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Gontijo M, Pereira Teles M, Martins Correia H, Pérez Jorge G, Rodrigues Santos Goes IC, Fasabi Flores AJ, Braz M, de Moraes Ceseti L, Zonzini Ramos P, Rosa e Silva I, Pereira Vidigal PM, Kobarg J, Miguez Couñago R, Alvarez-Martinez CE, Pereira C, Freire CSR, Almeida A, Brocchi M. Combined effect of SAR-endolysin LysKpV475 with polymyxin B and Salmonella bacteriophage phSE-5. MICROBIOLOGY (READING, ENGLAND) 2024; 170:001462. [PMID: 38739436 PMCID: PMC11170124 DOI: 10.1099/mic.0.001462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Accepted: 04/26/2024] [Indexed: 05/14/2024]
Abstract
Endolysins are bacteriophage (or phage)-encoded enzymes that catalyse the peptidoglycan breakdown in the bacterial cell wall. The exogenous action of recombinant phage endolysins against Gram-positive organisms has been extensively studied. However, the outer membrane acts as a physical barrier when considering the use of recombinant endolysins to combat Gram-negative bacteria. This study aimed to evaluate the antimicrobial activity of the SAR-endolysin LysKpV475 against Gram-negative bacteria as single or combined therapies, using an outer membrane permeabilizer (polymyxin B) and a phage, free or immobilized in a pullulan matrix. In the first step, the endolysin LysKpV475 in solution, alone and combined with polymyxin B, was tested in vitro and in vivo against ten Gram-negative bacteria, including highly virulent strains and multidrug-resistant isolates. In the second step, the lyophilized LysKpV475 endolysin was combined with the phage phSE-5 and investigated, free or immobilized in a pullulan matrix, against Salmonella enterica subsp. enterica serovar Typhimurium ATCC 13311. The bacteriostatic action of purified LysKpV475 varied between 8.125 μg ml-1 against Pseudomonas aeruginosa ATCC 27853, 16.25 μg ml-1 against S. enterica Typhimurium ATCC 13311, and 32.50 μg ml-1 against Klebsiella pneumoniae ATCC BAA-2146 and Enterobacter cloacae P2224. LysKpV475 showed bactericidal activity only for P. aeruginosa ATCC 27853 (32.50 μg ml-1) and P. aeruginosa P2307 (65.00 μg ml-1) at the tested concentrations. The effect of the LysKpV475 combined with polymyxin B increased against K. pneumoniae ATCC BAA-2146 [fractional inhibitory concentration index (FICI) 0.34; a value lower than 1.0 indicates an additive/combined effect] and S. enterica Typhimurium ATCC 13311 (FICI 0.93). A synergistic effect against S. enterica Typhimurium was also observed when the lyophilized LysKpV475 at ⅔ MIC was combined with the phage phSE-5 (m.o.i. of 100). The lyophilized LysKpV475 immobilized in a pullulan matrix maintained a significant Salmonella reduction of 2 logs after 6 h of treatment. These results demonstrate the potential of SAR-endolysins, alone or in combination with other treatments, in the free form or immobilized in solid matrices, which paves the way for their application in different areas, such as in biocontrol at the food processing stage, biosanitation of food contact surfaces and biopreservation of processed food in active food packing.
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Affiliation(s)
- Marco Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Mateus Pereira Teles
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970, Brazil
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Hugo Martins Correia
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Genesy Pérez Jorge
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
- Research Group Statistics and Mathematical Modeling Applied to Educational Quality (GEMMA), University of Sucre, Sincelejo, Sucre, Colombia
| | - Isabella Carolina Rodrigues Santos Goes
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Anthony Jhoao Fasabi Flores
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Márcia Braz
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Lucas de Moraes Ceseti
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Priscila Zonzini Ramos
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Ivan Rosa e Silva
- Laboratório Nacional de Biociências (LNBio), Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), Campinas, SP 13083-970, Brazil
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-871, Brazil
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Universidade Federal de Viçosa (UFV), Viçosa, MG 36570-900, Brazil
| | - Jörg Kobarg
- Faculdade de Ciências Farmacêuticas, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-871, Brazil
| | - Rafael Miguez Couñago
- Centro de Química Medicinal, Centro de Biologia Molecular e Engenharia Genética, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-970, Brazil
| | - Cristina Elisa Alvarez-Martinez
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
| | - Carla Pereira
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Carmen S. R. Freire
- CICECO – Aveiro Institute of Materials, Department of Chemistry, University of Aveiro, 3810-193, Aveiro, Portugal
| | - Adelaide Almeida
- Department of Biology, and Centre for Environmental and Marine Studies (CESAM), University of Aveiro, Aveiro, Portugal
| | - Marcelo Brocchi
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas, SP 13083-862, Brazil
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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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Montso PK, Kropinski AM, Mokoena F, Pierneef RE, Mlambo V, Ateba CN. Comparative genomics and proteomics analysis of phages infecting multi-drug resistant Escherichia coli O177 isolated from cattle faeces. Sci Rep 2023; 13:21426. [PMID: 38052835 PMCID: PMC10698182 DOI: 10.1038/s41598-023-48788-w] [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: 07/11/2023] [Accepted: 11/30/2023] [Indexed: 12/07/2023] Open
Abstract
The increasing prevalence of antimicrobial-resistant (AMR) pathogens has become a major global health concern. To address this challenge, innovative strategies such as bacteriophage therapy must be optimised. Genomic characterisation is a crucial step in identifying suitable phage candidates for combating AMR pathogens. The aim of this study was to characterise seven phages that infect the Escherichia coli O177 strain using a whole genome sequencing. The analysis of genome sequences revealed that these phages had linear dsDNA, with genome sizes spanning from 136, 483 to 166,791 bp and GC content varying from 35.39 to 43.63%. Taxonomically, the phages were classified under three different subfamilies (Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae) and three genera (Phapecoctavirus, Tequatrovirus, and Vequintavirus) within the class Caudoviricetes. In silico PhageAI analysis predicted that all the phages were virulent, with confidence levels between 96.07 and 97.26%. The phage genomes contained between 66 and 82 ORFs, which encode hypothetical and putative functional proteins. In addition, the phage genomes contained core genes associated with molecular processes such as DNA replication, transcription modulation, nucleotide metabolism, phage structure (capsid and tail), and lysis. None of the genomes carried genes associated with undesirable traits such as integrase, antimicrobial resistance, virulence, and toxins. The study revealed high genome and proteome homology among E. coli O177 phages and other known Escherichia phages. The results suggest that the seven phages are new members of the genera Phapecoctavirus, Tequatrovirus, and Vequintavirus under the subfamilies Stephanstirmvirinae, Tevenvirinae, and Vequintavirinae, respectively.
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Affiliation(s)
- Peter Kotsoana Montso
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa.
| | - Andrew M Kropinski
- Department Food Science, and Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Fortunate Mokoena
- Department of Biochemistry, Faculty of Natural and Agricultural Sciences, North-West University, Mmabatho, South Africa
| | - Rian Ewald Pierneef
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0001, South Africa
- Centre for Bioinformatics and Computational Biology, University of Pretoria, Pretoria, 0001, South Africa
- SARChI Chair: Marine Microbiomics, Microbiome@UP, Department of Biochemistry, Genetics and Microbiology, University of Pretoria (UP), Hatfield, Pretoria, South Africa
| | - Victor Mlambo
- Faculty of Agriculture and Natural Sciences, School of Agricultural Sciences, University of Mpumalanga, Mbombela, 1200, South Africa
| | - Collins Njie Ateba
- Food Security and Safety Focus Area, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
- Department of Microbiology, Faculty of Natural and Agricultural Sciences, North-West University, Private Bag X2046, Mmabatho, 2735, South Africa
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Soonthonsrima T, Htoo HH, Thiennimitr P, Srisuknimit V, Nonejuie P, Chaikeeratisak V. Phage-induced bacterial morphological changes reveal a phage-derived antimicrobial affecting cell wall integrity. Antimicrob Agents Chemother 2023; 67:e0076423. [PMID: 37843261 PMCID: PMC10648931 DOI: 10.1128/aac.00764-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 08/24/2023] [Indexed: 10/17/2023] Open
Abstract
In a looming post-antibiotic era, antibiotic alternatives have become key players in the combat against pathogens. Although recent advances in genomic research allow scientists to fully explore an organism's genome in the search for novel antibacterial molecules, laborious work is still needed in order to dissect each individual gene product for its antibacterial activity. Here, we exploited phage-induced bacterial morphological changes as anchors to explore and discover a potential phage-derived antimicrobial embedded in the phage genome. We found that, upon vibriophage KVP40 infection, Vibrio parahaemolyticus exhibited morphological changes similar to those observed when treated with mecillinam, a cell wall synthesis inhibitor, suggesting the mechanism of pre-killing that KVP40 exerts inside the bacterial cell upon sieging the host. Genome analysis revealed that, of all the annotated gene products in the KVP40 genome that are involved in cell wall degradation, lytic transglycosylase (LT) is of particular interest for subsequent functional studies. A single-cell morphological analysis revealed that heterologous expression of wild-type KVP40-LT induced similar bacterial morphological changes to those treated with the whole phage or mecillinam, prior to cell burst. On the contrary, neither the morphology nor the viability of the bacteria expressing signal-peptide truncated- or catalytic mutant E80A- KVP40-LT was affected, suggesting the necessity of these domains for the antibacterial activities. Altogether, this research paves the way for the future development of the discovery of phage-derived antimicrobials that is guided through phage-induced morphological changes.
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Affiliation(s)
- Tanapon Soonthonsrima
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Parameth Thiennimitr
- Department of Microbiology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Research Center of Microbial Diversity and Sustainable Utilization, Chiang Mai University, Chiang Mai, Thailand
| | - Veerasak Srisuknimit
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
- Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
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Jędrusiak A, Fortuna W, Majewska J, Górski A, Jończyk-Matysiak E. Phage Interactions with the Nervous System in Health and Disease. Cells 2023; 12:1720. [PMID: 37443756 PMCID: PMC10341288 DOI: 10.3390/cells12131720] [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: 05/08/2023] [Revised: 06/20/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The central nervous system manages all of our activities (e.g., direct thinking and decision-making processes). It receives information from the environment and responds to environmental stimuli. Bacterial viruses (bacteriophages, phages) are the most numerous structures occurring in the biosphere and are also found in the human organism. Therefore, understanding how phages may influence this system is of great importance and is the purpose of this review. We have focused on the effect of natural bacteriophages in the central nervous system, linking them to those present in the gut microbiota, creating the gut-brain axis network, as well as their interdependence. Importantly, based on the current knowledge in the field of phage application (e.g., intranasal) in the treatment of bacterial diseases associated with the brain and nervous system, bacteriophages may have significant therapeutic potential. Moreover, it was indicated that bacteriophages may influence cognitive processing. In addition, phages (via phage display technology) appear promising as a targeted therapeutic tool in the treatment of, among other things, brain cancers. The information collected and reviewed in this work indicates that phages and their impact on the nervous system is a fascinating and, so far, underexplored field. Therefore, the aim of this review is not only to summarize currently available information on the association of phages with the nervous system, but also to stimulate future studies that could pave the way for novel therapeutic approaches potentially useful in treating bacterial and non-bacterial neural diseases.
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Affiliation(s)
- Adam Jędrusiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
| | - Wojciech Fortuna
- Department of Neurosurgery, Wroclaw Medical University, Borowska 213, 54-427 Wroclaw, Poland;
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
| | - Joanna Majewska
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
| | - Andrzej Górski
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
- Phage Therapy Unit, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland
- Infant Jesus Hospital, The Medical University of Warsaw, 02-006 Warsaw, Poland
| | - Ewa Jończyk-Matysiak
- Bacteriophage Laboratory, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 53-114 Wroclaw, Poland; (A.J.); (J.M.); (A.G.)
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Lopez MES, Gontijo MTP, Cardoso RR, Batalha LS, Eller MR, Bazzolli DMS, Vidigal PMP, Mendonça RCS. Complete genome analysis of Tequatrovirus ufvareg1, a Tequatrovirus species inhibiting Escherichia coli O157:H7. Front Cell Infect Microbiol 2023; 13:1178248. [PMID: 37274318 PMCID: PMC10236363 DOI: 10.3389/fcimb.2023.1178248] [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: 03/02/2023] [Accepted: 04/27/2023] [Indexed: 06/06/2023] Open
Abstract
Introduction Bacteriophages infecting human pathogens have been considered potential biocontrol agents, and studying their genetic content is essential to their safe use in the food industry. Tequatrovirus ufvareg1 is a bacteriophage named UFV-AREG1, isolated from cowshed wastewater and previously tested for its ability to inhibit Escherichia coli O157:H7. Methods T. ufvareg1 was previously isolated using E. coli O157:H7 (ATCC 43895) as a bacterial host. The same strain was used for bacteriophage propagation and the one-step growth curve. The genome of the T. ufvareg1 was sequenced using 305 Illumina HiSeq, and the genome comparison was calculated by VIRIDIC and VIPTree. Results Here, we characterize its genome and compare it to other Tequatrovirus. T. ufvareg1 virions have an icosahedral head (114 x 86 nm) and a contracted tail (117 x 23 nm), with a latent period of 25 min, and an average burst size was 18 phage particles per infected E. coli cell. The genome of the bacteriophage T. ufvareg1 contains 268 coding DNA sequences (CDS) and ten tRNA genes distributed in both negative and positive strains. T. ufvareg1 genome also contains 40 promoters on its regulatory regions and two rho-independent terminators. T. ufvareg1 shares an average intergenomic similarity (VIRIDC) of 88.77% and an average genomic similarity score (VipTree) of 88.91% with eight four reference genomes for Tequatrovirus available in the NCBI RefSeq database. The pan-genomic analysis confirmed the high conservation of Tequatrovirus genomes. Among all CDS annotated in the T. ufvareg1 genome, there are 123 core genes, 38 softcore genes, 94 shell genes, and 13 cloud genes. None of 268 CDS was classified as being exclusive of T. ufvareg1. Conclusion The results in this paper, combined with other previously published findings, indicate that T. ufvareg1 bacteriophage is a potential candidate for food protection against E. coli O157:H7 in foods.
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Affiliation(s)
- Maryoris Elisa Soto Lopez
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Departamento de Ingeniería de Alimentos, Universidad de Córdoba, Montería, Colombia
| | - Marco Tulio Pardini Gontijo
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
- Department of Molecular Genetics and Microbiology, Duke University Medical Center, Duke University, Durham, NC, United States
| | - Rodrigo Rezende Cardoso
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Laís Silva Batalha
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
| | - Monique Renon Eller
- Departamento de Tecnologia de Alimentos, Universidade Federal de Viçosa, Viçosa, Minas Gerais, Brazil
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Abstract
Bacteriophage Mu is a paradigm coliphage studied mainly because of its use of transposition for genome replication. However, in extensive nonsense mutant screens, only one lysis gene has been identified, the endolysin gp22. This is surprising because in Gram-negative hosts, lysis by Caudovirales phages has been shown to require proteins which disrupt all three layers of the cell envelope. Usually this involves a holin, an endolysin, and a spanin targeting the cytoplasmic membrane, peptidoglycan (PG), and outer membrane (OM), respectively, with the holin determining the timing of lysis initiation. Here, we demonstrate that gp22 is a signal-anchor-release (SAR) endolysin and identify gp23 and gp23.1 as two-component spanin subunits. However, we find that Mu lacks a holin and instead encodes a membrane-tethered cytoplasmic protein, gp25, which is required for the release of the SAR endolysin. Mutational analysis showed that this dependence on gp25 is conferred by lysine residues at positions 6 and 7 of the short cytoplasmic domain of gp22. gp25, which we designate as a releasin, also facilitates the release of SAR endolysins from other phages. Moreover, the entire length of gp25, including its N-terminal transmembrane domain, belongs to a protein family, DUF2730, found in many Mu-like phages, including those with cytoplasmic endolysins. These results are discussed in terms of models for the evolution and mechanism of releasin function and a rationale for Mu lysis without holin control. IMPORTANCE Host cell lysis is the terminal event of the bacteriophage infection cycle. In Gram-negative hosts, lysis requires proteins that disrupt each of the three cell envelope components, only one of which has been identified in Mu: the endolysin gp22. We show that gp22 can be characterized as a SAR endolysin, a muralytic enzyme that activates upon release from the membrane to degrade the cell wall. Furthermore, we identify genes 23 and 23.1 as spanin subunits used for outer membrane disruption. Significantly, we demonstrate that Mu is the first known Caudovirales phage to lack a holin, a protein that disrupts the inner membrane and is traditionally known to release endolysins. In its stead, we report the discovery of a lysis protein, termed the releasin, which Mu uses for SAR endolysin release. This is an example of a system where the dynamic membrane localization of one protein is controlled by a secondary protein.
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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] [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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Virulence and DNA sequence analysis of Cronobacter spp. isolated from infant cereals. Int J Food Microbiol 2022; 376:109745. [DOI: 10.1016/j.ijfoodmicro.2022.109745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 05/21/2022] [Accepted: 05/23/2022] [Indexed: 11/20/2022]
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Functional Dissection of P1 Bacteriophage Holin-like Proteins Reveals the Biological Sense of P1 Lytic System Complexity. Int J Mol Sci 2022; 23:ijms23084231. [PMID: 35457047 PMCID: PMC9025707 DOI: 10.3390/ijms23084231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 04/01/2022] [Accepted: 04/07/2022] [Indexed: 02/01/2023] Open
Abstract
P1 is a model temperate myovirus. It infects different Enterobacteriaceae and can develop lytically or form lysogens. Only some P1 adaptation strategies to propagate in different hosts are known. An atypical feature of P1 is the number and organization of cell lysis-associated genes. In addition to SAR-endolysin Lyz, holin LydA, and antiholin LydB, P1 encodes other predicted holins, LydC and LydD. LydD is encoded by the same operon as Lyz, LydA and LydB are encoded by an unlinked operon, and LydC is encoded by an operon preceding the lydA gene. By analyzing the phenotypes of P1 mutants in known or predicted holin genes, we show that all the products of these genes cooperate with the P1 SAR-endolysin in cell lysis and that LydD is a pinholin. The contributions of holins/pinholins to cell lysis by P1 appear to vary depending on the host of P1 and the bacterial growth conditions. The pattern of morphological transitions characteristic of SAR-endolysin–pinholin action dominates during lysis by wild-type P1, but in the case of lydC lydD mutant it changes to that characteristic of classical endolysin-pinholin action. We postulate that the complex lytic system facilitates P1 adaptation to various hosts and their growth conditions.
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Hungaro HM, Vidigal PMP, do Nascimento EC, Gomes da Costa Oliveira F, Gontijo MTP, Lopez MES. Genomic Characterisation of UFJF_PfDIW6: A Novel Lytic Pseudomonas fluorescens-Phage with Potential for Biocontrol in the Dairy Industry. Viruses 2022; 14:v14030629. [PMID: 35337036 PMCID: PMC8951688 DOI: 10.3390/v14030629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2022] [Revised: 03/12/2022] [Accepted: 03/15/2022] [Indexed: 02/04/2023] Open
Abstract
In this study, we have presented the genomic characterisation of UFJF_PfDIW6, a novel lytic Pseudomonas fluorescens-phage with potential for biocontrol in the dairy industry. This phage showed a short linear double-stranded DNA genome (~42 kb) with a GC content of 58.3% and more than 50% of the genes encoding proteins with unknown functions. Nevertheless, UFJF_PfDIW6’s genome was organised into five functional modules: DNA packaging, structural proteins, DNA metabolism, lysogenic, and host lysis. Comparative genome analysis revealed that the UFJF_PfDIW6’s genome is distinct from other viral genomes available at NCBI databases, displaying maximum coverages of 5% among all alignments. Curiously, this phage showed higher sequence coverages (38–49%) when aligned with uncharacterised prophages integrated into Pseudomonas genomes. Phages compared in this study share conserved locally collinear blocks comprising genes of the modules’ DNA packing and structural proteins but were primarily differentiated by the composition of the DNA metabolism and lysogeny modules. Strategies for taxonomy assignment showed that UFJF_PfDIW6 was clustered into an unclassified genus in the Podoviridae clade. Therefore, our findings indicate that this phage could represent a novel genus belonging to the Podoviridae family.
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Affiliation(s)
- Humberto Moreira Hungaro
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
| | - Pedro Marcus Pereira Vidigal
- Núcleo de Análise de Biomoléculas (NuBioMol), Campus da UFV, Universidade Federal de Viçosa (UFV), Viçosa 36570-900, MG, Brazil;
| | - Edilane Cristina do Nascimento
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Felipe Gomes da Costa Oliveira
- Departamento de Ciências Farmacêuticas, Faculdade de Farmácia, Universidade Federal de Juiz de Fora (UFJF), Juiz de Fora 36036-900, MG, Brazil; (E.C.d.N.); (F.G.d.C.O.)
| | - Marco Túlio Pardini Gontijo
- Departamento de Genética, Evolução, Microbiologia e Imunologia, Instituto de Biologia, Universidade Estadual de Campinas (UNICAMP), Campinas 13083-872, SP, Brazil;
| | - Maryoris Elisa Soto Lopez
- Departamento de Engenharia de Alimentos, Universidade de Córdoba (UNICORDOBA), Córdoba 230002, Colombia
- Correspondence: (H.M.H.); (M.E.S.L.); Tel.: +55-32-2102-3804 (H.M.H.); +57-310-469-02-04 (M.E.S.L.)
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A phage cocktail in controlling phage resistance development in multidrug resistant Aeromonas hydrophila with great therapeutic potential. Microb Pathog 2021; 162:105374. [PMID: 34968644 DOI: 10.1016/j.micpath.2021.105374] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/19/2021] [Accepted: 12/24/2021] [Indexed: 10/19/2022]
Abstract
Aeromonas hydrophila (A. hydrophila) is an opportunistic pathogen of fish-human-livestock, which poses a threat to the development of aquaculture. Lytic phage has long been considered as an effective bactericidal agent. However, the rapid development of phage resistance seriously hinders the continuous application of lytic phages. In our study, a new bacteriophage vB_ AhaP_PZL-Ah8 was isolated from sewage and its characteristics and genome were investigated. Phage vB_ AhaP_PZL-Ah8 has been classified as the member of the Podoviridae family, which exhibited the latent period was about 30 min. As revealed from the genomic sequence analysis, vB_ AhaP_PZL-Ah8 covered a double-stranded genome of 40,855 bp (exhibiting 51.89% G + C content), with encoding 52 predicted open reading frames (ORFs). The results suggested that the combination of vB_ AhaP_PZL-Ah8 and another A. hydrophila phage vB_ AhaP_PZL-Ah1 could improve the therapeutic efficacy both in vitro and in vivo. The resistance mutation frequency of A. hydrophila cells infected with the mixture phage (vB_ AhaP_PZL-Ah8+ vB_ AhaP_PZL-Ah1) was significantly lower than cells treated with single phage (P <0.01). Phage therapy in vivo showed that the survival rate in the mixture phage treatment group was significantly higher than that in single phage treatment group.
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Gontijo MTP, Jorge GP, Brocchi M. Current Status of Endolysin-Based Treatments against Gram-Negative Bacteria. Antibiotics (Basel) 2021; 10:1143. [PMID: 34680724 PMCID: PMC8532960 DOI: 10.3390/antibiotics10101143] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 07/14/2021] [Accepted: 07/21/2021] [Indexed: 12/31/2022] Open
Abstract
The prevalence of multidrug-resistant Gram-negative bacteria is a public health concern. Bacteriophages and bacteriophage-derived lytic enzymes have been studied in response to the emergence of multidrug-resistant bacteria. The availability of tRNAs and endolysin toxicity during recombinant protein expression is circumvented by codon optimization and lower expression levels using inducible pET-type plasmids and controlled cultivation conditions, respectively. The use of polyhistidine tags facilitates endolysin purification and alters antimicrobial activity. Outer membrane permeabilizers, such as organic acids, act synergistically with endolysins, but some endolysins permeate the outer membrane of Gram-negative bacteria per se. However, the outer membrane permeation mechanisms of endolysins remain unclear. Other strategies, such as the co-administration of endolysins with polymyxins, silver nanoparticles, and liposomes confer additional outer membrane permeation. Engineered endolysins comprising domains for outer membrane permeation is also a strategy used to overcome the current challenges on the control of multidrug-resistant Gram-negative bacteria. Metagenomics is a new strategy for screening endolysins with interesting antimicrobial properties from uncultured phage genomes. Here, we review the current state of the art on the heterologous expression of endolysin, showing the potential of bacteriophage endolysins in controlling bacterial infections.
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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 13083-862, Brazil; (G.P.J.); (M.B.)
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