1
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Cushnie TPT, Luang-In V, Sexton DW. Necrophages and necrophiles: a review of their antibacterial defenses and biotechnological potential. Crit Rev Biotechnol 2024:1-18. [PMID: 39198023 DOI: 10.1080/07388551.2024.2389175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2023] [Revised: 03/20/2024] [Accepted: 04/04/2024] [Indexed: 09/01/2024]
Abstract
With antibiotic resistance on the rise, there is an urgent need for new antibacterial drugs and products to treat or prevent infection. Many such products in current use, for example human and veterinary antibiotics and antimicrobial food preservatives, were discovered and developed from nature. Natural selection acts on all living organisms and the presence of bacterial competitors or pathogens in an environment can favor the evolution of antibacterial adaptations. In this review, we ask if vultures, blow flies and other carrion users might be a good starting point for antibacterial discovery based on the selection pressure they are under from bacterial disease. Dietary details are catalogued for over 600 of these species, bacterial pathogens associated with the diets are described, and an overview of the antibacterial defenses contributing to disease protection is given. Biotechnological applications for these defenses are then discussed, together with challenges facing developers and possible solutions. Examples include use of (a) the antimicrobial peptide (AMP) gene sarcotoxin IA to improve crop resistance to bacterial disease, (b) peptide antibiotics such as serrawettin W2 as antibacterial drug leads, (c) lectins for targeted drug delivery, (d) bioconversion-generated chitin as an antibacterial biomaterial, (e) bacteriocins as antibacterial food preservatives and (f) mutualistic microbiota bacteria as alternatives to antibiotics in animal feed. We show that carrion users encounter a diverse range of bacterial pathogens through their diets and interactions, have evolved many antibacterial defenses, and are a promising source of genes, molecules, and microbes for medical, agricultural, and food industry product development.
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Affiliation(s)
- T P Tim Cushnie
- Faculty of Medicine, Mahasarakham University, Mueang, Maha Sarakham, Thailand
| | - Vijitra Luang-In
- Department of Biotechnology, Faculty of Technology, Mahasarakham University, Khamriang, Maha Sarakham, Thailand
| | - Darren W Sexton
- School of Pharmacy and Biomolecular Sciences, Liverpool John Moores University, Liverpool, UK
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2
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Fu Y, Yu S, Li J, Lao Z, Yang X, Lin Z. DeepMineLys: Deep mining of phage lysins from human microbiome. Cell Rep 2024; 43:114583. [PMID: 39110597 DOI: 10.1016/j.celrep.2024.114583] [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: 11/07/2023] [Revised: 06/21/2024] [Accepted: 07/19/2024] [Indexed: 09/01/2024] Open
Abstract
Vast shotgun metagenomics data remain an underutilized resource for novel enzymes. Artificial intelligence (AI) has increasingly been applied to protein mining, but its conventional performance evaluation is interpolative in nature, and these trained models often struggle to extrapolate effectively when challenged with unknown data. In this study, we present a framework (DeepMineLys [deep mining of phage lysins from human microbiome]) based on the convolutional neural network (CNN) to identify phage lysins from three human microbiome datasets. When validated with an independent dataset, our method achieved an F1-score of 84.00%, surpassing existing methods by 20.84%. We expressed 16 lysin candidates from the top 100 sequences in E. coli, confirming 11 as active. The best one displayed an activity 6.2-fold that of lysozyme derived from hen egg white, establishing it as the most potent lysin from the human microbiome. Our study also underscores several important issues when applying AI to biology questions. This framework should be applicable for mining other proteins.
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Affiliation(s)
- Yiran Fu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Shuting Yu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Jianfeng Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Zisha Lao
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China
| | - Xiaofeng Yang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
| | - Zhanglin Lin
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou, Guangdong 510006, China.
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3
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Zhydzetski A, Głowacka-Grzyb Z, Bukowski M, Żądło T, Bonar E, Władyka B. Agents Targeting the Bacterial Cell Wall as Tools to Combat Gram-Positive Pathogens. Molecules 2024; 29:4065. [PMID: 39274911 PMCID: PMC11396672 DOI: 10.3390/molecules29174065] [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: 07/28/2024] [Revised: 08/20/2024] [Accepted: 08/21/2024] [Indexed: 09/16/2024] Open
Abstract
The cell wall is an indispensable element of bacterial cells and a long-known target of many antibiotics. Penicillin, the first discovered beta-lactam antibiotic inhibiting the synthesis of cell walls, was successfully used to cure many bacterial infections. Unfortunately, pathogens eventually developed resistance to it. This started an arms race, and while novel beta-lactams, either natural or (semi)synthetic, were discovered, soon upon their application, bacteria were developing resistance. Currently, we are facing the threat of losing the race since more and more multidrug-resistant (MDR) pathogens are emerging. Therefore, there is an urgent need for developing novel approaches to combat MDR bacteria. The cell wall is a reasonable candidate for a target as it differentiates not only bacterial and human cells but also has a specific composition unique to various groups of bacteria. This ensures the safety and specificity of novel antibacterial agents that target this structure. Due to the shortage of low-molecular-weight candidates for novel antibiotics, attention was focused on peptides and proteins that possess antibacterial activity. Here, we describe proteinaceous agents of various origins that target bacterial cell wall, including bacteriocins and phage and bacterial lysins, as alternatives to classic antibiotic candidates for antimicrobial drugs. Moreover, advancements in protein chemistry and engineering currently allow for the production of stable, specific, and effective drugs. Finally, we introduce the concept of selective targeting of dangerous pathogens, exemplified by staphylococci, by agents specifically disrupting their cell walls.
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Affiliation(s)
- Aliaksandr Zhydzetski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Zuzanna Głowacka-Grzyb
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Michal Bukowski
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Tomasz Żądło
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
- Doctoral School of Exact and Natural Sciences, Jagiellonian University, Prof. St. Łojasiewicza St. 11, 30-348 Cracow, Poland
| | - Emilia Bonar
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
| | - Benedykt Władyka
- Department of Analytical Biochemistry, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Gronostajowa St. 7, 30-348 Cracow, Poland
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4
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Karyagina AS, Grishin AV, Kudinova AG, Bulygina IN, Koudan EV, Orlova PA, Datsenko VP, Zhulina AV, Grunina TM, Poponova MS, Krivozubov MS, Gromova MS, Strukova NV, Generalova MS, Nikitin KE, Shchetinin IV, Luchnikov LO, Zaitseva SV, Kirsanova MA, Statnik ES, Senatov FS, Lunin VG, Gromov AV. Dual-Functional Implant Based on Gellan-Xanthan Hydrogel with Diopside, BMP-2 and Lysostaphin for Bone Defect Repair and Control of Staphylococcal Infection. Macromol Biosci 2024:e2400205. [PMID: 39140453 DOI: 10.1002/mabi.202400205] [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: 04/25/2024] [Revised: 07/10/2024] [Indexed: 08/15/2024]
Abstract
A new dual-functional implant based on gellan-xanthan hydrogel with calcium-magnesium silicate ceramic diopside and recombinant lysostaphin and bone morphogenetic protein 2 (BMP-2)-ray is developed. In this composite, BMP-2 is immobilized on microparticles of diopside while lysostaphin is mixed directly into the hydrogel, providing sustained release of BMP-2 to allow gradual bone formation and rapid release of lysostaphin to eliminate infection immediately after implantation. Introduction of diopside of up to 3% (w/v) has a negligible effect on the mechanical properties of the hydrogel but provides a high sorption capacity for BMP-2. The hydrogels show good biocompatibility and antibacterial activity. Lysostaphin released from the implants over a 3 h period efficiently kills planktonic cells and completely destroys 24 h pre-formed biofilms of Staphylococcus aureus. Furthermore, in vivo experiments in a mouse model of critically-sized cranial defects infected with S. aureus show a complete lack of osteogenesis when implants contain only BMP-2, whereas, in the presence of lysostaphin, complete closure of the defect with newly formed mineralized bone tissue is observed. Thus, the new implantable gellan-xanthan hydrogel with diopside and recombinant lysostaphin and BMP-2 shows both osteogenic and antibacterial properties and represents a promising material for the treatment and/or prevention of osteomyelitis after bone trauma.
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Affiliation(s)
- Anna S Karyagina
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119992, Russia
- Institute of Biomedical Engineering, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Alexander V Grishin
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia
| | - Alina G Kudinova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Inna N Bulygina
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- Institute of Biomedical Engineering, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Elizaveta V Koudan
- Institute of Biomedical Engineering, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Polina A Orlova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Vera P Datsenko
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Anna V Zhulina
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Tatyana M Grunina
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia
| | - Maria S Poponova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Mikhail S Krivozubov
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Maria S Gromova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Natalia V Strukova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Maria S Generalova
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Kirill E Nikitin
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
| | - Igor V Shchetinin
- Material Science Department, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Lev O Luchnikov
- LASE - Laboratory of Advanced Solar Energy, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Svetlana V Zaitseva
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- Institute of Biomedical Engineering, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | | | - Eugene S Statnik
- "LUCh" Laboratory, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Fedor S Senatov
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- Institute of Biomedical Engineering, National University of Science and Technology "MISIS", Moscow, 119049, Russia
| | - Vladimir G Lunin
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
- All-Russia Research Institute of Agricultural Biotechnology, Russian Academy of Sciences, Moscow, 127550, Russia
| | - Alexander V Gromov
- Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Healthcare of the Russian Federation, Moscow, 123098, Russia
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Qiu Z, Yuan K, Cao H, Chen S, Chen F, Mo F, Guo G, Peng J. Cross-talk of MLST and transcriptome unveiling antibiotic resistance mechanism of carbapenem resistance Acinetobacter baumannii clinical strains isolated in Guiyang, China. Front Microbiol 2024; 15:1394775. [PMID: 38946905 PMCID: PMC11211267 DOI: 10.3389/fmicb.2024.1394775] [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: 03/02/2024] [Accepted: 05/23/2024] [Indexed: 07/02/2024] Open
Abstract
Introduction Acinetobacter baumannii (A. baumannii) is an important opportunistic pathogen causing nosocomial infection in the clinic. The occurrence rate of antibiotic resistance is increasing year by year, resulting in a highly serious situation of bacterial resistance. Methods To better understand the local epidemiology of multidrug-resistant A. baumannii, an investigation was conducted on the antibiotic resistance of different types of A. baumannii and its relationship with the genes of A. baumannii. Furthermore, the molecular mechanism underlying antibiotic resistance in A. baumannii was investigated through transcriptome analysis. Results These results showed that a total of 9 STs were detected. It was found that 99% of the strains isolated in the hospital belonged to the same STs, and the clone complex CC208 was widely distributed in various departments and all kinds of samples. Furthermore, these A. baumannii strains showed high resistance to ertapenem, biapenem, meropenem, and imipenem, among which the resistance to ertapenem was the strongest. The detection rate of bla OXA-51 gene in these carbapenem resistance A. baumannii (CRAB) reached 100%; Additionally, the transcriptome results showed that the resistance genes were up-regulated in resistance strains, and these genes involved in biofilm formation, efflux pumps, peptidoglycan biosynthesis, and chaperonin synthesis. Discussion These results suggest that the CC208 STs were the main clonal complex, and showed high carbapenem antibiotic resistance. All these resistant strains were distributed in various departments, but most of them were distributed in intensive care units (ICU). The bla OXA-23 was the main antibiotic resistance genotype; In summary, the epidemic trend of clinical A. baumannii in Guiyang, China was analyzed from the molecular level, and the resistance mechanism of A. baumannii to carbapenem antibiotics was analyzed with transcriptome, which provided a theoretical basis for better control of A. baumannii.
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Affiliation(s)
- Zhilang Qiu
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Kexin Yuan
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Huijun Cao
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Sufang Chen
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
| | - Feifei Chen
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
| | - Fei Mo
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
| | - Guo Guo
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
| | - Jian Peng
- Center for Clinical Laboratories, The Affiliated Hospital of Guizhou Medical University, Guiyang, China
- Key Laboratory of Infectious Immune and Antibody Engineering of Guizhou Province, Cellular Immunotherapy Engineering Research Center of Guizhou Province, School of Biology and Engineering/School of Basic Medical Sciences, Guizhou Medical University, Guiyang, China
- The Key and Characteristic Laboratory of Modern Pathogen Biology, Basic Medical College, Guizhou Medical University, Guiyang, China
- Translational Medicine Research Center, Guizhou Medical University, Guiyang, China
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6
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Sanz-Gaitero M, De Maesschalck V, Patel A, Longin H, Van Noort V, Rodriguez-Rubio L, van Ryne M, Danis-Wlodarczyk K, Drulis-Kawa Z, Mesnage S, van Raaij M, Lavigne R. Structural and Biochemical Characterization of a New Phage-Encoded Muramidase, KTN6 Gp46. PHAGE (NEW ROCHELLE, N.Y.) 2024; 5:53-62. [PMID: 39119210 PMCID: PMC11304755 DOI: 10.1089/phage.2023.0040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
Background Endolysins are phage-encoded lytic enzymes that degrade bacterial peptidoglycan at the end of phage lytic cycles to release new phage particles. These enzymes are being explored as an alternative to small-molecule antibiotics. Methods The crystal structure of KTN6 Gp46 was determined and compared with a ColabFold model. Cleavage specificity was examined using a peptidoglycan digest and reversed-phase high-performance liquid chromatography coupled to mass spectrometry (HPLC/MS). Results The structure of KTN6 Gp46 could be determined at 1.4 Å resolution, and key differences in loops of the putative peptidoglycan binding domain were identified in comparison with its closest known homologue, the endolysin of phage SPN1S. Reversed-phase HPLC/MS analysis of the reaction products following peptidoglycan digestion confirmed the muramidase activity of Gp46, consistent with structural predictions. Conclusion These insights into the structure and function of endolysins further expand the toolbox for endolysin engineering and explore their potential in enzyme-based antibacterial design strategies.
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Affiliation(s)
- Marta Sanz-Gaitero
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
- Department of Biological Sciences, Munster Technological University, Cork, Ireland
| | | | - Ankur Patel
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Hannelore Longin
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium
| | - Vera Van Noort
- Laboratory of Computational Systems Biology, KU Leuven, Leuven, Belgium
| | | | | | - Katarzyna Danis-Wlodarczyk
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, University of Wroclaw, Wroclaw, Poland
| | - Stephane Mesnage
- School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Mark van Raaij
- Centro Nacional de Biotecnologia, Consejo Superior de Investigaciones Cientificas, Madrid, Spain
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, Leuven, Belgium
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7
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Carratalá JV, Ferrer-Miralles N, Garcia-Fruitós E, Arís A. LysJEP8: A promising novel endolysin for combating multidrug-resistant Gram-negative bacteria. Microb Biotechnol 2024; 17:e14483. [PMID: 38864495 PMCID: PMC11167605 DOI: 10.1111/1751-7915.14483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 05/03/2024] [Accepted: 05/08/2024] [Indexed: 06/13/2024] Open
Abstract
Antimicrobial resistance (AMR) is an escalating global health crisis, driven by the overuse and misuse of antibiotics. Multidrug-resistant Gram-negative bacteria, such as Pseudomonas aeruginosa, Acinetobacter baumannii, and Klebsiella pneumoniae, are particularly concerning due to their high morbidity and mortality rates. In this context, endolysins, derived from bacteriophages, offer a promising alternative to traditional antibiotics. This study introduces LysJEP8, a novel endolysin derived from Escherichia phage JEP8, which exhibits remarkable antimicrobial activity against key Gram-negative members of the ESKAPE group. Comparative assessments highlight LysJEP8's superior performance in reducing bacterial survival rates compared to previously described endolysins, with the most significant impact observed against P. aeruginosa, and notable effects on A. baumannii and K. pneumoniae. The study found that LysJEP8, as predicted by in silico analysis, worked best at lower pH values but lost its effectiveness at salt concentrations close to physiological levels. Importantly, LysJEP8 exhibited remarkable efficacy in the disruption of P. aeruginosa biofilms. This research underscores the potential of LysJEP8 as a valuable candidate for the development of innovative antibacterial agents, particularly against Gram-negative pathogens, and highlights opportunities for further engineering and optimization to address AMR effectively.
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Affiliation(s)
- Jose Vicente Carratalá
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Barcelona, Spain
- Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Barcelona, Spain
- Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), Madrid, Spain
| | - Neus Ferrer-Miralles
- Institute of Biotechnology and Biomedicine, Autonomous University of Barcelona, Barcelona, Spain
- Department of Genetics and Microbiology, Autonomous University of Barcelona, Barcelona, Spain
- Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), Madrid, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Barcelona, Spain
| | - Anna Arís
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Barcelona, Spain
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8
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Lendel AM, Antonova NP, Grigoriev IV, Usachev EV, Gushchin VA, Vasina DV. Biofilm-disrupting effects of phage endolysins LysAm24, LysAp22, LysECD7, and LysSi3: breakdown the matrix. World J Microbiol Biotechnol 2024; 40:186. [PMID: 38683213 DOI: 10.1007/s11274-024-03999-9] [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: 01/26/2024] [Accepted: 04/21/2024] [Indexed: 05/01/2024]
Abstract
The ability of most opportunistic bacteria to form biofilms, coupled with antimicrobial resistance, hinder the efforts to control widespread infections, resulting in high risks of negative outcomes and economic costs. Endolysins are promising compounds that efficiently combat bacteria, including multidrug-resistant strains and biofilms, without a low probability of subsequent emergence of stable endolysin-resistant phenotypes. However, the details of antibiofilm effects of these enzymes are poorly understood. To elucidate the interactions of bacteriophage endolysins LysAm24, LysAp22, LysECD7, and LysSi3 with bacterial films formed by Gram-negative species, we estimated their composition and assessed the endolysins' effects on the most abundant exopolymers in vitro. The obtained data suggests a pronounced efficiency of these lysins against biofilms with high (Klebsiella pneumoniae) and low (Acinetobacter baumannii) matrix contents, or dual-species biofilms, resulting in at least a twofold loss of the biomass. These peptidoglycan hydrolases interacted diversely with protective compounds of biofilms such as extracellular DNA and polyanionic carbohydrates, indicating a spectrum of biofilm-disrupting effects for bacteriolytic phage enzymes. Specifically, we detected disruption of acid exopolysaccharides by LysAp22, strong DNA-binding capacity of LysAm24, both of these interactions for LysECD7, and neither of them for LysSi3.
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Affiliation(s)
- Anastasiya M Lendel
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098, Russia.
| | - Nataliia P Antonova
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Igor V Grigoriev
- Translational Biomedicine Laboratory, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Evgeny V Usachev
- Translational Biomedicine Laboratory, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Vladimir A Gushchin
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
| | - Daria V Vasina
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, 123098, Russia
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9
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Li Y, Luo L, Wang W, Hong B, Ma Y, Wang J. Characterization of a cell wall hydrolase with high activity against vegetative cells, spores and biofilm of Bacillus cereus. Int J Food Microbiol 2024; 414:110617. [PMID: 38335884 DOI: 10.1016/j.ijfoodmicro.2024.110617] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2023] [Revised: 12/17/2023] [Accepted: 02/04/2024] [Indexed: 02/12/2024]
Abstract
Bacillus cereus is a prevalent foodborne pathogen that induces food poisoning symptoms such as vomiting and diarrhea. Its capacity to form spores and biofilm enables it to withstand disinfectants and antimicrobials, leading to persistent contamination during food processing. Consequently, it is necessary to develop novel and efficient antimicrobial agents to control B. cereus, its spores, and biofilms. Peptidoglycan hydrolases have emerged as a promising and eco-friendly alternative owing to their specific lytic activity against pathogenic bacteria. Here, we identified and characterized a Lysozyme-like cell wall hydrolase Lys14579, from the genome of B. cereus ATCC 14579. Recombinant Lys14579 specifically lysed B. cereus without affecting other bacteria. Lys14579 exhibited strong lytic activity against B. cereus, effectively lysing B. cereus cell within 20 min at low concentration (10 μg/mL). It also inhibited the germination of B. cereus spores and prevented biofilm formation at 12.5 μg/mL. Moreover, Lys14579 displayed good antimicrobial stability with negligible hemolysis in mouse red blood cells and no cytotoxicity against RAW264.7 cells. Notably, Lys14579 effectively inhibited B. cereus in boiled rice and minced meat in a dose-dependent manner. Furthermore, bioinformatics analysis and point mutagenesis experiments revealed that Glu-47 was the catalytic site, and Asp-57, Gln-60, Ser-61 and Glu-63 were active-site residues related with the cell wall lytic activity. Taken together, Lys14579 could be a promising biocontrol agent against vegetative cells, spores, and biofilm of B. cereus in food industry.
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Affiliation(s)
- Yanmei Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Lun Luo
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Wenhai Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Bin Hong
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China
| | - Yi Ma
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China
| | - Jufang Wang
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510006, China; Guangdong Provincial Key Laboratory of Fermentation and Enzyme Engineering, South China University of Technology, Guangzhou 510006, China.
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10
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Dawood MAO, Abdo SE, El-Kassas S, El-Naggar K, Al Wakeel RA, Moustafa EM, Abou Asa S. Chicken egg lysozyme enhanced the growth performance, feed utilization, upregulated immune-related genes, and mitigated the impacts of Aeromonas hydrophila infection in Nile tilapia (Oreochromisniloticus). FISH & SHELLFISH IMMUNOLOGY 2024; 146:109377. [PMID: 38228249 DOI: 10.1016/j.fsi.2024.109377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Revised: 01/08/2024] [Accepted: 01/13/2024] [Indexed: 01/18/2024]
Abstract
Functional supplements, including lysozyme, are highly approved as immunostimulant and antibacterial agents with a high potential for use in aquaculture. In this regard, Nile tilapia was treated with lysozyme at 0, 0.5, 1, 1.5, and 3 g/kg for 60 days, then challenged with Aeromonas hydrophila. Fish were stocked in 15 glass aquaria (70 L each) with an equal initial weight of 10.72 ± 0.71 g per fish and 15 fish per aquarium. The regression analysis revealed that dietary lysozyme supplementation at 1.83-2 g/kg enhanced the growth performance, protein efficiency ratio, and protein productive value while reducing the feed conversion ratio of tilapia. Markedly, tilapia treated with lysozyme had a low mortality rate (30-50 %) compared to the control, which recorded a 70 % mortality rate after 15 days of challenge with A. hydrophila. The regression analysis also revealed that the highest lysozyme activity of tilapia-fed lysozyme for 60 days is achieved by 2.05 g/kg lysozyme. The expression of Nf-κb, IL-1β, and IL-8 genes is upregulated in tilapia-fed lysozyme at 0.5, 1, 1.5, and 3 g/kg for 60 days before and after A. hydrophila infection. The expression of GPX and CAT genes was higher in tilapia-fed lysozyme at 0.5, 1, 1.5, and 3 g/kg for 60 days before and after A. hydrophila infection. Before infection, the relative transcription of the lysozyme and C3 was upregulated in tilapia-fed lysozyme at 0.5, 1, 1.5, and 3 g/kg. However, lysozyme gene expression in tilapia treated with 0.5 g/kg lysozyme had no significant differences from those fed 0 g/kg lysozyme. After infection, the relative transcription of the lysozyme gene was upregulated in tilapia fed 1 and 1.5 g/kg, while tilapia fed 1 g/kg lysozyme had the highest C3 gene transcription. After infection, the hepatocytes in the livers of fish fed 0 g/kg lysozyme exhibited a noticeable fatty alteration, along with congestion, a light infiltration of inflammatory cells, and the start of necrosed cell regeneration. However, the livers of fish that received lysozyme were normal except for infiltrations of perivascular and interstitial mononuclear cells, depending on the supplementation dose. In conclusion, dietary lysozyme is recommended at 1.83-2.05 g/kg to gain high growth performance, immune response, and high resistance to A. hydrophila in Nile tilapia.
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Affiliation(s)
- Mahmoud A O Dawood
- Animal Production Department, Faculty of Agriculture, Kafrelsheikh University, Kafr El-Sheikh, 33516, Egypt; The Center for Applied Research on the Environment and Sustainability, The American University in Cairo, 11835, Cairo, Egypt.
| | - Safaa E Abdo
- Genetics and Genetic Engineering, Department of Animal Wealth Development, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt
| | - Seham El-Kassas
- Animal, Poultry and Fish Breeding and Production, Department of Animal Wealth Development, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt
| | - Karima El-Naggar
- Department of Nutrition and Veterinary Clinical Nutrition, Faculty of Veterinary Medicine, Alexandria University, 22758, Egypt
| | - Rasha A Al Wakeel
- Department of Physiology, Faculty of Veterinary Medicine, Kafrelsheikh University, Egypt
| | - Eman M Moustafa
- Department of Fish Diseases and Management, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El Sheikh, 33516, Egypt
| | - Samah Abou Asa
- Department of Veterinary Pathology, Faculty of Veterinary Medicine, Kafrelsheikh University, Kafr El Sheikh, 33516, Egypt
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11
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Carratalá JV, Arís A, Garcia-Fruitós E, Ferrer-Miralles N. Design strategies for positively charged endolysins: Insights into Artilysin development. Biotechnol Adv 2023; 69:108250. [PMID: 37678419 DOI: 10.1016/j.biotechadv.2023.108250] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Endolysins are bacteriophage-encoded enzymes that can specifically degrade the peptidoglycan layer of bacterial cell wall, making them an attractive tool for the development of novel antibacterial agents. The use of genetic engineering techniques for the production and modification of endolysins offers the opportunity to customize their properties and activity against specific bacterial targets, paving the way for the development of personalized therapies for bacterial infections. Gram-negative bacteria possess an outer membrane that can hinder the action of recombinantly produced endolysins. However, certain endolysins are capable of crossing the outer membrane by virtue of segments that share properties resembling those of cationic peptides. These regions increase the affinity of the endolysin towards the bacterial surface and assist in the permeabilization of the membrane. In order to improve the bactericidal effectiveness of endolysins, approaches have been implemented to increase their net charge, including the development of Artilysins containing positively charged amino acids at one end. At present, there are no specific guidelines outlining the steps for implementing these modifications. There is an ongoing debate surrounding the optimal location of positive charge, the need for a linker region, and the specific amino acid composition of peptides for modifying endolysins. The aim of this study is to provide clarity on these topics by analyzing and comparing the most effective modifications found in previous literature.
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Affiliation(s)
- Jose Vicente Carratalá
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain; Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain.
| | - Anna Arís
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
| | - Neus Ferrer-Miralles
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
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12
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Liu L, Jia X, Zhao X, Li T, Luo Z, Deng R, Peng B, Mao D, Liu H, Zheng Q. In vitro PCR verification that lysozyme inhibits nucleic acid replication and transcription. Sci Rep 2023; 13:6383. [PMID: 37076576 PMCID: PMC10115842 DOI: 10.1038/s41598-023-33228-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Accepted: 04/10/2023] [Indexed: 04/21/2023] Open
Abstract
Lysozyme can kill bacteria by its enzymatic activity or through a mechanism involving its cationic nature, which can facilitate electrostatic interactions with the viral capsid, the negatively charged parts of nucleic acids, and polymerase, so binding to nucleic acids may be another biological function of lysozyme. Here, PCR was used as a research tool to detect the effects of lysozyme on the replication and transcription of nucleic acids after treatment in different ways. We found that lysozyme and its hydrolysate can enter cells and inhibit PCR to varying degrees in vitro, and degraded lysozyme inhibited nucleic acid replication more effectively than intact lysozyme. The inhibition of lysozyme may be related to polymerase binding, and the sensitivity of different polymerases to lysozyme is inconsistent. Our findings provide a theoretical basis for further explaining the pharmacological effects of lysozyme, such as antibacterial, antiviral, anticancer, and immune regulatory activities, and directions for the development of new pharmacological effects of lysozyme and its metabolites.
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Affiliation(s)
- Lu Liu
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China
| | - Xu Jia
- Department of Pharmacy, Affiliated Hospital of North Sichuan Medical College, Nanchong, 637000, People's Republic of China
| | - Xiaoyang Zhao
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China
| | - Ting Li
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China
| | - Ziren Luo
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China
| | - Ranxi Deng
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China
| | - Bijia Peng
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China
| | - Danting Mao
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China
| | - Hong Liu
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China.
| | - Qian Zheng
- Medical Functional Experiment Center, North Sichuan Medical College, Nanchong, 637007, People's Republic of China.
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13
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Escobedo S, Pérez de Pipaon M, Rendueles C, Rodríguez A, Martínez B. Cell wall modifications that alter the exolytic activity of lactococcal phage endolysins have little impact on phage growth. Front Microbiol 2023; 14:1106049. [PMID: 36744092 PMCID: PMC9894900 DOI: 10.3389/fmicb.2023.1106049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 01/04/2023] [Indexed: 01/22/2023] Open
Abstract
Bacteriophages are a nuisance in the production of fermented dairy products driven by starter bacteria and strategies to reduce the risk of phage infection are permanently sought. Bearing in mind that the bacterial cell wall plays a pivotal role in host recognition and lysis, our goal was to elucidate to which extent modifications in the cell wall may alter endolysin activity and influence the outcome of phage infection in Lactococcus. Three lactococcal endolysins with distinct catalytic domains (CHAP, amidase and lysozyme) from phages 1,358, p2 and c2 respectively, were purified and their exolytic activity was tested against lactococcal mutants either overexpressing or lacking genes involved in the cell envelope stress (CES) response or in modifying peptidoglycan (PG) composition. After recombinant production in E. coli, Lys1358 (CHAP) and LysC2 (muramidase) were able to lyse lactococcal cells in turbidity reduction assays, but no activity of LysP2 was detected. The degree of PG acetylation, namely C6-O-acetylation and de-N-acetylation influenced the exolytic activity, being LysC2 more active against cells depleted of the PG deacetylase PgdA and the O-acetyl transferase OatA. On the contrary, both endolysins showed reduced activity on cells with an induced CES response. By measuring several growth parameters of phage c2 on these lactococcal mutants (lytic score, efficiency of plaquing, plaque size and one-step curves), a direct link between the exolytic activity of its endolysin and phage performance could not be stablished.
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14
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Arshinov IR, Antonova NP, Grigoriev IV, Pochtovyi AA, Tkachuk AP, Gushchin VA, Vasina DV. Engineered Endolysin LysECD7-SMAP Reveals Antimicrobial Synergy with Antibiotics and Restores Sensitivity in Gram-negative Pathogens. APPL BIOCHEM MICRO+ 2022. [DOI: 10.1134/s0003683822100027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
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15
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Razew A, Schwarz JN, Mitkowski P, Sabala I, Kaus-Drobek M. One fold, many functions-M23 family of peptidoglycan hydrolases. Front Microbiol 2022; 13:1036964. [PMID: 36386627 PMCID: PMC9662197 DOI: 10.3389/fmicb.2022.1036964] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2022] [Accepted: 10/05/2022] [Indexed: 12/02/2023] Open
Abstract
Bacterial cell walls are the guards of cell integrity. They are composed of peptidoglycan that provides rigidity to sustain internal turgor and ensures isolation from the external environment. In addition, they harbor the enzymatic machinery to secure cell wall modulations needed throughout the bacterial lifespan. The main players in this process are peptidoglycan hydrolases, a large group of enzymes with diverse specificities and different mechanisms of action. They are commonly, but not exclusively, found in prokaryotes. Although in most cases, these enzymes share the same molecular function, namely peptidoglycan hydrolysis, they are leveraged to perform a variety of physiological roles. A well-investigated family of peptidoglycan hydrolases is M23 peptidases, which display a very conserved fold, but their spectrum of lytic action is broad and includes both Gram- positive and Gram- negative bacteria. In this review, we summarize the structural, biochemical, and functional studies concerning the M23 family of peptidases based on literature and complement this knowledge by performing large-scale analyses of available protein sequences. This review has led us to gain new insight into the role of surface charge in the activity of this group of enzymes. We present relevant conclusions drawn from the analysis of available structures and indicate the main structural features that play a crucial role in specificity determination and mechanisms of latency. Our work systematizes the knowledge of the M23 family enzymes in the context of their unique antimicrobial potential against drug-resistant pathogens and presents possibilities to modulate and engineer their features to develop perfect antibacterial weapons.
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Affiliation(s)
| | | | | | - Izabela Sabala
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
| | - Magdalena Kaus-Drobek
- Laboratory of Protein Engineering, Mossakowski Medical Research Institute, Polish Academy of Sciences, Warsaw, Poland
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16
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Vacariu CM, Tanner ME. Recent Advances in the Synthesis and Biological Applications of Peptidoglycan Fragments. Chemistry 2022; 28:e202200788. [PMID: 35560956 DOI: 10.1002/chem.202200788] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2022] [Indexed: 11/09/2022]
Abstract
The biosynthesis, breakdown, and modification of peptidoglycan (PG) play vital roles in both bacterial viability and in the response of human physiology to bacterial infection. Studies on PG biochemistry are hampered by the fact that PG is an inhomogeneous insoluble macromolecule. Chemical synthesis is therefore an important means to obtain PG fragments that may serve as enzyme substrates and elicitors of the human immune response. This review outlines the recent advances in the synthesis and biochemical studies of PG fragments, PG biosynthetic intermediates (such as Park's nucleotides and PG lipids), and PG breakdown products (such as muramyl dipeptides and anhydro-muramic acid-containing fragments). A rich variety of synthetic approaches has been applied to preparing such compounds since carbohydrate, peptide, and phospholipid chemical methodologies must all be applied.
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Affiliation(s)
- Condurache M Vacariu
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
| | - Martin E Tanner
- Department of Chemistry, University of British Columbia, V6T 1Z1, Vancouver, British Columbia, Canada
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17
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Choi YJ, Kim S, Bae S, Kim Y, Chang HH, Kim J. Antibacterial Effects of Recombinant Endolysins in Disinfecting Medical Equipment: A Pilot Study. Front Microbiol 2022; 12:773640. [PMID: 35310392 PMCID: PMC8924034 DOI: 10.3389/fmicb.2021.773640] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 12/28/2021] [Indexed: 11/13/2022] Open
Abstract
Nosocomial infections caused by multidrug-resistant (MDR) bacteria are severe life-threatening factors. Endolysins (lysins) degrade the bacterial cell wall peptidoglycan and may help control pathogens, especially MDR bacteria prevalent in hospital settings. This study was conducted to verify the potential of lysin as disinfectant to kill bacteria contaminating medical devices that cause hospital infections. Eight catheters removed from hospitalized patients were collected and tested for their ability to kill bacteria contaminating the catheters using two lysins, LysSS and CHAP-161. Catheter-contaminating bacterial species were isolated and identified by 16s rRNA sequencing. From the eight catheters, bacteria were cultured from seven catheters, and five bacterial species (Bacillus megaterium, Bacillus muralis, Corynebacterium striatum, Enterococcus faecium, and Staphylococcus epidermidis) were identified. LysSS could inhibit catheter-contaminating bacteria, including C. striatum and S. epidermidis, compared with untreated controls but could not inhibit the growth of E. faecium. CHAP-161 showed more bactericidal effects than LysSS, but could not inhibit the growth of S. epidermidis. This study showed the potential of lysin as an alternative disinfectant for hazardous chemical disinfectants used in hospitals.
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Affiliation(s)
- Yoon-Jung Choi
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Shukho Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Sohyun Bae
- Department of Allergy and Infectious Diseases, Kyungpook National University Hospital, Daegu, South Korea
| | - Yoonjung Kim
- Department of Allergy and Infectious Diseases, Kyungpook National University Hospital, Daegu, South Korea
| | - Hyun-Ha Chang
- Department of Allergy and Infectious Diseases, Kyungpook National University Hospital, Daegu, South Korea
| | - Jungmin Kim
- Department of Microbiology, School of Medicine, Kyungpook National University, Daegu, South Korea
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18
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Schuch R, Cassino C, Vila-Farres X. Direct Lytic Agents: Novel, Rapidly Acting Potential Antimicrobial Treatment Modalities for Systemic Use in the Era of Rising Antibiotic Resistance. Front Microbiol 2022; 13:841905. [PMID: 35308352 PMCID: PMC8928733 DOI: 10.3389/fmicb.2022.841905] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 01/28/2022] [Indexed: 12/19/2022] Open
Abstract
Direct lytic agents (DLAs) are novel antimicrobial compounds with unique mechanisms of action based on rapid cell wall destabilization and bacteriolysis. DLAs include two classes of purified polypeptides—lysins (peptidoglycan hydrolase enzymes) and amurins (outer membrane targeting peptides). Their intended use is to kill bacteria in a manner that is complimentary to and synergistic with traditional antibiotics without selection for DLA resistance. Lysins were originally described as having activity against Gram-positive pathogens and of those, exebacase, is the first to have advanced into Phase 3 of clinical development. Recently, both engineered and native DLAs have now been described with potent bactericidal activity against a range of Gram-negative pathogens, including multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii. Importantly, novel DLAs targeting Gram-negatives, including the lysin CF-370 and the amurin peptides, are active in biological matrices (blood/serum) and, as such, offer promise for therapeutic use as systemically administered agents for the treatment of life-threatening invasive infections. In this review, DLAs are discussed as potential new classes of antimicrobial biologics that can be used to treat serious systemic infections.
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Novel Phage Lysin Abp013 against Acinetobacter baumannii. Antibiotics (Basel) 2022; 11:antibiotics11020169. [PMID: 35203772 PMCID: PMC8868305 DOI: 10.3390/antibiotics11020169] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Revised: 01/11/2022] [Accepted: 01/25/2022] [Indexed: 01/23/2023] Open
Abstract
As antimicrobial resistance (AMR) continues to pose an ever-growing global health threat, propelling us into a post-antibiotic era, novel alternative therapeutic agents are urgently required. Lysins are bacteriophage-encoded peptidoglycan hydrolases that display great potential as a novel class of antimicrobials for therapeutics. While lysins against Gram-positive bacteria are highly effective when applied exogenously, it is challenging for lysins to access and cleave the peptidoglycan of Gram-negative bacteria due to their outer membrane. In this study, we identify a novel phage lysin Abp013 against Acinetobacter baumannii. Abp013 exhibited significant lytic activity against multidrug-resistant strains of A. baumannii. Notably, we found that Abp013 was able to tolerate the presence of human serum by up to 10%. Using confocal microscopy and LIVE/DEAD staining, we show that Abp013 can access and kill the bacterial cells residing in the biofilm. These results highlight the intrinsic bacteriolytic property of Abp013, suggesting the promising use of Abp013 as a novel therapeutic agent.
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20
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Au A, Lee H, Ye T, Dave U, Rahman A. Bacteriophages: Combating Antimicrobial Resistance in Food-Borne Bacteria Prevalent in Agriculture. Microorganisms 2021; 10:microorganisms10010046. [PMID: 35056495 PMCID: PMC8778564 DOI: 10.3390/microorganisms10010046] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Revised: 12/14/2021] [Accepted: 12/22/2021] [Indexed: 01/21/2023] Open
Abstract
Through recent decades, the subtherapeutic use of antibiotics within agriculture has led to the widespread development of antimicrobial resistance. This problem not only impacts the productivity and sustainability of current agriculture but also has the potential to transfer antimicrobial resistance to human pathogens via the food supply chain. An increasingly popular alternative to antibiotics is bacteriophages to control bacterial diseases. Their unique bactericidal properties make them an ideal alternative to antibiotics, as many countries begin to restrict the usage of antibiotics in agriculture. This review analyses recent evidence from within the past decade on the efficacy of phage therapy on common foodborne pathogens, namely, Escherica coli, Staphylococcus aureus, Salmonella spp., and Campylobacter jejuni. This paper highlights the benefits and challenges of phage therapy and reveals the potential for phages to control bacterial populations both in food processing and livestock and the possibility for phages to replace subtherapeutic usage of antibiotics in the agriculture sector.
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Affiliation(s)
- Arnold Au
- Centre for Climate Change Research, University of Toronto, ONRamp@UTE, Toronto, ON M5G 1L5, Canada; (A.A.); (H.L.); (T.Y.); (U.D.)
- A.R. Environmental Solutions, ICUBE-University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Helen Lee
- Centre for Climate Change Research, University of Toronto, ONRamp@UTE, Toronto, ON M5G 1L5, Canada; (A.A.); (H.L.); (T.Y.); (U.D.)
- Faculty of Arts & Science, University of Toronto, Toronto, ON M5S 3G3, Canada
| | - Terry Ye
- Centre for Climate Change Research, University of Toronto, ONRamp@UTE, Toronto, ON M5G 1L5, Canada; (A.A.); (H.L.); (T.Y.); (U.D.)
- A.R. Environmental Solutions, ICUBE-University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Uday Dave
- Centre for Climate Change Research, University of Toronto, ONRamp@UTE, Toronto, ON M5G 1L5, Canada; (A.A.); (H.L.); (T.Y.); (U.D.)
- A.R. Environmental Solutions, ICUBE-University of Toronto, Mississauga, ON L5L 1C6, Canada
| | - Azizur Rahman
- Centre for Climate Change Research, University of Toronto, ONRamp@UTE, Toronto, ON M5G 1L5, Canada; (A.A.); (H.L.); (T.Y.); (U.D.)
- A.R. Environmental Solutions, ICUBE-University of Toronto, Mississauga, ON L5L 1C6, Canada
- Correspondence:
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21
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Ferraboschi P, Ciceri S, Grisenti P. Applications of Lysozyme, an Innate Immune Defense Factor, as an Alternative Antibiotic. Antibiotics (Basel) 2021; 10:1534. [PMID: 34943746 PMCID: PMC8698798 DOI: 10.3390/antibiotics10121534] [Citation(s) in RCA: 118] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/03/2021] [Accepted: 12/08/2021] [Indexed: 12/18/2022] Open
Abstract
Lysozyme is a ~14 kDa protein present in many mucosal secretions (tears, saliva, and mucus) and tissues of animals and plants, and plays an important role in the innate immunity, providing protection against bacteria, viruses, and fungi. Three main different types of lysozymes are known: the c-type (chicken or conventional type), the g-type (goose type), and the i-type (invertebrate type). It has long been the subject of several applications due to its antimicrobial properties. The problem of antibiotic resistance has stimulated the search for new molecules or new applications of known compounds. The use of lysozyme as an alternative antibiotic is the subject of this review, which covers the results published over the past two decades. This review is focused on the applications of lysozyme in medicine, (the treatment of infectious diseases, wound healing, and anti-biofilm), veterinary, feed, food preservation, and crop protection. It is available from a wide range of sources, in addition to the well-known chicken egg white, and its synergism with other compounds, endowed with antimicrobial activity, are also summarized. An overview of the modified lysozyme applications is provided in the form of tables.
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Affiliation(s)
- Patrizia Ferraboschi
- Department of Medical Biotechnology and Translational Medicine, University of Milan, Via C. Saldini 50, 20133 Milano, Italy;
| | - Samuele Ciceri
- Department of Pharmaceutical Sciences, University of Milan, Via L. Mangiagalli 25, 20133 Milano, Italy;
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Vasina DV, Antonova NP, Grigoriev IV, Yakimakha VS, Lendel AM, Nikiforova MA, Pochtovyi AA, Remizov TA, Usachev EV, Shevlyagina NV, Zhukhovitsky VG, Fursov MV, Potapov VD, Vorobev AM, Aleshkin AV, Laishevtsev AI, Makarov VV, Yudin SM, Tkachuk AP, Gushchin VA. Discovering the Potentials of Four Phage Endolysins to Combat Gram-Negative Infections. Front Microbiol 2021; 12:748718. [PMID: 34721353 PMCID: PMC8548769 DOI: 10.3389/fmicb.2021.748718] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/17/2021] [Indexed: 12/18/2022] Open
Abstract
Endolysin-based therapeutics are promising antibacterial agents and can successfully supplement the existing antibacterial drugs array. It is specifically important in the case of Gram-negative pathogens, e.g., ESKAPE group bacteria, which includes Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species, and are highly inclined to gain multiple antibiotic resistance. Despite numerous works devoted to the screening of new lytic enzymes and investigations of their biochemical properties, there are significant breaches in some aspects of their operating characteristics, including safety issues of endolysin use. Here, we provide a comprehensive study of the antimicrobial efficacy aspects of four Gram-negative bacteria-targeting endolysins LysAm24, LysAp22, LysECD7, and LysSi3, their in vitro and in vivo activity, and their biological safety. These endolysins possess a wide spectrum of action, are active against planktonic bacteria and bacterial biofilms, and are effective in wound and burn skin infection animal models. In terms of safety, these enzymes do not contribute to the development of short-term resistance, are not cytotoxic, and do not significantly affect the normal intestinal microflora in vivo. Our results provide a confident base for the development of effective and safe candidate dosage forms for the treatment of local and systemic infections caused by Gram-negative bacterial species.
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Affiliation(s)
- Daria V Vasina
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Nataliia P Antonova
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Igor V Grigoriev
- Translational Biomedicine Laboratory, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | | | - Anastasiya M Lendel
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Maria A Nikiforova
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Andrei A Pochtovyi
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Timofey A Remizov
- Translational Biomedicine Laboratory, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Evgeny V Usachev
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Natalia V Shevlyagina
- Laboratory of Indication and Ultrastructural Analysis of Microorganisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir G Zhukhovitsky
- Laboratory of Indication and Ultrastructural Analysis of Microorganisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,Russian Medical Academy of Continuing Professional Education (RMANPO), Ministry of Public Health, Moscow, Russia
| | - Mikhail V Fursov
- Aerobiological Laboratory, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Vasiliy D Potapov
- Aerobiological Laboratory, State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Aleksei M Vorobev
- Laboratory of Clinical Microbiology and Biotechnology of Bacteriophages, G. N. Gabrichevsky Moscow Research Institute for Epidemiology and Microbiology, Moscow, Russia
| | - Andrey V Aleshkin
- Laboratory of Clinical Microbiology and Biotechnology of Bacteriophages, G. N. Gabrichevsky Moscow Research Institute for Epidemiology and Microbiology, Moscow, Russia
| | - Aleksei I Laishevtsev
- Laboratory for Diagnostics and Control of Antibiotic Resistance of the Most Clinically Significant Pathogens of Animals, Federal State Budget Scientific Institution "Federal Scientific Centre VIEV" (FSC VIEV), Moscow, Russia
| | - Valentine V Makarov
- Center for Strategic Planning of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Sergey M Yudin
- Center for Strategic Planning of the Ministry of Health of the Russian Federation, Moscow, Russia
| | - Artem P Tkachuk
- Translational Biomedicine Laboratory, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia
| | - Vladimir A Gushchin
- Laboratory of Pathogen Population Variability Mechanisms, N. F. Gamaleya National Research Center for Epidemiology and Microbiology, Ministry of Health of the Russian Federation, Moscow, Russia.,Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia
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23
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PhaLP: A Database for the Study of Phage Lytic Proteins and Their Evolution. Viruses 2021; 13:v13071240. [PMID: 34206969 PMCID: PMC8310338 DOI: 10.3390/v13071240] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 01/22/2023] Open
Abstract
Phage lytic proteins are a clinically advanced class of novel enzyme-based antibiotics, so-called enzybiotics. A growing community of researchers develops phage lytic proteins with the perspective of their use as enzybiotics. A successful translation of enzybiotics to the market requires well-considered selections of phage lytic proteins in early research stages. Here, we introduce PhaLP, a database of phage lytic proteins, which serves as an open portal to facilitate the development of phage lytic proteins. PhaLP is a comprehensive, easily accessible and automatically updated database (currently 16,095 entries). Capitalizing on the rich content of PhaLP, we have mapped the high diversity of natural phage lytic proteins and conducted analyses at three levels to gain insight in their host-specific evolution. First, we provide an overview of the modular diversity. Secondly, datamining and interpretable machine learning approaches were adopted to reveal host-specific design rules for domain architectures in endolysins. Lastly, the evolution of phage lytic proteins on the protein sequence level was explored, revealing host-specific clusters. In sum, PhaLP can act as a starting point for the broad community of enzybiotic researchers, while the steadily improving evolutionary insights will serve as a natural inspiration for protein engineers.
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LysSAP26, a New Recombinant Phage Endolysin with a Broad Spectrum Antibacterial Activity. Viruses 2020; 12:v12111340. [PMID: 33238548 PMCID: PMC7700246 DOI: 10.3390/v12111340] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2020] [Revised: 11/18/2020] [Accepted: 11/19/2020] [Indexed: 12/11/2022] Open
Abstract
Multidrug-resistant (MDR) bacteria are a major threat to public health. Bacteriophage endolysins (lysins) are a promising alternative treatment to traditional antibiotics. However, the lysins currently under development are still underestimated. Herein, we cloned the lysin from the SAP-26 bacteriophage genome. The recombinant LysSAP26 protein inhibited the growth of carbapenem-resistant Acinetobacter baumannii, Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa, oxacillin-resistant Staphylococcus aureus, and vancomycin-resistant Enterococcus faecium with minimum inhibitory concentrations of 5~80 µg/mL. In animal experiments, mice infected with A. baumannii were protected by LysSAP26, with a 40% survival rate. Transmission electron microscopy analysis confirmed that LysSAP26 treatment resulted in the destruction of bacterial cell walls. LysSAP26 is a new endolysin that can be applied to treat MDR A. baumannii, E. faecium, S. aureus, K. pneumoniae, P. aeruginosa, and E. coli infections, targeting both Gram-positive and Gram-negative bacteria.
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