Bacteriophage Glycosylase-Depolymerase Confers Activity against Thermostable Geobacillus stearothermophilus via Capsule Degradation. Int J Mol Sci 2024; 25:722. [PMID: 38255796 PMCID: PMC10815759 DOI: 10.3390/ijms25020722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
The TP-84 bacteriophage, which infects Geobacillus stearothermophilus strain 10 (G. stearothermophilus), has a genome size of 47.7 kilobase pairs (kbps) and contains 81 predicted protein-coding ORFs. One of these, TP84_26 encodes a putative tail fiber protein possessing capsule depolymerase activity. In this study, we cloned the TP84_26 gene into a high-expression Escherichia coli (E. coli) system, modified its N-terminus with His-tag, expressed both the wild type gene and His-tagged variant, purified the recombinant depolymerase variants, and further evaluated their properties. We developed a direct enzymatic assay for the depolymerase activity toward G. stearothermophilus capsules. The recombinant TP84_26 protein variants effectively degraded the existing bacterial capsules and inhibited the formation of new ones. Our results provide insights into the novel TP84_26 depolymerase with specific activity against thermostable G. stearothermophilus and its role in the TP-84 life cycle. The identification and characterization of novel depolymerases, such as TP84_26, hold promise for innovative strategies to combat bacterial infections and improve various industrial processes.
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Affiliation(s)
- Beata Łubkowska
- Faculty of Health and Life Sciences, Gdansk University of Physical Education and Sport, K. Gorskiego 1, 80-336 Gdansk, Poland
| | - Ireneusz Sobolewski
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Katarzyna Adamowicz
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Agnieszka Zylicz-Stachula
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
| | - Piotr M. Skowron
- Faculty of Chemistry, Department of Molecular Biotechnology, University of Gdansk, Wita Stwosza 63, 80-308 Gdansk, Poland; (I.S.); (K.A.); (A.Z.-S.); (P.M.S.)
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7
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Wang H, Liu Y, Bai C, Leung SSY. Translating bacteriophage-derived depolymerases into antibacterial therapeutics: Challenges and prospects. Acta Pharm Sin B 2024; 14:155-169. [PMID: 38239242 PMCID: PMC10792971 DOI: 10.1016/j.apsb.2023.08.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 06/12/2023] [Accepted: 07/22/2023] [Indexed: 01/22/2024] Open
Abstract
Predatory bacteriophages have evolved a vast array of depolymerases for bacteria capture and deprotection. These depolymerases are enzymes responsible for degrading diverse bacterial surface carbohydrates. They are exploited as antibiofilm agents and antimicrobial adjuvants while rarely inducing bacterial resistance, making them an invaluable asset in the era of antibiotic resistance. Numerous depolymerases have been investigated preclinically, with evidence indicating that depolymerases with appropriate dose regimens can safely and effectively combat different multidrug-resistant pathogens in animal infection models. Additionally, some formulation approaches have been developed for improved stability and activity of depolymerases. However, depolymerase formulation is limited to liquid dosage form and remains in its infancy, posing a significant hurdle to their clinical translation, compounded by challenges in their applicability and manufacturing. Future development must address these obstacles for clinical utility. Here, after unravelling the history, diversity, and therapeutic use of depolymerases, we summarized the preclinical efficacy and existing formulation findings of recombinant depolymerases. Finally, the challenges and perspectives of depolymerases as therapeutics for humans were assessed to provide insights for their further development.
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Affiliation(s)
- Honglan Wang
- School of Pharmacy, the Chinese University of Hong Kong, Hong Kong SAR, China
| | - Yannan Liu
- Emergency Medicine Clinical Research Center, Beijing Chao-Yang Hospital, Capital Medical University, Beijing 100020, China
| | - Changqing Bai
- Department of Respiratory, Shenzhen University General Hospital, Shenzhen University Clinical Medical Academy, Guangdong 518055, China
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8
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Lukianova AA, Shneider MM, Evseev PV, Egorov MV, Kasimova AA, Shpirt AM, Shashkov AS, Knirel YA, Kostryukova ES, Miroshnikov KA. Depolymerisation of the Klebsiella pneumoniae Capsular Polysaccharide K21 by Klebsiella Phage K5. Int J Mol Sci 2023; 24:17288. [PMID: 38139119 PMCID: PMC10743669 DOI: 10.3390/ijms242417288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 12/05/2023] [Accepted: 12/07/2023] [Indexed: 12/24/2023] Open
Abstract
Klebsiella pneumoniae is a pathogen associated with various infection types, which often exhibits multiple antibiotic resistance. Phages, or bacterial viruses, have an ability to specifically target and destroy K. pneumoniae, offering a potential means of combatting multidrug-resistant infections. Phage enzymes are another promising therapeutic agent that can break down bacterial capsular polysaccharide, which shields K. pneumoniae from the immune response and external factors. In this study, Klebsiella phage K5 was isolated; this phage is active against Klebsiella pneumoniae with the capsular type K21. It was demonstrated that the phage can effectively lyse the host culture. The adsorption apparatus of the phage has revealed two receptor-binding proteins (RBPs) with predicted polysaccharide depolymerising activity. A recombinant form of both RBPs was obtained and experiments showed that one of them depolymerised the capsular polysaccharide K21. The structure of this polysaccharide and its degradation fragments were analysed. The second receptor-binding protein showed no activity on capsular polysaccharide of any of the 31 capsule types tested, so the substrate for this enzyme remains to be determined in the future. Klebsiella phage K5 may be considered a useful agent against Klebsiella infections.
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Affiliation(s)
- Anna A. Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia; (P.V.E.); (M.V.E.); (K.A.M.)
| | - Mikhail M. Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia; (P.V.E.); (M.V.E.); (K.A.M.)
| | - Peter V. Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia; (P.V.E.); (M.V.E.); (K.A.M.)
| | - Mikhail V. Egorov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia; (P.V.E.); (M.V.E.); (K.A.M.)
| | - Anastasiya A. Kasimova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, 119991 Moscow, Russia; (A.A.K.); (A.M.S.); (A.S.S.); (Y.A.K.)
| | - Anna M. Shpirt
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, 119991 Moscow, Russia; (A.A.K.); (A.M.S.); (A.S.S.); (Y.A.K.)
| | - Alexander S. Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, 119991 Moscow, Russia; (A.A.K.); (A.M.S.); (A.S.S.); (Y.A.K.)
| | - Yuriy A. Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky prosp. 47, 119991 Moscow, Russia; (A.A.K.); (A.M.S.); (A.S.S.); (Y.A.K.)
| | - Elena S. Kostryukova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine, Federal Medical Biological Agency, Malaya Pirogovskaya Str. 1, 119435 Moscow, Russia;
| | - Konstantin A. Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str. 16/10, 117997 Moscow, Russia; (P.V.E.); (M.V.E.); (K.A.M.)
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9
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Guo Z, Liu M, Zhang D. Potential of phage depolymerase for the treatment of bacterial biofilms. Virulence 2023; 14:2273567. [PMID: 37872768 PMCID: PMC10621286 DOI: 10.1080/21505594.2023.2273567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/30/2023] [Indexed: 10/25/2023] Open
Abstract
Resistance of bacteria to antibiotics is a major concern in medicine and veterinary science. The bacterial biofilm structures not only prevent the penetration of drugs into cells within the biofilm's interior but also aid in evasion of the host immune system. Hence, there is an urgent need to develop novel therapeutic approaches against bacterial biofilms. One potential strategy to counter biofilms is to use phage depolymerases that degrade the matrix structure of the bacteria and enable access to bacterial cells. This review mainly discusses the methods by which phage depolymerases enhance the efficacy of the human immune system and the therapeutic applications of some phage depolymerases, such as single phage depolymerase application, combined therapy with phage depolymerase and antibiotics, and phage depolymerase cocktails, for treating bacterial biofilms. This review also summarizes the relationship between bacterial biofilms and antibiotic resistance.
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Affiliation(s)
- Zhimin Guo
- Department of Laboratory Medicine, Infectious Diseases and Pathogen Biology Center, The First Hospital of Jilin University, Changchun, China
| | - Mengmeng Liu
- Department of Laboratory Medicine, The First Hospital of Jilin University, Changchun, China
| | - Dan Zhang
- Department of Hepatological Surgery, The First Hospital of Jilin University, Changchun, China
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10
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Maciejewska B, Squeglia F, Latka A, Privitera M, Olejniczak S, Switala P, Ruggiero A, Marasco D, Kramarska E, Drulis-Kawa Z, Berisio R. Klebsiella phage KP34gp57 capsular depolymerase structure and function: from a serendipitous finding to the design of active mini-enzymes against K. pneumoniae. mBio 2023; 14:e0132923. [PMID: 37707438 PMCID: PMC10653864 DOI: 10.1128/mbio.01329-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 07/19/2023] [Indexed: 09/15/2023] Open
Abstract
IMPORTANCE In this work, we determined the structure of Klebsiella phage KP34p57 capsular depolymerase and dissected the role of individual domains in trimerization and functional activity. The crystal structure serendipitously revealed that the enzyme can exist in a monomeric state once deprived of its C-terminal domain. Based on the crystal structure and site-directed mutagenesis, we localized the key catalytic residues in an intra-subunit deep groove. Consistently, we show that C-terminally trimmed KP34p57 variants are monomeric, stable, and fully active. The elaboration of monomeric, fully active phage depolymerases is innovative in the field, as no previous example exists. Indeed, mini phage depolymerases can be combined in chimeric enzymes to extend their activity ranges, allowing their use against multiple serotypes.
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Affiliation(s)
- Barbara Maciejewska
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Flavia Squeglia
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Agnieszka Latka
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Mario Privitera
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Sebastian Olejniczak
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Paulina Switala
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | | | - Daniela Marasco
- Department of Pharmacy, University of Naples Federico II, Napoli, Italy
| | - Eliza Kramarska
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wrocław, Wrocław, Poland
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, CNR, Napoli, Italy
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11
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Noreika A, Stankevičiūtė J, Rutkienė R, Meškys R, Kalinienė L. Exploring the enzymatic activity of depolymerase gp531 from Klebsiella pneumoniae jumbo phage RaK2. Virus Res 2023; 336:199225. [PMID: 37741345 PMCID: PMC10550766 DOI: 10.1016/j.virusres.2023.199225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 08/28/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Klebsiella pneumoniae poses a major global challenge due to its virulence, multidrug resistance, and nosocomial nature. Thus, bacteriophage-derived proteins are extensively being investigated as a means to combat this bacterium. In this study, we explored the enzymatic specificity of depolymerase gp531, encoded by the jumbo bacteriophage vB_KleM_RaK2 (RaK2). We used two different methods to modify the reducing end of the oligosaccharides released during capsule hydrolysis with gp531. Subsequent acidic cleavage with TFA, followed by TLC and HPLC-MS analyses, revealed that RaK2 gp531 is a β-(1→4)-endoglucosidase. The enzyme specifically recognizes and cleaves the capsular polysaccharide (CPS) of the Klebsiella pneumoniae K54 serotype, releasing K-unit monomers (the main product), dimers, and trimers. Depolymerase gp531 remains active from 10 to 50 °C and in the pH 3-8 range, indicating its stability and versatility. Additionally, we demonstrated that gp531's activity is not affected by CPS acetylation, which is influenced by the growth conditions of the bacterial culture. Overall, our findings provide valuable insights into the enzymatic activity of the first characterized depolymerase targeting the capsule of the clinically relevant K54 serotype of K. pneumoniae.
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Affiliation(s)
- Algirdas Noreika
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania.
| | - Jonita Stankevičiūtė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Rasa Rutkienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania
| | - Laura Kalinienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius, Lithuania.
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12
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Cai R, Ren Z, Zhao R, Lu Y, Wang X, Guo Z, Song J, Xiang W, Du R, Zhang X, Han W, Ru H, Gu J. Structural biology and functional features of phage-derived depolymerase Depo32 on Klebsiella pneumoniae with K2 serotype capsular polysaccharides. Microbiol Spectr 2023; 11:e0530422. [PMID: 37750730 PMCID: PMC10581125 DOI: 10.1128/spectrum.05304-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 08/03/2023] [Indexed: 09/27/2023] Open
Abstract
Hypervirulent Klebsiella pneumoniae with capsular polysaccharides (CPSs) causes severe nosocomial- and community-acquired infections. Phage-derived depolymerases can degrade CPSs from K. pneumoniae to attenuate bacterial virulence, but their antimicrobial mechanisms and clinical potential are not well understood. In the present study, Klebsiella phage GH-K3-derived depolymerase Depo32 (encoded by gene gp32) was identified to exhibit high efficiency in specifically degrading the CPSs of K2 serotype K. pneumoniae. The cryo-electron microscopy structure of trimeric Depo32 at a resolution up to 2.32 Å revealed potential catalytic centers in the cleft of each of the two adjacent subunits. K. pneumoniae subjected to Depo32 became more sensitive to phagocytosis by RAW264.7 cells and activated the cells by the mitogen-activated protein kinase signaling pathway. In addition, intranasal inoculation with Depo32 (a single dose of 200 µg, 20 µg daily for 3 days, or in combination with gentamicin) rescued all C57BL/6J mice infected with a lethal dose of K. pneumoniae K7 without interference from its neutralizing antibody. In summary, this work elaborates on the mechanism by which Depo32 targets the degradation of K2 serotype CPSs and its potential as an antivirulence agent. IMPORTANCE Depolymerases specific to more than 20 serotypes of Klebsiella spp. have been identified, but most studies only evaluated the single-dose treatment of depolymerases with relatively simple clinical evaluation indices and did not reveal the anti-infection mechanism of these depolymerases in depth. On the basis of determining the biological characteristics, the structure of Depo32 was analyzed by cryo-electron microscopy, and the potential active center was further identified. In addition, the effects of Depo32 on macrophage phagocytosis, signaling pathway activation, and serum killing were revealed, and the efficacy of the depolymerase (single treatment, multiple treatments, or in combination with gentamicin) against acute pneumonia caused by Klebsiella pneumoniae was evaluated. Moreover, the roles of the active sites of Depo32 were also elucidated in the in vitro and in vivo studies. Therefore, through structural biology, cell biology, and in vivo experiments, this study demonstrated the mechanism by which Depo32 targets K2 serotype K. pneumoniae infection.
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Affiliation(s)
- Ruopeng Cai
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Zhuolu Ren
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Rihong Zhao
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Yan Lu
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
| | - Xinwu Wang
- College of Animal Science and Technology, Jilin Agricultural Science and Technology University, Changchun, Jilin, China
| | - Zhimin Guo
- Infectious Diseases and Pathogen Biology Center, Clinical Laboratory Department, First Hospital of Jilin University, Changchun, Jilin, China
| | - Jinming Song
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Wentao Xiang
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
| | - Rui Du
- College of Animal Science and Technology, Jilin Agricultural University, Changchun, Jilin, China
- College of Chinese Medicine Materials, Jilin Agricultural University, Changchun, Jilin, China
| | - Xiaokang Zhang
- Faculty of Life and Health Sciences, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
- Inter disciplinary Center for Brain Information, The Brain Cognition and Brain Disease Institute, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, Guangdong, China
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, Guangdong, China
| | - Wenyu Han
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
| | - Heng Ru
- Zhejiang Provincial Key Laboratory for Cancer Molecular Cell Biology, Life Sciences Institute, Zhejiang University, Hangzhou, Zhejiang, China
| | - Jingmin Gu
- College of Veterinary Medicine, Jilin University, Changchun, Jilin, China
- Jiangsu Co-Innovation Center for the Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, Jiangsu, China
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13
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da Silva JD, Bens L, Santos AJDC, Lavigne R, Soares J, Melo LDR, Vallino M, Dias RS, Drulis-Kawa Z, de Paula SO, Wagemans J. Isolation and Characterization of the Acadevirus Members BigMira and MidiMira Infecting a Highly Pathogenic Proteus mirabilis Strain. Microorganisms 2023; 11:2141. [PMID: 37763984 PMCID: PMC10537623 DOI: 10.3390/microorganisms11092141] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 08/14/2023] [Accepted: 08/20/2023] [Indexed: 09/29/2023] Open
Abstract
Proteus mirabilis is an opportunistic pathogen and is responsible for more than 40% of all cases of catheter-associated urinary tract infections (CAUTIs). Healthcare-associated infections have been aggravated by the constant emergence of antibiotic-resistant bacterial strains. Because of this, the use of phages to combat bacterial infections gained renewed interest. In this study, we describe the biological and genomic features of two P. mirabilis phages, named BigMira and MidiMira. These phages belong to the Acadevirus genus (family Autographiviridae). BigMira and MidiMira are highly similar, differing only in four missense mutations in their phage tail fiber. These mutations are sufficient to impact the phages' depolymerase activity. Subsequently, the comparative genomic analysis of ten clinical P. mirabilis strains revealed differences in their antibiotic resistance profiles and lipopolysaccharide locus, with the latter potentially explaining the host range data of the phages. The massive presence of antimicrobial resistance genes, especially in the phages' isolation strain P. mirabilis MCS, highlights the challenges in treating infections caused by multidrug-resistant bacteria. The findings reinforce BigMira and MidiMira phages as candidates for phage therapy purposes.
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Affiliation(s)
- Jéssica Duarte da Silva
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Lene Bens
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
| | - Adriele J. do Carmo Santos
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
| | - José Soares
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
| | - Luís D. R. Melo
- Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal;
- LABBELS—Associate Laboratory, 4710-057 Braga, Portugal
| | - Marta Vallino
- Institute for Sustainable Plant Protection, National Research Council of Italy, 10135 Torino, Italy;
| | - Roberto Sousa Dias
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil;
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, 50-335 Wroclaw, Poland;
| | - Sérgio Oliveira de Paula
- Laboratory of Molecular Immunovirology, Department of Microbiology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil; (J.D.d.S.); (A.J.d.C.S.); (J.S.); (S.O.d.P.)
- Department of General Biology, Federal University of Viçosa, Viçosa 36570-900, MG, Brazil;
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Division of Animal and Human Health Engineering, KU Leuven, 3000 Leuven, Belgium; (L.B.); (R.L.)
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14
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Pas C, Latka A, Fieseler L, Briers Y. Phage tailspike modularity and horizontal gene transfer reveals specificity towards E. coli O-antigen serogroups. Virol J 2023; 20:174. [PMID: 37550759 PMCID: PMC10408124 DOI: 10.1186/s12985-023-02138-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 07/23/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND The interaction between bacteriophages and their hosts is intricate and highly specific. Receptor-binding proteins (RBPs) of phages such as tail fibers and tailspikes initiate the infection process. These RBPs bind to diverse outer membrane structures, including the O-antigen, which is a serogroup-specific sugar-based component of the outer lipopolysaccharide layer of Gram-negative bacteria. Among the most virulent Escherichia coli strains is the Shiga toxin-producing E. coli (STEC) pathotype dominated by a subset of O-antigen serogroups. METHODS Extensive phylogenetic and structural analyses were used to identify and validate specificity correlations between phage RBP subtypes and STEC O-antigen serogroups, relying on the principle of horizontal gene transfer as main driver for RBP evolution. RESULTS We identified O-antigen specific RBP subtypes for seven out of nine most prevalent STEC serogroups (O26, O45, O103, O104, O111, O145 and O157) and seven additional E. coli serogroups (O2, O8, O16, O18, 4s/O22, O77 and O78). Eight phage genera (Gamaleya-, Justusliebig-, Kaguna-, Kayfuna-, Kutter-, Lederberg-, Nouzilly- and Uetakeviruses) emerged for their high proportion of serogroup-specific RBPs. Additionally, we reveal sequence motifs in the RBP region, potentially serving as recombination hotspots between lytic phages. CONCLUSION The results contribute to a better understanding of mosaicism of phage RBPs, but also demonstrate a method to identify and validate new RBP subtypes for current and future emerging serogroups.
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Affiliation(s)
- Célia Pas
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
| | - Agnieszka Latka
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium
- Department of Pathogen Biology and Immunology, University of Wroclaw, Przybyszewskiego 63, 51-148, Wrocław, Poland
| | - Lars Fieseler
- Centre for Food Safety and Quality Management, ZHAW School of Life Sciences and Facility Management, Einsiedlerstrasse 31, 8820, Wädenswil, Switzerland
| | - Yves Briers
- Department of Biotechnology, Ghent University, Valentin Vaerwyckweg 1, 9000, Ghent, Belgium.
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15
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Dunstan RA, Bamert RS, Tan KS, Imbulgoda U, Barlow CK, Taiaroa G, Pickard DJ, Schittenhelm RB, Dougan G, Short FL, Lithgow T. Epitopes in the capsular polysaccharide and the porin OmpK36 receptors are required for bacteriophage infection of Klebsiella pneumoniae. Cell Rep 2023; 42:112551. [PMID: 37224021 DOI: 10.1016/j.celrep.2023.112551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 03/09/2023] [Accepted: 05/05/2023] [Indexed: 05/26/2023] Open
Abstract
To kill bacteria, bacteriophages (phages) must first bind to a receptor, triggering the release of the phage DNA into the bacterial cell. Many bacteria secrete polysaccharides that had been thought to shield bacterial cells from phage attack. We use a comprehensive genetic screen to distinguish that the capsule is not a shield but is instead a primary receptor enabling phage predation. Screening of a transposon library to select phage-resistant Klebsiella shows that the first receptor-binding event docks to saccharide epitopes in the capsule. We discover a second step of receptor binding, dictated by specific epitopes in an outer membrane protein. This additional and necessary event precedes phage DNA release to establish a productive infection. That such discrete epitopes dictate two essential binding events for phages has profound implications for understanding the evolution of phage resistance and what dictates host range, two issues critically important to translating knowledge of phage biology into phage therapies.
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Affiliation(s)
- Rhys A Dunstan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
| | - Rebecca S Bamert
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Kher Shing Tan
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Uvini Imbulgoda
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Christopher K Barlow
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - George Taiaroa
- Department of Infectious Diseases, University of Melbourne, at the Peter Doherty Institute for Infection and Immunity, Clayton, VIC, Australia
| | - Derek J Pickard
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ralf B Schittenhelm
- Monash Proteomics & Metabolomics Platform, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Francesca L Short
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia; Department of Medicine, University of Cambridge, Cambridge, UK; Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Trevor Lithgow
- Centre to Impact AMR, Monash University, Clayton, VIC, Australia; Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC, Australia.
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16
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Kasimova AA, Shneider MM, Evseev PV, Shelenkov AA, Mikhailova YV, Miroshnikov KA, Chebotar IV, Shagin DA. The structure of Klebsiella pneumoniae K108 capsular polysaccharide is similar to Escherichia coli colanic acid. Int J Biol Macromol 2023:125403. [PMID: 37330077 DOI: 10.1016/j.ijbiomac.2023.125403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 05/02/2023] [Accepted: 06/13/2023] [Indexed: 06/19/2023]
Abstract
The clinical isolate of Klebsiella pneumoniae 1333/P225 was revealed as containing a KL108 K. pneumoniae K locus for capsule biosynthesis. The gene cluster demonstrated a high level of sequence and arrangement similarity with that of the E. coli colanic acid biosynthesis gene cluster. The KL108 gene cluster includes a gene of WcaD polymerase responsible for joining oligosaccharide K units into capsular polysaccharide (CPS), acetyltransferase, pyruvyltransferasefive and genes for glycosyltransferases (Gtrs), four of which have homologues in genetic units of the colanic acid synthesis. The fifth Gtr is specific to this cluster. The work involved the use of sugar analysis, Smith degradation and one- and two-dimensional 1H and 13C NMR spectroscopy to establish the structure of the K108 CPS. The CPS repetitive K unit is composed of branched pentasaccharide with three monosaccharides in the backbone and a disaccharide side chain. The main chain is the same as for colanic acid but the side chain differs. Two bacteriophages infecting K. pneumoniae strain 1333/P225 were isolated and structural depolymerase genes were determined; depolymerases Dep108.1 and Dep108.2 were cloned, expressed and purified. It was demonstrated that both depolymerases specifically cleave the β-Glcp-(1→4)-α-Fucp linkage between K108 units in the CPS.
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Affiliation(s)
- Anastasiya A Kasimova
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Mikhail M Shneider
- M.M. Shemyakin and Y.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia.
| | - Peter V Evseev
- M.M. Shemyakin and Y.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | | | | | - Konstantin A Miroshnikov
- M.M. Shemyakin and Y.A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Science, Moscow, Russia
| | - Igor V Chebotar
- Pirogov Russian National Research Medical University, Moscow, Russia
| | - Dmitry A Shagin
- Pirogov Russian National Research Medical University, Moscow, Russia
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17
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Noreika A, Rutkiene R, Dumalakienė I, Vilienė R, Laurynėnas A, Povilonienė S, Skapas M, Meškys R, Kaliniene L. Insights into the Alcyoneusvirus Adsorption Complex. Int J Mol Sci 2023; 24:ijms24119320. [PMID: 37298271 DOI: 10.3390/ijms24119320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Revised: 05/23/2023] [Accepted: 05/24/2023] [Indexed: 06/12/2023] Open
Abstract
The structures of the Caudovirales phage tails are key factors in determining the host specificity of these viruses. However, because of the enormous structural diversity, the molecular anatomy of the host recognition apparatus has been elucidated in only a number of phages. Klebsiella viruses vB_KleM_RaK2 (RaK2) and phiK64-1, which form a new genus Alcyoneusvirus according to the ICTV, have perhaps one of the most structurally sophisticated adsorption complexes of all tailed viruses described to date. Here, to gain insight into the early steps of the alcyoneusvirus infection process, the adsorption apparatus of bacteriophage RaK2 is studied in silico and in vitro. We experimentally demonstrate that ten proteins, gp098 and gp526-gp534, previously designated as putative structural/tail fiber proteins (TFPs), are present in the adsorption complex of RaK2. We show that two of these proteins, gp098 and gp531, are essential for attaching to Klebsiella pneumoniae KV-3 cells: gp531 is an active depolymerase that recognizes and degrades the capsule of this particular host, while gp098 is a secondary receptor-binding protein that requires the coordinated action of gp531. Finally, we demonstrate that RaK2 long tail fibers consist of nine TFPs, seven of which are depolymerases, and propose a model for their assembly.
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Affiliation(s)
- Algirdas Noreika
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Rasa Rutkiene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Irena Dumalakienė
- Department of Immunology, State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08410 Vilnius, Lithuania
| | - Rita Vilienė
- Department of Immunology, State Research Institute Center for Innovative Medicine, Santariškių St. 5, LT-08410 Vilnius, Lithuania
| | - Audrius Laurynėnas
- Department of Bioanalysis, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Simona Povilonienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio Av. 3, LT-10257 Vilnius, Lithuania
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
| | - Laura Kaliniene
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Center, Vilnius University, Saulėtekio Av. 7, LT-10257 Vilnius, Lithuania
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18
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Latka A, Aertsen A, Boeckaerts D, Blasdel B, Ceyssens PJ, Garcia-Pino A, Gillis A, Lavigne R, Lima-Mendez G, Matthijnssens J, Onsea J, Peeters E, Pirnay JP, Thiry D, Vandenheuvel D, Van Mechelen E, Venneman J, Verbeken G, Wagemans J, Briers Y. Foundation of the Belgian Society for Viruses of Microbes and Meeting Report of Its Inaugural Symposium. Viruses 2023; 15:v15051213. [PMID: 37243298 DOI: 10.3390/v15051213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
The Belgian Society for Viruses of Microbes (BSVoM) was founded on 9 June 2022 to capture and enhance the collaborative spirit among the expanding community of microbial virus researchers in Belgium. The sixteen founders are affiliated to fourteen different research entities across academia, industry and government. Its inaugural symposium was held on 23 September 2022 in the Thermotechnical Institute at KU Leuven. The meeting program covered three thematic sessions launched by international keynote speakers: (1) virus-host interactions, (2) viral ecology, evolution and diversity and (3) present and future applications. During the one-day symposium, four invited keynote lectures, ten selected talks and eight student pitches were given along with 41 presented posters. The meeting hosted 155 participants from twelve countries.
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Affiliation(s)
- Agnieszka Latka
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
- Department of Pathogen Biology and Immunology, University of Wroclaw, 51-148 Wroclaw, Poland
| | - Abram Aertsen
- Laboratory of Food Microbiology, Department of Microbial and Molecular Systems, Faculty of Bioscience Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Dimitri Boeckaerts
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
- KERMIT, Department of Data Analysis and Mathematical Modelling, Ghent University, 9000 Ghent, Belgium
| | - Bob Blasdel
- Vésale Bioscience, Vésale Pharmaceutica, 5310 Noville-sur-Mehaigne, Belgium
| | | | - Abel Garcia-Pino
- Cellular and Molecular Microbiology, Faculté des Sciences, Université Libre de Bruxelles, Campus La Plaine, 1050 Brussels, Belgium
| | - Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, Université Catholique de Louvain, 1348 Louvain-la-Neuve, Belgium
| | - Rob Lavigne
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Gipsi Lima-Mendez
- Biology of Microorganisms Research Unit (URBM), Namur Research Institute for Life Sciences (NARILIS), Université de Namur ASBL, 5000 Namur, Belgium
| | - Jelle Matthijnssens
- Laboratory of Viral Metagenomics, Rega Institute, Department of Microbiology, Immunology and Transplantation, KU Leuven, 3000 Leuven, Belgium
| | - Jolien Onsea
- Department of Trauma Surgery, University Hospitals Leuven, 3000 Leuven, Belgium
- Department of Development and Regeneration, KU Leuven, 3000 Leuven, Belgium
| | - Eveline Peeters
- Research Group of Microbiology, Department of Bioengineering Sciences, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Jean-Paul Pirnay
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium
| | - Damien Thiry
- Veterinary Bacteriology, Department of Infectious and Parasitic Diseases, Fundamental and Applied Research for Animals and Health, Faculty of Veterinary Medicine, University of Liège, 4000 Liège, Belgium
| | - Dieter Vandenheuvel
- Department of Bioscience Engineering, University of Antwerp, 2020 Antwerp, Belgium
| | - Els Van Mechelen
- Research Centre Health & Water Technology, University of Applied Sciences, 9000 Gent, Belgium
| | - Jolien Venneman
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), 9820 Merelbeke, Belgium
| | - Gilbert Verbeken
- Laboratory for Molecular and Cellular Technology, Queen Astrid Military Hospital, 1120 Brussels, Belgium
| | - Jeroen Wagemans
- Laboratory of Gene Technology, Department of Biosystems, Faculty of Bioscience Engineering, KU Leuven, 3001 Leuven, Belgium
| | - Yves Briers
- Laboratory of Applied Biotechnology, Department of Biotechnology, Faculty of Bioscience Engineering, Ghent University, 9000 Gent, Belgium
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19
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Cambillau C, Goulet A. Exploring Host-Binding Machineries of Mycobacteriophages with AlphaFold2. J Virol 2023; 97:e0179322. [PMID: 36916948 PMCID: PMC10062164 DOI: 10.1128/jvi.01793-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 02/17/2023] [Indexed: 03/16/2023] Open
Abstract
Although more than 12,000 bacteriophages infecting mycobacteria (mycobacteriophages) have been isolated so far, there is a knowledge gap on their structure-function relationships. Here, we have explored the architecture of host-binding machineries from seven representative mycobacteriophages of the Siphoviridae family infecting Mycobacterium smegmatis, Mycobacterium abscessus, and Mycobacterium tuberculosis, using AlphaFold2 (AF2). AF2 enables confident structural analyses of large and flexible biological assemblies resistant to experimental methods, thereby opening new avenues to shed light on phage structure and function. Our results highlight the modularity and structural diversity of siphophage host-binding machineries that recognize host-specific receptors at the onset of viral infection. Interestingly, the studied mycobacteriophages' host-binding machineries present unique features compared with those of phages infecting other Gram-positive actinobacteria. Although they all assemble the classical Dit (distal tail), Tal (tail-associated lysin), and receptor-binding proteins, five of them contain two potential additional adhesion proteins. Moreover, we have identified brush-like domains formed of multiple polyglycine helices which expose hydrophobic residues as potential receptor-binding domains. These polyglycine-rich domains, which have been observed in only five native proteins, may be a hallmark of mycobacteriophages' host-binding machineries, and they may be more common in nature than expected. Altogether, the unique composition of mycobacteriophages' host-binding machineries indicate they might have evolved to bind to the peculiar mycobacterial cell envelope, which is rich in polysaccharides and mycolic acids. This work provides a rational framework to efficiently produce recombinant proteins or protein domains and test their host-binding function and, hence, to shed light on molecular mechanisms used by mycobacteriophages to infect their host. IMPORTANCE Mycobacteria include both saprophytes, such as the model system Mycobacterium smegmatis, and pathogens, such as Mycobacterium tuberculosis and Mycobacterium abscessus, that are poorly responsive to antibiotic treatments and pose a global public health problem. Mycobacteriophages have been collected at a very large scale over the last decade, and they have proven to be valuable tools for mycobacteria genetic manipulation, rapid diagnostics, and infection treatment. Yet, molecular mechanisms used by mycobacteriophages to infect their host remain poorly understood. Therefore, exploring the structural diversity of mycobacteriophages' host-binding machineries is important not only to better understand viral diversity and bacteriophage-host interactions, but also to rationally develop biotechnological tools. With the powerful protein structure prediction software AlphaFold2, which was publicly released a year ago, it is now possible to gain structural and functional insights on such challenging assemblies.
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Affiliation(s)
- Christian Cambillau
- School of Microbiology, University College Cork, Cork, Ireland
- AlphaGraphix, Formiguères, France
| | - Adeline Goulet
- Laboratoire d’Ingénierie des Systèmes Macromoléculaires, Institut de Microbiologie, Bioénergies et Biotechnologie, CNRS and Aix-Marseille Université, Marseille, France
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20
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Pertics BZ, Kovács T, Schneider G. Characterization of a Lytic Bacteriophage and Demonstration of Its Combined Lytic Effect with a K2 Depolymerase on the Hypervirulent Klebsiella pneumoniae Strain 52145. Microorganisms 2023; 11:microorganisms11030669. [PMID: 36985241 PMCID: PMC10051899 DOI: 10.3390/microorganisms11030669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 03/01/2023] [Accepted: 03/02/2023] [Indexed: 03/08/2023] Open
Abstract
Klebsiella pneumoniae is a nosocomial pathogen. Among its virulence factors is the capsule with a prominent role in defense and biofilm formation. Bacteriophages (phages) can evoke the lysis of bacterial cells. Due to the mode of action of their polysaccharide depolymerase enzymes, phages are typically specific for one bacterial strain and its capsule type. In this study, we characterized a bacteriophage against the capsule-defective mutant of the nosocomial K. pneumoniae 52145 strain, which lacks K2 capsule. The phage showed a relatively narrow host range but evoked lysis on a few strains with capsular serotypes K33, K21, and K24. Phylogenetic analysis showed that the newly isolated Klebsiella phage 731 belongs to the Webervirus genus in the Drexlerviridae family; it has a 31.084 MDa double-stranded, linear DNA with a length of 50,306 base pairs and a G + C content of 50.9%. Out of the 79 open reading frames (ORFs), we performed the identification of orf22, coding for a trimeric tail fiber protein with putative capsule depolymerase activity, along with the mapping of other putative depolymerases of phage 731 and homologous phages. Efficacy of a previously described recombinant K2 depolymerase (B1dep) was tested by co-spotting phage 731 on K. pneumoniae strains, and it was demonstrated that the B1dep-phage 731 combination allows the lysis of the wild type 52145 strain, originally resistant to the phage 731. With phage 731, we showed that B1dep is a promising candidate for use as a possible antimicrobial agent, as it renders the virulent strain defenseless against other phages. Phage 731 alone is also important due to its efficacy on K. pneumoniae strains possessing epidemiologically important serotypes.
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Affiliation(s)
- Botond Zsombor Pertics
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
| | - Tamás Kovács
- Department of Biotechnology, Nanophagetherapy Center, Enviroinvest Corporation, Kertváros St. 2., H-7632 Pécs, Hungary
| | - György Schneider
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Szigeti St. 12., H-7624 Pécs, Hungary
- Correspondence: ; Tel.: +36-72-536-200 (ext. 1908)
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21
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Nazir A, Song J, Chen Y, Liu Y. Phage-Derived Depolymerase: Its Possible Role for Secondary Bacterial Infections in COVID-19 Patients. Microorganisms 2023; 11:microorganisms11020424. [PMID: 36838389 PMCID: PMC9961776 DOI: 10.3390/microorganisms11020424] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/04/2023] [Accepted: 02/06/2023] [Indexed: 02/11/2023] Open
Abstract
As of 29 July 2022, there had been a cumulative 572,239,451 confirmed cases of COVID-19 worldwide, including 6,390,401 fatalities. COVID-19 patients with severe symptoms are usually treated with a combination of virus- and drug-induced immuno-suppression medicines. Critical clinical complications of the respiratory system due to secondary bacterial infections (SBIs) could be the reason for the high mortality rate in COVID-19 patients. Unfortunately, antimicrobial resistance is increasing daily, and only a few options are available in our antimicrobial armory. Hence, alternative therapeutic options such as enzymes derived from bacteriophages can be considered for treating SBIs in COVID-19 patients. In particular, phage-derived depolymerases have high antivirulent potency that can efficiently degrade bacterial capsular polysaccharides, lipopolysaccharides, and exopolysaccharides. They have emerged as a promising class of new antibiotics and their therapeutic role for bacterial infections is already confirmed in animal models. This review provides an overview of the rising incidence of SBIs among COVID-19 patients. We present a practicable novel workflow for phage-derived depolymerases that can easily be adapted for treating SBIs in COVID-19 patients.
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Affiliation(s)
| | | | - Yibao Chen
- Correspondence: (Y.C.); (Y.L.); Tel./Fax: +86-531-6665-5093 (Y.C. & Y.L.)
| | - Yuqing Liu
- Correspondence: (Y.C.); (Y.L.); Tel./Fax: +86-531-6665-5093 (Y.C. & Y.L.)
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22
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Klumpp J, Dunne M, Loessner MJ. A perfect fit: Bacteriophage receptor-binding proteins for diagnostic and therapeutic applications. Curr Opin Microbiol 2023; 71:102240. [PMID: 36446275 DOI: 10.1016/j.mib.2022.102240] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/26/2022] [Accepted: 10/31/2022] [Indexed: 11/27/2022]
Abstract
Bacteriophages are the most abundant biological entity on earth, acting as the predators and evolutionary drivers of bacteria. Owing to their inherent ability to specifically infect and kill bacteria, phages and their encoded endolysins and receptor-binding proteins (RBPs) have enormous potential for development into precision antimicrobials for treatment of bacterial infections and microbial disbalances; or as biocontrol agents to tackle bacterial contaminations during various biotechnological processes. The extraordinary binding specificity of phages and RBPs can be exploited in various areas of bacterial diagnostics and monitoring, from food production to health care. We review and describe the distinctive features of phage RBPs, explain why they are attractive candidates for use as therapeutics and in diagnostics, discuss recent applications using RBPs, and finally provide our perspective on how synthetic technology and artificial intelligence-driven approaches will revolutionize how we use these tools in the future.
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Affiliation(s)
- Jochen Klumpp
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Matthew Dunne
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland
| | - Martin J Loessner
- Institute of Food, Nutrition and Health, ETH Zurich, Schmelzbergstrasse 7, 8092 Zurich, Switzerland.
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23
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Leprince A, Mahillon J. Phage Adsorption to Gram-Positive Bacteria. Viruses 2023; 15:196. [PMID: 36680236 PMCID: PMC9863714 DOI: 10.3390/v15010196] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 01/03/2023] [Accepted: 01/06/2023] [Indexed: 01/12/2023] Open
Abstract
The phage life cycle is a multi-stage process initiated by the recognition and attachment of the virus to its bacterial host. This adsorption step depends on the specific interaction between bacterial structures acting as receptors and viral proteins called Receptor Binding Proteins (RBP). The adsorption process is essential as it is the first determinant of phage host range and a sine qua non condition for the subsequent conduct of the life cycle. In phages belonging to the Caudoviricetes class, the capsid is attached to a tail, which is the central player in the adsorption as it comprises the RBP and accessory proteins facilitating phage binding and cell wall penetration prior to genome injection. The nature of the viral proteins involved in host adhesion not only depends on the phage morphology (i.e., myovirus, siphovirus, or podovirus) but also the targeted host. Here, we give an overview of the adsorption process and compile the available information on the type of receptors that can be recognized and the viral proteins taking part in the process, with the primary focus on phages infecting Gram-positive bacteria.
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24
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Characterization of Novel Bacteriophage vB_KpnP_ZX1 and Its Depolymerases with Therapeutic Potential for K57 Klebsiella pneumoniae Infection. Pharmaceutics 2022; 14:pharmaceutics14091916. [PMID: 36145665 PMCID: PMC9505181 DOI: 10.3390/pharmaceutics14091916] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 09/04/2022] [Accepted: 09/08/2022] [Indexed: 11/17/2022] Open
Abstract
A novel temperate phage vB_KpnP_ZX1 was isolated from hospital sewage samples using the clinically derived K57-type Klebsiella pneumoniae as a host. Phage vB_KpnP_ZX1, encoding three lysogen genes, the repressor, anti-repressor, and integrase, is the fourth phage of the genus Uetakevirus, family Podoviridae, ever discovered. Phage vB_KpnP_ZX1 did not show ideal bactericidal effect on K. pneumoniae 111-2, but TEM showed that the depolymerase Dep_ZX1 encoded on the short tail fiber protein has efficient capsule degradation activity. In vitro antibacterial results show that purified recombinant Dep_ZX1 can significantly prevent the formation of biofilm, degrade the formed biofilm, and improve the sensitivity of the bacteria in the biofilm to the antibiotics kanamycin, gentamicin, and streptomycin. Furthermore, the results of animal experiments show that 50 µg Dep_ZX1 can protect all K. pneumoniae 111-2-infected mice from death, whereas the control mice infected with the same dose of K. pneumoniae 111-2 all died. The degradation activity of Dep_ZX1 on capsular polysaccharide makes the bacteria weaken their resistance to immune cells, such as complement-mediated serum killing and phagocytosis, which are the key factors for its therapeutic action. In conclusion, Dep_ZX1 is a promising anti-virulence agent for the K57-type K. pneumoniae infection or biofilm diseases.
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25
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Hua Y, Wu Y, Guo M, Ma R, Li Q, Hu Z, Chen H, Zhang X, Li H, Li Q, He P. Characterization and Functional Studies of a Novel Depolymerase Against K19-Type Klebsiella pneumoniae. Front Microbiol 2022; 13:878800. [PMID: 35814656 PMCID: PMC9257171 DOI: 10.3389/fmicb.2022.878800] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 05/31/2022] [Indexed: 12/14/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), a pathogen that causes severe nosocomial infections and yields a high mortality rate, poses a serious threat to global public health due to its high antimicrobial resistance. Bacteriophages encode polysaccharide-degrading enzymes referred to as depolymerases that cleave the capsular polysaccharide (CPS), one of the main virulence factors of K. pneumoniae. In this study, we identified and characterized a new capsule depolymerase K19-Dpo41 from K. pneumoniae bacteriophage SH-KP156570. Our characterization of K19-Dpo41 demonstrated that this depolymerase showed specific activities against K19-type K. pneumoniae. K19-Dpo41-mediated treatments promoted the sensitivity of a multidrug-resistant K19-type K. pneumoniae strain to the bactericidal effect of human serum and significantly increased the survival rate of Galleria mellonella infected with K19-type K. pneumoniae. Our results provided strong primary evidence that K19-Dpo41 was not only effective in capsular typing of K19-type K. pneumoniae but promising in terms of developing new alternative therapeutic strategies against K19-type CRKP infections in the future.
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Affiliation(s)
- Yunfen Hua
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongqin Wu
- College of Pharmaceutical Sciences, Zhejiang University of Technology, Hangzhou, China
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Minjie Guo
- Department of Nanoengineering, University of California, San Diego, La Jolla, CA, United States
| | - Ruijing Ma
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
| | - Qingchuan Li
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Zheyuan Hu
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hongrui Chen
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Xingyu Zhang
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- *Correspondence: Qingtian Li,
| | - Ping He
- Department of Immunology and Microbiology, Shanghai Jiao Tong University School of Medicine, Shanghai, China
- NHC Key Laboratory of Parasite and Vector Biology, National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention, Shanghai, China
- Ping He,
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26
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Tu IF, Lin TL, Yang FL, Lee IM, Tu WL, Liao JH, Ko TP, Wu WJ, Jan JT, Ho MR, Chou CY, Wang AHJ, Wu CY, Wang JT, Huang KF, Wu SH. Structural and biological insights into Klebsiella pneumoniae surface polysaccharide degradation by a bacteriophage K1 lyase: implications for clinical use. J Biomed Sci 2022; 29:9. [PMID: 35130876 PMCID: PMC8822698 DOI: 10.1186/s12929-022-00792-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/24/2022] [Indexed: 11/18/2022] Open
Abstract
Background K1 capsular polysaccharide (CPS)-associated Klebsiella pneumoniae is the primary cause of pyogenic liver abscesses (PLA) in Asia. Patients with PLA often have serious complications, ultimately leading to a mortality of ~ 5%. This K1 CPS has been reported as a promising target for development of glycoconjugate vaccines against K. pneumoniae infection. The pyruvylation and O-acetylation modifications on the K1 CPS are essential to the immune response induced by the CPS. To date, however, obtaining the fragments of K1 CPS that contain the pyruvylation and O-acetylation for generating glycoconjugate vaccines still remains a challenge. Methods We analyzed the digested CPS products with NMR spectroscopy and mass spectrometry to reveal a bacteriophage-derived polysaccharide depolymerase specific to K1 CPS. The biochemical and biophysical properties of the enzyme were characterized and its crystal structures containing bound CPS products were determined. We also performed site-directed mutagenesis, enzyme kinetic analysis, phage absorption and infectivity studies, and treatment of the K. pneumoniae-infected mice with the wild-type and mutant enzymes. Results We found a bacteriophage-derived polysaccharide lyase that depolymerizes the K1 CPS into fragments of 1–3 repeating trisaccharide units with the retention of the pyruvylation and O-acetylation, and thus the important antigenic determinants of intact K1 CPS. We also determined the 1.46-Å-resolution, product-bound crystal structure of the enzyme, revealing two distinct carbohydrate-binding sites in a trimeric β-helix architecture, which provide the first direct evidence for a second, non-catalytic, carbohydrate-binding site in bacteriophage-derived polysaccharide depolymerases. We demonstrate the tight interaction between the pyruvate moiety of K1 CPS and the enzyme in this second carbohydrate-binding site to be crucial to CPS depolymerization of the enzyme as well as phage absorption and infectivity. We also demonstrate that the enzyme is capable of protecting mice from K1 K. pneumoniae infection, even against a high challenge dose. Conclusions Our results provide insights into how the enzyme recognizes and depolymerizes the K1 CPS, and demonstrate the potential use of the protein not only as a therapeutic agent against K. pneumoniae, but also as a tool to prepare structurally-defined oligosaccharides for the generation of glycoconjugate vaccines against infections caused by this organism. Supplementary Information The online version contains supplementary material available at 10.1186/s12929-022-00792-4.
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Affiliation(s)
- I-Fan Tu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Tzu-Lung Lin
- Department of Microbiology, National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Feng-Ling Yang
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - I-Ming Lee
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Wei-Lin Tu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Jiahn-Haur Liao
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Tzu-Ping Ko
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Wen-Jin Wu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Jia-Tsrong Jan
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Meng-Ru Ho
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Ching-Yi Chou
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Andrew H-J Wang
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan
| | - Chung-Yi Wu
- Genomics Research Center, Academia Sinica, Taipei, 115, Taiwan
| | - Jin-Town Wang
- Department of Microbiology, National Taiwan University Hospital, Taipei, 100, Taiwan
| | - Kai-Fa Huang
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan.
| | - Shih-Hsiung Wu
- Institute of Biological Chemistry, Academia Sinica, No. 128 Academia Road Section 2, Nan‑Kang, Taipei, 115, Taiwan. .,Department of Chemistry, National Taiwan University, Taipei, 106, Taiwan.
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27
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Phenotypic and Genomic Comparison of Klebsiella pneumoniae Lytic Phages: vB_KpnM-VAC66 and vB_KpnM-VAC13. Viruses 2021; 14:v14010006. [PMID: 35062209 PMCID: PMC8778798 DOI: 10.3390/v14010006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/25/2022] Open
Abstract
Klebsiella pneumoniae is a human pathogen that worsens the prognosis of many immunocompromised patients. Here, we annotated and compared the genomes of two lytic phages that infect clinical strains of K. pneumoniae (vB_KpnM-VAC13 and vB_KpnM-VAC66) and phenotypically characterized vB_KpnM-VAC66 (time of adsorption of 12 min, burst size of 31.49 ± 0.61 PFU/infected cell, and a host range of 20.8% of the tested strains). Transmission electronic microscopy showed that vB_KpnM-VAC66 belongs to the Myoviridae family. The genomic analysis of the phage vB_KpnM-VAC66 revealed that its genome encoded 289 proteins. When compared to the genome of vB_KpnM-VAC13, they showed a nucleotide similarity of 97.56%, with a 93% of query cover, and the phylogenetic study performed with other Tevenvirinae phages showed a close common ancestor. However, there were 21 coding sequences which differed. Interestingly, the main differences were that vB_KpnM-VAC66 encoded 10 more homing endonucleases than vB_KpnM-VAC13, and that the nucleotidic and amino-acid sequences of the L-shaped tail fiber protein were highly dissimilar, leading to different three-dimensional protein predictions. Both phages differed significantly in their host range. These viruses may be useful in the development of alternative therapies to antibiotics or as a co-therapy increasing its antimicrobial potential, especially when addressing multidrug resistant (MDR) pathogens.
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28
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Dunstan RA, Bamert RS, Belousoff MJ, Short FL, Barlow CK, Pickard DJ, Wilksch JJ, Schittenhelm RB, Strugnell RA, Dougan G, Lithgow T. Mechanistic Insights into the Capsule-Targeting Depolymerase from a Klebsiella pneumoniae Bacteriophage. Microbiol Spectr 2021; 9:e0102321. [PMID: 34431721 PMCID: PMC8552709 DOI: 10.1128/spectrum.01023-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 08/02/2021] [Indexed: 02/07/2023] Open
Abstract
The production of capsular polysaccharides by Klebsiella pneumoniae protects the bacterial cell from harmful environmental factors such as antimicrobial compounds and infection by bacteriophages (phages). To bypass this protective barrier, some phages encode polysaccharide-degrading enzymes referred to as depolymerases to provide access to cell surface receptors. Here, we characterized the phage RAD2, which infects K. pneumoniae strains that produce the widespread, hypervirulence-associated K2-type capsular polysaccharide. Using transposon-directed insertion sequencing, we have shown that the production of capsule is an absolute requirement for efficient RAD2 infection by serving as a first-stage receptor. We have identified the depolymerase responsible for recognition and degradation of the capsule, determined that the depolymerase forms globular appendages on the phage virion tail tip, and present the cryo-electron microscopy structure of the RAD2 capsule depolymerase at 2.7-Å resolution. A putative active site for the enzyme was identified, comprising clustered negatively charged residues that could facilitate the hydrolysis of target polysaccharides. Enzymatic assays coupled with mass spectrometric analyses of digested oligosaccharide products provided further mechanistic insight into the hydrolase activity of the enzyme, which, when incubated with K. pneumoniae, removes the capsule and sensitizes the cells to serum-induced killing. Overall, these findings expand our understanding of how phages target the Klebsiella capsule for infection, providing a framework for the use of depolymerases as antivirulence agents against this medically important pathogen. IMPORTANCE Klebsiella pneumoniae is a medically important pathogen that produces a thick protective capsule that is essential for pathogenicity. Phages are natural predators of bacteria, and many encode diverse "capsule depolymerases" which specifically degrade the capsule of their hosts, an exploitable trait for potential therapies. We have determined the first structure of a depolymerase that targets the clinically relevant K2 capsule and have identified its putative active site, providing hints to its mechanism of action. We also show that Klebsiella cells treated with a recombinant form of the depolymerase are stripped of capsule, inhibiting their ability to grow in the presence of serum, demonstrating the anti-infective potential of these robust and readily producible enzymes against encapsulated bacterial pathogens such as K. pneumoniae.
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Affiliation(s)
- Rhys A. Dunstan
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Rebecca S. Bamert
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Matthew J. Belousoff
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Drug Discovery Biology Theme, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria, Australia
| | - Francesca L. Short
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Wellcome Sanger Institute, Hinxton, Cambridgeshire, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Christopher K. Barlow
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Derek J. Pickard
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Jonathan J. Wilksch
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Ralf B. Schittenhelm
- Monash Proteomics & Metabolomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia
| | - Richard A. Strugnell
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, Australia
| | - Gordon Dougan
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Trevor Lithgow
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
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29
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Identification of Receptor Binding Proteins in Flagellotropic Agrobacterium Phage 7-7-1. Viruses 2021; 13:v13071267. [PMID: 34209785 PMCID: PMC8310070 DOI: 10.3390/v13071267] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 06/22/2021] [Accepted: 06/23/2021] [Indexed: 12/14/2022] Open
Abstract
The rapid discovery of new and diverse bacteriophages has driven the innovation of approaches aimed at detailing interactions with their bacterial hosts. Previous studies on receptor binding proteins (RBPs) mainly relied on their identification in silico and are based on similarities to well-characterized systems. Thus, novel phage RBPs unlike those currently annotated in genomic and proteomic databases remain largely undiscovered. In this study, we employed a screen to identify RBPs in flagellotropic Agrobacterium phage 7-7-1. Flagellotropic phages utilize bacterial flagella as receptors. The screen identified three candidate RBPs, Gp4, Gp102, and Gp44. Homology modelling predicted that Gp4 is a trimeric, tail associated protein with a central β-barrel, while the structure and function of Gp102 and Gp44 are less obvious. Studies with purified Gp41-247 confirmed its ability to bind and interact with host cells, highlighting the robustness of the RBP screen. We also discovered that Gp41-247 inhibits the growth of host cells in a motility and lipopolysaccharide (LPS) dependent fashion. Hence, our results suggest interactions between Gp41-247, rotating flagellar filaments and host glycans to inhibit host cell growth, which presents an impactful and intriguing focus for future studies.
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Blundell-Hunter G, Enright MC, Negus D, Dorman MJ, Beecham GE, Pickard DJ, Wintachai P, Voravuthikunchai SP, Thomson NR, Taylor PW. Characterisation of Bacteriophage-Encoded Depolymerases Selective for Key Klebsiella pneumoniae Capsular Exopolysaccharides. Front Cell Infect Microbiol 2021; 11:686090. [PMID: 34222050 PMCID: PMC8253255 DOI: 10.3389/fcimb.2021.686090] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 04/30/2021] [Indexed: 01/12/2023] Open
Abstract
Capsular polysaccharides enable clinically important clones of Klebsiella pneumoniae to cause severe systemic infections in susceptible hosts. Phage-encoded capsule depolymerases have the potential to provide an alternative treatment paradigm in patients when multiple drug resistance has eroded the efficacy of conventional antibiotic chemotherapy. An investigation of 164 K. pneumoniae from intensive care patients in Thailand revealed a large number of distinct K types in low abundance but four (K2, K51, K1, K10) with a frequency of at least 5%. To identify depolymerases with the capacity to degrade capsules associated with these common K-types, 62 lytic phage were isolated from Thai hospital sewage water using K1, K2 and K51 isolates as hosts; phage plaques, without exception, displayed halos indicative of the presence of capsule-degrading enzymes. Phage genomes ranged in size from 41-348 kb with between 50 and 535 predicted coding sequences (CDSs). Using a custom phage protein database we were successful in applying annotation to 30 - 70% (mean = 58%) of these CDSs. The largest genomes, of so-called jumbo phage, carried multiple tRNAs as well as CRISPR repeat and spacer sequences. One of the smaller phage genomes was found to contain a putative Cas type 1E gene, indicating a history of host DNA acquisition in these obligate lytic phage. Whole-genome sequencing (WGS) indicated that some phage displayed an extended host range due to the presence of multiple depolymerase genes; in total, 42 candidate depolymerase genes were identified with up to eight in a single genome. Seven distinct virions were selected for further investigation on the basis of host range, phage morphology and WGS. Candidate genes for K1, K2 and K51 depolymerases were expressed and purified as his6-tagged soluble protein and enzymatic activity demonstrated against K. pneumoniae capsular polysaccharides by gel electrophoresis and Anton-Paar rolling ball viscometry. Depolymerases completely removed the capsule in K-type-specific fashion from K. pneumoniae cells. We conclude that broad-host range phage carry multiple enzymes, each with the capacity to degrade a single K-type, and any future use of these enzymes as therapeutic agents will require enzyme cocktails for utility against a range of K. pneumoniae infections.
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Affiliation(s)
| | - Mark C. Enright
- Department of Life Sciences, Manchester Metropolitan University, Manchester, United Kingdom
| | - David Negus
- School of Science & Technology, Nottingham Trent University, Nottingham, United Kingdom
| | - Matthew J. Dorman
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Gemma E. Beecham
- School of Pharmacy, University College London, London, United Kingdom
| | - Derek J. Pickard
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge, United Kingdom
| | | | | | - Nicholas R. Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
- Department of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Peter W. Taylor
- School of Pharmacy, University College London, London, United Kingdom
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Engineering the Modular Receptor-Binding Proteins of Klebsiella Phages Switches Their Capsule Serotype Specificity. mBio 2021; 12:mBio.00455-21. [PMID: 33947754 PMCID: PMC8262889 DOI: 10.1128/mbio.00455-21] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
The high specificity of bacteriophages is driven by their receptor-binding proteins (RBPs). Many Klebsiella bacteriophages target the capsular exopolysaccharide as the receptor and encode RBPs with depolymerase activity. The modular structure of these RBPs with an N-terminal structural module to attach the RBP to the phage tail, and a C-terminal specificity module for exopolysaccharide degradation, supports horizontal transfer as a major evolutionary driver for Klebsiella phage RBPs. We mimicked this natural evolutionary process by the construction of modular RBP chimeras, exchanging N-terminal structural modules and C-terminal specificity modules. All chimeras strictly follow the capsular serotype specificity of the C-terminal module. Transplanting chimeras with a K11 N-terminal structural RBP module in a Klebsiella phage K11 scaffold results in a capsular serotype switch and corresponding host range modification of the synthetic phages, demonstrating that horizontal transfer of C-terminal specificity modules offers Klebsiella phages an evolutionary highway for rapid adaptation to new capsular serotypes.
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Isolation and Characterization of a Novel Lytic Bacteriophage against the K2 Capsule-Expressing Hypervirulent Klebsiella pneumoniae Strain 52145, and Identification of Its Functional Depolymerase. Microorganisms 2021; 9:microorganisms9030650. [PMID: 33801047 PMCID: PMC8003838 DOI: 10.3390/microorganisms9030650] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2021] [Revised: 03/16/2021] [Accepted: 03/18/2021] [Indexed: 12/30/2022] Open
Abstract
Klebsiella pneumoniae is among the leading bacteria that cause nosocomial infections. The capsule of this Gram-negative bacterium is a dominant virulence factor, with a prominent role in defense and biofilm formation. Bacteriophages, which are specific for one bacterial strain and its capsule type, can evoke the lysis of bacterial cells, aided by polysaccharide depolymerase enzymes. In this study, we isolated and characterized a bacteriophage against the nosocomial K. pneumoniae 52145 strain with K2 capsular serotype. The phage showed a narrow host range and stable lytic activity, even when exposed to different temperatures or detergents. Preventive effect of the phage in a nasal colonization model was investigated in vivo. Phlyogenetic analysis showed that the newly isolated Klebsiella phage B1 belongs to the Webervirus genus in Drexlerviridae family. We identified the location of the capsule depolymerase gene of the new phage, which was amplified, cloned, expressed, and purified. The efficacy of the recombinant B1dep depolymerase was tested by spotting on K. pneumoniae strains and it was confirmed that the extract lowers the thickness of the bacterium lawn as it degrades the protective capsule on bacterial cells. As K. pneumoniae strains possessing the K2 serotype have epidemiological importance, the B1 phage and its depolymerase are promising candidates for use as possible antimicrobial agents.
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Townsend EM, Kelly L, Gannon L, Muscatt G, Dunstan R, Michniewski S, Sapkota H, Kiljunen SJ, Kolsi A, Skurnik M, Lithgow T, Millard AD, Jameson E. Isolation and Characterization of Klebsiella Phages for Phage Therapy. PHAGE (NEW ROCHELLE, N.Y.) 2021; 2:26-42. [PMID: 33796863 PMCID: PMC8006926 DOI: 10.1089/phage.2020.0046] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Introduction: Klebsiella is a clinically important pathogen causing a variety of antimicrobial resistant infections in both community and nosocomial settings, particularly pneumonia, urinary tract infection, and sepsis. Bacteriophage (phage) therapy is being considered a primary option for the treatment of drug-resistant infections of these types. Methods: We report the successful isolation and characterization of 30 novel, genetically diverse Klebsiella phages. Results: The isolated phages span six different phage families and nine genera, representing both lysogenic and lytic lifestyles. Individual Klebsiella phage isolates infected up to 11 of the 18 Klebsiella capsule types tested, and all 18 capsule-types were infected by at least one of the phages. Conclusions: Of the Klebsiella-infecting phages presented in this study, the lytic phages are most suitable for phage therapy, based on their broad host range, high virulence, short lysis period and given that they encode no known toxin or antimicrobial resistance genes. Phage isolates belonging to the Sugarlandvirus and Slopekvirus genera were deemed most suitable for phage therapy based on our characterization. Importantly, when applied alone, none of the characterized phages were able to suppress the growth of Klebsiella for more than 12 h, likely due to the inherent ease of Klebsiella to generate spontaneous phage-resistant mutants. This indicates that for successful phage therapy, a cocktail of multiple phages would be necessary to treat Klebsiella infections.
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Affiliation(s)
- Eleanor M. Townsend
- Department of Microbiology and Virology, School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, United Kingdom
| | - Lucy Kelly
- Department of Microbiology and Virology, School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, United Kingdom
| | - Lucy Gannon
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - George Muscatt
- Department of Microbiology and Virology, School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, United Kingdom
| | - Rhys Dunstan
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Slawomir Michniewski
- Department of Microbiology and Virology, School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, United Kingdom
| | - Hari Sapkota
- Department of Neuroscience, Psychology and Behaviour, University of Leicester, Leicester, United Kingdom
| | - Saija J. Kiljunen
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Anna Kolsi
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikael Skurnik
- Department of Bacteriology and Immunology, Human Microbiome Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Division of Clinical Microbiology, Helsinki University Hospital, HUSLAB, Helsinki, Finland
| | - Trevor Lithgow
- Infection and Immunity Program, Department of Microbiology, Biomedicine Discovery Institute, Monash University, Melbourne, Australia
| | - Andrew D. Millard
- Department of Genetics, University of Leicester, Leicester, United Kingdom
| | - Eleanor Jameson
- Department of Microbiology and Virology, School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, United Kingdom
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Identification of a Depolymerase Specific for K64-Serotype Klebsiella pneumoniae: Potential Applications in Capsular Typing and Treatment. Antibiotics (Basel) 2021; 10:antibiotics10020144. [PMID: 33535705 PMCID: PMC7912862 DOI: 10.3390/antibiotics10020144] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Revised: 01/25/2021] [Accepted: 01/29/2021] [Indexed: 01/08/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP), one of the major nosocomial pathogens, is increasingly becoming a serious threat to global public health. There is an urgent need to develop effective therapeutic and preventive approaches to combat the pathogen. Here, we identified and characterized a novel capsule depolymerase (K64-ORF41) derived from Klebsiella phage SH-KP152410, which showed specific activities for K. pneumoniae K64-serotype. We showed that this depolymerase could be used in the identification of K64 serotypes based on the capsular typing, and the results agreed well with those from the conventional serotyping method using antisera. From this study, we also identified K64 mutant strains, which showed typing discrepancy between wzi-sequencing based genotyping and depolymerase-based or antiserum-based typing methods. Further investigation indicated that the mutant strain has an insertion sequence (IS) in wcaJ, which led to the alteration of the capsular serotype structure. We further demonstrated that K64-ORF41 depolymerase could sensitize the bacteria to serum or neutrophil killing by degrading the capsular polysaccharide. In summary, the identified K64 depolymerase proves to be an accurate and reliable tool for capsular typing, which will facilitate the preventive intervention such as vaccine development. In addition, the polymerase may represent a potential and promising therapeutic biologics against CRKP-K64 infections.
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Loessner H, Schlattmeier I, Anders-Maurer M, Bekeredjian-Ding I, Rohde C, Wittmann J, Pokalyuk C, Krut O, Kamp C. Kinetic Fingerprinting Links Bacteria-Phage Interactions with Emergent Dynamics: Rapid Depletion of Klebsiella pneumoniae Indicates Phage Synergy. Antibiotics (Basel) 2020; 9:E408. [PMID: 32674401 PMCID: PMC7400656 DOI: 10.3390/antibiotics9070408] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 07/01/2020] [Accepted: 07/06/2020] [Indexed: 11/22/2022] Open
Abstract
The specific temporal evolution of bacterial and phage population sizes, in particular bacterial depletion and the emergence of a resistant bacterial population, can be seen as a kinetic fingerprint that depends on the manifold interactions of the specific phage-host pair during the course of infection. We have elaborated such a kinetic fingerprint for a human urinary tract Klebsiella pneumoniae isolate and its phage vB_KpnP_Lessing by a modeling approach based on data from in vitro co-culture. We found a faster depletion of the initially sensitive bacterial population than expected from simple mass action kinetics. A possible explanation for the rapid decline of the bacterial population is a synergistic interaction of phages which can be a favorable feature for phage therapies. In addition to this interaction characteristic, analysis of the kinetic fingerprint of this bacteria and phage combination revealed several relevant aspects of their population dynamics: A reduction of the bacterial concentration can be achieved only at high multiplicity of infection whereas bacterial extinction is hardly accomplished. Furthermore the binding affinity of the phage to bacteria is identified as one of the most crucial parameters for the reduction of the bacterial population size. Thus, kinetic fingerprinting can be used to infer phage-host interactions and to explore emergent dynamics which facilitates a rational design of phage therapies.
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Affiliation(s)
- Holger Loessner
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | - Insea Schlattmeier
- Goethe University Frankfurt, Institute of Mathematics, 60325 Frankfurt, Germany; (I.S.); (C.P.)
| | - Marie Anders-Maurer
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | | | - Christine Rohde
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Johannes Wittmann
- Leibniz Institute DSMZ German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany; (C.R.); (J.W.)
| | - Cornelia Pokalyuk
- Goethe University Frankfurt, Institute of Mathematics, 60325 Frankfurt, Germany; (I.S.); (C.P.)
| | - Oleg Krut
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
| | - Christel Kamp
- Paul-Ehrlich-Institut, 63225 Langen, Germany; (H.L.); (M.A.-M.); (I.B.-D.); (O.K.)
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