51
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Witeof AE, McClary W, Rea LT, Yang Q, Davis MM, Funke H, Catalano C, Randolph T. Atomic-Layer Deposition Processes Applied to Phage λ and a Phage-Like Particle Platform Yield Thermostable, Single-Shot Vaccines. J Pharm Sci 2022; 111:1354-1362. [DOI: 10.1016/j.xphs.2022.01.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 01/10/2022] [Accepted: 01/10/2022] [Indexed: 12/19/2022]
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52
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Sjahriani T, Wasito EB, Tyasningsih W. The Analysis of OmpA and Rz/Rz1 of Lytic Bacteriophage from Surabaya, Indonesia. SCIENTIFICA 2021; 2021:7494144. [PMID: 35096434 PMCID: PMC8794686 DOI: 10.1155/2021/7494144] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 11/28/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
A good strategy to conquer the Escherichia coli-cause food-borne disease could be bacteriophages. Porins are a type of β-barrel proteins with diffuse channels and OmpA, which has a role in hydrophilic transport, is the most frequent porin in E. coli; it was also chosen as the potential receptor of the phage. And the Rz/Rz1 was engaged in the breakup of the host bacterial external membrane. This study aimed to analyze the amino acid of OmpA and Rz/Rz1 of lytic bacteriophage from Surabaya, Indonesia. This study employed a sample of 8 bacteriophages from the previous study. The OmpA analysis method was mass spectrometry. Rz/Rz1 was analyzed using PCR, DNA sequencing, Expasy Translation, and Expasy ProtParam. The result obtained 10% to 29% sequence coverage of OmpA, carrying the ligand-binding site. The Rz/Rz1 gene shares a high percentage of 97.04% to 98.89% identities with the Siphoviridae isolate ctTwQ4, partial genome, and Myoviridae isolate cthRA4, partial genome. The Mann-Whitney statistical tests indicate the significant differences between Alanine, Aspartate, Glycine, Proline, Serine (p=0.011), Asparagine, Cysteine (p=0.009), Isoleucine (p=0.043), Lysine (p=0.034), Methionine (p=0.001), Threonine (p=0.018), and Tryptophan (p=0.007) of OmpA and Rz/Rz1. The conclusion obtained from this study is the fact that OmpA acts as Phage 1, Phage 2, Phage 3, Phage 5, and Phage 6 receptors for its peptide composition comprising the ligand binding site, and Rz/Rz1 participates in host bacteria lysis.
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Affiliation(s)
- Tessa Sjahriani
- Doctoral Program, Faculty of Medicine, Universitas Airlangga, Dr. Moestopo Road No. 47, Surabaya 60285, Indonesia
- Department of Microbiology, Faculty of Medicine, Universitas Malahayati, Pramuka Road No. 27, Bandar Lampung 35158, Indonesia
| | - Eddy Bagus Wasito
- Department of Microbiology, Faculty of Medicine, Universitas Airlangga, Dr. Moestopo Road No. 47, Surabaya 60285, Indonesia
| | - Wiwiek Tyasningsih
- Department of Microbiology, Faculty of Veterinary Medicine, Universitas Airlangga, C Campus, Mulyorejo Road, Surabaya 60115, Indonesia
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53
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Khalifa M, Few LL, Too WCS. Phage-Choline Kinase Inhibitor Combination to Control Pseudomonas aeruginosa: A Promising Combo. Mini Rev Med Chem 2021; 22:1281-1288. [PMID: 34961459 DOI: 10.2174/1389557521666211213160256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Revised: 09/09/2021] [Accepted: 10/25/2021] [Indexed: 11/22/2022]
Abstract
BACKGROUND Pseudomonas aeruginosa is one of the most prevalent opportunistic pathogens in humans that has thrived and proved to be difficult to control in this "post-antibiotic era." Antibiotic alternatives are necessary for fighting against this resilient bacterium. Even though phages might not be "the wonder drug" that solves everything, they still provide a viable option to combat P. aeruginosa and curb the threat it imposes. MAIN FINDINGS The combination of antibiotics with phages, however, poses a propitious treatment option for P. aeruginosa. Choline kinase (ChoK) is the enzyme that synthesizes phosphorylcholine subsequently incorporated into lipopolysaccharide located at the outer membrane of gram-negative bacteria. Recently, inhibition of ChoKs has been proposed as a promising antibacterial strategy. Successful docking of Hemicholinium-3, a choline kinase inhibitor, to the model structure of P. aeruginosa ChoK also supports the use of this inhibitor or its derivatives to inhibit the growth of this microorganism. CONCLUSION Therefore, the combination of the novel antimicrobial "choline kinase inhibitors (ChoKIs)" with a phage cocktail or synthetic phages as a potential treatment for P. aeruginosa infection has been proposed.
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Affiliation(s)
- Moad Khalifa
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan. Malaysia
| | - Ling Ling Few
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan. Malaysia
| | - Wei Cun See Too
- School of Health Sciences, Health Campus, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan. Malaysia
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54
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Marques AT, Tanoeiro L, Duarte A, Gonçalves L, Vítor JMB, Vale FF. Genomic Analysis of Prophages from Klebsiella pneumoniae Clinical Isolates. Microorganisms 2021; 9:2252. [PMID: 34835377 PMCID: PMC8617712 DOI: 10.3390/microorganisms9112252] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Revised: 10/15/2021] [Accepted: 10/25/2021] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae is an increasing threat to public health and represents one of the most concerning pathogens involved in life-threatening infections. The resistant and virulence determinants are coded by mobile genetic elements which can easily spread between bacteria populations and co-evolve with its genomic host. In this study, we present the full genomic sequences, insertion sites and phylogenetic analysis of 150 prophages found in 40 K. pneumoniae clinical isolates obtained from an outbreak in a Portuguese hospital. All strains harbored at least one prophage and we identified 104 intact prophages (69.3%). The prophage size ranges from 29.7 to 50.6 kbp, coding between 32 and 78 putative genes. The prophage GC content is 51.2%, lower than the average GC content of 57.1% in K. pneumoniae. Complete prophages were classified into three families in the order Caudolovirales: Myoviridae (59.6%), Siphoviridae (38.5%) and Podoviridae (1.9%). In addition, an alignment and phylogenetic analysis revealed nine distinct clusters. Evidence of recombination was detected within the genome of some prophages but, in most cases, proteins involved in viral structure, transcription, replication and regulation (lysogenic/lysis) were maintained. These results support the knowledge that prophages are diverse and widely disseminated in K. pneumoniae genomes, contributing to the evolution of this species and conferring additional phenotypes. Moreover, we identified K. pneumoniae prophages in a set of endolysin genes, which were found to code for proteins with lysozyme activity, cleaving the β-1,4 linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in the peptidoglycan network and thus representing genes with the potential for lysin phage therapy.
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Affiliation(s)
- Andreia T. Marques
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Luís Tanoeiro
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Av. Gama Pinto, 1649-003 Lisboa, Portugal;
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, 2829-511 Monte da Caparica, Portugal
| | - Luisa Gonçalves
- Clinical Pathology Unit, Hospital SAMS, Cidade de Gabela, 1849-017 Lisboa, Portugal;
| | - Jorge M. B. Vítor
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
| | - Filipa F. Vale
- Pathogen Genome Bioinformatics and Computational Biology, Research Institute for Medicines (iMed-ULisboa), Faculty of Pharmacy, Universidade de Lisboa, 1649-003 Lisboa, Portugal; (L.T.); (J.M.B.V.)
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55
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Zhang JT, Yang F, Du K, Li WF, Chen Y, Jiang YL, Li Q, Zhou CZ. Structure and assembly pattern of a freshwater short-tailed cyanophage Pam1. Structure 2021; 30:240-251.e4. [PMID: 34727518 DOI: 10.1016/j.str.2021.10.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 09/18/2021] [Accepted: 10/08/2021] [Indexed: 11/19/2022]
Abstract
Despite previous structural analyses of bacteriophages, quite little is known about the structures and assembly patterns of cyanophages. Using cryo-EM combined with crystallography, we solve the near-atomic-resolution structure of a freshwater short-tailed cyanophage, Pam1, which comprises a 400-Å-long tail and an icosahedral capsid of 650 Å in diameter. The outer capsid surface is reinforced by trimeric cement proteins with a β-sandwich fold, which structurally resemble the distal motif of Pam1's tailspike, suggesting its potential role in host recognition. At the portal vertex, the dodecameric portal and connected adaptor, followed by a hexameric needle head, form a DNA ejection channel, which is sealed by a trimeric needle. Moreover, we identify a right-handed rifling pattern that might help DNA to revolve along the wall of the ejection channel. Our study reveals the precise assembly pattern of a cyanophage and lays the foundation to support its practical biotechnological and environmental applications.
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Affiliation(s)
- Jun-Tao Zhang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Feng Yang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Kang Du
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Wei-Fang Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yuxing Chen
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Yong-Liang Jiang
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Qiong Li
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.
| | - Cong-Zhao Zhou
- Hefei National Laboratory for Physical Sciences at the Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, Anhui 230026, China.
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56
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Rao VB, Fokine A, Fang Q. The remarkable viral portal vertex: structure and a plausible model for mechanism. Curr Opin Virol 2021; 51:65-73. [PMID: 34619513 DOI: 10.1016/j.coviro.2021.09.004] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2021] [Revised: 08/23/2021] [Accepted: 09/12/2021] [Indexed: 01/20/2023]
Abstract
Many icosahedral viruses including tailed bacteriophages and herpes viruses have a unique portal vertex where a dodecameric protein ring is associated with a fivefold capsid shell. While the peripheral regions of the portal ring are involved in capsid assembly, its central channel is used to transport DNA into and out of capsid during genome packaging and infection. Though the atomic structure of this highly conserved, turbine-shaped, portal is known for nearly two decades, its molecular mechanism remains a mystery. Recent high-resolution in situ structures reveal various conformational states of the portal and the asymmetric interactions between the 12-fold portal and the fivefold capsid. These lead to a valve-like mechanism for this symmetry-mismatched portal vertex that regulates DNA flow through the channel, a critical function for high fidelity assembly of an infectious virion.
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Affiliation(s)
- Venigalla B Rao
- Bacteriophage Medical Research Center, Department of Biology, The Catholic University of America, Washington, DC 20064, USA.
| | - Andrei Fokine
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Qianglin Fang
- School of Public Health (Shenzhen), Sun Yat-sen University, Shenzhen, Guangdong, China
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57
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Dkhili S, Ribeiro M, Ghariani S, Yahia HB, Hillion M, Poeta P, Slama KB, Hébraud M, Igrejas G. Bacteriophages as Antimicrobial Agents? Proteomic Insights on Three Novel Lytic Bacteriophages Infecting ESBL-Producing Escherichia coli. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2021; 25:626-640. [PMID: 34559008 DOI: 10.1089/omi.2021.0122] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
With the emergence of multiresistant bacteria, the use of bacteriophages is gaining renewed interest as potential antimicrobial agents. The aim of this study was to analyze the structure of three lytic bacteriophages infecting Escherichia coli (SD1, SD2, and SD3) using a gel-based proteomics approach and the cellular response of this bacterium to phage SD1 infection at the proteome level. The combination of the results of 1-DE and 2-DE followed by mass spectrometry led to the identification of 3, 14, and 9 structure proteins for SD1, SD2, and SD3 phages, respectively. Different protein profiles with common proteins were noticed. We also analyzed phage-induced effects by comparing samples from infected cells to those of noninfected cells. We verified important changes in E. coli proteins expression during phage SD1 infection, where there was an overexpression of proteins involved in stress response. Our results indicated that viral infection caused bacterial oxidative stress and bacterial cells response to stress was orchestrated by antioxidant defense mechanisms. This article makes an empirical scientific contribution toward the concept of bacteriophages as potential antimicrobial agents. With converging ecological threats in the 21st century, novel approaches to address the innovation gaps in antimicrobial development are more essential than ever. Further research on bacteriophages is called for in this broader context of planetary health and integrative biology.
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Affiliation(s)
- Sadika Dkhili
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Miguel Ribeiro
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
| | - Salma Ghariani
- Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Houssem Ben Yahia
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Mélanie Hillion
- University Clermont Auvergne, INRAE, UMR0454 Microbiology Digestive Environment Health (MEDiS), Saint-Genès Champanelle, France.,INRAE, Metabolism Exploration Platform, Proteomic Component (PFEMcp), Saint-Genès Champanelle, France
| | - Patricia Poeta
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), Vila Real, Portugal
| | - Karim Ben Slama
- Laboratoire des Microorganismes et Biomolécules actives, Faculté des Sciences de Tunis, Université de Tunis El Manar, Tunis, Tunisie.,Institut Supérieur des Sciences Biologiques Appliquées de Tunis, Université de Tunis El Manar, Tunis, Tunisie
| | - Michel Hébraud
- University Clermont Auvergne, INRAE, UMR0454 Microbiology Digestive Environment Health (MEDiS), Saint-Genès Champanelle, France.,INRAE, Metabolism Exploration Platform, Proteomic Component (PFEMcp), Saint-Genès Champanelle, France
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology and University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,Functional Genomics and Proteomics Unity, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal.,LAQV-REQUIMTE, Faculty of Science and Technology, University Nova of Lisbon, Lisbon, Portugal
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58
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Erickson S, Paulson J, Brown M, Hahn W, Gil J, Barron-Montenegro R, Moreno-Switt AI, Eisenberg M, Nguyen MM. Isolation and engineering of a Listeria grayi bacteriophage. Sci Rep 2021; 11:18947. [PMID: 34556683 PMCID: PMC8460666 DOI: 10.1038/s41598-021-98134-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 09/03/2021] [Indexed: 01/02/2023] Open
Abstract
The lack of bacteriophages capable of infecting the Listeria species, Listeria grayi, is academically intriguing and presents an obstacle to the development of bacteriophage-based technologies for Listeria. We describe the isolation and engineering of a novel L. grayi bacteriophage, LPJP1, isolated from farm silage. With a genome over 200,000 base pairs, LPJP1 is the first and only reported jumbo bacteriophage infecting the Listeria genus. Similar to other Gram-positive jumbo phages, LPJP1 appeared to contain modified base pairs, which complicated initial attempts to obtain genomic sequence using standard methods. Following successful sequencing with a modified approach, a recombinant of LPJP1 encoding the NanoLuc luciferase was engineered using homologous recombination. This luciferase reporter bacteriophage successfully detected 100 stationary phase colony forming units of both subspecies of L. grayi in four hours. A single log phase colony forming unit was also sufficient for positive detection in the same time period. The recombinant demonstrated complete specificity for this particular Listeria species and did not infect 150 non-L. grayi Listeria strains nor any other bacterial genus. LPJP1 is believed to be the first reported lytic bacteriophage of L. grayi as well as the only jumbo bacteriophage to be successfully engineered into a luciferase reporter.
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Affiliation(s)
- Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA.
| | - John Paulson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Wendy Hahn
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA, 90062, USA
| | - Rocío Barron-Montenegro
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Andrea I Moreno-Switt
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile.,Millennium Initiative for Collaborative Research on Bacteria Resistance (MICROB-R), Santiago, Chile
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Minh M Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
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59
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Miroshnikov KA, Evseev PV, Lukianova AA, Ignatov AN. Tailed Lytic Bacteriophages of Soft Rot Pectobacteriaceae. Microorganisms 2021; 9:1819. [PMID: 34576713 PMCID: PMC8472413 DOI: 10.3390/microorganisms9091819] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 02/07/2023] Open
Abstract
The study of the ecological and evolutionary traits of Soft Rot Pectobacteriaceae (SRP) comprising genera Pectobacterium and Dickeya often involves bacterial viruses (bacteriophages). Bacteriophages are considered to be a prospective tool for the ecologically safe and highly specific protection of plants and harvests from bacterial diseases. Information concerning bacteriophages has been growing rapidly in recent years, and this has included new genomics-based principles of taxonomic distribution. In this review, we summarise the data on phages infecting Pectobacterium and Dickeya that are available in publications and genomic databases. The analysis highlights not only major genomic properties that assign phages to taxonomic families and genera, but also the features that make them potentially suitable for phage control applications. Specifically, there is a discussion of the molecular mechanisms of receptor recognition by the phages and problems concerning the evolution of phage-resistant mutants.
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Affiliation(s)
- Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
| | - Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Str., 16/10, 117997 Moscow, Russia
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Department of Biology, Lomonosov Moscow State University, Leninskie Gory, 1, bldg. 12, 119234 Moscow, Russia
| | - Alexander N Ignatov
- Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Str., 49, 127434 Moscow, Russia
- Agrobiotechnology Department, Agrarian and Technological Institute, RUDN University, Miklukho-Maklaya Str., 6, 117198 Moscow, Russia
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60
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Ramos-Vivas J, Elexpuru-Zabaleta M, Samano ML, Barrera AP, Forbes-Hernández TY, Giampieri F, Battino M. Phages and Enzybiotics in Food Biopreservation. Molecules 2021; 26:molecules26175138. [PMID: 34500572 PMCID: PMC8433972 DOI: 10.3390/molecules26175138] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/10/2021] [Accepted: 08/20/2021] [Indexed: 12/27/2022] Open
Abstract
Presently, biopreservation through protective bacterial cultures and their antimicrobial products or using antibacterial compounds derived from plants are proposed as feasible strategies to maintain the long shelf-life of products. Another emerging category of food biopreservatives are bacteriophages or their antibacterial enzymes called "phage lysins" or "enzybiotics", which can be used directly as antibacterial agents due to their ability to act on the membranes of bacteria and destroy them. Bacteriophages are an alternative to antimicrobials in the fight against bacteria, mainly because they have a practically unique host range that gives them great specificity. In addition to their potential ability to specifically control strains of pathogenic bacteria, their use does not generate a negative environmental impact as in the case of antibiotics. Both phages and their enzymes can favor a reduction in antibiotic use, which is desirable given the alarming increase in resistance to antibiotics used not only in human medicine but also in veterinary medicine, agriculture, and in general all processes of manufacturing, preservation, and distribution of food. We present here an overview of the scientific background of phages and enzybiotics in the food industry, as well as food applications of these biopreservatives.
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Affiliation(s)
- José Ramos-Vivas
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - María Elexpuru-Zabaleta
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
| | - María Luisa Samano
- Research Group on Foods, Nutritional Biochemistry and Health, Universidad Europea del Atlántico, 39011 Santander, Spain; (J.R.-V.); (M.E.-Z.); (M.L.S.)
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | - Alina Pascual Barrera
- Department of Project Management, Universidad Internacional Iberoamericana, Campeche 24560, Mexico;
| | | | - Francesca Giampieri
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
| | - Maurizio Battino
- Department of Clinical Sciences, Polytechnic University of Marche, 60131 Ancona, Italy
- International Research Center for Food Nutrition and Safety, Jiangsu University, Zhenjiang 212013, China
- Correspondence: (F.G.); (M.B.); Tel.: +339-071-220-4136 (F.G.); +339-071-220-4646 (M.B.)
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61
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Catala A, Dzieciatkowska M, Wang G, Gutierrez-Hartmann A, Simberg D, Hansen KC, D'Alessandro A, Catalano CE. Targeted Intracellular Delivery of Trastuzumab Using Designer Phage Lambda Nanoparticles Alters Cellular Programs in Human Breast Cancer Cells. ACS NANO 2021; 15:11789-11805. [PMID: 34189924 DOI: 10.1021/acsnano.1c02864] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
| Several diseases exhibit a high degree of heterogeneity and diverse reprogramming of cellular pathways. To address this complexity, additional strategies and technologies must be developed to define their scope and variability with the goal of improving current treatments. Nanomedicines derived from viruses are modular systems that can be easily adapted for combinatorial approaches, including imaging, biomarker targeting, and intracellular delivery of therapeutics. Here, we describe a "designer nanoparticle" system that can be rapidly engineered in a tunable and defined manner. Phage-like particles (PLPs) derived from bacteriophage lambda possess physiochemical properties compatible with pharmaceutical standards, and in vitro particle tracking and cell targeting are accomplished by simultaneous display of fluorescein-5-maleimide (F5M) and trastuzumab (Trz), respectively (Trz-PLPs). Trz-PLPs bind to the oncogenically active human epidermal growth factor receptor 2 (HER2) and are internalized by breast cancer cells of the HER2 overexpression subtype, but not by those lacking the HER2 amplification. Compared to treatment with Trz, robust internalization of Trz-PLPs results in higher intracellular concentrations of Trz, prolonged inhibition of cell growth, and modulated regulation of cellular programs associated with HER2 signaling, proliferation, metabolism, and protein synthesis. Given the implications to cancer pathogenesis and that dysregulated signaling and metabolism can lead to drug resistance and cancer cell survival, the present study identifies metabolic and proteomic liabilities that could be exploited by the PLP platform to enhance therapeutic efficacy. The lambda PLP system is robust and rapidly modifiable, which offers a platform that can be easily "tuned" for broad utility and tailored functionality.
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Affiliation(s)
- Alexis Catala
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Monika Dzieciatkowska
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Guankui Wang
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Arthur Gutierrez-Hartmann
- Departments of Biochemistry and Molecular Genetics and Medicine - Division of Endocrinology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Dmitri Simberg
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Kirk C Hansen
- Department of Biochemistry and Molecular Genetics, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Angelo D'Alessandro
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
- Departments of Biochemistry and Molecular Genetics and Medicine - Division of Hematology, School of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
| | - Carlos E Catalano
- Program in Structural Biology and Biochemistry, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado 80045, United States
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Šimoliūnienė M, Žukauskienė E, Truncaitė L, Cui L, Hutinet G, Kazlauskas D, Kaupinis A, Skapas M, de Crécy-Lagard V, Dedon PC, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_MED16-A Siphovirus Containing a 2'-Deoxy-7-amido-7-deazaguanosine-Modified DNA. Int J Mol Sci 2021; 22:7333. [PMID: 34298953 PMCID: PMC8306585 DOI: 10.3390/ijms22147333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 06/30/2021] [Accepted: 07/05/2021] [Indexed: 11/16/2022] Open
Abstract
A novel siphovirus, vB_PagS_MED16 (MED16) was isolated in Lithuania using Pantoea agglomerans strain BSL for the phage propagation. The double-stranded DNA genome of MED16 (46,103 bp) contains 73 predicted open reading frames (ORFs) encoding proteins, but no tRNA. Our comparative sequence analysis revealed that 26 of these ORFs code for unique proteins that have no reliable identity when compared to database entries. Based on phylogenetic analysis, MED16 represents a new genus with siphovirus morphology. In total, 35 MED16 ORFs were given a putative functional annotation, including those coding for the proteins responsible for virion morphogenesis, phage-host interactions, and DNA metabolism. In addition, a gene encoding a preQ0 DNA deoxyribosyltransferase (DpdA) is present in the genome of MED16 and the LC-MS/MS analysis indicates 2'-deoxy-7-amido-7-deazaguanosine (dADG)-modified phage DNA, which, to our knowledge, has never been experimentally validated in genomes of Pantoea phages. Thus, the data presented in this study provide new information on Pantoea-infecting viruses and offer novel insights into the diversity of DNA modifications in bacteriophages.
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Affiliation(s)
- Monika Šimoliūnienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Emilija Žukauskienė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Lidija Truncaitė
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Liang Cui
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
| | - Geoffrey Hutinet
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
| | - Darius Kazlauskas
- Department of Bioinformatics, Institute of Biotechnology, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Martynas Skapas
- Department of Characterisation of Materials Structure, Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Valérie de Crécy-Lagard
- Department of Microbiology and Cell Science, University of Florida, Gainesville, FL 32611, USA; (G.H.); (V.d.C.-L.)
- Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Peter C. Dedon
- Singapore-MIT Alliance for Research and Technology, Antimicrobial Resistance Interdisciplinary Research Group, Campus for Research Excellence and Technological Enterprise, Singapore 138602, Singapore; (L.C.); (P.C.D.)
- Department of Biological Engineering and Center for Environmental Health Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
| | - Eugenijus Šimoliūnas
- Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (M.Š.); (E.Ž.); (L.T.); (R.M.)
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Component Parts of Bacteriophage Virions Accurately Defined by a Machine-Learning Approach Built on Evolutionary Features. mSystems 2021; 6:e0024221. [PMID: 34042467 PMCID: PMC8269216 DOI: 10.1128/msystems.00242-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Antimicrobial resistance (AMR) continues to evolve as a major threat to human health, and new strategies are required for the treatment of AMR infections. Bacteriophages (phages) that kill bacterial pathogens are being identified for use in phage therapies, with the intention to apply these bactericidal viruses directly into the infection sites in bespoke phage cocktails. Despite the great unsampled phage diversity for this purpose, an issue hampering the roll out of phage therapy is the poor quality annotation of many of the phage genomes, particularly for those from infrequently sampled environmental sources. We developed a computational tool called STEP3 to use the “evolutionary features” that can be recognized in genome sequences of diverse phages. These features, when integrated into an ensemble framework, achieved a stable and robust prediction performance when benchmarked against other prediction tools using phages from diverse sources. Validation of the prediction accuracy of STEP3 was conducted with high-resolution mass spectrometry analysis of two novel phages, isolated from a watercourse in the Southern Hemisphere. STEP3 provides a robust computational approach to distinguish specific and universal features in phages to improve the quality of phage cocktails and is available for use at http://step3.erc.monash.edu/. IMPORTANCE In response to the global problem of antimicrobial resistance, there are moves to use bacteriophages (phages) as therapeutic agents. Selecting which phages will be effective therapeutics relies on interpreting features contributing to shelf-life and applicability to diagnosed infections. However, the protein components of the phage virions that dictate these properties vary so much in sequence that best estimates suggest failure to recognize up to 90% of them. We have utilized this diversity in evolutionary features as an advantage, to apply machine learning for prediction accuracy for diverse components in phage virions. We benchmark this new tool showing the accurate recognition and evaluation of phage component parts using genome sequence data of phages from undersampled environments, where the richest diversity of phage still lies.
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Ben-Zaken H, Kraitman R, Coppenhagen-Glazer S, Khalifa L, Alkalay-Oren S, Gelman D, Ben-Gal G, Beyth N, Hazan R. Isolation and Characterization of Streptococcus mutans Phage as a Possible Treatment Agent for Caries. Viruses 2021; 13:825. [PMID: 34063251 PMCID: PMC8147482 DOI: 10.3390/v13050825] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/27/2021] [Accepted: 04/29/2021] [Indexed: 12/22/2022] Open
Abstract
Streptococcus mutans is a key bacterium in dental caries, one of the most prevalent chronic infectious diseases. Conventional treatment fails to specifically target the pathogenic bacteria, while tending to eradicate commensal bacteria. Thus, caries remains one of the most common and challenging diseases. Phage therapy, which involves the use of bacterial viruses as anti-bacterial agents, has been gaining interest worldwide. Nevertheless, to date, only a few phages have been isolated against S. mutans. In this study, we describe the isolation and characterization of a new S. mutans phage, termed SMHBZ8, from hundreds of human saliva samples that were collected, filtered, and screened. The SMHBZ8 genome was sequenced and analyzed, visualized by TEM, and its antibacterial properties were evaluated in various states. In addition, we tested the lytic efficacy of SMHBZ8 against S. mutans in a human cariogenic dentin model. The isolation and characterization of SMHBZ8 may be the first step towards developing a potential phage therapy for dental caries.
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Affiliation(s)
- Hadar Ben-Zaken
- Department of Prosthodontics, Hadassah School of Dental Medicine, Hebrew University, Jerusalem 91120, Israel; (H.B.-Z.); (R.K.); (G.B.-G.); (N.B.)
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Sciences, School of Dental Medicine, The Hebrew University, Jerusalem 91120, Israel; (S.C.-G.); (L.K.); (S.A.-O.); (D.G.)
| | - Reut Kraitman
- Department of Prosthodontics, Hadassah School of Dental Medicine, Hebrew University, Jerusalem 91120, Israel; (H.B.-Z.); (R.K.); (G.B.-G.); (N.B.)
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Sciences, School of Dental Medicine, The Hebrew University, Jerusalem 91120, Israel; (S.C.-G.); (L.K.); (S.A.-O.); (D.G.)
| | - Shunit Coppenhagen-Glazer
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Sciences, School of Dental Medicine, The Hebrew University, Jerusalem 91120, Israel; (S.C.-G.); (L.K.); (S.A.-O.); (D.G.)
| | - Leron Khalifa
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Sciences, School of Dental Medicine, The Hebrew University, Jerusalem 91120, Israel; (S.C.-G.); (L.K.); (S.A.-O.); (D.G.)
| | - Sivan Alkalay-Oren
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Sciences, School of Dental Medicine, The Hebrew University, Jerusalem 91120, Israel; (S.C.-G.); (L.K.); (S.A.-O.); (D.G.)
| | - Daniel Gelman
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Sciences, School of Dental Medicine, The Hebrew University, Jerusalem 91120, Israel; (S.C.-G.); (L.K.); (S.A.-O.); (D.G.)
| | - Gilad Ben-Gal
- Department of Prosthodontics, Hadassah School of Dental Medicine, Hebrew University, Jerusalem 91120, Israel; (H.B.-Z.); (R.K.); (G.B.-G.); (N.B.)
| | - Nurit Beyth
- Department of Prosthodontics, Hadassah School of Dental Medicine, Hebrew University, Jerusalem 91120, Israel; (H.B.-Z.); (R.K.); (G.B.-G.); (N.B.)
| | - Ronen Hazan
- Institute of Biomedical and Oral Research (IBOR), Faculty of Dental Sciences, School of Dental Medicine, The Hebrew University, Jerusalem 91120, Israel; (S.C.-G.); (L.K.); (S.A.-O.); (D.G.)
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Abdelsattar AS, Dawoud A, Makky S, Nofal R, Aziz RK, El-Shibiny A. Bacteriophages: from isolation to application. Curr Pharm Biotechnol 2021; 23:337-360. [PMID: 33902418 DOI: 10.2174/1389201022666210426092002] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 01/29/2021] [Accepted: 03/11/2021] [Indexed: 11/22/2022]
Abstract
Bacteriophages are considered as a potential alternative to fight pathogenic bacteria during the antibiotic resistance era. With their high specificity, they are being widely used in various applications: medicine, food industry, agriculture, animal farms, biotechnology, diagnosis, etc. Many techniques have been designed by different researchers for phage isolation, purification, and amplification, each of which has strengths and weaknesses. However, all aim at having a reasonably pure phage sample that can be further characterized. Phages can be characterized based on their physiological, morphological or inactivation tests. Microscopy, in particular, has opened a wide gate not only for visualizing phage morphological structure, but also for monitoring biochemistry and behavior. Meanwhile, computational analysis of phage genomes provides more details about phage history, lifestyle, and potential for toxigenic or lysogenic conversion, which translate to safety in biocontrol and phage therapy applications. This review summarizes phage application pipelines at different levels and addresses specific restrictions and knowledge gaps in the field. Recently developed computational approaches, which are used in phage genome analysis, are critically assessed. We hope that this assessment provides researchers with useful insights for selection of suitable approaches for Phage-related research aims and applications.
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Affiliation(s)
- Abdallah S Abdelsattar
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Alyaa Dawoud
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Salsabil Makky
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Rana Nofal
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
| | - Ramy K Aziz
- Department of Microbiology and Immunology, Faculty of Pharmacy, Cairo University, Qasr El-Ainy St, Cairo. Egypt
| | - Ayman El-Shibiny
- Center for Microbiology and Phage Therapy, Zewail City of Science and Technology, October Gardens, 6th of October City, Giza, 12578. Egypt
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Žukauskienė E, Šimoliūnienė M, Truncaitė L, Skapas M, Kaupinis A, Valius M, Meškys R, Šimoliūnas E. Pantoea Bacteriophage vB_PagS_AAS23: A Singleton of the Genus Sauletekiovirus. Microorganisms 2021; 9:668. [PMID: 33807116 PMCID: PMC8004638 DOI: 10.3390/microorganisms9030668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2021] [Revised: 03/18/2021] [Accepted: 03/19/2021] [Indexed: 11/16/2022] Open
Abstract
A cold-adapted siphovirus, vB_PagS_AAS23 (AAS23) was isolated in Lithuania using the Pantoea agglomerans strain AUR for the phage propagation. The double-stranded DNA genome of AAS23 (51,170 bp) contains 92 probable protein encoding genes, and no genes for tRNA. A comparative sequence analysis revealed that 25 of all AAS23 open reading frames (ORFs) code for unique proteins that have no reliable identity to database entries. Based on the phylogenetic analysis, AAS23 has no close relationship to other viruses publicly available to date and represents a single species of the genus Sauletekiovirus within the family Drexlerviridae. The phage is able to form plaques in bacterial lawns even at 4 °C and demonstrates a depolymerase activity. Thus, the data presented in this study not only provides the information on Pantoea-infecting bacteriophages, but also offers novel insights into the diversity of cold-adapted viruses and their potential to be used as biocontrol agents.
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Affiliation(s)
- Emilija Žukauskienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Monika Šimoliūnienė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Lidija Truncaitė
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Martynas Skapas
- Center for Physical Sciences and Technology, Saulėtekio av. 3, LT-10257 Vilnius, Lithuania;
| | - Algirdas Kaupinis
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Mindaugas Valius
- Proteomics Centre, Institute of Biochemistry, Life Sciences Centre, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (A.K.); (M.V.)
| | - Rolandas Meškys
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
| | - Eugenijus Šimoliūnas
- Life Sciences Centre, Department of Molecular Microbiology and Biotechnology, Institute of Biochemistry, Vilnius University, Saulėtekio av. 7, LT-10257 Vilnius, Lithuania; (E.Ž.); (M.Š.); (R.M.)
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Enhancement of Antimicrobial Activity of Alginate Films with a Low Amount of Carbon Nanofibers (0.1% w/w). APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11052311] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The World Health Organization has called for new effective and affordable alternative antimicrobial materials for the prevention and treatment of microbial infections. In this regard, calcium alginate has previously been shown to possess antiviral activity against the enveloped double-stranded DNA herpes simplex virus type 1. However, non-enveloped viruses are more resistant to inactivation than enveloped ones. Thus, the viral inhibition capacity of calcium alginate and the effect of adding a low amount of carbon nanofibers (0.1% w/w) were explored here against a non-enveloped double-stranded DNA virus model for the first time. The results of this study showed that neat calcium alginate films partly inactivated this type of non-enveloped virus and that including that extremely low percentage of carbon nanofibers (CNFs) significantly enhanced its antiviral activity. These calcium alginate/CNFs composite materials also showed antibacterial properties against the Gram-positive Staphylococcus aureus bacterial model and no cytotoxic effects in human keratinocyte HaCaT cells. Since alginate-based materials have also shown antiviral activity against four types of enveloped positive-sense single-stranded RNA viruses similar to SARS-CoV-2 in previous studies, these novel calcium alginate/carbon nanofibers composites are promising as broad-spectrum antimicrobial biomaterials for the current COVID-19 pandemic.
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68
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Yilmaz B, Mooser C, Keller I, Li H, Zimmermann J, Bosshard L, Fuhrer T, Gomez de Agüero M, Trigo NF, Tschanz-Lischer H, Limenitakis JP, Hardt WD, McCoy KD, Stecher B, Excoffier L, Sauer U, Ganal-Vonarburg SC, Macpherson AJ. Long-term evolution and short-term adaptation of microbiota strains and sub-strains in mice. Cell Host Microbe 2021; 29:650-663.e9. [PMID: 33662276 DOI: 10.1016/j.chom.2021.02.001] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/23/2020] [Accepted: 01/28/2021] [Indexed: 12/18/2022]
Abstract
Isobiotic mice, with an identical stable microbiota composition, potentially allow models of host-microbial mutualism to be studied over time and between different laboratories. To understand microbiota evolution in these models, we carried out a 6-year experiment in mice colonized with 12 representative taxa. Increased non-synonymous to synonymous mutation rates indicate positive selection in multiple taxa, particularly for genes annotated for nutrient acquisition or replication. Microbial sub-strains that evolved within a single taxon can stably coexist, consistent with niche partitioning of ecotypes in the complex intestinal environment. Dietary shifts trigger rapid transcriptional adaptation to macronutrient and micronutrient changes in individual taxa and alterations in taxa biomass. The proportions of different sub-strains are also rapidly altered after dietary shift. This indicates that microbial taxa within a mouse colony adapt to changes in the intestinal environment by long-term genomic positive selection and short-term effects of transcriptional reprogramming and adjustments in sub-strain proportions.
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Affiliation(s)
- Bahtiyar Yilmaz
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Catherine Mooser
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Irene Keller
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland
| | - Hai Li
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Jakob Zimmermann
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Lars Bosshard
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland; CMPG, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Tobias Fuhrer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Mercedes Gomez de Agüero
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Nerea Fernandez Trigo
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Heidi Tschanz-Lischer
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland
| | - Julien P Limenitakis
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | | | - Kathy D McCoy
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, 80336 Munich, Germany; German Center for Infection Research (DZIF), partner site LMU Munich, 80539 Munich, Germany
| | - Laurent Excoffier
- Interfaculty Bioinformatics Unit and Swiss Institute of Bioinformatics, University of Bern, Bern, 3012, Switzerland; CMPG, Institute of Ecology and Evolution, University of Bern, 3012 Bern, Switzerland
| | - Uwe Sauer
- Institute of Molecular Systems Biology, Swiss Federal Institute of Technology (ETH) Zürich, 8093 Zürich, Switzerland
| | - Stephanie C Ganal-Vonarburg
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland
| | - Andrew J Macpherson
- Maurice Müller Laboratories, Department for Biomedical Research, University of Bern, 3008 Bern, Switzerland; Department of Visceral Surgery and Medicine, Bern University Hospital, University of Bern, 3008 Bern, Switzerland.
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69
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Host cell volume explains differences in the size of DsDNA viruses. Virus Res 2021; 295:198321. [PMID: 33515605 DOI: 10.1016/j.virusres.2021.198321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 12/19/2020] [Accepted: 01/23/2021] [Indexed: 11/23/2022]
Abstract
The nearly 3 orders of magnitude variation in size observed among double-stranded DNA viruses (dsDNA) has important ecological consequences, but the factors responsible for this variation remain poorly understood. Here we first evaluate if a relationship exists between the genome size of diverse dsDNA viruses and their hosts in single-celled organisms (prokaryotes and eukaryotes). We find that dsDNA genome size increases systematically, though less than proportionally, with host genome size. We next evaluate possible relationships between virus size, host size and burst size in an analysis that includes both single-celled and multicellular hosts where genome size and cell volume are not as highly correlated. Here we find that virus volume increases sublinearly with host cell volume (but not genome size) across species, and that virus burst volume (burst size * virus volume) increases with host cell volume. These findings suggest that the size and number of dsDNA viruses produced by a particular host may be constrained by the volume of the infected host cell. This may be useful for better understanding virus-host population dynamics, and ultimately, a better understanding of which viruses may infect which hosts (i.e., host specificity) and the likelihood of cross-species transmission events (i.e., host jumping).
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M. Iyer L, Anantharaman V, Krishnan A, Burroughs AM, Aravind L. Jumbo Phages: A Comparative Genomic Overview of Core Functions and Adaptions for Biological Conflicts. Viruses 2021; 13:v13010063. [PMID: 33466489 PMCID: PMC7824862 DOI: 10.3390/v13010063] [Citation(s) in RCA: 48] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 02/07/2023] Open
Abstract
Jumbo phages have attracted much attention by virtue of their extraordinary genome size and unusual aspects of biology. By performing a comparative genomics analysis of 224 jumbo phages, we suggest an objective inclusion criterion based on genome size distributions and present a synthetic overview of their manifold adaptations across major biological systems. By means of clustering and principal component analysis of the phyletic patterns of conserved genes, all known jumbo phages can be classified into three higher-order groups, which include both myoviral and siphoviral morphologies indicating multiple independent origins from smaller predecessors. Our study uncovers several under-appreciated or unreported aspects of the DNA replication, recombination, transcription and virion maturation systems. Leveraging sensitive sequence analysis methods, we identify novel protein-modifying enzymes that might help hijack the host-machinery. Focusing on host–virus conflicts, we detect strategies used to counter different wings of the bacterial immune system, such as cyclic nucleotide- and NAD+-dependent effector-activation, and prevention of superinfection during pseudolysogeny. We reconstruct the RNA-repair systems of jumbo phages that counter the consequences of RNA-targeting host effectors. These findings also suggest that several jumbo phage proteins provide a snapshot of the systems found in ancient replicons preceding the last universal ancestor of cellular life.
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Affiliation(s)
- Lakshminarayan M. Iyer
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Vivek Anantharaman
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - Arunkumar Krishnan
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Berhampur, Odisha 760010, India;
| | - A. Maxwell Burroughs
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
| | - L. Aravind
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA; (L.M.I.); (V.A.); (A.M.B.)
- Correspondence:
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71
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Esterman ES, Wolf YI, Kogay R, Koonin EV, Zhaxybayeva O. Evolution of DNA packaging in gene transfer agents. Virus Evol 2021; 7:veab015. [PMID: 33732503 PMCID: PMC7947584 DOI: 10.1093/ve/veab015] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Gene transfer agents (GTAs) are virus-like particles encoded and produced by many bacteria and archaea. Unlike viruses, GTAs package fragments of the host genome instead of the genes that encode the components of the GTA itself. As a result of this non-specific DNA packaging, GTAs can transfer genes within bacterial and archaeal communities. GTAs clearly evolved from viruses and are thought to have been maintained in prokaryotic genomes due to the advantages associated with their DNA transfer capacity. The most-studied GTA is produced by the alphaproteobacterium Rhodobacter capsulatus (RcGTA), which packages random portions of the host genome at a lower DNA density than usually observed in tailed bacterial viruses. How the DNA packaging properties of RcGTA evolved from those of the ancestral virus remains unknown. To address this question, we reconstructed the evolutionary history of the large subunit of the terminase (TerL), a highly conserved enzyme used by viruses and GTAs to package DNA. We found that RcGTA-like TerLs grouped within viruses that employ the headful packaging strategy. Because distinct mechanisms of viral DNA packaging correspond to differences in the TerL amino acid sequence, our finding suggests that RcGTA evolved from a headful packaging virus. Headful packaging is the least sequence-specific mode of DNA packaging, which would facilitate the switch from packaging of the viral genome to packaging random pieces of the host genome during GTA evolution.
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Affiliation(s)
- Emma S Esterman
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Yuri I Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Roman Kogay
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Olga Zhaxybayeva
- Department of Biological Sciences, Dartmouth College, Hanover, NH 03755, USA
- Department of Computer Science, Dartmouth College, Hanover, NH 03755, USA
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74
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Huang L, Xiang Y. Structures of the tailed bacteriophages that infect Gram-positive bacteria. Curr Opin Virol 2020; 45:65-74. [DOI: 10.1016/j.coviro.2020.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Revised: 07/07/2020] [Accepted: 09/06/2020] [Indexed: 01/04/2023]
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75
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Discovering the Molecular Determinants of Phaeobacter inhibens Susceptibility to Phaeobacter Phage MD18. mSphere 2020; 5:5/6/e00898-20. [PMID: 33148823 PMCID: PMC7643831 DOI: 10.1128/msphere.00898-20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Bacteriophages have immense potential as antibiotic therapies and in genetic engineering. Understanding the mechanisms that bacteriophages implement to infect their hosts will allow researchers to manipulate these systems and adapt them to specific bacterial targets. In this study, we isolated a bacteriophage capable of infecting the marine alphaproteobacterium Phaeobacter inhibens and determined its mechanism of infection. Phaeobacter virus MD18, a novel species of bacteriophage isolated in Woods Hole, MA, exhibits potent lytic ability against P. inhibens and appears to be of the Siphoviridae morphotype. The genomic sequence of MD18 displayed significant similarity to another siphophage, the recently discovered Roseobacter phage DSS3P8, but genomic and phylogenetic analyses, assessing host range and a search of available metagenomes are all consistent with the conclusion that Phaeobacter phage MD18 is a novel lytic phage. We incubated MD18 with a library of barcoded P. inhibens transposon insertion mutants and identified 22 genes that appear to be required for phage predation of this host. Network analysis of these genes using genomic position, Gene Ontology (GO) term enrichment, and protein associations revealed that these genes are enriched for roles in assembly of a type IV pilus (T4P) and regulators of cellular morphology. Our results suggest that T4P serve as receptors for a novel marine virus that targets P. inhibens. IMPORTANCE Bacteriophages are useful nonantibiotic therapeutics for bacterial infections as well as threats to industries utilizing bacterial agents. This study identified Phaeobacter virus MD18, a phage antagonist of Phaeobacter inhibens, a bacterium with promising use as a probiotic for aquatic farming industries. Genomic analysis suggested that Phaeobacter phage MD18 has evolved to enhance its replication in P. inhibens by adopting favorable tRNA genes as well as through genomic sequence adaptation to resemble host codon usage. Lastly, a high-throughput analysis of P. inhibens transposon insertion mutants identified genes that modulate host susceptibility to phage MD18 and implicated the type IV pilus as the likely receptor recognized for adsorption. This study marks the first characterization of the relationship between P. inhibens and an environmentally sampled phage, which informs our understanding of natural threats to the bacterium and may promote the development of novel phage technologies for genetic manipulation of this host.
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76
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Nguyen MM, Gil J, Brown M, Cesar Tondo E, Soraya Martins de Aquino N, Eisenberg M, Erickson S. Accurate and sensitive detection of Salmonella in foods by engineered bacteriophages. Sci Rep 2020; 10:17463. [PMID: 33060781 PMCID: PMC7567081 DOI: 10.1038/s41598-020-74587-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/28/2020] [Indexed: 12/17/2022] Open
Abstract
Salmonella is a major causative agent of foodborne illness and rapid identification of this pathogen is essential to prevent disease. Currently most assays require high bacterial burdens or prolonged enrichment to achieve acceptable performance. A reduction in testing time without loss of sensitivity is critical to allow food processors to safely decrease product holding time. To meet this need, a method was developed to detect Salmonella using luciferase reporter bacteriophages. Bacteriophages were engineered to express NanoLuc, a novel optimized luciferase originating from the deep-sea shrimp Oplophorus gracilirostris. NanoLuc-expressing bacteriophages had a limit of detection of 10-100 CFU per mL in culture without enrichment. Luciferase reporters demonstrated a broad host range covering all Salmonella species with one reporter detecting 99.3% of 269 inclusivity strains. Cross-reactivity was limited and only observed with other members of the Enterobacteriaceae family. In food matrix studies, a cocktail of engineered bacteriophages accurately detected 1 CFU in either 25 g of ground turkey with a 7 h enrichment or 100 g of powdered infant formula with a 16 h enrichment. Use of the NanoLuc reporter assay described herein resulted in a considerable reduction in enrichment time without a loss of sensitivity.
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Affiliation(s)
- Minh M Nguyen
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA
| | - Jose Gil
- Laboratory Corporation of America Holdings, Los Angeles, CA, 90062, USA
| | - Matthew Brown
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Eduardo Cesar Tondo
- Laboratório de Microbiologia e Controle de Alimentos, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul (ICTA/UFRGS), Porto Alegre, RS, 91501-970, Brazil
| | - Nathanyelle Soraya Martins de Aquino
- Laboratório de Microbiologia e Controle de Alimentos, Instituto de Ciência e Tecnologia de Alimentos, Universidade Federal do Rio Grande do Sul (ICTA/UFRGS), Porto Alegre, RS, 91501-970, Brazil
| | - Marcia Eisenberg
- Laboratory Corporation of America Holdings, Burlington, NC, 27215, USA
| | - Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN, 55112, USA.
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Hardy JM, Dunstan RA, Grinter R, Belousoff MJ, Wang J, Pickard D, Venugopal H, Dougan G, Lithgow T, Coulibaly F. The architecture and stabilisation of flagellotropic tailed bacteriophages. Nat Commun 2020; 11:3748. [PMID: 32719311 PMCID: PMC7385642 DOI: 10.1038/s41467-020-17505-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 07/01/2020] [Indexed: 12/31/2022] Open
Abstract
Flagellotropic bacteriophages engage flagella to reach the bacterial surface as an effective means to increase the capture radius for predation. Structural details of these viruses are of great interest given the substantial drag forces and torques they face when moving down the spinning flagellum. We show that the main capsid and auxiliary proteins form two nested chainmails that ensure the integrity of the bacteriophage head. Core stabilising structures are conserved in herpesviruses suggesting their ancestral origin. The structure of the tail also reveals a robust yet pliable assembly. Hexameric rings of the tail-tube protein are braced by the N-terminus and a β-hairpin loop, and interconnected along the tail by the splayed β-hairpins. By contrast, we show that the β-hairpin has an inhibitory role in the tail-tube precursor, preventing uncontrolled self-assembly. Dyads of acidic residues inside the tail-tube present regularly-spaced motifs well suited to DNA translocation into bacteria through the tail.
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Affiliation(s)
- Joshua M Hardy
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia
| | - Rhys A Dunstan
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Rhys Grinter
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Matthew J Belousoff
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Jiawei Wang
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia
| | - Derek Pickard
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Hariprasad Venugopal
- Ramaciotti Centre for Cryo-Electron Microscopy, Monash University, Clayton, VIC, Australia
| | - Gordon Dougan
- Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Hills Road, Cambridge, UK
| | - Trevor Lithgow
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Microbiology, Monash University, Clayton, VIC, Australia.
| | - Fasséli Coulibaly
- Infection & Immunity Program, Biomedicine Discovery Institute & Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC, Australia.
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A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection. Viruses 2020; 12:v12080797. [PMID: 32722163 PMCID: PMC7472136 DOI: 10.3390/v12080797] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 12/13/2022] Open
Abstract
The lactococcal virulent phage p2 is a model for studying the Skunavirus genus, the most prevalent group of phages causing milk fermentation failures in cheese factories worldwide. This siphophage infects Lactococcus lactis MG1363, a model strain used to study Gram-positive lactic acid bacteria. The structural proteins of phage p2 have been thoroughly described, while most of its non-structural proteins remain uncharacterized. Here, we developed an integrative approach, making use of structural biology, genomics, physiology, and proteomics to provide insights into the function of ORF47, the most conserved non-structural protein of unknown function among the Skunavirus genus. This small phage protein, which is composed of three α-helices, was found to have a major impact on the bacterial proteome during phage infection and to significantly reduce the emergence of bacteriophage-insensitive mutants.
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79
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A Cut above the Rest: Characterization of the Assembly of a Large Viral Icosahedral Capsid. Viruses 2020; 12:v12070725. [PMID: 32635654 PMCID: PMC7411985 DOI: 10.3390/v12070725] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 11/17/2022] Open
Abstract
The head of Salmonella virus SPN3US is composed of ~50 different proteins and is unusual because within its packaged genome there is a mass (>40 MDa) of ejection or E proteins that enter the Salmonella cell. The assembly mechanisms of this complex structure are poorly understood. Previous studies showed that eight proteins in the mature SPN3US head had been cleaved by the prohead protease. In this study, we present the characterization of SPN3US prohead protease mutants using transmission electron microscopy and mass spectrometry. In the absence of the prohead protease, SPN3US head formation was severely impeded and proheads accumulated on the Salmonella inner membrane. This impediment is indicative of proteolysis being necessary for the release and subsequent DNA packaging of proheads in the wild-type phage. Proteomic analyses of gp245- proheads that the normal proteolytic processing of head proteins had not occurred. Assays of a recombinant, truncated form of the protease found it was active, leading us to hypothesize that the C-terminal propeptide has a role in targeting the protease into the prohead core. Our findings provide new evidence regarding the essential role of proteolysis for correct head assembly in this remarkable parasite.
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80
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Schüler MA, Stegmann BA, Poehlein A, Daniel R, Dürre P. Genome sequence analysis of the temperate bacteriophage TBP2 of the solvent producer Clostridium saccharoperbutylacetonicum N1-4 (HMT, ATCC 27021). FEMS Microbiol Lett 2020; 367:5866474. [PMID: 32614389 DOI: 10.1093/femsle/fnaa103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 06/23/2020] [Indexed: 11/13/2022] Open
Abstract
The genus Clostridium consists of a diverse group of pathogenic and non-pathogenic bacteria. The non-pathogenic clostridia contain several solventogenic members of industrial importance, such as Clostridium acetobutylicum or C. beijerinckii. In the process of acetone-butanol-ethanol (ABE) fermentation, these strains are used in large scale fermentation plants since almost 100 years. Soon after establishment of the first plants, the fermentation processes suffered from different bacteriophage infections worldwide. A limited set of studies addressing bacteriophages in solventogenic clostridia have been conducted since then. In this study, we present the genome sequence of the temperate bacteriophage TBP2 of the solventogenic strain C. saccharoperbutylacetonicum N1-4 (HMT) that is used for ABE fermentation. The phage genome consists of 38 039 bp and includes 48 open reading frames. Sequence analysis indicates that the genome encloses random parts of the bacterial genome in addition to its own DNA. It represents the first fully sequenced genome of a temperate bacteriophage infecting solventogenic clostridia.
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Affiliation(s)
- Miriam A Schüler
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Benjamin A Stegmann
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
| | - Anja Poehlein
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Rolf Daniel
- Genomic and Applied Microbiology & Göttingen Genomics Laboratory, Georg-August University, Grisebachstr. 8, D-37077 Göttingen, Germany
| | - Peter Dürre
- Institut für Mikrobiologie und Biotechnologie, Universität Ulm, Albert-Einstein-Allee 11, D-89081, Ulm, Germany
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81
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Mutagenic Analysis of a DNA Translocating Tube's Interior Surface. Viruses 2020; 12:v12060670. [PMID: 32580341 PMCID: PMC7354561 DOI: 10.3390/v12060670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/17/2020] [Accepted: 06/18/2020] [Indexed: 01/06/2023] Open
Abstract
Bacteriophage ϕX174 uses a decamer of DNA piloting proteins to penetrate its host. These proteins oligomerize into a cell wall-spanning tube, wide enough for genome passage. While the inner surface of the tube is primarily lined with inward-facing amino acid side chains containing amide and guanidinium groups, there is a 28 Å-long section near the tube’s C-terminus that does not exhibit this motif. The majority of the inward-facing residues in this region are conserved across the three ϕX174-like clades, suggesting that they play an important role during genome delivery. To test this hypothesis, and explore the general function of the tube’s inner surface, non-glutamine residues within this region were mutated to glutamine, while existing glutamine residues were changed to serine. Four of the resulting mutants had temperature-dependent phenotypes. Virion assembly, host attachment, and virion eclipse, defined as the cell’s ability to inactivate the virus, were not affected. Genome delivery, however, was inhibited. The results support a model in which a balance of forces governs genome delivery: potential energy provided by the densely packaged viral genome and/or an osmotic gradient move the genome into the cell, while the tube’s inward facing glutamine residues exert a frictional force, or drag, that controls genome release.
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82
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Soleimani Sasani M, Eftekhar F. Potential of a Bacteriophage Isolated from Wastewater in Treatment of Lobar Pneumonia Infection Induced by Klebsiella pneumoniae in Mice. Curr Microbiol 2020; 77:2650-2655. [PMID: 32451685 DOI: 10.1007/s00284-020-02041-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 05/18/2020] [Indexed: 12/21/2022]
Abstract
The potential of bacteriophages as alternative treatment for multidrug-resistant (MDR) Klebsiella pneumoniae-related infections has recently gained much interest. The purpose of this research was to isolate and characterize a K. pneumoniae-specific lytic phage with the potential to treat experimental lobar pneumonia induced by K. pneumoniae in mice. A lytic phage was isolated from an urban wastewater sample in Tehran and characterized by transmission electron microscopy (TEM), thermal, pH, and chloroform stability before being employed for treatment of mice infected with K. pneumoniae in an experimental model of lobar pneumonia. BALB/C mice were challenged by intranasal inoculation with 108 colony-forming units (CFU/ml) of K. pneumoniae ATCC 10031 followed by an intraperitoneal injection of the isolated phage using 1010 and 109 plaque-forming units (PFU/ml) simultaneously or 24 h post infection. Control groups of mice received bacteria or bacteriophage alone. Mice were euthanized daily up to 7 days post infection and examined for abnormality in their lungs and livers followed by determining the number of phages and bacteria in plasma and lung homogenates. The isolated phage (vB_KpnM-Teh.1) belonged to the Myoviridae family, was stable at 37 °C, pH 7, and was resistant to chloroform. Treatment of mice with a single dose of phage simultaneously at the time of infection, or 24 h post infection, resulted in seven and five logs decrease of CFU/ml in the lung homogenates up to 3 days after phage administration, respectively. The isolated phage may have the potential as a therapeutic agent against K. pneumoniae infections.
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Affiliation(s)
- Mahboubeh Soleimani Sasani
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, G.C., Tehran, Iran
| | - Fereshteh Eftekhar
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, G.C., Tehran, Iran.
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83
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Bleriot I, Trastoy R, Blasco L, Fernández-Cuenca F, Ambroa A, Fernández-García L, Pacios O, Perez-Nadales E, Torre-Cisneros J, Oteo-Iglesias J, Navarro F, Miró E, Pascual A, Bou G, Martínez-Martínez L, Tomas M. Genomic analysis of 40 prophages located in the genomes of 16 carbapenemase-producing clinical strains of Klebsiella pneumoniae. Microb Genom 2020; 6:e000369. [PMID: 32375972 PMCID: PMC7371120 DOI: 10.1099/mgen.0.000369] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2019] [Accepted: 03/31/2020] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is the clinically most important species within the genus Klebsiella and, as a result of the continuous emergence of multi-drug resistant (MDR) strains, the cause of severe nosocomial infections. The decline in the effectiveness of antibiotic treatments for infections caused by MDR bacteria has generated particular interest in the study of bacteriophages. In this study, we characterized a total of 40 temperate bacteriophages (prophages) with a genome range of 11.454-84.199 kb, predicted from 16 carbapenemase-producing clinical strains of K. pneumoniae belonging to different sequence types, previously identified by multilocus sequence typing. These prophages were grouped into the three families in the order Caudovirales (27 prophages belonging to the family Myoviridae, 10 prophages belonging to the family Siphoviridae and 3 prophages belonging to the family Podoviridae). Genomic comparison of the 40 prophage genomes led to the identification of four prophages isolated from different strains and of genome sizes of around 33.3, 36.1, 39.6 and 42.6 kb. These prophages showed sequence similarities (query cover >90 %, identity >99.9 %) with international Microbe Versus Phage (MVP) (http://mvp.medgenius.info/home) clusters 4762, 4901, 3499 and 4280, respectively. Phylogenetic analysis revealed the evolutionary proximity among the members of the four groups of the most frequently identified prophages in the bacterial genomes studied (33.3, 36.1, 39.6 and 42.6 kb), with bootstrap values of 100 %. This allowed the prophages to be classified into three clusters: A, B and C. Interestingly, these temperate bacteriophages did not infect the highest number of strains as indicated by a host-range assay, these results could be explained by the development of superinfection exclusion mechanisms. In addition, bioinformatic analysis of the 40 identified prophages revealed the presence of 2363 proteins. In total, 59.7 % of the proteins identified had a predicted function, mainly involving viral structure, transcription, replication and regulation (lysogenic/lysis). Interestingly, some proteins had putative functions associated with bacterial virulence (toxin expression and efflux pump regulators), phage defence profiles such as toxin-antitoxin modules, an anti-CRISPR/Cas9 protein, TerB protein (from terZABCDE operon) and methyltransferase proteins.
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Affiliation(s)
- Ines Bleriot
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Rocío Trastoy
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Lucia Blasco
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Felipe Fernández-Cuenca
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Antón Ambroa
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Laura Fernández-García
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Olga Pacios
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
| | - Elena Perez-Nadales
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Julian Torre-Cisneros
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Jesús Oteo-Iglesias
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Reference and Research Laboratory for Antibiotic Resistance and Health Care Infections, National Centre for Microbiology, Institute of Health Carlos III, Majadahonda, Madrid, Spain
| | - Ferran Navarro
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Elisenda Miró
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Microbiology Department, Sant Pau Hospital, Autonomous University of Barcelona (Bellaterra), Barcelona, Spain
| | - Alvaro Pascual
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Clinical Unit for Infectious Diseases, Microbiology and Preventive Medicine, Hospital Universitario Virgen Macarena. Deparment of Microbiology and Medicine, University of Seville, Seville, Spain
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - German Bou
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
| | - Luis Martínez-Martínez
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
- Microbiology Unit, Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University Hospital Reina Sofía, University of Córdoba, Cordoba, Spain
| | - Maria Tomas
- Microbiology Department, Research Institute Biomedical A Coruña (INIBIC), Hospital A Coruña (CHUAC), University of A Coruña (UDC), A Coruña, Spain
- Study Group on Mechanisms of Action and Resistance to Antimicrobials (GEMARA), Spanish Society of Infectious Diseases and Clinical Microbiology (SEIMC), Madrid
- Spanish Network for the Research in Infectious Diseases, REIPI, Seville, Spain
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84
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Herridge WP, Shibu P, O’Shea J, Brook TC, Hoyles L. Bacteriophages of Klebsiella spp., their diversity and potential therapeutic uses. J Med Microbiol 2020; 69:176-194. [PMID: 31976857 PMCID: PMC7431098 DOI: 10.1099/jmm.0.001141] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022] Open
Abstract
Klebsiella spp. are commensals of the human microbiota, and a leading cause of opportunistic nosocomial infections. The incidence of multidrug resistant (MDR) strains of Klebsiella pneumoniae causing serious infections is increasing, and Klebsiella oxytoca is an emerging pathogen. Alternative strategies to tackle infections caused by these bacteria are required as strains become resistant to last-resort antibiotics such as colistin. Bacteriophages (phages) are viruses that can infect and kill bacteria. They and their gene products are now being considered as alternatives or adjuncts to antimicrobial therapies. Several in vitro and in vivo studies have shown the potential for lytic phages to combat MDR K. pneumoniae infections. Ready access to cheap sequencing technologies has led to a large increase in the number of genomes available for Klebsiella-infecting phages, with these phages being heterogeneous at the whole-genome level. This review summarizes our current knowledge on phages of Klebsiella spp. and highlights technological and biological issues relevant to the development of phage-based therapies targeting these bacteria.
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Affiliation(s)
- Warren P. Herridge
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Preetha Shibu
- Life Sciences, University of Westminster, 115 Cavendish Street, London W1W 6UW, UK
| | - Jessica O’Shea
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Thomas C. Brook
- Life Sciences, University of Westminster, 115 Cavendish Street, London W1W 6UW, UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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85
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Walker S, Arsuaga J, Hiltner L, Calderer MC, Vázquez M. Fine structure of viral dsDNA encapsidation. Phys Rev E 2020; 101:022703. [PMID: 32168691 DOI: 10.1103/physreve.101.022703] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023]
Abstract
Unraveling the mechanisms of packing of DNA inside viral capsids is of fundamental importance to understanding the spread of viruses. It could also help develop new applications to targeted drug delivery devices for a large range of therapies. In this article, we present a robust, predictive mathematical model and its numerical implementation to aid the study and design of bacteriophage viruses for application purposes. Exploiting the analogies between the columnar hexagonal chromonic phases of encapsidated viral DNA and chromonic aggregates formed by plank-shaped molecular compounds, we develop a first-principles effective mechanical model of DNA packing in a viral capsid. The proposed expression of the packing energy, which combines relevant aspects of the liquid crystal theory, is developed from the model of hexagonal columnar phases, together with that describing configurations of polymeric liquid crystals. The method also outlines a parameter selection strategy that uses available data for a collection of viruses, aimed at applications to viral design. The outcome of the work is a mathematical model and its numerical algorithm, based on the method of finite elements, and computer simulations to identify and label the ordered and disordered regions of the capsid and calculate the inner pressure. It also presents the tools for the local reconstruction of the DNA "scaffolding" and the center curve of the filament within the capsid.
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Affiliation(s)
- Shawn Walker
- Department of Mathematics, 303 Lockett Hall, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Javier Arsuaga
- Department of Cellular and Molecular Biology, Briggs Hall 09, and Department of Mathematics, MSB 2115, University of California Davis, Davis, California 95616, USA
| | - Lindsey Hiltner
- School of Mathematics, 507 Vincent Hall, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - M Carme Calderer
- School of Mathematics, 507 Vincent Hall, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Mariel Vázquez
- Department of Microbiology and Molecular Genetics, Briggs Hall 09, and Department of Mathematics, MSB 2150, University of California Davis, Davis, California 95616, USA
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86
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Lukianova AA, Shneider MM, Evseev PV, Shpirt AM, Bugaeva EN, Kabanova AP, Obraztsova EA, Miroshnikov KK, Senchenkova SN, Shashkov AS, Toschakov SV, Knirel YA, Ignatov AN, Miroshnikov KA. Morphologically Different Pectobacterium brasiliense Bacteriophages PP99 and PP101: Deacetylation of O-Polysaccharide by the Tail Spike Protein of Phage PP99 Accompanies the Infection. Front Microbiol 2020; 10:3147. [PMID: 32038580 PMCID: PMC6989608 DOI: 10.3389/fmicb.2019.03147] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 12/29/2019] [Indexed: 01/31/2023] Open
Abstract
Soft rot caused by numerous species of Pectobacterium and Dickeya is a serious threat to the world production of potatoes. The application of bacteriophages to combat bacterial infections in medicine, agriculture, and the food industry requires the selection of comprehensively studied lytic phages and the knowledge of their infection mechanism for more rational composition of therapeutic cocktails. We present the study of two bacteriophages, infective for the Pectobacterium brasiliense strain F152. Podoviridae PP99 is a representative of the genus Zindervirus, and Myoviridae PP101 belongs to the still unclassified genomic group. The structure of O-polysaccharide of F152 was established by sugar analysis and 1D and 2D NMR spectroscopy: → 4)-α-D-Manp6Ac-(1→ 2)-α-D-Manp-(1→ 3)-β-D-Galp-(1→
3↑1α-l-6dTalpAc0−2 The recombinant tail spike protein of phage PP99, gp55, was shown to deacetylate the side chain talose residue of bacterial O-polysaccharide, thus providing the selective attachment of the phage to the cell surface. Both phages demonstrate lytic behavior, thus being prospective for therapeutic purposes.
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Affiliation(s)
- Anna A Lukianova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Department of Biology, Lomonosov Moscow State University, Moscow, Russia
| | - Mikhail M Shneider
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Peter V Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Anna M Shpirt
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Anastasia P Kabanova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia.,Research Center "PhytoEngineering" Ltd., Rogachevo, Moscow, Russia
| | - Ekaterina A Obraztsova
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Kirill K Miroshnikov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Sofiya N Senchenkova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Alexander S Shashkov
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | - Stepan V Toschakov
- Winogradsky Institute of Microbiology, Federal Research Center "Fundamentals of Biotechnology", Russian Academy of Sciences, Moscow, Russia
| | - Yuriy A Knirel
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Moscow, Russia
| | | | - Konstantin A Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow, Russia
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87
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Benler S, Hung SH, Vander Griend JA, Peters GA, Rohwer F, Segall AM. Gp4 is a nuclease required for morphogenesis of T4-like bacteriophages. Virology 2020; 543:7-12. [PMID: 32056848 DOI: 10.1016/j.virol.2020.01.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2019] [Revised: 01/15/2020] [Accepted: 01/15/2020] [Indexed: 11/26/2022]
Abstract
An essential step in the morphogenesis of tailed bacteriophages is the joining of heads and tails to form infectious virions. Our understanding of the maturation of complete virus particles remains incomplete. Through an unknown mechanism, phage T4 gene product 4 (gp4) plays an essential role in the head-tail joining step of T4-like phages. Alignment of T4 gp4 homologs identified a type II restriction endonuclease motif. Purified gp4 from both T4 and a marine T4-like bacteriophage, YC, have non-specific nuclease activity in vitro. Mutation of a single conserved amino acid residue in the endonuclease fold of T4 and YC gp4 abrogates nuclease activity. When expressed in trans, the wild type T4 gp4, but neither the mutated T4 protein nor the YC homolog, rescues a T4 gene 4 amber mutant phage. Thus the nuclease activity appears essential for morphogenesis, potentially by cleaving packaged DNA to enable the joining of heads to tails.
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Affiliation(s)
- Sean Benler
- Department of Biology and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
| | - Shr-Hau Hung
- Department of Biology and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Jacob A Vander Griend
- Department of Biology and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Gregory A Peters
- Department of Biology and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Forest Rohwer
- Department of Biology and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA
| | - Anca M Segall
- Department of Biology and Viral Information Institute, San Diego State University, 5500 Campanile Drive, San Diego, CA, 92182, USA.
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88
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A newly isolated roseophage represents a distinct member of Siphoviridae family. Virol J 2019; 16:128. [PMID: 31694663 PMCID: PMC6836515 DOI: 10.1186/s12985-019-1241-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 10/10/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Members of the Roseobacter lineage are a major group of marine heterotrophic bacteria because of their wide distribution, versatile lifestyles and important biogeochemical roles. Bacteriophages, the most abundant biological entities in the ocean, play important roles in shaping their hosts' population structures and mediating genetic exchange between hosts. However, our knowledge of roseophages (bacteriophages that infect Roseobacter) is far behind that of their host counterparts, partly reflecting the need to isolate and analyze the phages associated with this ecologically important bacterial clade. METHODS vB_DshS-R4C (R4C), a novel virulent roseophage that infects Dinoroseobacter shibae DFL12T, was isolated with the double-layer agar method. The phage morphology was visualized with transmission electron microscopy. We characterized R4C in-depth with a genomic analysis and investigated the distribution of the R4C genome in different environments with a metagenomic recruitment analysis. RESULTS The double-stranded DNA genome of R4C consists of 36,291 bp with a high GC content of 66.75%. It has 49 genes with low DNA and protein homologies to those of other known phages. Morphological and phylogenetic analyses suggested that R4C is a novel member of the family Siphoviridae and is most closely related to phages in the genus Cronusvirus. However, unlike the Cronusvirus phages, R4C encodes an integrase, implying its ability to establish a lysogenic life cycle. A terminal analysis shows that, like that of λ phage, the R4C genome utilize the 'cohesive ends' DNA-packaging mechanism. Significantly, homologues of the R4C genes are more prevalent in coastal areas than in the open ocean. CONCLUSIONS Information about this newly discovered phage extends our understanding of bacteriophage diversity, evolution, and their roles in different environments.
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89
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Freitag-Pohl S, Jasilionis A, Håkansson M, Svensson LA, Kovačič R, Welin M, Watzlawick H, Wang L, Altenbuchner J, Płotka M, Kaczorowska AK, Kaczorowski T, Nordberg Karlsson E, Al-Karadaghi S, Walse B, Aevarsson A, Pohl E. Crystal structures of the Bacillus subtilis prophage lytic cassette proteins XepA and YomS. Acta Crystallogr D Struct Biol 2019; 75:1028-1039. [PMID: 31692476 PMCID: PMC6834076 DOI: 10.1107/s2059798319013330] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Accepted: 09/28/2019] [Indexed: 11/23/2022] Open
Abstract
As part of the Virus-X Consortium that aims to identify and characterize novel proteins and enzymes from bacteriophages and archaeal viruses, the genes of the putative lytic proteins XepA from Bacillus subtilis prophage PBSX and YomS from prophage SPβ were cloned and the proteins were subsequently produced and functionally characterized. In order to elucidate the role and the molecular mechanism of XepA and YomS, the crystal structures of these proteins were solved at resolutions of 1.9 and 1.3 Å, respectively. XepA consists of two antiparallel β-sandwich domains connected by a 30-amino-acid linker region. A pentamer of this protein adopts a unique dumbbell-shaped architecture consisting of two discs and a central tunnel. YomS (12.9 kDa per monomer), which is less than half the size of XepA (30.3 kDa), shows homology to the C-terminal part of XepA and exhibits a similar pentameric disc arrangement. Each β-sandwich entity resembles the fold of typical cytoplasmic membrane-binding C2 domains. Only XepA exhibits distinct cytotoxic activity in vivo, suggesting that the N-terminal pentameric domain is essential for this biological activity. The biological and structural data presented here suggest that XepA disrupts the proton motive force of the cytoplasmatic membrane, thus supporting cell lysis.
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Affiliation(s)
| | - Andrius Jasilionis
- Division of Biotechnology, Lund University, PO Box 124, SE-221 00 Lund, Sweden
| | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Rebeka Kovačič
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | - Hildegard Watzlawick
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Lei Wang
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Josef Altenbuchner
- Institut for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Magdalena Płotka
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Anna Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | - Tadeusz Kaczorowski
- Department of Microbiology, Faculty of Biology, University of Gdańsk, Kladki 24, 80-824 Gdańsk, Poland
| | | | | | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 63 Lund, Sweden
| | | | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, England
- Department of Biosciences, Durham University, South Road, Durham DH1 3LE, England
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90
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Dixit AB, Ray K, Black LW. A viral small terminase subunit (TerS) twin ring pac synapsis DNA packaging model is supported by fluorescent fusion proteins. Virology 2019; 536:39-48. [PMID: 31400548 PMCID: PMC6760839 DOI: 10.1016/j.virol.2019.07.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 07/22/2019] [Accepted: 07/24/2019] [Indexed: 11/23/2022]
Abstract
A bacteriophage T4 DNA "synapsis model" proposes that the bacteriophage T4 terminase small subunit (TerS) apposes two pac site containing dsDNA homologs to gauge concatemer maturation adequate for packaging initiation. N-terminus, C-terminus, or both ends modified fusion Ter S proteins retain function. Replacements of the TerS gene in the T4 genome with fusion genes encoding larger (18-45 kDa) TerS-eGFP and TerS-mCherry fluorescent fusion proteins function without significant change in phenotype. Co-infection and co-expression by T4 phages encoding TerS-eGFP and TerS-mCherry shows in vivo FRET in infected bacteria comparable to that of the purified, denatured and then renatured, mixed fusion proteins in vitro. FRET of purified, denatured-renatured, mixed temperature sensitive and native TerS fusion proteins at low and high temperature in vitro shows that TerS ring-like oligomer formation is essential for function in vivo. Super-resolution STORM and PALM microscopy of intercalating dye YOYO-1 DNA and photoactivatable TerS-PAmCherry-C1 fusions support accumulation of TerS dimeric or multiple ring-like oligomer structures containing DNA and gp16-mCherry in vivo as well as in vitro to regulate pac site cutting.
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Affiliation(s)
- Aparna Banerjee Dixit
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Krishanu Ray
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA; Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Lindsay W Black
- Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, MD, 21201, USA.
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91
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Jin H, Jiang YL, Yang F, Zhang JT, Li WF, Zhou K, Ju J, Chen Y, Zhou CZ. Capsid Structure of a Freshwater Cyanophage Siphoviridae Mic1. Structure 2019; 27:1508-1516.e3. [DOI: 10.1016/j.str.2019.07.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 06/11/2019] [Accepted: 07/12/2019] [Indexed: 02/06/2023]
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92
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Serwer P, Wright ET, Lee JC. High murine blood persistence of phage T3 and suggested strategy for phage therapy. BMC Res Notes 2019; 12:560. [PMID: 31488211 PMCID: PMC6729040 DOI: 10.1186/s13104-019-4597-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Accepted: 08/31/2019] [Indexed: 12/11/2022] Open
Abstract
OBJECTIVE Our immediate objective is to determine whether infectivity of lytic podophage T3 has a relatively high persistence in the blood of a mouse, as suggested by previous data. Secondarily, we determine whether the T3 surface has changed during this mouse passage. The surface is characterized by native agarose gel electrophoresis (AGE). Beyond our current data, the long-term objective is optimization of phages chosen for therapy of all bacteremias and associated sepsis. RESULTS We find that the persistence of T3 in mouse blood is higher by over an order of magnitude than the previously reported persistence of (1) lysogenic phages lambda and P22, and (2) lytic phage T7, a T3 relative. We explain these differences via the lysogenic character of lambda and P22, and the physical properties of T7. For the future, we propose testing a new, AGE-based strategy for rapidly screening for high-persistence, lytic, environmental podophages that have phage therapy-promoting physical properties.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900 USA
| | - Elena T. Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900 USA
| | - John C. Lee
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX 78229-3900 USA
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93
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Abstract
The continuous evolvement of bacterial resistance to most, if not all, available antibiotics is a worldwide problem. These strains, frequently isolated from military-associated environments, have created an urgent need to develop supplementary anti-infective modalities. One of the leading directions is phage therapy, which includes the administration of bacteriophages, viruses that specifically target bacteria, as biotherapies. Although neglected in the West until recent years, bacteriophages have been widely studied and clinically administered in the former Soviet Union and Eastern Europe for over a century, where they were found to be incredibly efficient at battling numerous infectious diseases.In this review, we discuss the high potential of phage therapy as a solution for resistant bacterial infectious diseases relating to military medicine. By describing the historical development and knowledge acquired on phage therapy, we define the advantages of bacteriophages for combating resistant bacteria in multiple settings, such as trauma injuries and foodborne illnesses, as a preventive tool and therapy against biological warfare agents, and more. We also present the most recent successful clinical applications of bacteriophages in military settings worldwide.We believe that augmenting military medicine by integrating phage therapy is an important and required step in preparedness for the rapidly approaching post-antibiotic era.
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94
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Deaton J, Yu FB, Quake SR. Mini-Metagenomics and Nucleotide Composition Aid the Identification and Host Association of Novel Bacteriophage Sequences. ACTA ACUST UNITED AC 2019; 3:e1900108. [PMID: 32648690 DOI: 10.1002/adbi.201900108] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 07/10/2019] [Indexed: 11/07/2022]
Abstract
A broad spectrum of metagenomic and single cell sequencing techniques have become popular for dissecting environmental microbial diversity, leading to the characterization of thousands of novel microbial lineages. In addition to recovering bacterial and archaeal genomes, metagenomic assembly can also produce genomes of viruses that infect microbial cells. Because of their diversity, lack of marker genes, and small genome size, identifying novel bacteriophage sequences from metagenomic data is often challenging, especially when the objective is to establish phage-host relationships. The present work describes a computational approach that uses supervised learning to classify metagenomic contigs as phage or non-phage as well as assigning phage taxonomy based on tetranucleotide frequencies. Furthermore, the method assigns phage-host relationships using co-occurrence statistics derived from a recently developed mini-metagenomic experimental technique. This work evaluates method performance at identifying viral contigs and predicting taxonomic classification using publicly available references. Then, using two mini-metagenomic datasets, over 100 novel phage contigs from hot spring samples of Yellowstone National Park are identified and assigned to putative microbial hosts. Results of this work demonstrate the value of combining viral sequence identification with mini-metagenomic experimental methods to understand the microbial ecosystem.
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Affiliation(s)
- Jonathan Deaton
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, USA
| | - Feiqiao Brian Yu
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, USA.,Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA
| | - Stephen R Quake
- Department of Bioengineering, Stanford University, 443 Via Ortega, Stanford, CA, 94305, USA.,Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA, 94158, USA
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95
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Complete Genome Sequence of the Novel Klebsiella pneumoniae Phage Marfa. Microbiol Resour Announc 2019; 8:8/29/e00748-19. [PMID: 31320440 PMCID: PMC6639630 DOI: 10.1128/mra.00748-19] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Here, we describe the complete genome sequence of the T4-like Klebsiella pneumoniae myophage Marfa. In its 168,532-bp genome, Marfa has 289 genes, for which 122 gene functions were predicted. Many similar proteins are shared between Marfa and phage T4, as well as its closest phage relatives. Here, we describe the complete genome sequence of the T4-like Klebsiella pneumoniae myophage Marfa. In its 168,532-bp genome, Marfa has 289 genes, for which 122 gene functions were predicted. Many similar proteins are shared between Marfa and phage T4, as well as its closest phage relatives.
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96
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Xu J, Wang D, Gui M, Xiang Y. Structural assembly of the tailed bacteriophage ϕ29. Nat Commun 2019; 10:2366. [PMID: 31147544 PMCID: PMC6542822 DOI: 10.1038/s41467-019-10272-3] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Accepted: 04/24/2019] [Indexed: 11/30/2022] Open
Abstract
The mature virion of the tailed bacteriophage ϕ29 is an ~33 MDa complex that contains more than 450 subunits of seven structural proteins assembling into a prolate head and a short non-contractile tail. Here, we report the near-atomic structures of the ϕ29 pre-genome packaging head (prohead), the mature virion and the genome-emptied virion. Structural comparisons suggest local rotation or oscillation of the head-tail connector upon DNA packaging and release. Termination of the DNA packaging occurs through pressure-dependent correlative positional and conformational changes in the connector. The funnel-shaped tail lower collar attaches the expanded narrow end of the connector and has a 180-Å long, 24-strand β barrel narrow stem tube that undergoes conformational changes upon genome release. The appendages form an interlocked assembly attaching the tail around the collar. The membrane active long loops at the distal end of the tail knob exit during the late stage of infection and form the cone-shaped tip of a largely hydrophobic helix barrel, prepared for membrane penetration. Mature particles of bacteriophage ϕ29 consist of a 33-MDa complex formed by over 450 subunits, assembled into a head and a short tail. Here, Xu et al. report the near-atomic structures of the ϕ29 prohead, the mature virion and the genome-emptied virion, providing insights into DNA packaging and release.
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Affiliation(s)
- Jingwei Xu
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.,Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093, Zürich, Switzerland
| | - Dianhong Wang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China
| | - Miao Gui
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.,Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, 02115, USA
| | - Ye Xiang
- Beijing Advanced Innovation Center for Structural Biology, Beijing Frontier Research Center for Biological Structure, Center for Infectious Disease Research, Department of Basic Medical Sciences, School of Medicine, Tsinghua University, 100084, Beijing, China.
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97
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Habusha M, Tzipilevich E, Fiyaksel O, Ben‐Yehuda S. A mutant bacteriophage evolved to infect resistant bacteria gained a broader host range. Mol Microbiol 2019; 111:1463-1475. [DOI: 10.1111/mmi.14231] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/19/2019] [Indexed: 02/04/2023]
Affiliation(s)
- Michal Habusha
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
| | - Elhanan Tzipilevich
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
| | - Osher Fiyaksel
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
| | - Sigal Ben‐Yehuda
- Department of Microbiology and Molecular Genetics Institute for Medical Research Israel‐Canada (IMRIC), The Hebrew University‐Hadassah Medical School, The Hebrew University of Jerusalem Jerusalem Israel
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98
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McNulty R, Cardone G, Gilcrease EB, Baker TS, Casjens SR, Johnson JE. Cryo-EM Elucidation of the Structure of Bacteriophage P22 Virions after Genome Release. Biophys J 2019; 114:1295-1301. [PMID: 29590587 DOI: 10.1016/j.bpj.2018.01.026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/24/2017] [Accepted: 01/17/2018] [Indexed: 11/19/2022] Open
Abstract
Genome ejection proteins are required to facilitate transport of bacteriophage P22 double-stranded DNA safely through membranes of Salmonella. The structures and locations of all proteins in the context of the mature virion are known, with the exception of three ejection proteins. Furthermore, the changes that occur to the proteins residing in the mature virion upon DNA release are not fully understood. We used cryogenic electron microscopy to obtain what is, to our knowledge, the first asymmetric reconstruction of mature bacteriophage P22 after double-stranded DNA has been extruded from the capsid-a state representative of one step during viral infection. Results of icosahedral and asymmetric reconstructions at estimated resolutions of 7.8 and 12.5 Å resolutions, respectively, are presented. The reconstruction shows tube-like protein density extending from the center of the tail assembly. The portal protein does not revert to the more contracted, procapsid state, but instead maintains an extended and splayed barrel structure. These structural details contribute to our understanding of the molecular mechanism of P22 phage infection and also set the foundation for future exploitation serving engineering purposes.
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Affiliation(s)
- Reginald McNulty
- Laboratory of Gene Regulation and Signal Transduction, Department of Pharmacology, School of Medicine, University of California, San Diego, La Jolla, California.
| | - Giovanni Cardone
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California
| | - Eddie B Gilcrease
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - Timothy S Baker
- Department of Chemistry and BiochemistryUniversity of California, San Diego, La Jolla, California; Division of Biological Sciences, University of California, San Diego, La Jolla, California
| | - Sherwood R Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah
| | - John E Johnson
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, California.
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99
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Frosiniuk A, Kolchanov DS, Milichko VA, Vinogradov AV, Vinogradov VV. Optical interference-based sensors for the visual detection of nano-scale objects. NANOSCALE 2019; 11:6343-6351. [PMID: 30887996 DOI: 10.1039/c9nr00616h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
In this study, we present a new concept for the simple visual detection of nano-scale objects in solutions. To achieve this goal, we developed chromogen-free interference-based sensors that provided a color visible reaction directly after the interaction of the analyte with the substrate. The effect is based on the strong optical interference occurring at the interface between the inkjet printed sol-gel titania film (a layer with high refractive index) and the adsorbed nano-sized objects (layer with low refractive index), which can be detected even with the naked eye. Herein, we have developed a synthetic strategy for the inkjet printing of interference sensors with controllable color change through thickness adjustment.
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Affiliation(s)
- Anna Frosiniuk
- ITMO University, International Laboratory "Solution Chemistry of Advanced Materials and Technologies", Lomonosova 9, 191002, Saint Petersburg, Russia.
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100
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Engineering of receptor-binding proteins in bacteriophages and phage tail-like bacteriocins. Biochem Soc Trans 2019; 47:449-460. [PMID: 30783013 DOI: 10.1042/bst20180172] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/21/2019] [Accepted: 01/28/2019] [Indexed: 12/23/2022]
Abstract
Bacteriophages and phage tail-like bacteriocins (PTLBs) rely on receptor-binding proteins (RBPs) located in tail fibers or spikes for an initial and specific interaction with susceptible bacteria. Bacteriophages kill bacteria through a lytic, replicative cycle, whereas PTLBs kill the target through membrane depolarization in a single hit mechanism. Extensive efforts in the engineering of RBPs of both phages and PTLBs have been undertaken to obtain a greater understanding of the structural organization of RBPs. In addition, a major goal of engineering RBPs of phages and PTLBs is the production of antibacterials with a customized spectrum. Swapping of the RBP of phages and PTLBs results in a shift in activity spectrum in accordance with the spectrum of the new RBP. The engineering of strictly virulent phages with new RBPs required significant technical advances in the past decades, whereas the engineering of RBPs of PTLBs relied on the traditional molecular techniques used for the manipulation of bacteria and was thus relatively straightforward. While phages and PTLBs share their potential for specificity tuning, specific features of phages such as their lytic killing mechanism, their self-replicative nature and thus different pharmacokinetics and their potential to co-evolve are clear differentiators compared with PTLBs in terms of their antibacterial use.
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