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Javid M, Shahverdi AR, Ghasemi A, Moosavi-Movahedi AA, Ebrahim-Habibi A, Sepehrizadeh Z. Decoding the Structure-Function Relationship of the Muramidase Domain in E. coli O157.H7 Bacteriophage Endolysin: A Potential Building Block for Chimeric Enzybiotics. Protein J 2024:10.1007/s10930-024-10195-z. [PMID: 38662183 DOI: 10.1007/s10930-024-10195-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/23/2024] [Indexed: 04/26/2024]
Abstract
Bacteriophage endolysins are potential alternatives to conventional antibiotics for treating multidrug-resistant gram-negative bacterial infections. However, their structure-function relationships are poorly understood, hindering their optimization and application. In this study, we focused on the individual functionality of the C-terminal muramidase domain of Gp127, a modular endolysin from E. coli O157:H7 bacteriophage PhaxI. This domain is responsible for the enzymatic activity, whereas the N-terminal domain binds to the bacterial cell wall. Through protein modeling, docking experiments, and molecular dynamics simulations, we investigated the activity, stability, and interactions of the isolated C-terminal domain with its ligand. We also assessed its expression, solubility, toxicity, and lytic activity using the experimental data. Our results revealed that the C-terminal domain exhibits high activity and toxicity when tested individually, and its expression is regulated in different hosts to prevent self-destruction. Furthermore, we validated the muralytic activity of the purified refolded protein by zymography and standardized assays. These findings challenge the need for the N-terminal binding domain to arrange the active site and adjust the gap between crucial residues for peptidoglycan cleavage. Our study shed light on the three-dimensional structure and functionality of muramidase endolysins, thereby enriching the existing knowledge pool and laying a foundation for accurate in silico modeling and the informed design of next-generation enzybiotic treatments.
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Affiliation(s)
- Mehri Javid
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | | | - Azadeh Ebrahim-Habibi
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
- Biosensor Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy & Biotechnology Research Center, Tehran University of Medical Sciences, Tehran, Iran.
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Asadi M, Taheri-Anganeh M, Ranjbar M, Khatami SH, Maleksabet A, Mostafavi-Pour Z, Ghasemi Y, Keshavarzi A, Savardashtaki A. LYZ2-SH3b as a novel and efficient enzybiotic against methicillin-resistant Staphylococcus aureus. BMC Microbiol 2023; 23:257. [PMID: 37704938 PMCID: PMC10500863 DOI: 10.1186/s12866-023-03002-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 09/04/2023] [Indexed: 09/15/2023] Open
Abstract
BACKGROUND Enzybiotics are promising alternatives to conventional antibiotics for drug-resistant infections. Exolysins, as a class of enzybiotics, show antibacterial effects against methicillin-resistant Staphylococcus aureus (MRSA). This study evaluated a novel exolysin containing an SH3b domain for its antibacterial activity against MRSA. METHODS This study designed a chimeric exolysin by fusing the Cell-binding domain (SH3b) from Lysostaphin with the lytic domain (LYZ2) from the gp61 enzyme. Subsequently, LYZ2-SH3b was cloned and expressed in Escherichia coli (E. coli). Finally, the antibacterial effects of LYZ2-SH3b compared with LYZ2 and vancomycin against reference and clinical isolates of MRSA were measured using the disc diffusion method, the minimal inhibitory concentration (MIC), and the minimal bactericidal concentration (MBC) assays. RESULTS Analysis of bioinformatics showed that LYZ2-SH3b was stable, soluble, and non-allergenic. Protein purification was performed with a 0.8 mg/ml yield for LYZ2-SH3b. The plate lysis assay results indicated that, at the same concentrations, LYZ2-SH3b has a more inhibitory effect than LYZ2. The MICs of LYZ2 were 4 µg/mL (ATCC 43,300) and 8 µg/mL (clinical isolate ST239), whereas, for LYZ2-SH3b, they were 2 µg/mL (ATCC 43,300) and 4 µg/mL (clinical isolate ST239). This suggests a higher efficiency of LYZ2-SH3b compared to LYZ2. Furthermore, the MBCs of LYZ2 were 4 µg/mL (ATCC 43,300) and 8 µg/mL (clinical isolate ST239), whereas, for LYZ2-SH3b, they were 2 µg/mL (ATCC 43,300) and 4 µg/mL (clinical isolate ST239), thus confirming the superior lytic activity of LYZ2-SH3b over LYZ2. CONCLUSIONS The study suggests that phage endolysins, such as LYZ2-SH3b, may represent a promising new approach to treating MRSA infections, particularly in cases where antibiotic resistance is a concern. But further studies are needed.
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Affiliation(s)
- Marzieh Asadi
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences Shiraz, Shiraz, Iran
- Student Research Committee, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mortaza Taheri-Anganeh
- Cellular and Molecular Research Center, Cellular and Molecular Medicine Research Institute, Urmia University of Medical Sciences, Urmia, Iran
| | - Maryam Ranjbar
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences Shiraz, Shiraz, Iran
| | - Seyyed Hossein Khatami
- Department of Clinical Biochemistry, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Amir Maleksabet
- Department of Medical Biotechnology, School of Advanced Technologies in Medicine, Mazandaran University of Medical Sciences, Sari, Iran
| | - Zohreh Mostafavi-Pour
- Recombinant Protein Laboratory, Department of Biochemistry, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Younes Ghasemi
- Pharmaceutical Sciences Research Center, Shiraz University of Medical Science, Shiraz, Iran
| | | | - Amir Savardashtaki
- Department of Medical Biotechnology, School of Advanced Medical Sciences and Technologies, Shiraz University of Medical Sciences Shiraz, Shiraz, Iran.
- Infertility Research Center, Shiraz University of Medical Sciences, Shiraz, Iran.
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Gadallah EE, El-Borai AM, El-Aassar SA, Beltagy EA. Purification, characterization, immobilization and applications of an enzybiotic β-1,3-1,4-glucanase produced from halotolerant marine Halomonas meridiana ES021. World J Microbiol Biotechnol 2023; 39:89. [PMID: 36740637 PMCID: PMC9899757 DOI: 10.1007/s11274-023-03527-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2022] [Accepted: 01/17/2023] [Indexed: 02/07/2023]
Abstract
Extracellular β-1,3-1,4-glucanase-producing strain Halomonas meridiana ES021 was isolated from Gabal El-Zeit off shore, Red Sea, Egypt. The Extracellular enzyme was partially purified by precipitation with 75% acetone followed by anion exchange chromatography on DEAE-cellulose, where a single protein band was determined with molecular mass of approximately 72 kDa. The Km value was 0.62 mg β-1,3-1,4-glucan/mL and Vmax value was 7936 U/mg protein. The maximum activity for the purified enzyme was observed at 40 °C, pH 5.0, and after 10 min of the reaction. β-1,3-1,4-glucanase showed strong antibacterial effect against Bacillus subtilis, Streptococcus agalactiae and Vibrio damsela. It also showed antifungal effect against Penicillium sp. followed by Aspergillus niger. No toxicity was observed when tested on Artemia salina. Semi-purified β-1,3-1,4-glucanase was noticed to be effective in clarification of different juices at different pH values and different time intervals. The maximum clarification yields were 51.61% and 66.67% on mango juice at 40 °C and pH 5.3 for 2 and 4 h, respectively. To our knowledge, this is the first report of β-1,3-1,4-glucanase enzyme from halotolerant Halomonas species.
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Affiliation(s)
- Eman E Gadallah
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt.
| | - Aliaa M El-Borai
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Samy A El-Aassar
- Botany and Microbiology Department, Faculty of Science, Alexandria University, Alexandria, Egypt
| | - Ehab A Beltagy
- National Institute of Oceanography and Fisheries (NIOF), Cairo, Egypt
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Gontijo MTP, Teles MP, Vidigal PMP, Brocchi M. Expanding the Database of Signal-Anchor-Release Domain Endolysins Through Metagenomics. Probiotics Antimicrob Proteins 2022; 14:603-612. [PMID: 35525881 DOI: 10.1007/s12602-022-09948-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/03/2022] [Indexed: 10/18/2022]
Abstract
Endolysins are bacteriophage-derived lytic enzymes with antimicrobial activity. The action of endolysins against Gram-negative bacteria remains a challenge due to the physical protection of the outer membrane. However, recent research has demonstrated that signal-anchor-release (SAR) endolysins permeate the outer membrane of Gram-negative bacteria. This study investigates 2628 putative endolysin genes identified in 183,298 bacteriophage genomes. Previously, bioinformatic approaches resulted in a database of 66 SAR endolysins. This manuscript almost doubles the list with 53 additional SAR endolysin candidates. Forty-eight of the putative SAR endolysins described in this study contained one muramidase catalytic domain, and five included additional cell wall-binding domains at the C-terminus. For the moment, SAR domains are found in four protein families: glycoside hydrolase family 19 (GH19), glycoside hydrolase family 24 (GH24), glycoside hydrolase family 25 (GH25), and glycoside hydrolase family 108 (GH108). These SAR lysis are clustered in eight groups based on biochemical properties and domain presence/absence. Therefore, in this study, we expand the arsenal of endolysin candidates that might act against Gram-negative bacteria and develop a consult database for antimicrobial proteins derived from bacteriophages.
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Affiliation(s)
- Marco Túlio Pardini Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Rua Monteiro Lobato 255, Campinas, São Paulo, 13083-862, Brazil.
| | - Mateus Pereira Teles
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Rua Monteiro Lobato 255, Campinas, São Paulo, 13083-862, Brazil.,Faculdade de Farmácia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Rua Cândido Portinari 200, Campinas, São Paulo, 13083-862, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa (UFV), Vila Gianetti, Casa 21, Campus da UFV, Viçosa, Minas Gerais, 36570-900, Brazil
| | - Marcelo Brocchi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Cidade Universitária Zeferino Vaz, Rua Monteiro Lobato 255, Campinas, São Paulo, 13083-862, Brazil
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Gontijo MTP, Vidigal PMP, Lopez MES, Brocchi M. Bacteriophages that infect Gram-negative bacteria as source of signal-arrest-release motif lysins. Res Microbiol 2020; 172:103794. [PMID: 33347948 DOI: 10.1016/j.resmic.2020.103794] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/13/2020] [Accepted: 12/15/2020] [Indexed: 01/23/2023]
Abstract
Treatment of infections caused by multidrug-resistant (MDR) Gram-negative bacteria is challenging, a potential solution for which is the use of bacteriophage-derived lytic enzymes. However, the exogenous action of bacteriophage lysins against Gram-negative bacteria is hindered due to the presence of an impermeable outer membrane in these bacteria. Nevertheless, recent research has demonstrated that some lysins are capable of permeating the outer membrane of Gram-negative bacteria with the help of signal peptides. In the present study, we investigated the genomes of 309 bacteriophages that infect Gram-negative pathogens of clinical interest in order to determine the evolutionary markers of signal peptide-containing lysins. Complete genomes displayed 265 putative lysins, of which 17 (6.41%) contained signal-arrest-release motifs and 41 (15.47%) contained cleavable signal peptides. There was no apparent relationship between host specificity and lysin diversity. Nevertheless, the evolution of lysin genes might not be independent of the rest of the bacteriophage genome once pan-genome clustering and lysin diversity appear to be correlated. In addition, signal peptide- and signal-arrest-release-containing lysins were monophyletically distributed in the protein cladogram, suggesting that the natural selection of holin-independent lysins is divergent. Our study screened 58 (21.89%) out of 265 potential candidates for in vitro experimentation against MDR bacteria.
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Affiliation(s)
- Marco Túlio Pardini Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato 255, Campinas, São Paulo, 13083-862, Brazil.
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa (UFV), Vila Gianetti, Casa 21, Campus da UFV, Viçosa, Minas Gerais, 36570-900, Brazil.
| | - Maryoris Elisa Soto Lopez
- Departamento de Ingeniería de Alimentos, Universidad de Córdoba (UNICORDOBA), Carrera 6 77-305, Montería, 230002, Colombia.
| | - Marcelo Brocchi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Rua Monteiro Lobato 255, Campinas, São Paulo, 13083-862, Brazil.
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Simmons M, Morales CA, Oakley BB, Seal BS. Recombinant Expression of a Putative Amidase Cloned from the Genome of Listeria monocytogenes that Lyses the Bacterium and its Monolayer in Conjunction with a Protease. Probiotics Antimicrob Proteins 2016; 4:1-10. [PMID: 26781731 DOI: 10.1007/s12602-011-9084-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Listeria monocytogenes is a Gram-positive, non-spore forming, catalase-positive rod that is a major bacterial food-borne disease agent associated with uncooked meats, including poultry, uncooked vegetables, soft cheeses, and unpasteurized milk. The bacterium may be carried by animals without signs of disease, can replicate at refrigeration temperatures, and is frequently associated with biofilms. There is a need to discover innovative pathogen intervention technologies for this bacterium. Consequently, bioinformatic analyses were used to identify genes encoding lytic protein sequences in the genomes of L. monocytogenes isolates. PCR primers were designed that amplified nucleotide sequences of a putative N-acetylmuramoyl-L-alanine amidase gene from L. monocytogenes strain 4b. The resultant amplification product was cloned into an expression vector, propagated in Escherichia coli Rosetta strains, and the recombinant protein was purified to homogeneity. Gene and protein sequencing confirmed that the predicted and chemically determined amino acid sequence of the recombinant protein designated PlyLM was a putative N-acetylmuramoyl-L-alanine amidase. The recombinant lytic protein was capable of lysing both the parental L. monocytogenes strain as well as other strains of the bacterium in spot and MIC/MIB assays, but was not active against other bacteria beyond the genus. A microtiter plate assay was utilized to assay for the ability of the recombinant lysin protein to potentially aid with digestion of a L. monocytogenes biofilm. Protease or lysozyme digestion alone did not significantly reduce the L. monocytogenes biofilm. Although the recombinant protein alone reduced the biofilm by only 20%, complete digestion of the bacterial monolayer was accomplished in conjunction with a protease.
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Affiliation(s)
- Mustafa Simmons
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, 950 College Station Road, 30605, Athens, GA, USA
| | - Cesar A Morales
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, 950 College Station Road, 30605, Athens, GA, USA
| | - Brian B Oakley
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, 950 College Station Road, 30605, Athens, GA, USA
| | - Bruce S Seal
- Poultry Microbiology Safety Research Unit, Richard B. Russell Agricultural Research Center, Agricultural Research Service, USDA, 950 College Station Road, 30605, Athens, GA, USA.
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