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Zheng K, Liang Y, Paez-Espino D, Zou X, Gao C, Shao H, Sung YY, Mok WJ, Wong LL, Zhang YZ, Tian J, Chen F, Jiao N, Suttle CA, He J, McMinn A, Wang M. Identification of hidden N4-like viruses and their interactions with hosts. mSystems 2023; 8:e0019723. [PMID: 37702511 PMCID: PMC10654107 DOI: 10.1128/msystems.00197-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 07/19/2023] [Indexed: 09/14/2023] Open
Abstract
IMPORTANCE The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.
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Affiliation(s)
- Kaiyang Zheng
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yantao Liang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - David Paez-Espino
- DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, California, USA
- Mammoth Biosciences Inc., South San Francisco, California, USA
| | - Xiao Zou
- Qingdao Central Hospital, Qingdao, China
| | - Chen Gao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Hongbing Shao
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
| | - Yeong Yik Sung
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Wen Jye Mok
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Li Lian Wong
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu (UMT), Kuala Terengganu, Malaysia
| | - Yu-Zhong Zhang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- State Key Laboratory of Microbial Technology, Marine Biotechnology Research Center, Shandong University, Qingdao, China
| | - Jiwei Tian
- Key Laboratory of Physical Oceanography, Ministry of Education, Ocean University of China, Qingdao, China
| | - Feng Chen
- Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, Maryland, USA
| | - Nianzhi Jiao
- State Key Laboratory of Marine Environmental Sciences, Institute of Marine Microbes and Ecospheres, Xiamen University, Xiamen, China
| | - Curtis A. Suttle
- Department of Earth, Ocean and Atmospheric Sciences, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Microbiology and Immunology, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
- Department of Botany, Institute for the Oceans and Fisheries, The University of British Columbia, Vancouver, British Columbia, Canada
| | - Jianfeng He
- SOA Key Laboratory for Polar Science, Polar Research Institute of China, Shanghai, China
| | - Andrew McMinn
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Min Wang
- Key Laboratory of Polar Oceanography and Global Ocean Change, Frontiers Science Center for Deep Ocean Multispheres and Earth System, College of Marine Life Sciences, Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao, China
- UMT-OUC Joint Centre for Marine Studies, Qingdao, China
- The Affiliated Hospital of Qingdao University, Qingdao, China
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Bulssico J, PapukashvilI I, Espinosa L, Gandon S, Ansaldi M. Phage-antibiotic synergy: Cell filamentation is a key driver of successful phage predation. PLoS Pathog 2023; 19:e1011602. [PMID: 37703280 PMCID: PMC10519598 DOI: 10.1371/journal.ppat.1011602] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Revised: 09/25/2023] [Accepted: 08/07/2023] [Indexed: 09/15/2023] Open
Abstract
Phages are promising tools to fight antibiotic-resistant bacteria, and as for now, phage therapy is essentially performed in combination with antibiotics. Interestingly, combined treatments including phages and a wide range of antibiotics lead to an increased bacterial killing, a phenomenon called phage-antibiotic synergy (PAS), suggesting that antibiotic-induced changes in bacterial physiology alter the dynamics of phage propagation. Using single-phage and single-cell techniques, each step of the lytic cycle of phage HK620 was studied in E. coli cultures treated with either ceftazidime, cephalexin or ciprofloxacin, three filamentation-inducing antibiotics. In the presence of sublethal doses of antibiotics, multiple stress tolerance and DNA repair pathways are triggered following activation of the SOS response. One of the most notable effects is the inhibition of bacterial division. As a result, a significant fraction of cells forms filaments that stop dividing but have higher rates of mutagenesis. Antibiotic-induced filaments become easy targets for phages due to their enlarged surface areas, as demonstrated by fluorescence microscopy and flow cytometry techniques. Adsorption, infection and lysis occur more often in filamentous cells compared to regular-sized bacteria. In addition, the reduction in bacterial numbers caused by impaired cell division may account for the faster elimination of bacteria during PAS. We developed a mathematical model to capture the interaction between sublethal doses of antibiotics and exposition to phages. This model shows that the induction of filamentation by sublethal doses of antibiotics can amplify the replication of phages and therefore yield PAS. We also use this model to study the consequences of PAS on the emergence of antibiotic resistance. A significant percentage of hyper-mutagenic filamentous bacteria are effectively killed by phages due to their increased susceptibility to infection. As a result, the addition of even a very low number of bacteriophages produced a strong reduction of the mutagenesis rate of the entire bacterial population. We confirm this prediction experimentally using reporters for bacterial DNA repair. Our work highlights the multiple benefits associated with the combination of sublethal doses of antibiotics with bacteriophages.
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Affiliation(s)
- Julián Bulssico
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Irina PapukashvilI
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
- Faculty of Exact and Natural Sciences, Ivane Javakhishvili Tbilisi State University, Tbilisi, Georgia
| | - Leon Espinosa
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
| | - Sylvain Gandon
- CEFE, CNRS, Univ Montpellier, EPHE, IRD, Montpellier, France
| | - Mireille Ansaldi
- Laboratoire de Chimie Bactérienne, UMR7283, Centre National de la Recherche Scientifique, Aix-Marseille Université, Marseille, France
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Sultan-Alolama MI, Amin A, Vijayan R, El-Tarabily KA. Isolation, Characterization, and Comparative Genomic Analysis of Bacteriophage Ec_MI-02 from Pigeon Feces Infecting Escherichia coli O157:H7. Int J Mol Sci 2023; 24:ijms24119506. [PMID: 37298457 DOI: 10.3390/ijms24119506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 05/23/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
The most significant serotype of Shiga-toxigenic Escherichia coli that causes foodborne illnesses is Escherichia coli O157:H7. Elimination of E. coli O157:H7 during food processing and storage is a possible solution. Bacteriophages have a significant impact on bacterial populations in nature due to their ability to lyse their bacterial host. In the current study, a virulent bacteriophage, Ec_MI-02, was isolated from the feces of a wild pigeon in the United Arab Emirates (UAE) for potential future use as a bio-preservative or in phage therapy. Using a spot test and an efficiency of plating analysis, Ec_MI-02 was found to infect in addition to the propagation host, E. coli O157:H7 NCTC 12900, five different serotypes of E. coli O157:H7 (three clinical samples from infected patients, one from contaminated green salad, and one from contaminated ground beef). Based on morphology and genome analysis, Ec_MI-02 belongs to the genus Tequatrovirus under the order Caudovirales. The adsorption rate constant (K) of Ec_MI-02 was found to be 1.55 × 10-8 mL/min. The latent period was 50 min with a burst size of almost 10 plaque forming units (pfu)/host cell in the one-step growth curve when the phage Ec_MI-02 was cultivated using the propagation host E. coli O157:H7 NCTC 12900. Ec_MI-02 was found to be stable at a wide range of pH, temperature, and commonly used laboratory disinfectants. Its genome is 165,454 bp long with a GC content of 35.5% and encodes 266 protein coding genes. Ec_MI-02 has genes encoding for rI, rII, and rIII lysis inhibition proteins, which supports the observation of delayed lysis in the one-step growth curve. The current study provides additional evidence that wild birds could also be a good natural reservoir for bacteriophages that do not carry antibiotic resistance genes and could be good candidates for phage therapy. In addition, studying the genetic makeup of bacteriophages that infect human pathogens is crucial for ensuring their safe usage in the food industry.
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Affiliation(s)
- Mohamad Ismail Sultan-Alolama
- Zayed Complex for Herbal Research and Traditional Medicine, Research and Innovation Center, Department of Health, Abu Dhabi 5674, United Arab Emirates
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Amr Amin
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
| | - Ranjit Vijayan
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- The Big Data Analytics Center, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Al Ain P.O. Box 17666, United Arab Emirates
| | - Khaled A El-Tarabily
- Department of Biology, College of Science, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Khalifa Center for Genetic Engineering and Biotechnology, United Arab Emirates University, Al Ain P.O. Box 15551, United Arab Emirates
- Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
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Kamyab H, Torkashvand N, Shahverdi AR, Khoshayand MR, Sharifzadeh M, Sepehrizadeh Z. Isolation, characterization, and genomic analysis of vB_PaeS_TUMS_P81, a lytic bacteriophage against Pseudomonas aeruginosa. Virus Genes 2023; 59:132-41. [PMID: 36357763 DOI: 10.1007/s11262-022-01954-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2022] [Accepted: 10/30/2022] [Indexed: 11/12/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that can lead to nosocomial infections which are in turn life threatening. The increase in antibiotic resistance, at an alarming rate, has resulted in a pressing need for alternative therapeutic approaches such as phage therapy, which hold promise according to several studies. This study featured the isolation and characterization of vB_PaeS_TUMS_P81, a new lytic Pseudomonas phage. The whole-genome sequencing indicated that it has a genome of 73,167 bp containing 93 predicted coding sequences. Genes involved in virulence or lysogeny pathway were nowhere to be found in the genome, so it is potentially safe when it comes to therapeutic applications. Genomic and phylogenetic analysis indicated that vB_PaeS_TUMS_P81 is a member of the genus Litunavirus, belonging to Schitoviridae family. The present study lays the groundwork for further research on treatment of P. aeruginosa infections.
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Kamyab H, Torkashvand N, Shahverdi AR, Khoshayand MR, Sharifzadeh M, Sepehrizadeh Z. Isolation, characterization, and genomic analysis of vB_PaeP_TUMS_P121, a new lytic bacteriophage infecting Pseudomonas aeruginosa. Arch Virol 2022; 168:8. [PMID: 36565337 DOI: 10.1007/s00705-022-05692-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 11/28/2022] [Indexed: 12/25/2022]
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that can cause life-threatening nosocomial infections. The alarming increase in antibiotic resistance has led to an urgent need for alternative therapeutic approaches, such as phage therapy, which has shown promising results in many studies. In this study, P121, a new lytic Pseudomonas phage, was isolated and characterized. Whole-genome sequencing showed that it has a genome of 73,001 bp that contains 91 predicted coding sequences. No genes involved in virulence or lysogeny were found in the genome, thus making it potentially safe for therapeutic applications. Genomic and phylogenetic analysis indicated that P121 is a member of the genus Litunavirus, family Schitoviridae. The present study provides some basic information for further research on treatment of P. aeruginosa infections.
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Affiliation(s)
- Haniyeh Kamyab
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Narges Torkashvand
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Ahmad Reza Shahverdi
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Khoshayand
- Department of Food and Drug Control, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Mohammad Sharifzadeh
- Department of Pharmacology and Toxicology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran
| | - Zargham Sepehrizadeh
- Department of Pharmaceutical Biotechnology and Biotechnology Research Center, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, Iran.
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Lin LC, Tsai YC. Isolation and characterization of a Vibrio owensii phage phi50-12. Sci Rep 2022; 12:16390. [PMID: 36180722 PMCID: PMC9525291 DOI: 10.1038/s41598-022-20831-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Accepted: 09/19/2022] [Indexed: 11/09/2022] Open
Abstract
Vibrio owensii is a widely distributed marine vibrio species that causes acute hepatopancreatic necrosis in the larvae of Panulirus ornatus and Penaeus vannamei, and is also associated with Montipora white syndrome in corals. We characterized V. owensii GRA50-12 as a potent pathogen using phenotypic, biochemical, and zebrafish models. A virulent phage, vB_VowP_phi50-12 (phi50-12), belonging to the N4-like Podoviridae, was isolated from the same habitat as that of V. owensii GRA50-12 and characterized. This phage possesses a unique sequence with no similar hits in the public databases and has a short latent time (30 min), a large burst size (106 PFU/infected cell), and a wide range of pH and temperature stabilities. Moreover, phi50-12 also demonstrated a strong lysis ability against V. owensii GRA50-12. SDS-PAGE revealed at least nine structural proteins, four of which were confirmed using LC–MS/MS analysis. The size of the phi50-12 genome was 68,059 bp, with 38.5% G + C content. A total of 101 ORFs were annotated, with 17 ORFs having closely related counterparts in the N4-like vibrio phage. Genomic sequencing confirmed the absence of antibiotic resistance genes or virulence factors. Comparative studies have shown that phi50-12 has a unique genomic arrangement, except for the well-conserved core regions of the N4-like phages. Phylogenetic analysis demonstrated that it belonged to a group of smaller genomes of N4-like vibrio phages. The therapeutic effect in the zebrafish model suggests that phi50-12 could be a potential candidate for application in the treatment of V. owensii infection or as a biocontrol agent. However, further research must be carried out to confirm the efficacy of phage50-12.
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Affiliation(s)
- Ling-Chun Lin
- Masters Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien, 97004, Taiwan.
| | - Yu-Chuan Tsai
- Masters Program in Biomedical Sciences, School of Medicine, Tzu Chi University, No. 701, Sec. 3, Zhongyang Rd., Hualien, 97004, Taiwan
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Farquharson EL, Nugen SR. Enterobacteria Phage Ac3's Genome Annotation and Host Range Analysis Against the ECOR Reference Library. Phage (New Rochelle) 2022; 3:165-170. [PMID: 36199530 PMCID: PMC9527048 DOI: 10.1089/phage.2022.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Host range analyses and genome sequencing/annotation of bacteriophage isolates allow more effective development of tools for applications in medicine, agriculture, and the environment and expand our understanding of phage biology. Here we present the complete sequence of phage Ac3's assembled and annotated genome (accession OK040907). Originally referred to simply as "3," Ac3 has previously been described as a T4-like bacteriophage belonging to the Myoviridae family in the Caudovirales order of tailed bacteriophages. Using a combination of spot tests and full plate plaque assays, Ac3's permissive and adsorptive host range were evaluated against the ECOR Reference Library; a panel of 72 Escherichia coli isolates meant to represent the diversity of E. coli. Spot assays revealed that Ac3 could adsorb to 43 of the 72 strains (59.7%), whereas plaque assays demonstrated Ac3's ability to complete replication within 27 of the 72 strains (37.5%). By overlaying spot test and plaque assay results, 16 of the 45 nonpermissive ECOR strains (35.5%) were highlighted as being able to support Ac3's adsorption and tail contraction, but not its replication. Further characterization of Ac3 is still needed, however, the study presented here provides a solid starting point for future research.
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Affiliation(s)
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, New York, USA
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Juškauskas A, Zajančkauskaitė A, Meškys R, Ger M, Kaupinis A, Valius M, Truncaitė L. Interaction between Phage T4 Protein RIII and Host Ribosomal Protein S1 Inhibits Endoribonuclease RegB Activation. Int J Mol Sci 2022; 23:9483. [PMID: 36012768 DOI: 10.3390/ijms23169483] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/16/2022] [Accepted: 08/20/2022] [Indexed: 11/17/2022] Open
Abstract
Lytic viruses of bacteria (bacteriophages, phages) are intracellular parasites that take over hosts' biosynthetic processes for their propagation. Most of the knowledge on the host hijacking mechanisms has come from the studies of the lytic phage T4, which infects Escherichia coli. The integrity of T4 development is achieved by strict control over the host and phage processes and by adjusting them to the changing infection conditions. In this study, using in vitro and in vivo biochemical methods, we detected the direct interaction between the T4 protein RIII and ribosomal protein S1 of the host. Protein RIII is known as a cytoplasmic antiholin, which plays a role in the lysis inhibition function of T4. However, our results show that RIII also acts as a viral effector protein mainly targeting S1 RNA-binding domains that are central for all the activities of this multifunctional protein. We confirm that the S1-RIII interaction prevents the S1-dependent activation of endoribonuclease RegB. In addition, we propose that by modulating the multiple processes mediated by S1, RIII could act as a regulator of all stages of T4 infection including the lysis inhibition state.
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El-Sayed D, Elsayed T, Amin N, Al-Shahaby A, Goda H. Evaluating the Phenotypic and Genomic Characterization of Some Egyptian Phages Infecting Shiga Toxin-Producing Escherichia coli O157:H7 for the Prospective Application in Food Bio-Preservation. Biology 2022; 11:biology11081180. [PMID: 36009807 PMCID: PMC9404725 DOI: 10.3390/biology11081180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 07/21/2022] [Accepted: 08/01/2022] [Indexed: 11/16/2022]
Abstract
Simple Summary Shiga toxin-producing Escherichia coli (STEC) represents a hazardous health problem because it causes various human gastrointestinal tract diseases, for example, bloody diarrhea and hemorrhagic colitis. The major concern of STEC O157:H7 resulted from its biological characteristics, including low infective dose, ability to express different virulence factors and multidrug resistance of some species. Principally, the human outbreaks of STEC O157:H7 are associated with consumption of undercooked or contaminated bovine dairy and meat products. Treatments of E. coli infections have been increasingly complicated as a result of the development of antibiotic resistance. For this reason, as well as the increasing consumer demand for safe food products, it has become important to apply alternative effective and eco-friendly approaches, such as using lytic phages, to control the growth of pathogenic bacteria in food. This study focused on evaluating the applicability of locally isolated lytic phages specific to Shiga toxin-producing Escherichia coli O157:H7 as prospective biocontrol agents in food. Our findings presented two phages with promising biological and genomic characteristics to be applied in food bio-preservation. Abstract Shiga toxin-producing E. coli (STEC) is considered a worldwide public health and food safety problem. Despite the implementation of various different approaches to control food safety, outbreaks persist. The aim of study is to evaluate the applicability of phages, isolated against STEC O157:H7, as prospective food bio-preservatives. Considering the relatively wide host range and greatest protein diversity, two phages (STEC P2 and P4) from four were furtherly characterized. Complete genome analysis confirmed the absence of toxins and virulence factors—encoding genes. The results confirmed the close relation of STEC P2 to phages of Myoviridae, and STEC P4 to the Podoviridae family. The phages retained higher lytic competence of 90.4 and 92.68% for STEC P2 and P4, respectively with the HTST pasteurization. The strong acidic (pH 1) and alkaline (pH 13) conditions had influential effect on the surviving counts of the two phages. The lowest survivability of 63.37 and 86.36% in STEC P2 and P4 lysate, respectively appeared in 2% bile salt solution after 3 h. The results confirmed the strong effect of simulated gastric fluid (SGF) on the survivability of the two phages comparing with simulated intestinal fluid (SIF). Therefore, the two phages could be applied as a natural alternative for food preservation.
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Carmody CM, Farquharson EL, Nugen SR. Enterobacteria Phage SV76 Host Range and Genomic Characterization. Phage (New Rochelle) 2022; 3:59-63. [PMID: 35495085 PMCID: PMC9041521 DOI: 10.1089/phage.2022.0005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Background Increasing the quantity and detail of bacteriophage genomic data is critical to broadening our understanding of how bacteriophages operate to allow us to harness their unique properties for biotechnology advancements. Here we present the complete sequence of phage SV76's assembled and annotated genome (Accession OM339528). SV76 has previously been classified as a T4-like bacteriophage belonging to the Tequatrovirus genus within the Myoviridae family of contractile tailed bacteriophages. Materials and Methods Whole genome sequencing, assembly, and annotation was performed on SV76. Double-agar spot assays were utilized to determine SV76's host range against a panel of 72 Escherichia coli isolates meant to represent the diversity of E. coli, as well as a series of knockouts designed to identify required receptor binding proteins. The genome and host range were compared to the closely related phage, T2. Results Spot assays revealed that SV76 could plaque on 10 of the 72 strains (13.9 %) and nine of the nine E. coli K12 single gene knockout of known phage receptors (100%). SV76 did not plate on a ΔfadL E. coli indicating suggesting a requirement as a receptor binding protein. Conclusions SV76 is closely related to T2 with similar host ranges within ECOR. This study presents novel host range and genomic data on SV76 phage, providing a foundation for future studies to further characterize SV76 to understand more about SV76 and other T4-like phages that can be applied to create novel biotechnologies.
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Affiliation(s)
| | | | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, New York, USA.,Address correspondence to: Sam R. Nugen, PhD, Department of Food Science, Cornell University, 411 Tower Road, Ithaca, NY 14853, USA
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Saheb Kashaf S, Proctor DM, Deming C, Saary P, Hölzer M, Taylor ME, Kong HH, Segre JA, Almeida A, Finn RD. Integrating cultivation and metagenomics for a multi-kingdom view of skin microbiome diversity and functions. Nat Microbiol 2022; 7:169-179. [PMID: 34952941 PMCID: PMC8732310 DOI: 10.1038/s41564-021-01011-w] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 10/28/2021] [Indexed: 12/23/2022]
Abstract
Human skin functions as a physical barrier to foreign pathogen invasion and houses numerous commensals. Shifts in the human skin microbiome have been associated with conditions ranging from acne to atopic dermatitis. Previous metagenomic investigations into the role of the skin microbiome in health or disease have found that much of the sequenced data do not match reference genomes, making it difficult to interpret metagenomic datasets. We combined bacterial cultivation and metagenomic sequencing to assemble the Skin Microbial Genome Collection (SMGC), which comprises 622 prokaryotic species derived from 7,535 metagenome-assembled genomes and 251 isolate genomes. The metagenomic datasets that we generated were combined with publicly available skin metagenomic datasets to identify members and functions of the human skin microbiome. The SMGC collection includes 174 newly identified bacterial species and 12 newly identified bacterial genera, including the abundant genus 'Candidatus Pellibacterium', which has been newly associated with the skin. The SMGC increases the characterized set of known skin bacteria by 26%. We validated the SMGC metagenome-assembled genomes by comparing them with sequenced isolates obtained from the same samples. We also recovered 12 eukaryotic species and assembled thousands of viral sequences, including newly identified clades of jumbo phages. The SMGC enables classification of a median of 85% of skin metagenomic sequences and provides a comprehensive view of skin microbiome diversity, derived primarily from samples obtained in North America.
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Affiliation(s)
- Sara Saheb Kashaf
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Diana M Proctor
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Clay Deming
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Paul Saary
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
| | - Martin Hölzer
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK
- Methodology and Research Infrastructure, MF1 Bioinformatics, Robert Koch Institute, Berlin, Germany
| | - Monica E Taylor
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Heidi H Kong
- Dermatology Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julia A Segre
- Microbial Genomics Section, Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Alexandre Almeida
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.
| | - Robert D Finn
- European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton, UK.
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12
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Barron-Montenegro R, García R, Dueñas F, Rivera D, Opazo-Capurro A, Erickson S, Moreno-Switt AI. Comparative Analysis of Felixounavirus Genomes Including Two New Members of the Genus That Infect Salmonella Infantis. Antibiotics (Basel) 2021; 10:806. [PMID: 34356727 PMCID: PMC8300805 DOI: 10.3390/antibiotics10070806] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Revised: 06/28/2021] [Accepted: 06/29/2021] [Indexed: 11/16/2022] Open
Abstract
Salmonella spp. is one of the most common foodborne pathogens worldwide; therefore, its control is highly relevant for the food industry. Phages of the Felixounavirus genus have the characteristic that one phage can infect a large number of different Salmonella serovars and, thus, are proposed as an alternative to antimicrobials in food production. Here, we describe two new members of the Felixounavirus genus named vB_Si_35FD and vB_Si_DR94, which can infect Salmonella Infantis. These new members were isolated and sequenced, and a subsequent comparative genomic analysis was conducted including 23 publicly available genomes of Felixounaviruses that infect Salmonella. The genomes of vB_Si_35FD and vB_Si_DR94 are 85,818 and 85,730 bp large and contain 129 and 125 coding sequences, respectively. The genomes did not show genes associated with virulence or antimicrobial resistance, which could be useful for candidates to use as biocontrol agents. Comparative genomics revealed that closely related Felixounavirus are found in distinct geographical locations and that this genus has a conserved genomic structure despite its worldwide distribution. Our study revealed a highly conserved structure of the phage genomes, and the two newly described phages could represent promising biocontrol candidates against Salmonella spp. from a genomic viewpoint.
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Affiliation(s)
- Rocío Barron-Montenegro
- Laboratorio de Investigación en Agentes Antimicrobianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile; (R.B.-M.); (A.O.-C.)
- Escuela de Medicina Veterinaria, Facultad de Agronomía e Ingeniería Forestal, Facultad de Ciencias Biológicas, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago 7550000, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Lo Barnechea, Santiago 7690000, Chile;
| | - Rodrigo García
- Laboratorio de Microbiología, Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso 2340000, Chile;
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Fernando Dueñas
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8320000, Chile;
| | - Dácil Rivera
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Lo Barnechea, Santiago 7690000, Chile;
- Escuela de Medicina Veterinaria, Facultad de Ciencias de la Vida, Universidad Andres Bello, Santiago 8320000, Chile;
| | - Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antimicrobianos, Departamento de Microbiología, Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción 4030000, Chile; (R.B.-M.); (A.O.-C.)
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Lo Barnechea, Santiago 7690000, Chile;
| | - Stephen Erickson
- Laboratory Corporation of America Holdings, New Brighton, MN 55112, USA;
| | - 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 7550000, Chile
- Millennium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Lo Barnechea, Santiago 7690000, Chile;
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13
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Wong S, Alattas H, Slavcev RA. A snapshot of the λ T4rII exclusion (Rex) phenotype in Escherichia coli. Curr Genet 2021; 67:739-745. [PMID: 33877398 DOI: 10.1007/s00294-021-01183-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/20/2021] [Accepted: 03/25/2021] [Indexed: 10/21/2022]
Abstract
The lambda (λ) T4rII exclusion (Rex) phenotype is defined as the inability of T4rII to propagate in Escherichia coli lysogenized by bacteriophage λ. The Rex system requires the presence of two lambda immunity genes, rexA and rexB, to exclude T4 (rIIA-rIIB) from plating on a lawn of E. coli λ lysogens. The onset of the Rex phenotype by T4rII infection imparts a harsh cellular environment that prevents T4rII superinfection while killing the majority of the cell population. Since the discovery of this powerful exclusion system in 1955 by Seymour Benzer, few mechanistic models have been proposed to explain the process of Rex activation and the physiological manifestations associated with Rex onset. For the first time, key host proteins have recently been linked to Rex, including σE, σS, TolA, and other membrane proteins. Together with the known Rex system components, the RII proteins of bacteriophage T4 and the Rex proteins from bacteriophage λ, we are closer than ever to solving the mystery that has eluded investigators for over six decades. Here, we review the fundamental Rex components in light of this new knowledge.
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Affiliation(s)
- Shirley Wong
- School of Pharmacy, University of Waterloo, ON, N2L 3G1, Canada
| | - Hibah Alattas
- School of Pharmacy, University of Waterloo, ON, N2L 3G1, Canada.
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14
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Grabowski Ł, Łepek K, Stasiłojć M, Kosznik-Kwaśnicka K, Zdrojewska K, Maciąg-Dorszyńska M, Węgrzyn G, Węgrzyn A. Bacteriophage-encoded enzymes destroying bacterial cell membranes and walls, and their potential use as antimicrobial agents. Microbiol Res 2021; 248:126746. [PMID: 33773329 DOI: 10.1016/j.micres.2021.126746] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 03/06/2021] [Accepted: 03/08/2021] [Indexed: 01/22/2023]
Abstract
Appearance of pathogenic bacteria resistant to most, if not all, known antibiotics is currently one of the most significant medical problems. Therefore, development of novel antibacterial therapies is crucial for efficient treatment of bacterial infections in the near future. One possible option is to employ enzymes, encoded by bacteriophages, which cause destruction of bacterial cell membranes and walls. Bacteriophages use such enzymes to destroy bacterial host cells at the final stage of their lytic development, in order to ensure effective liberation of progeny virions. Nevertheless, to use such bacteriophage-encoded proteins in medicine and/or biotechnology, it is crucial to understand details of their biological functions and biochemical properties. Therefore, in this review article, we will present and discuss our current knowledge on the processes of bacteriophage-mediated bacterial cell lysis, with special emphasis on enzymes involved in them. Regulation of timing of the lysis is also discussed. Finally, possibilities of the practical use of these enzymes as antibacterial agents will be underlined and perspectives of this aspect will be presented.
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Affiliation(s)
- Łukasz Grabowski
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Krzysztof Łepek
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Małgorzata Stasiłojć
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Katarzyna Kosznik-Kwaśnicka
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Karolina Zdrojewska
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Monika Maciąg-Dorszyńska
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdansk, Wita Stwosza 59, 80-308, Gdansk, Poland.
| | - Alicja Węgrzyn
- Laboratory of Phage Therapy, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822, Gdansk, Poland.
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15
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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: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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16
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Wittmann J, Turner D, Millard AD, Mahadevan P, Kropinski AM, Adriaenssens EM. From Orphan Phage to a Proposed New Family-the Diversity of N4-Like Viruses. Antibiotics (Basel) 2020; 9:E663. [PMID: 33008130 PMCID: PMC7650795 DOI: 10.3390/antibiotics9100663] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/28/2020] [Accepted: 09/29/2020] [Indexed: 01/29/2023] Open
Abstract
Escherichia phage N4 was isolated in 1966 in Italy and has remained a genomic orphan for a long time. It encodes an extremely large virion-associated RNA polymerase unique for bacterial viruses that became characteristic for this group. In recent years, due to new and relatively inexpensive sequencing techniques the number of publicly available phage genome sequences expanded rapidly. This revealed new members of the N4-like phage group, from 33 members in 2015 to 115 N4-like viruses in 2020. Using new technologies and methods for classification, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV) has moved the classification and taxonomy of bacterial viruses from mere morphological approaches to genomic and proteomic methods. The analysis of 115 N4-like genomes resulted in a huge reassessment of this group and the proposal of a new family "Schitoviridae", including eight subfamilies and numerous new genera.
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Affiliation(s)
- Johannes Wittmann
- Leibniz Institute DSMZ–German Collection of Microorganisms and Cell Cultures, 38124 Braunschweig, Germany
| | - Dann Turner
- Department of Applied Sciences, University of the West of England, Bristol BS16 1QY, UK;
| | - Andrew D. Millard
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH UK;
| | | | - Andrew M. Kropinski
- Department of Food Science, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Department of Pathobiology, University of Guelph, Guelph, ON N1G 2W1, Canada
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17
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Buttimer C, Lynch C, Hendrix H, Neve H, Noben JP, Lavigne R, Coffey A. Isolation and Characterization of Pectobacterium Phage vB_PatM_CB7: New Insights into the Genus Certrevirus. Antibiotics (Basel) 2020; 9:E352. [PMID: 32575906 PMCID: PMC7344957 DOI: 10.3390/antibiotics9060352] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/18/2020] [Accepted: 06/19/2020] [Indexed: 12/20/2022] Open
Abstract
To date, Certrevirus is one of two genera of bacteriophage (phage), with phages infecting Pectobacterium atrosepticum, an economically important phytopathogen that causes potato blackleg and soft rot disease. This study provides a detailed description of Pectobacterium phage CB7 (vB_PatM_CB7), which specifically infects P. atrosepticum. Host range, morphology, latent period, burst size and stability at different conditions of temperature and pH were examined. Analysis of its genome (142.8 kbp) shows that the phage forms a new species of Certrevirus, sharing sequence similarity with other members, highlighting conservation within the genus. Conserved elements include a putative early promoter like that of the Escherichia coli sigma70 promoter, which was found to be shared with other genus members. A number of dissimilarities were observed, relating to DNA methylation and nucleotide metabolism. Some members do not have homologues of a cytosine methylase and anaerobic nucleotide reductase subunits NrdD and NrdG, respectively. Furthermore, the genome of CB7 contains one of the largest numbers of homing endonucleases described in a single phage genome in the literature to date, with a total of 23 belonging to the HNH and LAGLIDADG families. Analysis by RT-PCR of the HNH homing endonuclease residing within introns of genes for the large terminase, DNA polymerase, ribonucleotide reductase subunits NrdA and NrdB show that they are splicing competent. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was also performed on the virion of CB7, allowing the identification of 26 structural proteins-20 of which were found to be shared with the type phages of the genera of Vequintavirus and Seunavirus. The results of this study provide greater insights into the phages of the Certrevirus genus as well as the subfamily Vequintavirinae.
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Affiliation(s)
- Colin Buttimer
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
| | - Caoimhe Lynch
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
| | - Hanne Hendrix
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Horst Neve
- Department of Microbiology and Biotechnology, Max Rubner-Institut, 24103 Kiel, Germany;
| | - Jean-Paul Noben
- Biomedical Research Institute and Transnational University Limburg, Hasselt University, 3590 Hasselt, Belgium;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Leuven, Belgium; (H.H.); (R.L.)
| | - Aidan Coffey
- Department of Biological Sciences, Cork Institute of Technology, T12 P928 Cork, Ireland; (C.B.); (C.L.)
- APC Microbiome Institute, University College, T12 YT20 Cork, Ireland
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18
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Krieger IV, Kuznetsov V, Chang JY, Zhang J, Moussa SH, Young RF, Sacchettini JC. The Structural Basis of T4 Phage Lysis Control: DNA as the Signal for Lysis Inhibition. J Mol Biol 2020; 432:4623-4636. [PMID: 32562709 DOI: 10.1016/j.jmb.2020.06.013] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 06/10/2020] [Accepted: 06/12/2020] [Indexed: 02/05/2023]
Abstract
Optimal phage propagation depends on the regulation of the lysis of the infected host cell. In T4 phage infection, lysis occurs when the holin protein (T) forms lesions in the host membrane. However, the lethal function of T can be blocked by an antiholin (RI) during lysis inhibition (LIN). LIN sets if the infected cell undergoes superinfection, then the lysis is delayed until host/phage ratio becomes more favorable for the release of progeny. It has been thought that a signal derived from the superinfection is required to activate RI. Here we report structures that suggest a radically different model in which RI binds to T irrespective of superinfection, causing it to accumulate in a membrane as heterotetrameric 2RI-2T complex. Moreover, we show the complex binds non-specifically to DNA, suggesting that the gDNA from the superinfecting phage serves as the LIN signal and that stabilization of the complex by DNA binding is what defines LIN. Finally, we show that soluble domain of free RI crystallizes in a domain-swapped homotetramer, which likely works as a sink for RI molecules released from the RI-T complex to ensure efficient lysis. These results constitute the first structural basis and a new model not only for the historic LIN phenomenon but also for the temporal regulation of phage lysis in general.
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Affiliation(s)
- Inna V Krieger
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Vladimir Kuznetsov
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Jeng-Yih Chang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Department of Biochemistry and Biophysics
| | - Junjie Zhang
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Department of Biochemistry and Biophysics
| | - Samir H Moussa
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Department of Biochemistry and Biophysics
| | - Ryland F Young
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Department of Biochemistry and Biophysics
| | - James C Sacchettini
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA.
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19
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Hays SG, Seed KD. Dominant Vibrio cholerae phage exhibits lysis inhibition sensitive to disruption by a defensive phage satellite. eLife 2020; 9:e53200. [PMID: 32329714 PMCID: PMC7182436 DOI: 10.7554/elife.53200] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 04/01/2020] [Indexed: 12/28/2022] Open
Abstract
Bacteria, bacteriophages that prey upon them, and mobile genetic elements (MGEs) compete in dynamic environments, evolving strategies to sense the milieu. The first discovered environmental sensing by phages, lysis inhibition, has only been characterized and studied in the limited context of T-even coliphages. Here, we discover lysis inhibition in the etiological agent of the diarrheal disease cholera, Vibrio cholerae, infected by ICP1, a phage ubiquitous in clinical samples. This work identifies the ICP1-encoded holin, teaA, and antiholin, arrA, that mediate lysis inhibition. Further, we show that an MGE, the defensive phage satellite PLE, collapses lysis inhibition. Through lysis inhibition disruption a conserved PLE protein, LidI, is sufficient to limit the phage produced from infection, bottlenecking ICP1. These studies link a novel incarnation of the classic lysis inhibition phenomenon with conserved defensive function of a phage satellite in a disease context, highlighting the importance of lysis timing during infection and parasitization.
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Affiliation(s)
- Stephanie G Hays
- Department of Plant and Microbial Biology, University of CaliforniaBerkeleyUnited States
| | - Kimberley D Seed
- Department of Plant and Microbial Biology, University of CaliforniaBerkeleyUnited States
- Chan Zuckerberg BiohubSan FranciscoUnited States
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20
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Yuan Y, Xi H, Dai J, Zhong Y, Lu S, Wang T, Yang L, Guan Y, Wang P. The characteristics and genome analysis of the novel Y. pestis phage JC221. Virus Res 2020; 283:197982. [PMID: 32315702 DOI: 10.1016/j.virusres.2020.197982] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 10/24/2022]
Abstract
The pathogen of plague is Yersinia pestis (Y. pestis), one of the deadliest pathogens in the world and belonging to the family Enterobacteriaceae. In this work, the biological characteristics and complete genome sequence analysis of a novel lytic Y. pestis-specific phage JC221 isolated from Yunnan Province, China, was studied. JC221 belongs to the Myoviridae family and has a regular icosahedral head and a long contractile tail. The double-stranded DNA genome of JC221 contains 174,931 bp, and the G + C content is 41.23 %. There are 274 predicted genes, of which only 103 hits of genes or gene products are found in database searches, and there are no known virulence-related or antibiotic resistance genes. The genome sequence of JC221 showed <80 % identity to other phages, and evolutionary analysis revealed that bacteriophage JC221 belongs to the Yersinia phage cluster. Furthermore, the bacteriophage could completely lyse most of the tested Y. pestis strains (12/13) at 28 °C and 37 °C, and some Shigella strains could be lysed at 37°C. Morphological and genomic analysis indicated that JC221 is a new Y. pestis phage and a new member of the Tequatrovirus phages. The novel Y. pestis phage JC221 has important reference value for the study of environmental microecology and epidemiology of plague foci.
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Affiliation(s)
- Yue Yuan
- School of Public Health, Kunming Medical University, Kunming, 650106, PR China; Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
| | - Hengyu Xi
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, PR China.
| | - Jiaxin Dai
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, PR China.
| | - Youhong Zhong
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
| | - Shuguang Lu
- Department of Microbiology, School of Basic Medical Sciences, Army Military Medical University, Chongqing, 400030, PR China.
| | - Tianqi Wang
- College of Clinical Medicine, Jilin University, Changchun, 130021, PR China.
| | - Lihua Yang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
| | - Yuan Guan
- Key Laboratory of Zoonosis Research, Ministry of Education, College of Veterinary Medicine, Jilin University, Changchun, 130062, PR China.
| | - Peng Wang
- Yunnan Key Laboratory for Zoonosis Control and Prevention, Yunnan Institute for Endemic Disease Control and Prevention, Dali, 671000, PR China.
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21
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Gao M, Qin Y, Fan H, Zhang X, Li P, Liu H, Pei G, Mi Z, Xu X, Tong Y, Bai C. Characteristics and complete genome sequence of the virulent Vibrio alginolyticus phage VAP7, isolated in Hainan, China. Arch Virol 2020; 165:947-53. [PMID: 32130520 DOI: 10.1007/s00705-020-04535-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2019] [Accepted: 12/27/2019] [Indexed: 02/08/2023]
Abstract
A novel Vibrio alginolyticus phage, VAP7, was isolated from seawater collected from Sanya, Hainan province, China. Whole-genome sequencing analysis revealed that phage VAP7 has a linear, double-stranded DNA genome of 144,685 bp with an average G+C content of 41.9% and a high degree of sequence similarity to Vibrio phage VP-1. Annotation results identified 193 open reading frames and one transfer RNA-encoding gene in the phage genome. The morphology and the results of phylogenetic analysis suggest that VAP7 should be classified as a new member of the family Ackermannviridae. Moreover, phage VAP7 grew over a wide pH (5.0-10.0) and temperature (4-40 °C) range. Host-range experiments revealed that VAP7 could infect 31 Vibrio alginolyticus strains. Thus, VAP7 infecting Vibrio alginolyticus strains represents a potential new candidate for use in phage therapy.
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Cubo MT, Alías-Villegas C, Balsanelli E, Mesa D, de Souza E, Espuny MR. Diversity of Sinorhizobium (Ensifer) meliloti Bacteriophages in the Rhizosphere of Medicago marina: Myoviruses, Filamentous and N4-Like Podovirus. Front Microbiol 2020; 11:22. [PMID: 32038600 PMCID: PMC6992544 DOI: 10.3389/fmicb.2020.00022] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 01/07/2020] [Indexed: 02/02/2023] Open
Abstract
Using different Sinorhizobium meliloti strains as hosts, we isolated eight new virulent phages from the rhizosphere of the coastal legume Medicago marina. Half of the isolated phages showed a very narrow host range while the other half exhibited a wider host range within the strains tested. Electron microscopy studies showed that phages M_ort18, M_sf1.2, and M_sf3.33 belonged to the Myoviridae family with feature long, contractile tails and icosaedral head. Phages I_sf3.21 and I_sf3.10T appeared to have filamentous shape and produced turbid plaques, which is a characteristic of phages from the Inoviridae family. Phage P_ort11 is a member of the Podoviridae, with an icosahedral head and a short tail and was selected for further characterization and genome sequencing. P_ort11 contained linear, double-stranded DNA with a length of 75239 bp and 103 putative open reading frames. BLASTP analysis revealed strong similarities to Escherichia phage N4 and other N4-like phages. This is the first report of filamentous and N4-like phages that infect S. meliloti.
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Affiliation(s)
- María Teresa Cubo
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Cynthia Alías-Villegas
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
| | - Eduardo Balsanelli
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Dany Mesa
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - Emanuel de Souza
- Department of Biochemistry and Molecular Biology, Universidade Federal do Paraná, Curitiba, Brazil
| | - María Rosario Espuny
- Departamento de Microbiología, Facultad de Biología, Universidad de Sevilla, Seville, Spain
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Abedon ST. Look Who's Talking: T-Even Phage Lysis Inhibition, the Granddaddy of Virus-Virus Intercellular Communication Research. Viruses 2019; 11:v11100951. [PMID: 31623057 PMCID: PMC6832632 DOI: 10.3390/v11100951] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 09/15/2019] [Accepted: 09/30/2019] [Indexed: 12/13/2022] Open
Abstract
That communication can occur between virus-infected cells has been appreciated for nearly as long as has virus molecular biology. The original virus communication process specifically was that seen with T-even bacteriophages-phages T2, T4, and T6-resulting in what was labeled as a lysis inhibition. Another proposed virus communication phenomenon, also seen with T-even phages, can be described as a phage-adsorption-induced synchronized lysis-inhibition collapse. Both are mediated by virions that were released from earlier-lysing, phage-infected bacteria. Each may represent ecological responses, in terms of phage lysis timing, to high local densities of phage-infected bacteria, but for lysis inhibition also to locally reduced densities of phage-uninfected bacteria. With lysis inhibition, the outcome is a temporary avoidance of lysis, i.e., a lysis delay, resulting in increased numbers of virions (greater burst size). Synchronized lysis-inhibition collapse, by contrast, is an accelerated lysis which is imposed upon phage-infected bacteria by virions that have been lytically released from other phage-infected bacteria. Here I consider some history of lysis inhibition, its laboratory manifestation, its molecular basis, how it may benefit expressing phages, and its potential ecological role. I discuss as well other, more recently recognized examples of virus-virus intercellular communication.
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Affiliation(s)
- Stephen T Abedon
- Department of Microbiology, The Ohio State University, Mansfield, OH 44906, USA.
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24
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Latino L, Midoux C, Vergnaud G, Pourcel C. Investigation of Pseudomonas aeruginosa strain PcyII-10 variants resisting infection by N4-like phage Ab09 in search for genes involved in phage adsorption. PLoS One 2019; 14:e0215456. [PMID: 30990839 PMCID: PMC6467409 DOI: 10.1371/journal.pone.0215456] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 04/02/2019] [Indexed: 12/20/2022] Open
Abstract
Bacteria and their bacteriophages coexist and coevolve for the benefit of both in a mutualistic association. Multiple mechanisms are used by bacteria to resist phages in a trade-off between survival and maintenance of fitness. In vitro studies allow inquiring into the fate of virus and host in different conditions aimed at mimicking natural environment. We analyse here the mutations emerging in a clinical Pseudomonas aeruginosa strain in response to infection by Ab09, a N4-like lytic podovirus and describe a variety of chromosomal deletions and mutations conferring resistance. Some deletions result from illegitimate recombination taking place during long-term maintenance of the phage genome. Phage variants with mutations in a tail fiber gene are selected during pseudolysogeny with the capacity to infect resistant cells and produce large plaques. These results highlight the complex host/phage association and suggest that phage Ab09 promotes bacterial chromosome rearrangements. Finally this study points to the possible role of two bacterial genes in Ab09 phage adhesion to the cell, rpsB encoding protein S2 of the 30S ribosomal subunit and ORF1587 encoding a Wzy-like membrane protein involved in LPS biosynthesis.
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Affiliation(s)
- Libera Latino
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Cédric Midoux
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Gilles Vergnaud
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Christine Pourcel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
- * E-mail: ,
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25
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El-Dougdoug N, Cucic S, Abdelhamid A, Brovko L, Kropinski A, Griffiths M, Anany H. Control of Salmonella Newport on cherry tomato using a cocktail of lytic bacteriophages. Int J Food Microbiol 2019; 293:60-71. [DOI: 10.1016/j.ijfoodmicro.2019.01.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Revised: 01/03/2019] [Accepted: 01/04/2019] [Indexed: 12/11/2022]
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26
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Fernandes S, São-José C. Enzymes and Mechanisms Employed by Tailed Bacteriophages to Breach the Bacterial Cell Barriers. Viruses 2018; 10:E396. [PMID: 30060520 DOI: 10.3390/v10080396] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Revised: 07/23/2018] [Accepted: 07/26/2018] [Indexed: 01/07/2023] Open
Abstract
Monoderm bacteria possess a cell envelope made of a cytoplasmic membrane and a cell wall, whereas diderm bacteria have and extra lipid layer, the outer membrane, covering the cell wall. Both cell types can also produce extracellular protective coats composed of polymeric substances like, for example, polysaccharidic capsules. Many of these structures form a tight physical barrier impenetrable by phage virus particles. Tailed phages evolved strategies/functions to overcome the different layers of the bacterial cell envelope, first to deliver the genetic material to the host cell cytoplasm for virus multiplication, and then to release the virion offspring at the end of the reproductive cycle. There is however a major difference between these two crucial steps of the phage infection cycle: virus entry cannot compromise cell viability, whereas effective virion progeny release requires host cell lysis. Here we present an overview of the viral structures, key protein players and mechanisms underlying phage DNA entry to bacteria, and then escape of the newly-formed virus particles from infected hosts. Understanding the biological context and mode of action of the phage-derived enzymes that compromise the bacterial cell envelope may provide valuable information for their application as antimicrobials.
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27
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Puxty RJ, Evans DJ, Millard AD, Scanlan DJ. Energy limitation of cyanophage development: implications for marine carbon cycling. ISME J 2018; 12:1273-1286. [PMID: 29379179 PMCID: PMC5931967 DOI: 10.1038/s41396-017-0043-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Revised: 11/25/2017] [Accepted: 12/09/2017] [Indexed: 11/16/2022]
Abstract
Marine cyanobacteria are responsible for ~25% of the fixed carbon that enters the ocean biosphere. It is thought that abundant co-occurring viruses play an important role in regulating population dynamics of cyanobacteria and thus the cycling of carbon in the oceans. Despite this, little is known about how viral infections ‘play-out’ in the environment, particularly whether infections are resource or energy limited. Photoautotrophic organisms represent an ideal model to test this since available energy is modulated by the incoming light intensity through photophosphorylation. Therefore, we exploited phototrophy of the environmentally relevant marine cyanobacterium Synechococcus and monitored growth of a cyanobacterial virus (cyanophage). We found that light intensity has a marked effect on cyanophage infection dynamics, but that this is not manifest by a change in DNA synthesis. Instead, cyanophage development appears energy limited for the synthesis of proteins required during late infection. We posit that acquisition of auxiliary metabolic genes (AMGs) involved in light-dependent photosynthetic reactions acts to overcome this limitation. We show that cyanophages actively modulate expression of these AMGs in response to light intensity and provide evidence that such regulation may be facilitated by a novel mechanism involving light-dependent splicing of a group I intron in a photosynthetic AMG. Altogether, our data offers a mechanistic link between diurnal changes in irradiance and observed community level responses in metabolism, i.e., through an irradiance-dependent, viral-induced release of dissolved organic matter (DOM).
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Affiliation(s)
- Richard J Puxty
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, UK
| | - David J Evans
- School of Biology and BSRC, Biomolecular Sciences Building, North Haugh, St Andrews, KY16 9AJ, UK
| | - Andrew D Millard
- Department of Infection, Immunity and Inflammation, University of Leicester, Leicester, LE1 9HNL, UK
| | - David J Scanlan
- School of Life Sciences, University of Warwick, Coventry, West Midlands, CV4 7AL, UK.
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28
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De Sordi L, Khanna V, Debarbieux L. The Gut Microbiota Facilitates Drifts in the Genetic Diversity and Infectivity of Bacterial Viruses. Cell Host Microbe 2017; 22:801-808.e3. [PMID: 29174401 DOI: 10.1016/j.chom.2017.10.010] [Citation(s) in RCA: 99] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Revised: 09/11/2017] [Accepted: 09/29/2017] [Indexed: 01/12/2023]
Abstract
The intestinal microbiota and human health are intimately linked, but interactions between bacteria and bacteriophages in the context of the mammalian intestine remain largely unexplored. We used comparative population genomics to study a tripartite network consisting of a virulent bacteriophage, its bacterial host, and a phage-insensitive bacterial strain both in vitro and within the murine gut. The bacteriophage adapted to infect the insensitive strain when the three partners co-existed in the gut of conventional mice, but not in dixenic mice or in planktonic cultures. The molecular changes associated with modifications in the bacteriophage host spectrum included single amino acid substitutions and an unusual homologous intragenomic recombination event within the genome of the bacteriophage. An intermediate bacterial host isolated from the murine microbiota mediated bacteriophage adaptation. Our data indicate that by offering access to new hosts, the microbiota shifts the genetic diversity of bacteriophages, thereby promoting long-term persistence of bacteriophage populations.
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29
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Xing S, Ma T, Zhang X, Huang Y, Mi Z, Sun Q, An X, Fan H, Wu S, Wei L, Tong Y. First complete genome sequence of a virulent bacteriophage infecting the opportunistic pathogen Serratia rubidaea. Arch Virol 2017; 162:2021-2028. [PMID: 28265773 DOI: 10.1007/s00705-017-3300-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2016] [Accepted: 02/14/2017] [Indexed: 10/20/2022]
Abstract
A Serratia rubidaea phage, vB_Sru IME250, was isolated from hospital sewage. The morphology suggested that phage vB_Sru IME250 should be classified as a member of the family Myoviridae. High-throughput sequencing revealed that the phage genome has 154,938 nucleotides and consists of 193 coding DNA sequences, 90 of which have putative functions. The genome of vB_Sru IME250 is a linear, double-stranded DNA with an average GC content of 40.04%. The phage has a relatively high similarity to Klebsiella phage 0507-KN2-1, with a genome coverage of 84%.
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Affiliation(s)
- Shaozhen Xing
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Taping Ma
- Department of Immunology, Basic Medical College, Hebei Medical University, Shijiazhuang, 050017, People's Republic of China.,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, 050017, People's Republic of China
| | - Xianglilan Zhang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Yong Huang
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Zhiqiang Mi
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Qiang Sun
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Xiaoping An
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Hang Fan
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China
| | - Shuhui Wu
- Department of Pathogenic Biology and Immunology, School of Basic Medicine, Hebei University of Chinese Medicine, Shijiazhuang, 050000, China.
| | - Lin Wei
- Department of Immunology, Basic Medical College, Hebei Medical University, Shijiazhuang, 050017, People's Republic of China. .,Key Laboratory of Immune Mechanism and Intervention on Serious Disease in Hebei Province, Shijiazhuang, 050017, People's Republic of China.
| | - Yigang Tong
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, 100071, People's Republic of China.
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30
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Bryan D, El-Shibiny A, Hobbs Z, Porter J, Kutter EM. Bacteriophage T4 Infection of Stationary Phase E. coli: Life after Log from a Phage Perspective. Front Microbiol 2016; 7:1391. [PMID: 27660625 PMCID: PMC5014867 DOI: 10.3389/fmicb.2016.01391] [Citation(s) in RCA: 93] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 08/23/2016] [Indexed: 01/26/2023] Open
Abstract
Virtually all studies of phage infections investigate bacteria growing exponentially in rich media. In nature, however, phages largely encounter non-growing cells. Bacteria entering stationary phase often activate well-studied stress defense mechanisms that drastically alter the cell, facilitating its long-term survival. An understanding of phage-host interactions in such conditions is of major importance from both an ecological and therapeutic standpoint. Here, we show that bacteriophage T4 can efficiently bind to, infect and kill E. coli in stationary phase, both in the presence and absence of a functional stationary-phase sigma factor, and explore the response of T4-infected stationary phase cells to the addition of fresh nutrients 5 or 24 h after that infection. An unexpected new mode of response has been identified. "Hibernation" mode is a persistent but reversible dormant state in which the infected cells make at least some phage enzymes, but halt phage development until appropriate nutrients become available before producing phage particles. Our evidence indicates that the block in hibernation mode occurs after the middle-mode stage of phage development; host DNA breakdown and the incorporation of the released nucleotides into phage DNA indicate that the enzymes of the nucleotide synthesizing complex, under middle-mode control, have been made and assembled into a functional state. Once fresh glucose and amino acids become available, the standard lytic infection process rapidly resumes and concentrations of up to 10(11) progeny phage (an average of about 40 phage per initially present cell) are produced. All evidence is consistent with the hibernation-mode control point lying between middle mode and late mode T4 gene expression. We have also observed a "scavenger" response, where the infecting phage takes advantage of whatever few nutrients are available to produce small quantities of progeny within 2 to 5 h after infection. The scavenger response seems able to produce no more than an average of one phage per originally available cell, and few if any further progeny are produced by cells in this mode even if fresh nutrients are made available later.
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Affiliation(s)
- Daniel Bryan
- Kutter Bacteriophage Lab, The Evergreen State College Olympia, WA, USA
| | - Ayman El-Shibiny
- Kutter Bacteriophage Lab, The Evergreen State CollegeOlympia, WA, USA; Biomedical Sciences, University of Science and Technology, Zewail City of Science and TechnologyGiza, Egypt; Faculty of Environmental Agricultural Sciences, Arish UniversityArish, Egypt
| | - Zack Hobbs
- Kutter Bacteriophage Lab, The Evergreen State College Olympia, WA, USA
| | - Jillian Porter
- Kutter Bacteriophage Lab, The Evergreen State College Olympia, WA, USA
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31
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Chen Y, Young R. The Last r Locus Unveiled: T4 RIII Is a Cytoplasmic Antiholin. J Bacteriol 2016; 198:2448-57. [PMID: 27381920 DOI: 10.1128/JB.00294-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 06/27/2016] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED The latent period of phage T4, normally ∼25 min, can be extended indefinitely if the infected cell is superinfected after 5 min. This phenomenon, designated lysis inhibition (LIN), was first described in the 1940s and is genetically defined by mutations in diverse T4 r genes. RI, the main effector of LIN, has been shown to be secreted to the periplasm, where, upon activation by superinfection with a T-even virion, it binds to the C-terminal periplasmic domain of the T4 holin T and blocks its lethal permeabilization of the cytoplasmic membrane. Another r locus, rIII, has been the subject of conflicting reports. In this study, we show that RIII, an 82-amino-acid protein, is also required for LIN in both Escherichia coli B strains and E. coli K-12 strains. In T4ΔrIII infections, LIN was briefly established but was unstable. The overexpression of a cloned rIII gene alone impeded T-mediated lysis temporarily. However, coexpression of rIII and rI resulted in a stable LIN state. Bacterial two-hybrid assays and pulldown assays showed that RIII interacts with the cytoplasmic N terminus of T, which is a critical domain for holin function. We conclude that RIII is a T4 antiholin that blocks membrane hole formation by interacting directly with the holin. Accordingly, we propose an augmented model for T4 LIN that involves the stabilization of a complex of three proteins in two compartments of the cell: RI interacting with the C terminus of T in the periplasm and RIII interacting with the N terminus of T in the cytoplasm. IMPORTANCE Lysis inhibition is a unique feature of phage T4 in response to environmental conditions, effected by the antiholin RI, which binds to the periplasmic domain of the T holin and blocks its hole-forming function. Here we report that the T4 gene rIII encodes a cytoplasmic antiholin that, together with the main antiholin, RI, inhibits holin T by forming a complex of three proteins spanning two cell compartments.
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32
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Wittmann J, Klumpp J, Moreno Switt AI, Yagubi A, Ackermann HW, Wiedmann M, Svircev A, Nash JH, Kropinski AM. Taxonomic reassessment of N4-like viruses using comparative genomics and proteomics suggests a new subfamily - "Enquartavirinae". Arch Virol 2015; 160:3053-62. [PMID: 26395091 DOI: 10.1007/s00705-015-2609-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 09/09/2015] [Indexed: 10/23/2022]
Abstract
The GenBank database currently contains sequence data for 33 N4-like viruses, with only one, Escherichia phage N4, being formally recognized by the ICTV. The genus N4likevirus is uniquely characterized by that fact that its members possess an extremely large, virion-associated RNA polymerase. Using a variety of proteomic, genomic and phylogenetic tools, we have demonstrated that the N4-like phages are not monophyletic and that N4 is actually a genomic orphan. We propose to create four new genera: "G7cvirus" (consisting of phages G7C, IME11, KBNP21, vB_EcoP_PhAPEC5, vB_EcoP_PhAPEC7, Bp4, EC1-UPM and pSb-1), "Lit1virus" (LIT1, PA26 and vB_PaeP_C2-10_Ab09), "Sp58virus" (SP058 and SP076), and "Dss3virus" (DSS3φ2 and EE36φ1). We propose that coliphage N4, the members of "G7cvirus", Erwinia phage Ea9-2, and Achromobacter phage JWAlpha should be considered members of the same subfamily, which we tentatively call the "Enquartavirinae".
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33
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Alves DR, Perez-Esteban P, Kot W, Bean JE, Arnot T, Hansen LH, Enright MC, Jenkins ATA. A novel bacteriophage cocktail reduces and disperses Pseudomonas aeruginosa biofilms under static and flow conditions. Microb Biotechnol 2015; 9:61-74. [PMID: 26347362 PMCID: PMC4720417 DOI: 10.1111/1751-7915.12316] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2015] [Revised: 08/10/2015] [Accepted: 08/11/2015] [Indexed: 01/21/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic human pathogen that forms highly stable communities - biofilms, which contribute to the establishment and maintenance of infections. The biofilm state and intrinsic/acquired bacterial resistance mechanisms contribute to resistance/tolerance to antibiotics that is frequently observed in P. aeruginosa isolates. Here we describe the isolation and characterization of six novel lytic bacteriophages: viruses that infect bacteria, which together efficiently infect and kill a wide range of P. aeruginosa clinical isolates. The phages were used to formulate a cocktail with the potential to eliminate P. aeruginosa PAO1 planktonic cultures. Two biofilm models were studied, one static and one dynamic, and the phage cocktail was assessed for its ability to reduce and disperse the biofilm biomass. For the static model, after 4 h of contact with the phage suspension (MOI 10) more than 95% of biofilm biomass was eliminated. In the flow biofilm model, a slower rate of activity by the phage was observed, but 48 h after addition of the phage cocktail the biofilm was dispersed, with most cells eliminated (> 4 logs) comparing with the control. This cocktail has the potential for development as a therapeutic to control P. aeruginosa infections, which are predominantly biofilm centred.
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Affiliation(s)
- Diana R Alves
- Department of Chemistry, University of Bath, Bath, Claverton Down, BA2 7AY, UK
| | - P Perez-Esteban
- Department of Chemical Engineering, University of Bath, Bath, Claverton Down, BA2 7AY, UK
| | - W Kot
- Department of Environmental Science, Aarhus Universitet, Frederiksborgvej 399, Postboks, 358, Roskilde, DK-4000, Denmark
| | - J E Bean
- Department of Chemistry, University of Bath, Bath, Claverton Down, BA2 7AY, UK
| | - T Arnot
- Department of Chemical Engineering, University of Bath, Bath, Claverton Down, BA2 7AY, UK
| | - L H Hansen
- Department of Environmental Science, Aarhus Universitet, Frederiksborgvej 399, Postboks, 358, Roskilde, DK-4000, Denmark
| | - Mark C Enright
- School of Healthcare Sciences, Manchester Metropolitan University, John Dalton Building, Chester Street, Manchester, M1 5GD, UK
| | - A Tobias A Jenkins
- Department of Chemistry, University of Bath, Bath, Claverton Down, BA2 7AY, UK
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34
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Abstract
The development of the molecular biology of bacteriophage such as T4, lambda and filamentous phages was described and the process that the fundamental knowledge obtained in this field has subsequently led us to the technology of phage display was introduced.
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35
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Abstract
t is the holin gene for coliphage T4, encoding a 218-amino-acid (aa) protein essential for the inner membrane hole formation that initiates lysis and terminates the phage infection cycle. T is predicted to be an integral membrane protein that adopts an N(in)-C(out) topology with a single transmembrane domain (TMD). This holin topology is different from those of the well-studied holins S105 (3 TMDs; N(out)-C(in)) of the coliphage lambda and S68 (2 TMDs; N(in)-C(in)) of the lambdoid phage 21. Here, we used random mutagenesis to construct a library of lysis-defective alleles of t to discern residues and domains important for holin function and for the inhibition of lysis by the T4 antiholin, RI. The results show that mutations in all 3 topological domains (N-terminal cytoplasmic, TMD, and C-terminal periplasmic) can abrogate holin function. Additionally, several lysis-defective alleles in the C-terminal domain are no longer competent in binding RI. Taken together, these results shed light on the roles of the previously uncharacterized N-terminal and C-terminal domains in lysis and its real-time regulation.
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36
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Wittmann J, Dreiseikelmann B, Rohde M, Meier-Kolthoff JP, Bunk B, Rohde C. First genome sequences of Achromobacter phages reveal new members of the N4 family. Virol J 2014; 11:14. [PMID: 24468270 PMCID: PMC3915230 DOI: 10.1186/1743-422x-11-14] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 01/21/2014] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND Multi-resistant Achromobacter xylosoxidans has been recognized as an emerging pathogen causing nosocomially acquired infections during the last years. Phages as natural opponents could be an alternative to fight such infections. Bacteriophages against this opportunistic pathogen were isolated in a recent study. This study shows a molecular analysis of two podoviruses and reveals first insights into the genomic structure of Achromobacter phages so far. METHODS Growth curve experiments and adsorption kinetics were performed for both phages. Adsorption and propagation in cells were visualized by electron microscopy. Both phage genomes were sequenced with the PacBio RS II system based on single molecule, real-time (SMRT) technology and annotated with several bioinformatic tools. To further elucidate the evolutionary relationships between the phage genomes, a phylogenomic analysis was conducted using the genome Blast Distance Phylogeny approach (GBDP). RESULTS In this study, we present the first detailed analysis of genome sequences of two Achromobacter phages so far. Phages JWAlpha and JWDelta were isolated from two different waste water treatment plants in Germany. Both phages belong to the Podoviridae and contain linear, double-stranded DNA with a length of 72329 bp and 73659 bp, respectively. 92 and 89 putative open reading frames were identified for JWAlpha and JWDelta, respectively, by bioinformatic analysis with several tools. The genomes have nearly the same organization and could be divided into different clusters for transcription, replication, host interaction, head and tail structure and lysis. Detailed annotation via protein comparisons with BLASTP revealed strong similarities to N4-like phages. CONCLUSIONS Analysis of the genomes of Achromobacter phages JWAlpha and JWDelta and comparisons of different gene clusters with other phages revealed that they might be strongly related to other N4-like phages, especially of the Escherichia group. Although all these phages show a highly conserved genomic structure and partially strong similarities at the amino acid level, some differences could be identified. Those differences, e.g. the existence of specific genes for replication or host interaction in some N4-like phages, seem to be interesting targets for further examination of function and specific mechanisms, which might enlighten the mechanism of phage establishment in the host cell after infection.
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Affiliation(s)
- Johannes Wittmann
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Brigitte Dreiseikelmann
- Department of Microbiology/Genetechnology, Faculty of Biology, University of Bielefeld, Bielefeld, Germany
| | - Manfred Rohde
- Helmholtz Centre for Infection Research, Department of Medical Microbiology, Central Facility for Microscopy, Braunschweig, Germany
| | - Jan P Meier-Kolthoff
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Boyke Bunk
- Bioinformatics, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Christine Rohde
- Department of Microorganisms, Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
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Fouts DE, Klumpp J, Bishop-Lilly KA, Rajavel M, Willner KM, Butani A, Henry M, Biswas B, Li M, Albert MJ, Loessner MJ, Calendar R, Sozhamannan S. Whole genome sequencing and comparative genomic analyses of two Vibrio cholerae O139 Bengal-specific Podoviruses to other N4-like phages reveal extensive genetic diversity. Virol J 2013; 10:165. [PMID: 23714204 PMCID: PMC3670811 DOI: 10.1186/1743-422x-10-165] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Accepted: 05/21/2013] [Indexed: 11/23/2022] Open
Abstract
Background Vibrio cholerae O139 Bengal is the only serogroup other than O1 implicated in cholera epidemics. We describe the isolation and characterization of an O139 serogroup-specific phage, vB_VchP_VchO139-I (ϕVchO139-I) that has similar host range and virion morphology as phage vB_VchP_JA1 (ϕJA1) described previously. We aimed at a complete molecular characterization of both phages and elucidation of their genetic and structural differences and assessment of their genetic relatedness to the N4-like phage group. Methods Host-range analysis and plaque morphology screening were done for both ϕJA1 and ϕVchO139-I. Both phage genomes were sequenced by a 454 and Sanger hybrid approach. Genomes were annotated and protein homologies were determined by Blast and HHPred. Restriction profiles, PFGE patterns and data on the physical genome structure were acquired and phylogenetic analyses were performed. Results The host specificity of ϕJA1 has been attributed to the unique capsular O-antigen produced by O139 strains. Plaque morphologies of the two phages were different; ϕVchO139-I produced a larger halo around the plaques than ϕJA1. Restriction profiles of ϕJA1 and ϕVchO139-I genomes were also different. The genomes of ϕJA1 and ϕVchO139-I consisted of linear double-stranded DNA of 71,252 and 70,938 base pairs. The presence of direct terminal repeats of around 1974 base pairs was demonstrated. Whole genome comparison revealed single nucleotide polymorphisms, small insertions/deletions and differences in gene content. Both genomes had 79 predicted protein encoding sequences, of which only 59 were identical between the two closely related phages. They also encoded one tRNA-Arg gene, an intein within the large terminase gene, and four homing endonuclease genes. Whole genome phylogenetic analyses of ϕJA1 and ϕVchO139-I against other sequenced N4-like phages delineate three novel subgroups or clades within this phage family. Conclusions The closely related phages feature significant genetic differences, in spite of being morphologically identical. The phage morphology, genetic organization, genomic content and large terminase protein based phylogeny support the placement of these two phages in the Podoviridae family, more specifically within the N4-like phage group. The physical genome structure of ϕJA1 could be demonstrated experimentally. Our data pave the way for potential use of ϕJA1 and ϕVchO139-I in Vibrio cholerae typing and control.
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38
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Golec P, Karczewska-Golec J, Voigt B, Albrecht D, Schweder T, Hecker M, Węgrzyn G, Łoś M. Proteomic profiles and kinetics of development of bacteriophage T4 and its rI and rIII mutants in slowly growing Escherichia coli. J Gen Virol 2012; 94:896-905. [PMID: 23239571 DOI: 10.1099/vir.0.048686-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage T4 survival in its natural environment requires adjustment of phage development to the slow bacterial growth rate or the initiation of mechanisms of pseudolysogeny or lysis inhibition (LIN). While phage-encoded RI and probably RIII proteins seem to be crucial players in pseudolysogeny and LIN phenomena, the identity of proteins involved in the regulation of T4 development in slowly growing bacteria has remained unknown. In this work, using a chemostat system, we studied the development of wild-type T4 (T4wt) and its rI (T4rI) and rIII (T4rIII) mutants in slowly growing bacteria, where T4 did not initiate LIN or pseudolysogeny. We determined eclipse periods, phage propagation times, latent periods and burst sizes of T4wt, T4rI and T4rIII. We also compared intracellular proteomes of slowly growing Escherichia coli infected with either T4wt or the mutants. Using two-dimensional PAGE analyses we found 18 differentially expressed proteins from lysates of infected cells. Proteins whose amounts were different in cells harbouring T4wt and the mutants are involved in processes of replication, phage-host interactions or they constitute virion components. Our data indicate that functional RI and RIII proteins - apart from their already known roles in LIN and pseudolysogeny - are also necessary for the regulation of phage T4 development in slowly growing bacteria. This regulation may be more complicated than previously anticipated, with many factors influencing T4 development in its natural habitat.
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Affiliation(s)
- Piotr Golec
- Laboratory of Molecular Biology (affiliated with the University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Joanna Karczewska-Golec
- Laboratory of Molecular Bacteriology, Intercollegiate Faculty of Biotechnology, University of Gdańsk and Medical University of Gdańsk, Dębinki 1, 80-211 Gdańsk, Poland
| | - Birgit Voigt
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, F.-L.-Jahn-Str. 15, 17489 Greifswald, Germany
| | - Dirk Albrecht
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, F.-L.-Jahn-Str. 15, 17489 Greifswald, Germany
| | - Thomas Schweder
- Department of Pharmaceutical Biotechnology, Institute of Pharmacy, Ernst-Moritz-Arndt-University of Greifswald, Felix-Hausdorff-Str. 3, 17489 Greifswald, Germany
| | - Michael Hecker
- Institute for Microbiology, Ernst-Moritz-Arndt-University of Greifswald, F.-L.-Jahn-Str. 15, 17489 Greifswald, Germany
| | - Grzegorz Węgrzyn
- Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Marcin Łoś
- Phage Consultants, Partyzantów10/18, 80-254 Gdańsk, Poland.,Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.,Department of Molecular Biology, University of Gdańsk, Wita Stwosza 59, 80-308 Gdańsk, Poland
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Kutter EM, Skutt-Kakaria K, Blasdel B, El-Shibiny A, Castano A, Bryan D, Kropinski AM, Villegas A, Ackermann HW, Toribio AL, Pickard D, Anany H, Callaway T, Brabban AD. Characterization of a ViI-like phage specific to Escherichia coli O157:H7. Virol J 2011; 8:430. [PMID: 21899740 PMCID: PMC3184105 DOI: 10.1186/1743-422x-8-430] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2011] [Accepted: 09/07/2011] [Indexed: 12/16/2022] Open
Abstract
Phage vB_EcoM_CBA120 (CBA120), isolated against Escherichia coli O157:H7 from a cattle feedlot, is morphologically very similar to the classic phage ViI of Salmonella enterica serovar Typhi. Until recently, little was known genetically or physiologically about the ViI-like phages, and none targeting E. coli have been described in the literature. The genome of CBA120 has been fully sequenced and is highly similar to those of both ViI and the Shigella phage AG3. The core set of structural and replication-related proteins of CBA120 are homologous to those from T-even phages, but generally are more closely related to those from T4-like phages of Vibrio, Aeromonas and cyanobacteria than those of the Enterobacteriaceae. The baseplate and method of adhesion to the host are, however, very different from those of either T4 or the cyanophages. None of the outer baseplate proteins are conserved. Instead of T4's long and short tail fibers, CBA120, like ViI, encodes tail spikes related to those normally seen on podoviruses. The 158 kb genome, like that of T4, is circularly permuted and terminally redundant, but unlike T4 CBA120 does not substitute hmdCyt for cytosine in its DNA. However, in contrast to other coliphages, CBA120 and related coliphages we have isolated cannot incorporate 3H-thymidine (3H-dThd) into their DNA. Protein sequence comparisons cluster the putative "thymidylate synthase" of CBA120, ViI and AG3 much more closely with those of Delftia phage φW-14, Bacillus subtilis phage SPO1, and Pseudomonas phage YuA, all known to produce and incorporate hydroxymethyluracil (hmdUra).
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Affiliation(s)
| | | | - Bob Blasdel
- The Evergreen State College, Olympia, WA, USA
- Department of Microbiology, The Ohio State University, Columbus, OH
| | - Ayman El-Shibiny
- The Evergreen State College, Olympia, WA, USA
- Faculty of Environmental Agricultural Sciences, Suez Canal University, Egypt
| | - Anna Castano
- The Evergreen State College, Olympia, WA, USA
- Department of Pediatric Neurology, University of Colorado Children's Hospital, Denver, CO
| | | | - Andrew M Kropinski
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, Canada
- Department of Molecular & Cellular Biology, University of Guelph, ON, Canada
| | - Andre Villegas
- Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, Canada
| | | | - Ana L Toribio
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, England, UK
| | - Derek Pickard
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, England, UK
| | - Hany Anany
- Canadian Research Institute for Food Safety, University of Guelph, ON, Canada
- Microbiology Department, Ain Shams University, Cairo, Egypt
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40
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Burch LH, Zhang L, Chao FG, Xu H, Drake JW. The bacteriophage T4 rapid-lysis genes and their mutational proclivities. J Bacteriol 2011; 193:3537-45. [PMID: 21571993 PMCID: PMC3133318 DOI: 10.1128/jb.00138-11] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2011] [Accepted: 05/03/2011] [Indexed: 11/20/2022] Open
Abstract
Like most phages with double-stranded DNA, phage T4 exits the infected host cell by a lytic process requiring, at a minimum, an endolysin and a holin. Unlike most phages, T4 can sense superinfection (which signals the depletion of uninfected host cells) and responds by delaying lysis and achieving an order-of-magnitude increase in burst size using a mechanism called lysis inhibition (LIN). T4 r mutants, which are unable to conduct LIN, produce distinctly large, sharp-edged plaques. The discovery of r mutants was key to the foundations of molecular biology, in particular to discovering and characterizing genetic recombination in T4, to redefining the nature of the gene, and to exploring the mutation process at the nucleotide level of resolution. A number of r genes have been described in the past 7 decades with various degrees of clarity. Here we describe an extensive and perhaps saturating search for T4 r genes and relate the corresponding mutational spectra to the often imperfectly known physiologies of the proteins encoded by these genes. Focusing on r genes whose mutant phenotypes are largely independent of the host cell, the genes are rI (which seems to sense superinfection and signal the holin to delay lysis), rIII (of poorly defined function), rIV (same as sp and also of poorly defined function), and rV (same as t, the holin gene). We did not identify any mutations that might correspond to a putative rVI gene, and we did not focus on the famous rII genes because they appear to affect lysis only indirectly.
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Affiliation(s)
- Lauranell H. Burch
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Leilei Zhang
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Frank G. Chao
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - Hong Xu
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
| | - John W. Drake
- Laboratory of Molecular Genetics, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709
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41
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Raya RR, Oot RA, Moore-Maley B, Wieland S, Callaway TR, Kutter EM, Brabban AD. Naturally resident and exogenously applied T4-like and T5-like bacteriophages can reduce Escherichia coli O157:H7 levels in sheep guts. Bacteriophage 2011; 1:15-24. [PMID: 21687531 PMCID: PMC3109454 DOI: 10.4161/bact.1.1.14175] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/11/2010] [Revised: 11/01/2010] [Accepted: 11/06/2010] [Indexed: 11/19/2022]
Abstract
In preparing sheep for an in vivo Escherichia coli O157:H7 eradication trial, we found that 20/39 members of a single flock were naturally colonized by O157:H7-infecting phages. Characterization showed these were all one phage type (subsequently named CEV2) infecting 15/16 O157:H7, 7/72 ECOR and common lab strains. Further characterization by PFGE (genome∼120 kb), restriction enzyme digest (DNA appears unmodified), receptor studies (FhuA but not TonB is required for infection) and sequencing (>95% nucleotide identity) showed it is a close relative of the classically studied coliphage T5. Unlike T5, CEV2 infects O157:H7 in vitro, both aerobically and anaerobically, rapidly adsorbing and killing, but resistant mutants regrew within 24 h. When used together with T4-like CEV1 (MOI ∼2 per phage), bacterial killing was longer lasting. CEV2 did not reproduce when co-infecting the same cell as CEV1, presumably succumbing to CEV1's ability to shut off transcription of cytosine-containing DNA. In vivo sheep trials to remove resident O157:H7 showed that a cocktail of CEV2 and CEV1 (∼10(11) total PFU) applied once orally was more effective (>99.9% reduction) than CEV1 alone (∼99%) compared to the untreated phage-free control. Those sheep naturally carrying CEV2, receiving no additional phage treatment, had the lowest O157:H7 levels (∼99.99% reduction). These data suggest that phage cocktails are more effective than individual phage in removing O157:H7 that have taken residence if the phage work in concert with one another and that naturally resident O157:H7-infecting phages may prevent O157:H7 gut colonization and be one explanation for the transient O157:H7 colonization in ruminants.
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Affiliation(s)
- Raul R Raya
- The Evergreen State College; Olympia, WA USA
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42
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Golec P, Wiczk A, Łoś JM, Konopa G, Węgrzyn G, Łoś M. Persistence of bacteriophage T4 in a starved Escherichia coli culture: evidence for the presence of phage subpopulations. J Gen Virol 2010; 92:997-1003. [PMID: 21177930 DOI: 10.1099/vir.0.027326-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Bacteriophage T4 is able to adjust its development to the growth parameters of the host cell. Here, we present evidence for the production of two different subpopulations of phage particles, which differ in their ability to infect starved Escherichia coli cells. The ability of phage T4 to produce a fraction of virions unable to infect starved cells is linked to the functions of genes rI and rIII, as well as rIIA. This may represent the adaptation of phage T4 in order to persist in unfavourable environmental conditions.
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Affiliation(s)
- Piotr Golec
- Laboratory of Molecular Biology (affiliated with The University of Gdańsk), Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Kładki 24, 80-822 Gdańsk, Poland
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Eshelman CM, Vouk R, Stewart JL, Halsne E, Lindsey HA, Schneider S, Gualu M, Dean AM, Kerr B. Unrestricted migration favours virulent pathogens in experimental metapopulations: evolutionary genetics of a rapacious life history. Philos Trans R Soc Lond B Biol Sci 2010; 365:2503-13. [PMID: 20643740 DOI: 10.1098/rstb.2010.0066] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Understanding pathogen infectivity and virulence requires combining insights from epidemiology, ecology, evolution and genetics. Although theoretical work in these fields has identified population structure as important for pathogen life-history evolution, experimental tests are scarce. Here, we explore the impact of population structure on life-history evolution in phage T4, a viral pathogen of Escherichia coli. The host-pathogen system is propagated as a metapopulation in which migration between subpopulations is either spatially restricted or unrestricted. Restricted migration favours pathogens with low infectivity and low virulence. Unrestricted migration favours pathogens that enter and exit their hosts quickly, although they are less productive owing to rapid extirpation of the host population. The rise of such 'rapacious' phage produces a 'tragedy of the commons', in which better competitors lower productivity. We have now identified a genetic basis for a rapacious life history. Mutations at a single locus (rI) cause increased virulence and are sufficient to account for a negative relationship between phage competitive ability and productivity. A higher frequency of rI mutants under unrestricted migration signifies the evolution of rapaciousness in this treatment. Conversely, spatially restricted migration favours a more 'prudent' pathogen strategy, in which the tragedy of the commons is averted. As our results illustrate, profound epidemiological and ecological consequences of life-history evolution in a pathogen can have a simple genetic cause.
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Affiliation(s)
- Christal M Eshelman
- Department of Biology, University of Washington, Box 351800, Seattle, WA 98195, USA
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44
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Golec P, Wiczk A, Majchrzyk A, Łoś JM, Węgrzyn G, Łoś M. A role for accessory genes rI.-1 and rI.1 in the regulation of lysis inhibition by bacteriophage T4. Virus Genes 2010; 41:459-68. [PMID: 20945083 DOI: 10.1007/s11262-010-0532-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2010] [Accepted: 09/17/2010] [Indexed: 11/29/2022]
Abstract
Lysis inhibition (LIN) is a known feature of the T-even family of bacteriophages. Despite its historical role in the development of modern molecular genetics, many aspects of this phenomenon remain mostly unexplained. The key element of LIN is an interaction between two phage-encoded proteins, the T holin and the RI antiholin. This interaction is stabilized by RIII. In this report, we demonstrate the results of genetic experiments which suggest a synergistic action of two accessory proteins of bacteriophage T4, RI.-1, and RI.1 with RIII in the regulation of LIN.
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Abstract
The host range of a bacteriophage is defined by what bacterial genera, species and strains it can lyse; it is one of the defining biological characteristics of a particular bacterial virus. Because of host factors such as masking by O antigens that affects injection and the presence of restriction endonucleases, the relative efficiency of plating (EOP), that is, the titer of the phage on a given bacterial cell line compared to the maximum titer observed, may vary considerably. This chapter describes rapid procedures for determining the host range and relative EOP on each host of any phage.
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46
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Abstract
Bacteriophage growth may be differentiated into sequential steps: (i) phage collision with an adsorption-susceptible bacterium, (ii) virion attachment, (iii) virion nucleic acid uptake, (iv) an eclipse period during which infections synthesize phage proteins and nucleic acid, (v) a "post-eclipse" period during which virions mature, (vi) a virion release step, and (vii) a diffusion-delimited period of virion extracellular search for bacteria to adsorb (1). The latent period begins at the point of virion attachment (ii) and/or nucleic acid uptake (iii) and ends with infection termination, spanning both the eclipse (iv) and the post-eclipse maturation (v) periods. For lytic phages, latent-period termination occurs at lysis, i.e., at the point of phage-progeny release (vi). A second compound step is phage adsorption, which, depending upon one's perspective, can begin with virion release (vi), may include the virion extracellular search (vii), certainly involves virion collision with (i) and then attachment to (ii) a bacterium, and ends either with irreversible virion attachment to bacteria (ii) or with phage nucleic acid uptake into cytoplasm (iii). Thus, the phage life cycle, particularly for virulent phages, consists of an adsorption period, virion attachment/nucleic acid uptake, a latent period, and virion release ((2), p. 13, citing d'Herelle). The duration of these steps together define the phage generation time and help to define rates of phage population growth. Also controlling rates of phage population growth is the number of phage progeny produced per infection: the phage burst size. In this chapter we present protocols for determining phage growth parameters, particularly phage rate of adsorption, latent period, eclipse period, and burst size.
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Affiliation(s)
- Paul Hyman
- MedCentral College of Nursing, Mansfield, OH, USA
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47
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Abstract
Background Taking as a pattern, the T4 and lambda viruses interacting with each other and with their Gram-negative host, Escherichia coli, a general model is constructed for the evolution of 'gentle' or temperate pathogens. This model is not simply either pure group or kin selection, but probably is common in a variety of host-parasite pairs in various taxonomic groups. The proposed mechanism is that for its own benefit the pathogen evolved ways to protect its host from attack by other pathogens and this has incidentally protected the host. Although appropriate mechanisms would have been developed and excluded related viral species and also other quite different pathogens, the important advance would have been when other individuals of the same species that arrive at the host subsequent to the first infecting one were excluded. Results Such a class of mechanisms would not compete one genotype with another, but simply would be of benefit to the first pathogen that had attacked a host organism. Conclusion This would tend to protect and extend the life of the host against the detrimental effects of a secondarily infecting pathogen. This leads to the pathogens becoming more temperate via the now favorable co-evolution with its host, which basically protects both host and virus against other pathogens but may cause slowing of the growth of the primary infecting pathogen. Evolution by a 'gentle' strategy would be favored as long as the increased wellbeing of the host also favored the eventual transmission of the early infecting pathogen to other hosts.
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Affiliation(s)
- Arthur L Koch
- Biology Department, Indiana University, Bloomington, IN 47405-6801, USA.
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48
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Comeau AM, Tétart F, Trojet SN, Prère MF, Krisch H. Phage-Antibiotic Synergy (PAS): beta-lactam and quinolone antibiotics stimulate virulent phage growth. PLoS One 2007; 2:e799. [PMID: 17726529 PMCID: PMC1949050 DOI: 10.1371/journal.pone.0000799] [Citation(s) in RCA: 254] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Accepted: 07/25/2007] [Indexed: 11/29/2022] Open
Abstract
Although the multiplication of bacteriophages (phages) has a substantial impact on the biosphere, comparatively little is known about how the external environment affects phage production. Here we report that sub-lethal concentrations of certain antibiotics can substantially stimulate the host bacterial cell's production of some virulent phage. For example, a low dosage of cefotaxime, a cephalosporin, increased an uropathogenic Escherichia coli strain's production of the phage ΦMFP by more than 7-fold. We name this phenomenon Phage-Antibiotic Synergy (PAS). A related effect was observed in diverse host-phage systems, including the T4-like phages, with β-lactam and quinolone antibiotics, as well as mitomycin C. A common characteristic of these antibiotics is that they inhibit bacterial cell division and trigger the SOS system. We therefore examined the PAS effect within the context of the bacterial SOS and filamentation responses. We found that the PAS effect appears SOS-independent and is primarily a consequence of cellular filamentation; it is mimicked by cells that constitutively filament. The fact that completely unrelated phages manifest this phenomenon suggests that it confers an important and general advantage to the phages.
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Affiliation(s)
- André M. Comeau
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse, Toulouse, France
| | - Françoise Tétart
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse, Toulouse, France
| | - Sabrina N. Trojet
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse, Toulouse, France
| | - Marie-Françoise Prère
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse, Toulouse, France
- Laboratoire de Bactériologie, Institut Fédératif de Biologie, Centre Hospitalier Universitaire de Toulouse, Toulouse, France
| | - H.M. Krisch
- Laboratoire de Microbiologie et Génétique Moléculaires, Centre National de la Recherche Scientifique, Université Paul Sabatier-Toulouse, Toulouse, France
- * To whom correspondence should be addressed. E-mail:
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Abstract
Lysis inhibition (LIN) of T4-infected cells was one of the foundational experimental systems for modern molecular genetics. In LIN, secondary infection of T4-infected cells results in a dramatically protracted infection cycle in which intracellular phage and endolysin accumulation can continue for hours. At the molecular level, this is due to the inhibition of the holin, T, by the antiholin, RI. RI is only 97 residues and contains an N-terminal hydrophobic domain and a C-terminal hydrophilic domain; expression of the latter domain fused to a secretory signal sequence is sufficient to impose LIN, due to its specific interaction with the periplasmic domain of the T holin. Here we show that the N-terminal sequence comprises a signal anchor release (SAR) domain, which causes the secretion of RI in a membrane-tethered form and then its subsequent release into the periplasm, without proteolytic processing. Moreover, the SAR domain confers both functional lability and DegP-mediated proteolytic instability on the released form of RI, although LIN is not affected in a degP host. These results are discussed in terms of a model for the activation of RI in the establishment of the LIN state.
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Affiliation(s)
- Tram Anh T Tran
- Department of Biochemistry and Biophysics, Texas A&M University, 2128 TAMU, College Station, TX 77843-2128, USA
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50
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Kerr B, Neuhauser C, Bohannan BJM, Dean AM. Local migration promotes competitive restraint in a host-pathogen 'tragedy of the commons'. Nature 2006; 442:75-8. [PMID: 16823452 DOI: 10.1038/nature04864] [Citation(s) in RCA: 251] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2006] [Accepted: 05/04/2006] [Indexed: 11/09/2022]
Abstract
Fragmented populations possess an intriguing duplicity: even if subpopulations are reliably extinction-prone, asynchrony in local extinctions and recolonizations makes global persistence possible. Migration is a double-edged sword in such cases: too little migration prevents recolonization of extinct patches, whereas too much synchronizes subpopulations, raising the likelihood of global extinction. Both edges of this proverbial sword have been explored by manipulating the rate of migration within experimental populations. However, few experiments have examined how the evolutionary ecology of fragmented populations depends on the pattern of migration. Here, we show that the migration pattern affects both coexistence and evolution within a community of bacterial hosts (Escherichia coli) and viral pathogens (T4 coliphage) distributed across a large network of subpopulations. In particular, different patterns of migration select for distinct pathogen strategies, which we term 'rapacious' and 'prudent'. These strategies define a 'tragedy of the commons': rapacious phage displace prudent variants for shared host resources, but prudent phage are more productive when alone. We find that prudent phage dominate when migration is spatially restricted, while rapacious phage evolve under unrestricted migration. Thus, migration pattern alone can determine whether a de novo tragedy of the commons is resolved in favour of restraint.
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Affiliation(s)
- Benjamin Kerr
- Department of Biology, University of Washington, Box 351800, Seattle, Washington 98195-1800, USA.
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