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Kovacs CJ, Antonacci A, Graham A, Jessup F, Rankin W, Brasko B, Maguire F, Washington MA, Kua SC, Burpo FJ, Barnhill JC. Comparing Methods to Genetically Engineer Bacteriophage and Increase Host Range. Mil Med 2024; 189:e1488-e1496. [PMID: 38780999 DOI: 10.1093/milmed/usae226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Revised: 11/15/2023] [Accepted: 04/30/2024] [Indexed: 05/25/2024] Open
Abstract
INTRODUCTION Antibacterial resistance is an emerging problem in military medicine. Disruptions to the health care systems in war-torn countries that result from ongoing conflict can potentially exacerbate this problem and increase the risk to U.S. forces in the deployed environment. Therefore, novel therapies are needed to mitigate the impact of these potentially devastating infections on military operations. Bacteriophages are viruses that infect and kill bacteria. They can be delivered as therapeutic agents and offer a promising alternative to traditional antibiotic chemotherapy. There are several potential benefits to their use, including high specificity and comparative ease of use in the field setting. However, the process of engineering phages for military medical applications can be a laborious and time-consuming endeavor. This review examines available techniques and compares their efficacy. MATERIALS AND METHODS This review evaluates the scientific literature on the development and application of four methods of bacteriophage genome engineering and their consideration in the context of military applications. Preffered Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were followed for a systematic review of available literature that met criteria for analysis and inclusion. The research completed for this review article originated from the United States Military Academy's library "Scout" search engine, which compiles results from 254 available databases (including PubMed, Google Scholar, and SciFinder). Particular attention was focused on identifying useful mechanistic insight into the nature of the engineering technique, the ease of use, and the applicability of the technique to countering the problem of antimicrobial resistance in the military setting. RESULTS A total of 52 studies were identified that met inclusion criteria following PRISMA guidelines. The bioengineering techniques analyzed included homologous recombination (12 articles), in vivo recombineering (9 articles), bacteriophage recombineering of electroporated DNA (7 articles), and the CRISPR-Cas system (10 articles). Rates of success and fidelity varied across each platform, and comparative benefits and drawbacks are considered. CONCLUSIONS Each of the phage engineering techniques addressed herein varies in amount of effort and overall success rate. CRISPR-Cas-facilitated modification of phage genomes presents a highly efficient method that does not require a lengthy purification and screening process. It therefore appears to be the method best suited for military medical applications.
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Affiliation(s)
- Christopher J Kovacs
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
- Defense Threat Reduction Agency, Fort Belvoir, VA 22060, USA
| | - Alessia Antonacci
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Abigail Graham
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Faye Jessup
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - William Rankin
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Brianna Brasko
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Fiona Maguire
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Michael A Washington
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - Siang C Kua
- Department of Clinical Investigation, Dwight D. Eisenhower Army Medical Center, Fort Gordon, GA 30905, USA
| | - F John Burpo
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
| | - Jason C Barnhill
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY 10996, USA
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2
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Jacoby ML, Hogg GD, Assaad MR, Williamson KE. Seasonal trends in lysogeny in an Appalachian oak-hickory forest soil. Appl Environ Microbiol 2024; 90:e0140823. [PMID: 38084945 PMCID: PMC10807418 DOI: 10.1128/aem.01408-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2023] [Accepted: 10/22/2023] [Indexed: 12/23/2023] Open
Abstract
Since 1989, investigations into viral ecology have revealed how bacteriophages can influence microbial dynamics within ecosystems at global scales. Most of the information we know about temperate phages, which can integrate themselves into the host genome and remain dormant via a process called lysogeny, has come from research in aquatic ecosystems. Soil environments remain under-studied, and more research is necessary to fully understand the range of impacts phage infections have on the soil bacteria they infect. The aims of this study were to compare the efficacy of different prophage-inducing agents and to elucidate potential temporal trends in lysogeny within a soil bacterial community. In addition to mitomycin C and acyl-homoserine lactones, our results indicated that halosulfuron methyl herbicides may also be potent inducing agents. In optimizing chemical induction assays, we determined that taking steps to reduce background virus particles and starve cells was critical in obtaining consistent results. A clear seasonal trend in inducible lysogeny was observed in an Appalachian oak-hickory forest soil. The average monthly air temperature was negatively correlated with inducible fraction and burst size, supporting the idea that lysogeny provides a mechanism for phage persistence when temperatures are low and host metabolism is slower. Furthermore, the inducible fraction was negatively correlated with both soil bacterial and soil viral abundance, supporting the idea that lysogeny provides a mechanism for temperate phage persistence when host density is lower. The present study is the first of its kind to reveal clear seasonal trends in inducible lysogeny in any soil.IMPORTANCELysogeny is a relationship in which certain viruses that infect bacteria (phages) may exist within their bacterial host cell as a segment of nucleic acid. In this state, the phage genome is protected from environmental damage and retains the potential to generate progeny particles in the future. It is thought that lysogeny provides a mechanism for long-term persistence for phages when host density is low or hosts are starved-two conditions likely to be found in soils. In the present study, we provide the first known evidence for a seasonal trend in lysogeny in a forest soil. Based on clear relationships observed between lysogeny, temperature, and soil microbial abundance, we find support for previous hypotheses regarding the factors governing lysogeny.
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Affiliation(s)
- Melaina L. Jacoby
- Center for Vaccine Research, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham D. Hogg
- American Type Culture Collection, Manassas, Virginia, USA
| | | | - Kurt E. Williamson
- Biology Department, College of William & Mary, Williamsburg, Virginia, USA
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Zamora-Caballero S, Chmielowska C, Quiles-Puchalt N, Brady A, Gallego Del Sol F, Mancheño-Bonillo J, Felipe-Ruíz A, Meijer WJJ, Penadés JR, Marina A. Antagonistic interactions between phage and host factors control arbitrium lysis-lysogeny decision. Nat Microbiol 2024; 9:161-172. [PMID: 38177302 PMCID: PMC10769878 DOI: 10.1038/s41564-023-01550-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 11/07/2023] [Indexed: 01/06/2024]
Abstract
Phages can use a small-molecule communication arbitrium system to coordinate lysis-lysogeny decisions, but the underlying mechanism remains unknown. Here we determined that the arbitrium system in Bacillus subtilis phage phi3T modulates the bacterial toxin-antitoxin system MazE-MazF to regulate the phage life cycle. We show that phi3T expresses AimX and YosL, which bind to and inactivate MazF. AimX also inhibits the function of phi3T_93, a protein that promotes lysogeny by binding to MazE and releasing MazF. Overall, these mutually exclusive interactions promote the lytic cycle of the phage. After several rounds of infection, the phage-encoded AimP peptide accumulates intracellularly and inactivates the phage antiterminator AimR, a process that eliminates aimX expression from the aimP promoter. Therefore, when AimP increases, MazF activity promotes reversion back to lysogeny, since AimX is absent. Altogether, our study reveals the evolutionary strategy used by arbitrium to control lysis-lysogeny by domesticating and fine-tuning a phage-defence mechanism.
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Grants
- Wellcome Trust
- Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)
- Regional Government of Valencia | Conselleria d'Educació, Investigació, Cultura i Esport (Conselleria d'Educació, Investigació, Cultura i Esport de la Generalitat Valenciana)
- NYSE Euronext
- European Commission NextGenerationEU fund (EU 2020/2094), through CSIC’s Global Health Platform (PTI Salud Global). Block allocation group (BAG) DLS Proposal MX28394, ALBA Proposal 2020074406 and ESRF proposal MX-2452
- grants PID2019-108541GB-I00 and PID2022-137201NB-I00 from Spanish Government (Ministerio de Ciencia e Innovación), PROMETEO/2020/012 by Valencian Government
- MR/M003876/1, MR/V000772/1 and MR/S00940X/1 from the Medical Research Council (UK), BB/N002873/1, BB/V002376/1 and BB/S003835/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), ERC-ADG-2014 Proposal n° 670932 Dut-signal (from EU), and Wellcome Trust 201531/Z/16/Z
- RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)
- RCUK | Medical Research Council (MRC)
- Wellcome Trust (Wellcome)
- EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)
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Affiliation(s)
- Sara Zamora-Caballero
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Cora Chmielowska
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
| | - Nuria Quiles-Puchalt
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Department of Biomedical Sciences, Faculty of Health Sciences, Universidad CEU Cardenal Herrera, CEU Universities, Alfara del Patriarca, Spain
| | - Aisling Brady
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, UK
| | - Francisca Gallego Del Sol
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Javier Mancheño-Bonillo
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Alonso Felipe-Ruíz
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain
| | - Wilfried J J Meijer
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Universidad Autónoma, Cantoblanco, Madrid, Spain
| | - José R Penadés
- Centre for Bacterial Resistance Biology, Imperial College London, London, UK.
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV)-CSIC and CIBER de Enfermedades Raras (CIBERER)-ISCIII, Valencia, Spain.
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Jansen D, Falony G, Vieira-Silva S, Simsek C, Marcelis T, Caenepeel C, Machiels K, Raes J, Vermeire S, Matthijnssens J. Community Types of the Human Gut Virome are Associated with Endoscopic Outcome in Ulcerative Colitis. J Crohns Colitis 2023; 17:1504-1513. [PMID: 37052201 PMCID: PMC10588789 DOI: 10.1093/ecco-jcc/jjad061] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Indexed: 04/14/2023]
Abstract
BACKGROUND Inflammatory bowel disease [IBD] is a major debilitating disease. Recently, the gut microbiota has gained attention as an important factor involved in the pathophysiology of IBD. As a complement to the established bacterial 'enterotypes' associated with IBD, we focused here on viruses. We investigated the intestinal virome of IBD patients undergoing biological therapy for the presence of virome configurations associated with IBD, and to uncover how those configurations are associated with therapeutic success. METHODS Viral-like particle enrichment followed by deep sequencing was performed on 432 faecal samples from 181 IBD patients starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into 'viral community types', respectively. RESULTS Patients were stratified based on unsupervised clustering into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated with the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Crassvirales and Malgrandaviricetes phages. During post-interventional analysis, endoscopic outcome was associated with gut virome composition. Remitting UC patients had a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Pre-interventional analyses also identified five novel phages associated with treatment success. CONCLUSIONS This study proposed two gut virome configurations that may be involved in the pathophysiology of IBD. Interestingly, those viral configurations are further associated with therapeutic success, suggesting a potential clinical relevance.
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Affiliation(s)
- Daan Jansen
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Gwen Falony
- KU Leuven, Department of Microbiology Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
- Center for Microbiology, VIB, B-3000 Leuven, Belgium
| | - Sara Vieira-Silva
- KU Leuven, Department of Microbiology Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
- Institute of Medical Microbiology and Hygiene, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
- Institute of Molecular Biology (IMB), Mainz, Germany
| | - Ceren Simsek
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Tine Marcelis
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
| | - Clara Caenepeel
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Kathleen Machiels
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jeroen Raes
- KU Leuven, Department of Microbiology Immunology and Transplantation, Rega Institute, Laboratory of Molecular Bacteriology, Leuven, Belgium
- Center for Microbiology, VIB, B-3000 Leuven, Belgium
| | - Séverine Vermeire
- KU Leuven, Translational Research Center for Gastrointestinal Disorders (TARGID), University Hospitals Leuven, Leuven, Belgium
| | - Jelle Matthijnssens
- KU Leuven, Department of Microbiology, Immunology and Transplantation, Rega Institute, Laboratory of Viral Metagenomics, Leuven, Belgium
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5
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Chee MSJ, Serrano E, Chiang YN, Harling-Lee J, Man R, Bacigalupe R, Fitzgerald JR, Penadés JR, Chen J. Dual pathogenicity island transfer by piggybacking lateral transduction. Cell 2023; 186:3414-3426.e16. [PMID: 37541198 DOI: 10.1016/j.cell.2023.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Revised: 03/30/2023] [Accepted: 07/03/2023] [Indexed: 08/06/2023]
Abstract
Lateral transduction (LT) is the process by which temperate phages mobilize large sections of bacterial genomes. Despite its importance, LT has only been observed during prophage induction. Here, we report that superantigen-carrying staphylococcal pathogenicity islands (SaPIs) employ a related but more versatile and complex mechanism of gene transfer to drive chromosomal hypermobility while self-transferring with additional virulence genes from the host. We found that after phage infection or prophage induction, activated SaPIs form concatamers in the bacterial chromosome by switching between parallel genomic tracks in replication bubbles. This dynamic life cycle enables SaPIbov1 to piggyback its LT of staphylococcal pathogenicity island vSaα, which encodes an array of genes involved in host-pathogen interactions, allowing both islands to be mobilized intact and transferred in a single infective particle. Our findings highlight previously unknown roles of pathogenicity islands in bacterial virulence and show that their evolutionary impact extends beyond the genes they carry.
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Affiliation(s)
- Melissa Su Juan Chee
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Ester Serrano
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Yin Ning Chiang
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Joshua Harling-Lee
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - Rebecca Man
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - Rodrigo Bacigalupe
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH259RG, UK
| | - José R Penadés
- School of Infection and Immunity, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK; Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113 Moncada, Spain; Centre for Bacterial Resistance Biology, Imperial College London, London SW7 2AZ, UK.
| | - John Chen
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore.
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6
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Hwang S, Kang JY. To burst or hide. Structure 2023; 31:893-894. [PMID: 37541191 DOI: 10.1016/j.str.2023.07.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 07/07/2023] [Accepted: 07/11/2023] [Indexed: 08/06/2023]
Abstract
The transcription activator of the λ phage, CII, determines whether the phage will undergo the lytic or the lysogenic pathway. In a report by Zhao et al. in this issue of Structure, the cryo-EM structure of the λCII-dependent transcription activation complex reveals how λCII activates the PRE promoter to turn on the lysogenic pathway.
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Affiliation(s)
- Seungha Hwang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea
| | - Jin Young Kang
- Department of Chemistry, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.
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7
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King RA, Babbs M, Baugh K, Hamilton C. Isolation and Characterization of Phages That Bypass the Requirement for RNA-Mediated Antitermination. PHAGE (NEW ROCHELLE, N.Y.) 2023; 4:82-89. [PMID: 37350996 PMCID: PMC10282786 DOI: 10.1089/phage.2023.0008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/24/2023]
Abstract
Introduction The rpoCY75N mutation in the zinc-binding domain of the β' subunit of Escherichia coli RNA polymerase blocks the RNA-based mechanism of transcription antitermination utilized by bacteriophage HK022. Materials and Methods Mutant phages that overcome the block imposed by the rpoCY75N mutation are described. These phages, designated "orc" (overcomes rpoC), carry mutations that create new promoters. Promoter activity was assessed by cloning the respective regions from the wild-type and orc phages into a promoterless lacZ reporter vector. Results Reporter assays showed that the sequence originating from orc phages had significant promoter activity when compared with the equivalent sequence cloned from the parental phage. Conclusions The newly created promoters facilitate the expression of phage genes that are essential for growth on the rpoCY75N strain by bypassing transcription terminators. The small plaque phenotype of orc phages, when grown on the mutant host, suggests that suppression of the rpoCY75N mutation is incomplete.
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Affiliation(s)
- Rodney A. King
- Biology Department, Western Kentucky University, Bowling Green, Kentucky, USA
| | - Millicent Babbs
- Owensboro Family Medicine, University of Louisville, Owensboro, Kentucky, USA
| | - Kimberly Baugh
- Department of Pharmacy, Franciscan Health Lafayette East, Lafayette, Indiana, USA
| | - Courtney Hamilton
- Department of Psychiatry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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8
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Prolič-Kalinšek M, Volkov AN, Hadži S, Van Dyck J, Bervoets I, Charlier D, Loris R. Structural basis of DNA binding by YdaT, a functional equivalent of the CII repressor in the cryptic prophage CP-933P from Escherichia coli O157:H7. Acta Crystallogr D Struct Biol 2023; 79:245-258. [PMID: 36876434 PMCID: PMC9986795 DOI: 10.1107/s2059798323001249] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
YdaT is a functional equivalent of the CII repressor in certain lambdoid phages and prophages. YdaT from the cryptic prophage CP-933P in the genome of Escherichia coli O157:H7 is functional as a DNA-binding protein and recognizes a 5'-TTGATTN6AATCAA-3' inverted repeat. The DNA-binding domain is a helix-turn-helix (HTH)-containing POU domain and is followed by a long α-helix (α6) that forms an antiparallel four-helix bundle, creating a tetramer. The loop between helix α2 and the recognition helix α3 in the HTH motif is unusually long compared with typical HTH motifs, and is highly variable in sequence and length within the YdaT family. The POU domains have a large degree of freedom to move relative to the helix bundle in the free structure, but their orientation becomes fixed upon DNA binding.
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Affiliation(s)
- Maruša Prolič-Kalinšek
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Alexander N Volkov
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Večna pot 113, 1000 Ljubljana, Slovenia
| | - Jeroen Van Dyck
- Department of Chemistry, Universiteit Antwerpen, Groenenborgerlaan 171, 2020 Antwerpen, Belgium
| | - Indra Bervoets
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Daniel Charlier
- Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
| | - Remy Loris
- Structural Biology Brussels, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussel, Belgium
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Miyata T, Taniguchi I, Nakamura K, Gotoh Y, Yoshimura D, Itoh T, Hirai S, Yokoyama E, Ohnishi M, Iyoda S, Ogura Y, Hayashi T. Alteration of a Shiga toxin-encoding phage associated with a change in toxin production level and disease severity in Escherichia coli. Microb Genom 2023; 9:mgen000935. [PMID: 36821793 PMCID: PMC9997748 DOI: 10.1099/mgen.0.000935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023] Open
Abstract
Among the nine clades of Shiga toxin (Stx)-producing Escherichia coli O157:H7, clade 8 is thought to be highly pathogenic, as it causes severe disease more often than other clades. Two subclades have been proposed, but there are conflicting reports on intersubclade differences in Stx2 levels, although Stx2 production is a risk factor for severe disease development. The global population structure of clade 8 has also yet to be fully elucidated. Here, we present genome analyses of a global clade 8 strain set (n=510), including 147 Japanese strains sequenced in this study. The complete genome sequences of 18 of the 147 strains were determined to perform detailed clade-wide genome analyses together with 17 publicly available closed genomes. Intraclade variations in Stx2 production level and disease severity were also re-evaluated within the phylogenetic context. Based on phylogenomic analysis, clade 8 was divided into four lineages corresponding to the previously proposed SNP genotypes (SGs): SG8_30, SG8_31A, SG8_31B and SG8_32. SG8_30 and the common ancestor of the other SGs were first separated, with SG8_31A and SG8_31B emerging from the latter and SG8_32 emerging from SG8_31B. Comparison of 35 closed genomes revealed the overall structure of chromosomes and pO157 virulence plasmids and the prophage contents to be well conserved. However, Stx2a phages exhibit notable genomic diversity, even though all are integrated into the argW locus, indicating that subtype changes in Stx2a phage occurred from the γ subtype to its variant (γ_v1) in SG8_31A and from γ to δ in SG8_31B and SG8_32 via replacement of parts or almost entire phage genomes, respectively. We further show that SG8_30 strains (all carrying γ Stx2a phages) produce significantly higher levels of Stx2 and cause severe disease more frequently than SG8_32 strains (all carrying δ Stx2a phages). Clear conclusions on SG8_31A and SG8_31B cannot be made due to the small number of strains available, but as SG8_31A (carrying γ_v1 Stx2a phages) contains strains that produce much more Stx2 than SG8_30 strains, attention should also be paid to this SG.
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Affiliation(s)
- Tatsuya Miyata
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Department of Pediatrics, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Itsuki Taniguchi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Keiji Nakamura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Yasuhiro Gotoh
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
| | - Dai Yoshimura
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Takehiko Itoh
- School of Life Science and Technology, Tokyo Institute of Technology, Meguro, Tokyo 152-8550, Japan
| | - Shinichiro Hirai
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan.,Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Musashi-Murayama, Tokyo 208-0011, Japan
| | - Eiji Yokoyama
- Division of Bacteriology, Chiba Prefectural Institute of Public Health, Chiba 260-8715, Japan
| | - Makoto Ohnishi
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Sunao Iyoda
- Department of Bacteriology I, National Institute of Infectious Diseases, Shinjuku, Tokyo 162-8640, Japan
| | - Yoshitoshi Ogura
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan.,Division of Microbiology, Department of Infectious Medicine, Kurume University School of Medicine, Kurume, Fukuoka 830-0011, Japan
| | - Tetsuya Hayashi
- Department of Bacteriology, Graduate School of Medical Sciences, Kyushu University, Fukuoka 812-8582, Japan
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10
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Feiss M, Young R, Ramsey J, Adhya S, Georgopoulos C, Hendrix RW, Hatfull GF, Gilcrease EB, Casjens SR. Hybrid Vigor: Importance of Hybrid λ Phages in Early Insights in Molecular Biology. Microbiol Mol Biol Rev 2022; 86:e0012421. [PMID: 36165780 PMCID: PMC9799177 DOI: 10.1128/mmbr.00124-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Laboratory-generated hybrids between phage λ and related phages played a seminal role in establishment of the λ model system, which, in turn, served to develop many of the foundational concepts of molecular biology, including gene structure and control. Important λ hybrids with phages 21 and 434 were the earliest of such phages. To understand the biology of these hybrids in full detail, we determined the complete genome sequences of phages 21 and 434. Although both genomes are canonical members of the λ-like phage family, they both carry unsuspected bacterial virulence gene types not previously described in this group of phages. In addition, we determined the sequences of the hybrid phages λ imm21, λ imm434, and λ h434 imm21. These sequences show that the replacements of λ DNA by nonhomologous segments of 21 or 434 DNA occurred through homologous recombination in adjacent sequences that are nearly identical in the parental phages. These five genome sequences correct a number of errors in published sequence fragments of the 21 and 434 genomes, and they point out nine nucleotide differences from Sanger's original λ sequence that are likely present in most extant λ strains in laboratory use today. We discuss the historical importance of these hybrid phages in the development of fundamental tenets of molecular biology and in some of the earliest gene cloning vectors. The 434 and 21 genomes reinforce the conclusion that the genomes of essentially all natural λ-like phages are mosaics of sequence modules from a pool of exchangeable segments.
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Affiliation(s)
- Michael Feiss
- Department of Microbiology and Immunology, Carver College of Medicine, University of Iowa, Iowa City, Iowa, USA
| | - Ryland Young
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Jolene Ramsey
- Center for Phage Technology, Texas A&M AgriLife Research, College Station, Texas, USA
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Sankar Adhya
- Laboratory of Molecular Biology, Center for Cancer Research, The National Cancer Institute, Bethesda, Maryland, USA
| | - Costa Georgopoulos
- Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Roger W. Hendrix
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Graham F. Hatfull
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Pittsburgh Bacteriophage Institute, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Eddie B. Gilcrease
- Department of Civil and Environmental Engineering, University of Utah, Salt Lake City, Utah, USA
| | - Sherwood R. Casjens
- Division of Microbiology and Immunology, Pathology Department, University of Utah School of Medicine, Salt Lake City, Utah, USA
- School of Biological Sciences, University of Utah, Salt Lake City, Utah, USA
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11
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Lee HJ, Kim HJ, Lee SJ. Control of λ Lysogenic Escherichia coli Cells by Synthetic λ Phage Carrying cIantisense. ACS Synth Biol 2022; 11:3829-3835. [PMID: 36326101 PMCID: PMC9680875 DOI: 10.1021/acssynbio.2c00409] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Indexed: 11/05/2022]
Abstract
Enterobacterial phage λ is a temperate phage that infects Escherichia coli and has a lytic-lysogenic life cycle. CI, a λ repressor, regulates the expression of lytic transcripts and acts as a major genetic switch that determines the lysogenic state. To manipulate the genome of phage λ, the CRISPR-Cas9 genome editing system was constructed in lysogenic E. coli MG1655 cells. For instance, we successfully changed cI857 to cIWT in the phage genome through Cas9-mediated single-nucleotide editing. A lytic phage was prepared by introducing an amber mutation in the middle of the cI gene, but it could not lyse lysogenic MG1655 cells. We prepared a phage expressing cI antisense mRNA by reverse substitution of the cI gene. Lysis of λ cI857 lysogenic cells occurred by the infection of the λ cIantisense. These results suggest an effective lysogenic cell control method by a synthetic phage expressing antisense mRNA of the genetic switch gene. It is expected to be applied as a tool to control harmful lysogenic microorganisms.
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Affiliation(s)
- Ho Joung Lee
- Department of Systems Biotechnology
and Institute of Microbiomics, Chung-Ang
University, Anseong 17546, Republic of Korea
| | - Hyun Ju Kim
- Department of Systems Biotechnology
and Institute of Microbiomics, Chung-Ang
University, Anseong 17546, Republic of Korea
| | - Sang Jun Lee
- Department of Systems Biotechnology
and Institute of Microbiomics, Chung-Ang
University, Anseong 17546, Republic of Korea
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12
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Lakshminarasimhan A. Prophage induction therapy: Activation of the lytic phase in prophages for the elimination of pathogenic bacteria. Med Hypotheses 2022. [DOI: 10.1016/j.mehy.2022.110980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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13
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Miguel-Romero L, Alqasmi M, Bacarizo J, Tan JA, Cogdell RJ, Chen J, Byron O, Christie GE, Marina A, Penadés JR. Non-canonical Staphylococcus aureus pathogenicity island repression. Nucleic Acids Res 2022; 50:11109-11127. [PMID: 36200825 PMCID: PMC9638917 DOI: 10.1093/nar/gkac855] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 09/08/2022] [Accepted: 09/23/2022] [Indexed: 11/14/2022] Open
Abstract
Mobile genetic elements control their life cycles by the expression of a master repressor, whose function must be disabled to allow the spread of these elements in nature. Here, we describe an unprecedented repression-derepression mechanism involved in the transfer of Staphylococcus aureus pathogenicity islands (SaPIs). Contrary to the classical phage and SaPI repressors, which are dimers, the SaPI1 repressor StlSaPI1 presents a unique tetrameric conformation never seen before. Importantly, not just one but two tetramers are required for SaPI1 repression, which increases the novelty of the system. To derepress SaPI1, the phage-encoded protein Sri binds to and induces a conformational change in the DNA binding domains of StlSaPI1, preventing the binding of the repressor to its cognate StlSaPI1 sites. Finally, our findings demonstrate that this system is not exclusive to SaPI1 but widespread in nature. Overall, our results characterize a novel repression-induction system involved in the transfer of MGE-encoded virulence factors in nature.
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Affiliation(s)
- Laura Miguel-Romero
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ, UK
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
| | - Mohammed Alqasmi
- Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, G12 8TA, UK
- College of Applied Medical Sciences, Shaqra University, Shaqra City 15572, Saudi Arabia
| | - Julio Bacarizo
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ, UK
- Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113 Moncada, Spain
| | - Jason A Tan
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | | | - John Chen
- Infectious Diseases Translational Research Programme and Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore
| | - Olwyn Byron
- School of Life Sciences, University of Glasgow, Glasgow, G12 8QQ,UK
| | - Gail E Christie
- Department of Microbiology and Immunology, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Alberto Marina
- Instituto de Biomedicina de Valencia (IBV), CSIC and CIBER de Enfermedades Raras (CIBERER), Valencia, Spain
| | - José R Penadés
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, SW7 2AZ, UK
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14
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Abstract
Mycobacteriophages-bacteriophages infecting Mycobacterium hosts-contribute substantially to our understanding of viral diversity and evolution, provide resources for advancing Mycobacterium genetics, are the basis of high-impact science education programs, and show considerable therapeutic potential. Over 10,000 individual mycobacteriophages have been isolated by high school and undergraduate students using the model organism Mycobacterium smegmatis mc2155 and 2,100 have been completely sequenced, giving a high-resolution view of the phages that infect a single common host strain. The phage genomes are revealed to be highly diverse and architecturally mosaic and are replete with genes of unknown function. Mycobacteriophages have provided many widely used tools for Mycobacterium genetics including integration-proficient vectors and recombineering systems, as well as systems for efficient delivery of reporter genes, transposons, and allelic exchange substrates. The genomic insights and engineering tools have facilitated exploration of phages for treatment of Mycobacterium infections, although their full therapeutic potential has yet to be realized.
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15
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Homologs of the Escherichia coli F Element Protein TraR, Including Phage Lambda Orf73, Directly Reprogram Host Transcription. mBio 2022; 13:e0095222. [PMID: 35583320 PMCID: PMC9239242 DOI: 10.1128/mbio.00952-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Bacterial cells and their associated plasmids and bacteriophages encode numerous small proteins of unknown function. One example, the 73-amino-acid protein TraR, is encoded by the transfer operon of the conjugative F plasmid of Escherichia coli. TraR is a distant homolog of DksA, a protein found in almost all proteobacterial species that is required for ppGpp to regulate transcription during the stringent response. TraR and DksA increase or decrease transcription initiation depending on the kinetic features of the promoter by binding directly to RNA polymerase without binding to DNA. Unlike DksA, whose full activity requires ppGpp as a cofactor, TraR is fully active by itself and unaffected by ppGpp. TraR belongs to a family of divergent proteins encoded by proteobacterial bacteriophages and other mobile elements. Here, we experimentally addressed whether other members of the TraR family function like the F element-encoded TraR. Purified TraR and all 5 homologs that were examined bound to RNA polymerase, functioned at lower concentrations than DksA, and complemented a dksA-null strain for growth on minimal medium. One of the homologs, λ Orf73, encoded by bacteriophage lambda, was examined in greater detail. λ Orf73 slowed host growth and increased phage burst size. Mutational analysis suggested that λ Orf73 and TraR have a similar mechanism for inhibiting rRNA and r-protein promoters. We suggest that TraR and its homologs regulate host transcription to divert cellular resources to phage propagation or conjugation without induction of ppGpp and a stringent response.
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16
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Landa KJ, Mossman LM, Whitaker RJ, Rapti Z, Clifton SM. Phage-Antibiotic Synergy Inhibited by Temperate and Chronic Virus Competition. Bull Math Biol 2022; 84:54. [PMID: 35316421 DOI: 10.1007/s11538-022-01006-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Accepted: 02/10/2022] [Indexed: 12/12/2022]
Abstract
As antibiotic resistance grows more frequent for common bacterial infections, alternative treatment strategies such as phage therapy have become more widely studied in the medical field. While many studies have explored the efficacy of antibiotics, phage therapy, or synergistic combinations of phages and antibiotics, the impact of virus competition on the efficacy of antibiotic treatment has not yet been considered. Here, we model the synergy between antibiotics and two viral types, temperate and chronic, in controlling bacterial infections. We demonstrate that while combinations of antibiotic and temperate viruses exhibit synergy, competition between temperate and chronic viruses inhibits bacterial control with antibiotics. In fact, our model reveals that antibiotic treatment may counterintuitively increase the bacterial load when a large fraction of the bacteria are antibiotic resistant, and both chronic and temperate phages are present.
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Affiliation(s)
- Kylie J Landa
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA
| | - Lauren M Mossman
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA
| | - Rachel J Whitaker
- Department of Microbiology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Zoi Rapti
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
- Department of Mathematics, University of Illinois at Urbana-Champaign, Urbana, IL, 61801, USA
| | - Sara M Clifton
- Department of Mathematics, Statistics, and Computer Science, St. Olaf College, Northfield, MN, 55057, USA.
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17
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Chitboonthavisuk C, Luo CH, Huss P, Fernholz M, Raman S. Engineering a Dynamic Controllable Infectivity Switch in Bacteriophage T7. ACS Synth Biol 2022; 11:286-296. [PMID: 34985866 PMCID: PMC9059553 DOI: 10.1021/acssynbio.1c00414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Abstract
Transcriptional repressors play an important role in regulating phage life cycle. Here, we examine how synthetic transcription repressors can be used in bacteriophage T7 to create a dynamic, controllable infectivity switch. We engineered T7 phage by replacing a large region of the early phage genome with different combinations of ligand-responsive promoters and ribosome binding sites (RBS) designed to control the phage RNA polymerase, gp1. Phages with engineered infectivity switch are fully viable at levels comparable to wildtype T7, when not repressed, indicating the phage can be engineered without loss of fitness. The most effective switch used a TetR-responsive promoter and an attenuated RBS, resulting in a 2-fold increase in latent period and a 10-fold decrease in phage titer when repressed. Phage activity can be further tuned using different inducer concentrations. Our study provides a proof of concept for how a simple synthetic circuit introduced into the phage genome enables user control over phage infectivity.
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Affiliation(s)
- Chutikarn Chitboonthavisuk
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Chun Huai Luo
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Phil Huss
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Microbiology Doctoral Training Program, University of Wisconsin-Madison
| | - Mikayla Fernholz
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Srivatsan Raman
- Dept. of Biochemistry, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Bacteriology, Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
- Dept. of Chemical & Biological Eng., Univ. of Wisconsin-Madison, Madison, WI, 53706, USA
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18
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Bistable Expression of a Toxin-Antitoxin System Located in a Cryptic Prophage of Escherichia coli O157:H7. mBio 2021; 12:e0294721. [PMID: 34844426 PMCID: PMC8630535 DOI: 10.1128/mbio.02947-21] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Type II toxin-antitoxin (TA) systems are classically composed of two genes that encode a toxic protein and a cognate antitoxin protein. Both genes are organized in an operon whose expression is autoregulated at the level of transcription by the antitoxin-toxin complex, which binds operator DNA through the antitoxin’s DNA-binding domain. Here, we investigated the transcriptional regulation of a particular TA system located in the immunity region of a cryptic lambdoid prophage in the Escherichia coli O157:H7 EDL933 strain. This noncanonical paaA2-parE2 TA operon contains a third gene, paaR2, that encodes a transcriptional regulator that was previously shown to control expression of the TA. We provide direct evidence that the PaaR2 is a transcriptional regulator which shares functional similarities to the lambda CI repressor. Expression of the paaA2-parE2 TA operon is regulated by two other transcriptional regulators, YdaS and YdaT, encoded within the same region. We argue that YdaS and YdaT are analogous to lambda Cro and CII and that they do not constitute a TA system, as previously debated. We show that PaaR2 primarily represses the expression of YdaS and YdaT, which in turn controls the expression of paaR2-paaA2-parE2 operon. Overall, our results show that the paaA2-parE2 TA is embedded in an intricate lambdoid prophage-like regulation network. Using single-cell analysis, we observed that the entire locus exhibits bistability, which generates diversity of expression in the population. Moreover, we confirmed that paaA2-parE2 is addictive and propose that it could limit genomic rearrangements within the immunity region of the CP-933P cryptic prophage.
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19
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Bacteriophage self-counting in the presence of viral replication. Proc Natl Acad Sci U S A 2021; 118:2104163118. [PMID: 34916284 DOI: 10.1073/pnas.2104163118] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/04/2021] [Indexed: 11/18/2022] Open
Abstract
When host cells are in low abundance, temperate bacteriophages opt for dormant (lysogenic) infection. Phage lambda implements this strategy by increasing the frequency of lysogeny at higher multiplicity of infection (MOI). However, it remains unclear how the phage reliably counts infecting viral genomes even as their intracellular number increases because of replication. By combining theoretical modeling with single-cell measurements of viral copy number and gene expression, we find that instead of hindering lambda's decision, replication facilitates it. In a nonreplicating mutant, viral gene expression simply scales with MOI rather than diverging into lytic (virulent) and lysogenic trajectories. A similar pattern is followed during early infection by wild-type phage. However, later in the infection, the modulation of viral replication by the decision genes amplifies the initially modest gene expression differences into divergent trajectories. Replication thus ensures the optimal decision-lysis upon single-phage infection and lysogeny at higher MOI.
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20
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Fillol-Salom A, Bacigalupe R, Humphrey S, Chiang YN, Chen J, Penadés JR. Lateral transduction is inherent to the life cycle of the archetypical Salmonella phage P22. Nat Commun 2021; 12:6510. [PMID: 34751192 PMCID: PMC8575938 DOI: 10.1038/s41467-021-26520-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 10/01/2021] [Indexed: 11/08/2022] Open
Abstract
Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with early prophage excision followed by DNA replication and packaging (ERP). This temporal program is considered universal for P22-like temperate phages, though there is no direct evidence to support the timing and sequence of these events. Here we report that the long-standing ERP program is an observation of the experimentally favored Salmonella phage P22 tsc229 heat-inducible mutant, and that wild-type P22 actually follows the replication-packaging-excision (RPE) program. We find that P22 tsc229 excises early after induction, but P22 delays excision to just before it is detrimental to phage production. This allows P22 to engage in lateral transduction. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation.
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Affiliation(s)
- Alfred Fillol-Salom
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK
| | - Rodrigo Bacigalupe
- Dep. Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113, Moncada, Spain
- The Rega Institute for Medical Research, KU Leuven, 3000, Leuven, Belgium
| | - Suzanne Humphrey
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK
| | - Yin Ning Chiang
- Department of Microbiology and Immunology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, Singapore
| | - John Chen
- Department of Microbiology and Immunology, Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore, Singapore.
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8TA, UK.
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, London, SW7 2AZ, UK.
- Dep. Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113, Moncada, Spain.
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21
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Elghondakly A, Wu CH, Klupt S, Goodson J, Winkler WC. A NusG Specialized Paralog That Exhibits Specific, High-Affinity RNA-Binding Activity. J Mol Biol 2021; 433:167100. [PMID: 34119489 DOI: 10.1016/j.jmb.2021.167100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 05/17/2021] [Accepted: 06/05/2021] [Indexed: 10/21/2022]
Abstract
Bacterial NusG associates with RNA polymerase (RNAP) through its N-terminal domain, while the C-terminal domain (CTD) forms dynamic interactions with Rho, S10, NusB and NusA to affect transcription elongation. While virtually all bacteria encode for a core NusG, many also synthesize paralogs that transiently bind RNAP to alter expression of targeted genes. Yet, despite the importance of the genes they regulate, most of the subfamilies of NusG paralogs (e.g., UpxY, TaA, ActX and LoaP) have not been investigated in depth. Herein, we discover that LoaP requires a small RNA hairpin located within the 5' leader region of its targeted operons. LoaP binds the RNA element with nanomolar affinity and high specificity, in contrast to other NusG proteins, which have not been shown to exhibit RNA-binding activity. These data reveal a sequence feature that can be used to identify LoaP-regulated operons. This discovery also expands the repertoire of macromolecular interactions exhibited by the NusG CTD during transcription elongation to include an RNA ligand.
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Affiliation(s)
- Amr Elghondakly
- The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States
| | - Chih Hao Wu
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Steven Klupt
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Jonathan Goodson
- The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States
| | - Wade C Winkler
- The University of Maryland, Department of Chemistry and Biochemistry, College Park, MD, United States; The University of Maryland, Department of Cell Biology and Molecular Genetics, College Park, MD, United States.
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22
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Abstract
Bacteriophages are the most diverse and abundant biological entities on the Earth and require host bacteria to replicate. Because of this obligate relationship, in addition to the challenging conditions of surrounding environments, phages must integrate information about extrinsic and intrinsic factors when infecting their host. This integration helps to determine whether the infection becomes lytic or lysogenic, which likely influences phage spreading and long-term survival. Although a variety of environmental and physiological clues are known to modulate lysis-lysogeny decisions, the social interplay among phages and host populations has been overlooked until recently. A growing body of evidence indicates that cell-cell communication in bacteria and, more recently, peptide-based communication among phage-phage populations, affect phage-host interactions by controlling phage lysis-lysogeny decisions and phage counter-defensive strategies in bacteria. Here, we explore and discuss the role of signal molecules as well as quorum sensing and quenching factors that mediate phage-host interactions. Our aim is to provide an overview of population-dependent mechanisms that influence phage replication, and how social communication may affect the dynamics and evolution of microbial communities, including their implications in phage therapy.
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23
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Temperate and chronic virus competition leads to low lysogen frequency. J Theor Biol 2021; 523:110710. [PMID: 33839160 DOI: 10.1016/j.jtbi.2021.110710] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Revised: 04/04/2021] [Accepted: 04/05/2021] [Indexed: 11/23/2022]
Abstract
The canonical bacteriophage is obligately lytic: the virus infects a bacterium and hijacks cell functions to produce large numbers of new viruses which burst from the cell. These viruses are well-studied, but there exist a wide range of coexisting virus lifestyles that are less understood. Temperate viruses exhibit both a lytic cycle and a latent (lysogenic) cycle, in which viral genomes are integrated into the bacterial host. Meanwhile, chronic (persistent) viruses use cell functions to produce more viruses without killing the cell; chronic viruses may also exhibit a latent stage in addition to the productive stage. Here, we study the ecology of these competing viral strategies. We demonstrate the conditions under which each strategy is dominant, which aids in control of human bacterial infections using viruses. We find that low lysogen frequencies provide competitive advantages for both virus types; however, chronic viruses maximize steady state density by eliminating lysogeny entirely, while temperate viruses exhibit a non-zero 'sweet spot' lysogen frequency. Viral steady state density maximization leads to coexistence of temperate and chronic viruses, explaining the presence of multiple viral strategies in natural environments.
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24
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Abstract
Bacteriophages are viruses whose ubiquity in nature and remarkable specificity to their host bacteria enable an impressive and growing field of tunable biotechnologies in agriculture and public health. Bacteriophage capsids, which house and protect their nucleic acids, have been modified with a range of functionalities (e.g., fluorophores, nanoparticles, antigens, drugs) to suit their final application. Functional groups naturally present on bacteriophage capsids can be used for electrostatic adsorption or bioconjugation, but their impermanence and poor specificity can lead to inconsistencies in coverage and function. To overcome these limitations, researchers have explored both genetic and chemical modifications to enable strong, specific bonds between phage capsids and their target conjugates. Genetic modification methods involve introducing genes for alternative amino acids, peptides, or protein sequences into either the bacteriophage genomes or capsid genes on host plasmids to facilitate recombinant phage generation. Chemical modification methods rely on reacting functional groups present on the capsid with activated conjugates under the appropriate solution pH and salt conditions. This review surveys the current state-of-the-art in both genetic and chemical bacteriophage capsid modification methodologies, identifies major strengths and weaknesses of methods, and discusses areas of research needed to propel bacteriophage technology in development of biosensors, vaccines, therapeutics, and nanocarriers.
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Affiliation(s)
| | - Julie M. Goddard
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
| | - Sam R. Nugen
- Department of Food Science, Cornell University, Ithaca, NY 14853, USA
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25
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Tridgett M, Ababi M, Osgerby A, Ramirez Garcia R, Jaramillo A. Engineering Bacteria to Produce Pure Phage-like Particles for Gene Delivery. ACS Synth Biol 2021; 10:107-114. [PMID: 33317264 DOI: 10.1021/acssynbio.0c00467] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Natural and engineered phages have been used in many applications, but their use to deliver user-defined genetic cargoes has been hampered by contamination with replicative phage, restricting use of the technology beyond the laboratory. Here we present a method to produce transducing particles without contamination. In addition, we demonstrate the use of a helper phage-free transducing particle preparation as an antimicrobial agent. This will pave the way for the development of new phage-based technologies with greater scope than lytic phage therapy.
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Affiliation(s)
- Matthew Tridgett
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
| | - Maria Ababi
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, U.K
| | - Alexander Osgerby
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
| | - Robert Ramirez Garcia
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
| | - Alfonso Jaramillo
- School of Life Sciences, Gibbet Hill Campus, The University of Warwick, Coventry, CV4 7AL, U.K
- CNRS, Paris, 75016, France
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Abstract
Antibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship. Most bacteria and archaea are infected by latent viruses that change their physiology and responses to environmental stress. We use a population model of the bacterium-phage relationship to examine the role that latent phage play in the bacterial population over time in response to antibiotic treatment. We demonstrate that the stress induced by antibiotic administration, even if bacteria are resistant to killing by antibiotics, is sufficient to control the infection under certain conditions. This work expands the breadth of understanding of phage-antibiotic synergy to include both temperate and chronic viruses persisting in their latent form in bacterial populations. IMPORTANCE Antibiotic resistance is a growing concern for management of common bacterial infections. Here, we show that antibiotics can be effective at subinhibitory levels when bacteria carry latent phage. Our findings suggest that specific treatment strategies based on the identification of latent viruses in individual bacterial strains may be an effective personalized medicine approach to antibiotic stewardship.
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Tang Q, Feng M, Hou B, Ye J, Wu H, Zhang H. Prophage protein RacR activates lysozyme LysN, causing the growth defect of E. coli JM83. Sci Rep 2019; 9:12537. [PMID: 31467306 PMCID: PMC6715736 DOI: 10.1038/s41598-019-48690-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Accepted: 08/01/2019] [Indexed: 11/09/2022] Open
Abstract
Prophage enriched the prokaryotic genome, and their transcriptional factors improved the protein expression network of the host. In this study, we uncovered a new prophage-prophage interaction in E. coli JM83. The Rac prophage protein RacR (GenBank accession no. AVI55875.1) directly activated the transcription of φ80dlacZΔM15 prophage lysozyme encoding gene 19 (GenBank accession no. ACB02445.1, renamed it lysN, lysozyme nineteen), resulting in the growth defect of JM83. This phenomenon also occurred in DH5α, but not in BL21(DE3) and MG1655 due to the genotype differences. However, deletion of lysN could not completely rescued JM83 from the growth arrest, indicating that RacR may regulate other related targets. In addition, passivation of RacR regulation was found in the late period of growth of JM83, and it was transmissible to daughter cells. Altogether, our study revealed part of RacR regulatory network, which suggested some advanced genetic strategies in bacteria.
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Affiliation(s)
- Qiongwei Tang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Meilin Feng
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Bingbing Hou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Jiang Ye
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China
| | - Haizhen Wu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. .,Department of Applied Biology, East China University of Science and Technology, Shanghai, China.
| | - Huizhan Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai, China. .,Department of Applied Biology, East China University of Science and Technology, Shanghai, China.
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29
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Ainuddin U, Khurram M, Hasan SMR. Cloning the λ Switch: Digital and Markov Representations. IEEE Trans Nanobioscience 2019; 18:428-436. [PMID: 30946673 DOI: 10.1109/tnb.2019.2908669] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
The lysis-lysogeny switch in E. coli due to infection from lambda phage has been extensively studied and explained by scientists of molecular biology. The bacterium either survives with the viral strand of deoxyribonucleic acid (DNA) or dies producing hundreds of viruses for propagation of infection. Many proteins transcribed after infection by λ phage take part in determining the fate of the bacterium, but two proteins that play a key role in this regard are the cI and cro dimers, which are transcribed off the viral DNA. This paper presents a novel modeling mechanism for the lysis-lysogeny switch, by transferring the interactions of the main proteins, the lambda right operator and promoter regions and the ribonucleic acid (RNA) polymerase, to a finite state machine (FSM), to determine cell fate. The FSM, and thus derived is implemented in field-programmable gate array (FPGA), and simulations have been run in random conditions. A Markov model has been created for the same mechanism. Steady state analysis has been conducted for the transition matrix of the Markov model, and the results have been generated to show the steady state probability of lysis with various model values. In this paper, it is hoped to lay down guidelines to convert biological processes into computing machines.
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30
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Chen J, Quiles-Puchalt N, Chiang YN, Bacigalupe R, Fillol-Salom A, Chee MSJ, Fitzgerald JR, Penadés JR. Genome hypermobility by lateral transduction. Science 2018; 362:207-212. [PMID: 30309949 DOI: 10.1126/science.aat5867] [Citation(s) in RCA: 133] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 08/14/2018] [Indexed: 02/01/2023]
Abstract
Genetic transduction is a major evolutionary force that underlies bacterial adaptation. Here we report that the temperate bacteriophages of Staphylococcus aureus engage in a distinct form of transduction we term lateral transduction. Staphylococcal prophages do not follow the previously described excision-replication-packaging pathway but instead excise late in their lytic program. Here, DNA packaging initiates in situ from integrated prophages, and large metameric spans including several hundred kilobases of the S. aureus genome are packaged in phage heads at very high frequency. In situ replication before DNA packaging creates multiple prophage genomes so that lateral-transducing particles form during normal phage maturation, transforming parts of the S. aureus chromosome into hypermobile regions of gene transfer.
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Affiliation(s)
- John Chen
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore.
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Yin Ning Chiang
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore
| | - Rodrigo Bacigalupe
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - Alfred Fillol-Salom
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Melissa Su Juan Chee
- Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, 5 Science Drive 2, Singapore
| | - J Ross Fitzgerald
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh EH25 9RG, UK
| | - José R Penadés
- Institute of Infection, Immunity, and Inflammation, College of Medical, Veterinary, and Life Sciences, University of Glasgow, Glasgow G12 8TA, UK. .,Departamento de Ciencias Biomédicas, Universidad CEU Cardenal Herrera, 46113 Moncada, Spain.,MRC-University of Glasgow Centre for Virus Research, Glasgow G61 1QH, UK
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31
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Guan J, Ibarra D, Zeng L. The role of side tail fibers during the infection cycle of phage lambda. Virology 2018; 527:57-63. [PMID: 30463036 DOI: 10.1016/j.virol.2018.11.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Revised: 11/07/2018] [Accepted: 11/08/2018] [Indexed: 11/17/2022]
Abstract
Bacteriophage λ has served as an important model for molecular biology and different cellular processes over the past few decades. In 1992, the phage strain used in most laboratories around the world, thought of as λ wild type, was discovered to carry a mutation in the stf gene which encodes four side tail fibers. Up to now, the role of the side tail fibers during the infection cycle, especially at the single-cell level, remains largely unknown. Here we utilized fluorescent reporter systems to characterize the effect of the side tail fibers on phage infection. We found that the side tail fibers interfere with phage DNA ejection process, most likely through the binding with their receptors, OmpC, leading to a more frequent failed infection. However, the side tail fibers do not seem to affect the lysis-lysogeny decision-making or lysis time.
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Affiliation(s)
- Jingwen Guan
- Molecular and Environmental Plant Science, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - David Ibarra
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA
| | - Lanying Zeng
- Molecular and Environmental Plant Science, Texas A&M University, College Station, TX 77843, USA; Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA.
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32
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Manning KA, Quiles-Puchalt N, Penadés JR, Dokland T. A novel ejection protein from bacteriophage 80α that promotes lytic growth. Virology 2018; 525:237-247. [PMID: 30308422 DOI: 10.1016/j.virol.2018.09.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Revised: 09/28/2018] [Accepted: 09/28/2018] [Indexed: 12/30/2022]
Abstract
Many staphylococcal bacteriophages encode a minor capsid protein between the genes for the portal and scaffolding proteins. In Staphylococcus aureus bacteriophage 80α, this protein, called gp44, is essential for the production of viable phage, but dispensable for the phage-mediated mobilization of S. aureus pathogenicity islands. We show here that gp44 is not required for capsid assembly, DNA packaging or ejection of the DNA, nor for generalized transduction of plasmids. An 80α Δ44 mutant could be complemented in trans by gp44 expressed from a plasmid, indicating that gp44 plays a post-injection role in the host. Our results show that gp44 is an ejection (pilot) protein that is involved in deciding the fate of the phage DNA after injection. Our data are consistent with a model in which gp44 acts as a regulatory protein that promotes progression to the lytic cycle.
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Affiliation(s)
- Keith A Manning
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Nuria Quiles-Puchalt
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - José R Penadés
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Terje Dokland
- Department of Microbiology, University of Alabama at Birmingham, Birmingham, AL 35294, USA.
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33
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Shao Q, Cortes MG, Trinh JT, Guan J, Balázsi G, Zeng L. Coupling of DNA Replication and Negative Feedback Controls Gene Expression for Cell-Fate Decisions. iScience 2018; 6:1-12. [PMID: 30240603 PMCID: PMC6137276 DOI: 10.1016/j.isci.2018.07.006] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Revised: 05/21/2018] [Accepted: 07/09/2018] [Indexed: 11/16/2022] Open
Abstract
Cellular decision-making arises from the expression of genes along a regulatory cascade, which leads to a choice between distinct phenotypic states. DNA dosage variations, often introduced by replication, can significantly affect gene expression to ultimately bias decision outcomes. The bacteriophage lambda system has long served as a paradigm for cell-fate determination, yet the effect of DNA replication remains largely unknown. Here, through single-cell studies and mathematical modeling we show that DNA replication drastically boosts cI expression to allow lysogenic commitment by providing more templates. Conversely, expression of CII, the upstream regulator of cI, is surprisingly robust to DNA replication due to the negative autoregulation of the Cro repressor. Our study exemplifies how living organisms can not only utilize DNA replication for gene expression control but also implement mechanisms such as negative feedback to allow the expression of certain genes to be robust to dosage changes resulting from DNA replication.
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Affiliation(s)
- Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Michael G Cortes
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Applied Mathematics and Statistics, Stony Brook University, Stony Brook, NY, USA
| | - Jimmy T Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA
| | - Jingwen Guan
- Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA; Molecular and Environmental Plant Science, Texas A&M University, College Station, TX 77843, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, NY, USA; Department of Biomedical Engineering, Stony Brook University, Stony Brook, NY, USA.
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843, USA; Center for Phage Technology, Texas A&M University, College Station, TX 77843, USA; Molecular and Environmental Plant Science, Texas A&M University, College Station, TX 77843, USA.
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Complementation Studies of Bacteriophage λ O Amber Mutants by Allelic Forms of O Expressed from Plasmid, and O-P Interaction Phenotypes. Antibiotics (Basel) 2018; 7:antibiotics7020031. [PMID: 29621200 PMCID: PMC6022878 DOI: 10.3390/antibiotics7020031] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Revised: 03/25/2018] [Accepted: 04/03/2018] [Indexed: 11/17/2022] Open
Abstract
λ genes O and P are required for replication initiation from the bacteriophage λ origin site, oriλ, located within gene O. Questions have persisted for years about whether O-defects can indeed be complemented in trans. We show the effect of original null mutations in O and the influence of four origin mutations (three are in-frame deletions and one is a point mutation) on complementation. This is the first demonstration that O proteins with internal deletions can complement for O activity, and that expression of the N-terminal portion of gene P can completely prevent O complementation. We show that O-P co-expression can limit the lethal effect of P on cell growth. We explore the influence of the contiguous small RNA OOP on O complementation and P-lethality.
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35
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The Bacteriophage Lambda CII Phenotypes for Complementation, Cellular Toxicity and Replication Inhibition Are Suppressed in cII-oop Constructs Expressing the Small RNA OOP. Viruses 2018. [PMID: 29518935 PMCID: PMC5869508 DOI: 10.3390/v10030115] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The temperate bacteriophage lambda (λ) CII protein is a positive regulator of transcription from promoter pE, a component of the lysogenic response. The expression of cII was examined in vectors devoid of phage transcription-modulating elements. Their removal enabled evaluating if the expression of the small RNA OOP, on its own, could suppress CII activities, including complementing for a lysogenic response, cell toxicity and causing rapid cellular loss of ColE1 plasmids. The results confirm that OOP RNA expression from the genetic element pO-oop-to can prevent the ability of plasmid-encoded CII to complement for a lysogenic response, suggesting that it serves as a powerful regulatory pivot in λ development. Plasmids with a pO promoter sequence of 45 nucleotides (pO45), containing the −10 and −35 regions for oop, were non-functional; whereas, plasmids with pO94 prevented CII complementation, CII-dependent plasmid loss and suppressed CII toxicity, suggesting the pO promoter has an extended DNA sequence. All three CII activities were eliminated by the deletion of the COOH-terminal 20 amino acids of CII. Host mutations in the hflA locus, in pcnB and in rpoB influenced CII activities. These studies suggest that the COOH-terminal end of CII likely interacts with the β-subunit of RNA polymerase.
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36
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Lambda phage genetic switch as a system with critical behaviour. J Theor Biol 2017; 431:32-38. [PMID: 28754287 DOI: 10.1016/j.jtbi.2017.07.024] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2016] [Revised: 07/12/2017] [Accepted: 07/25/2017] [Indexed: 11/21/2022]
Abstract
Critical behaviour pervades scientific disciplines as diverse as geology, economy or sociology. The critical behaviour of cell control systems is an open issue whose role has not yet been fully explored. The control of the expression of lambda phage DNA in the host cell can be classified as a system with critical behaviour. Lambda phage is a virus that infects Escherichia coli. Its core genes maintain one of two states; lysogeny or lysis. Current knowledge of the lambda phage genetic network allows to build a computational model of transcriptional control of the genes involved in the lytic-lysogenic switch and to simulate the temporal changes of their expression. Here, we focused on the computational simulation of these gene expressions to demonstrate critical behaviour of the system.
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Psyllids, It’s What’s on the Inside That Counts: Community Cross Talk Facilitates Prophage Interactions. mSphere 2017; 2:mSphere00227-17. [PMID: 28612849 PMCID: PMC5463028 DOI: 10.1128/msphere.00227-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Despite the availability of massive microbial community data sets (e.g., metagenomes), there is still a lack of knowledge on what molecular mechanisms facilitate cross talk between microbes and prophage within a community context. Despite the availability of massive microbial community data sets (e.g., metagenomes), there is still a lack of knowledge on what molecular mechanisms facilitate cross talk between microbes and prophage within a community context. A study published in mSphere by Jain and colleagues (M. Jain, L. A. Fleites, and D. W. Gabriel, mSphere 2:e00171-17, 2017, https://doi.org/10.1128/mSphereDirect.00171-17) reports on an intriguing new twist of how a prophage of the bacterium “Candidatus Liberibacter asiaticus” may have its lytic cycle suppressed partly because of a protein that is expressed by a cooccurring bacterium, Wolbachia. Both of these microbes coexist along with other microbial tenants inside their sap-feeding insect host, a psyllid. Although these results are still preliminary and alternative hypotheses need to be tested, these results suggest an interesting new dimension on how regulation of microbial genomes occurs in a community context.
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Sunderland KS, Yang M, Mao C. Phage-Enabled Nanomedicine: From Probes to Therapeutics in Precision Medicine. Angew Chem Int Ed Engl 2017; 56:1964-1992. [PMID: 27491926 PMCID: PMC5311110 DOI: 10.1002/anie.201606181] [Citation(s) in RCA: 114] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Indexed: 01/08/2023]
Abstract
Both lytic and temperate bacteriophages (phages) can be applied in nanomedicine, in particular, as nanoprobes for precise disease diagnosis and nanotherapeutics for targeted disease treatment. Since phages are bacteria-specific viruses, they do not naturally infect eukaryotic cells and are not toxic to them. They can be genetically engineered to target nanoparticles, cells, tissues, and organs, and can also be modified with functional abiotic nanomaterials for disease diagnosis and treatment. This Review will summarize the current use of phage structures in many aspects of precision nanomedicine, including ultrasensitive biomarker detection, enhanced bioimaging for disease diagnosis, targeted drug and gene delivery, directed stem cell differentiation, accelerated tissue formation, effective vaccination, and nanotherapeutics for targeted disease treatment. We will also propose future directions in the area of phage-based nanomedicines, and discuss the state of phage-based clinical trials.
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Affiliation(s)
- Kegan S Sunderland
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019, USA
| | - Mingying Yang
- Institute of Applied Bioresource Research, College of Animal Science, Zhejiang University, Yuhangtang Road 866, Hangzhou, Zhejiang, 310058, China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry, Stephenson Life Sciences Research Center, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma, 73019, USA
- School of Materials Science and Engineering, Zhejiang University, Hangzhou, Zhejiang, 310027, China
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Trinh JT, Székely T, Shao Q, Balázsi G, Zeng L. Cell fate decisions emerge as phages cooperate or compete inside their host. Nat Commun 2017; 8:14341. [PMID: 28165024 PMCID: PMC5303824 DOI: 10.1038/ncomms14341] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Accepted: 12/19/2016] [Indexed: 01/02/2023] Open
Abstract
The system of the bacterium Escherichia coli and its virus, bacteriophage lambda, is paradigmatic for gene regulation in cell-fate development, yet insight about its mechanisms and complexities are limited due to insufficient resolution of study. Here we develop a 4-colour fluorescence reporter system at the single-virus level, combined with computational models to unravel both the interactions between phages and how individual phages determine cellular fates. We find that phages cooperate during lysogenization, compete among each other during lysis, and that confusion between the two pathways occasionally occurs. Additionally, we observe that phage DNAs have fluctuating cellular arrival times and vie for resources to replicate, enabling the interplay during different developmental paths, where each phage genome may make an individual decision. These varied strategies could separate the selection for replication-optimizing beneficial mutations during lysis from sequence diversification during lysogeny, allowing rapid adaptation of phage populations for various environments.
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Affiliation(s)
- Jimmy T. Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
| | - Tamás Székely
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
| | - Gábor Balázsi
- The Louis and Beatrice Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York 11794, USA
- Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York 11794, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas 77843, USA
- Center for Phage Technology, Texas A&M University, College Station, Texas 77843, USA
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40
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Chen M, Zhang L, Xin S, Yao H, Lu C, Zhang W. Inducible Prophage Mutant of Escherichia coli Can Lyse New Host and the Key Sites of Receptor Recognition Identification. Front Microbiol 2017; 8:147. [PMID: 28203234 PMCID: PMC5285337 DOI: 10.3389/fmicb.2017.00147] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 01/20/2017] [Indexed: 12/17/2022] Open
Abstract
The use of bacteriophages as therapeutic agents is hindered by their narrow and specific host range, and by a lack of the knowledge concerning the molecular mechanism of receptor recognition. Two P2-like coliphages, named P88 and pro147, were induced from Escherichia coli strains K88 and DE147, respectively. A comparison of the genomes of these two and other P2-like coliphages obtained from GenBank showed that the tail fiber protein genes, which are the key genes for receptor recognition in other myoviridae phages, showed more diversity than the conserved lysin, replicase, and terminase genes. Firstly, replacing hypervariable region 2 (HR2: amino acids 716-746) of the tail fiber protein of P88 with that of pro147 changed the host range of P88. Then, replacing six amino acids in HR2 with the corresponding residues from pro147 altered the host range only in these mutants with changes at position 730 (leucine) and 744 (glutamic acid). Thus, we predicted that these amino acids are vital to establish the host range of P88. This study provided a vector of lysogenic bacteria that could be used to change or expand the phage host range of P88. These results illustrated that, in P2-like phage P88, the tail fiber protein determined the receptor recognition. Amino acids 716-746 and the amino acids at positions 730 and 744 were important for receptor recognition.
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Affiliation(s)
- Mianmian Chen
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Lei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Sipei Xin
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Huochun Yao
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Chengping Lu
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
| | - Wei Zhang
- College of Veterinary Medicine, Nanjing Agricultural University Nanjing, China
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41
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Sunderland KS, Yang M, Mao C. Nanomedizin auf Phagenbasis: von Sonden zu Therapeutika für eine Präzisionsmedizin. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201606181] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Kegan S. Sunderland
- Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center University of Oklahoma 101 Stephenson Parkway Norman Oklahoma 73019 USA
| | - Mingying Yang
- Institute of Applied Bioresource Research College of Animal Science Zhejiang University Yuhangtang Road 866 Hangzhou Zhejiang 310058 China
| | - Chuanbin Mao
- Department of Chemistry and Biochemistry Stephenson Life Sciences Research Center University of Oklahoma 101 Stephenson Parkway Norman Oklahoma 73019 USA
- School of Materials Science and Engineering Zhejiang University Hangzhou Zhejiang 310027 China
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42
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Pires DP, Cleto S, Sillankorva S, Azeredo J, Lu TK. Genetically Engineered Phages: a Review of Advances over the Last Decade. Microbiol Mol Biol Rev 2016; 80:523-43. [PMID: 27250768 PMCID: PMC4981678 DOI: 10.1128/mmbr.00069-15] [Citation(s) in RCA: 238] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Soon after their discovery in the early 20th century, bacteriophages were recognized to have great potential as antimicrobial agents, a potential that has yet to be fully realized. The nascent field of phage therapy was adversely affected by inadequately controlled trials and the discovery of antibiotics. Although the study of phages as anti-infective agents slowed, phages played an important role in the development of molecular biology. In recent years, the increase in multidrug-resistant bacteria has renewed interest in the use of phages as antimicrobial agents. With the wide array of possibilities offered by genetic engineering, these bacterial viruses are being modified to precisely control and detect bacteria and to serve as new sources of antibacterials. In applications that go beyond their antimicrobial activity, phages are also being developed as vehicles for drug delivery and vaccines, as well as for the assembly of new materials. This review highlights advances in techniques used to engineer phages for all of these purposes and discusses existing challenges and opportunities for future work.
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Affiliation(s)
- Diana P Pires
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Sara Cleto
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Sanna Sillankorva
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Joana Azeredo
- Centre of Biological Engineering, University of Minho, Braga, Portugal
| | - Timothy K Lu
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
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Shao Q, Trinh JT, McIntosh CS, Christenson B, Balázsi G, Zeng L. Lysis-lysogeny coexistence: prophage integration during lytic development. Microbiologyopen 2016; 6. [PMID: 27530202 PMCID: PMC5300877 DOI: 10.1002/mbo3.395] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 06/30/2016] [Indexed: 11/11/2022] Open
Abstract
The infection of Escherichia coli cells by bacteriophage lambda results in bifurcated means of propagation, where the phage decides between the lytic and lysogenic pathways. Although traditionally thought to be mutually exclusive, increasing evidence suggests that this lysis-lysogeny decision is more complex than once believed, but exploring its intricacies requires an improved resolution of study. Here, with a newly developed fluorescent reporter system labeling single phage and E. coli DNAs, these two distinct pathways can be visualized by following the DNA movements in vivo. Surprisingly, we frequently observed an interesting "lyso-lysis" phenomenon in lytic cells, where phage integrates its DNA into the host, a characteristic event of the lysogenic pathway, followed by cell lysis. Furthermore, the frequency of lyso-lysis increases with the number of infecting phages, and specifically, with CII activity. Moreover, in lytic cells, the integration site attB on the E. coli genome migrates toward the polar region over time, leading to more spatial overlap with the phage DNA and frequent colocalization/collision of attB and phage DNA, possibly contributing to a higher chance for DNA integration.
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Affiliation(s)
- Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.,Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Jimmy T Trinh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.,Center for Phage Technology, Texas A&M University, College Station, Texas, USA
| | - Colby S McIntosh
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA
| | - Brita Christenson
- Department of Biology and Biochemistry, University of Northwestern - St. Paul, St. Paul, Minnesota, USA
| | - Gábor Balázsi
- Laufer Center for Physical & Quantitative Biology, Stony Brook University, Stony Brook, New York, USA.,Department of Biomedical Engineering, Stony Brook University, Stony Brook, New York, USA
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas, USA.,Center for Phage Technology, Texas A&M University, College Station, Texas, USA
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45
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Reconstruction and Application of Protein-Protein Interaction Network. Int J Mol Sci 2016; 17:ijms17060907. [PMID: 27338356 PMCID: PMC4926441 DOI: 10.3390/ijms17060907] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2016] [Revised: 05/31/2016] [Accepted: 06/03/2016] [Indexed: 11/17/2022] Open
Abstract
The protein-protein interaction network (PIN) is a useful tool for systematic investigation of the complex biological activities in the cell. With the increasing interests on the proteome-wide interaction networks, PINs have been reconstructed for many species, including virus, bacteria, plants, animals, and humans. With the development of biological techniques, the reconstruction methods of PIN are further improved. PIN has gradually penetrated many fields in biological research. In this work we systematically reviewed the development of PIN in the past fifteen years, with respect to its reconstruction and application of function annotation, subsystem investigation, evolution analysis, hub protein analysis, and regulation mechanism analysis. Due to the significant role of PIN in the in-depth exploration of biological process mechanisms, PIN will be preferred by more and more researchers for the systematic study of the protein systems in various kinds of organisms.
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46
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Shao Q, Hawkins A, Zeng L. Phage DNA dynamics in cells with different fates. Biophys J 2016; 108:2048-60. [PMID: 25902444 DOI: 10.1016/j.bpj.2015.03.027] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 02/24/2015] [Accepted: 03/17/2015] [Indexed: 11/27/2022] Open
Abstract
Bacteriophage λ begins its infection cycle by ejecting its DNA into its host Escherichia coli cell, after which either a lytic or a lysogenic pathway is followed, resulting in different cell fates. In this study, using a new technique to monitor the spatiotemporal dynamics of the phage DNA in vivo, we found that the phage DNA moves via two distinct modes, localized motion and motion spanning the whole cell. One or the other motion is preferred, depending on where the phage DNA is ejected into the cell. By examining the phage DNA trajectories, we found the motion to be subdiffusive. Moreover, phage DNA motion is the same in the early phase of the infection cycle, irrespective of whether the lytic or lysogenic pathway is followed; hence, cell-fate decision-making appears not to be correlated with the phage DNA motion. However, after the cell commits to one pathway or the other, phage DNA movement slows during the late phase of the lytic cycle, whereas it remains the same during the entire lysogenic cycle. Throughout the infection cycle, phage DNA prefers the regions around the quarter positions of the cell.
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Affiliation(s)
- Qiuyan Shao
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas; Center for Phage Technology, Texas A&M University, College Station, Texas
| | - Alexander Hawkins
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas; Center for Phage Technology, Texas A&M University, College Station, Texas
| | - Lanying Zeng
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, Texas; Center for Phage Technology, Texas A&M University, College Station, Texas.
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Nedialkova LP, Sidstedt M, Koeppel MB, Spriewald S, Ring D, Gerlach RG, Bossi L, Stecher B. Temperate phages promote colicin-dependent fitness of Salmonella enterica serovar Typhimurium. Environ Microbiol 2015; 18:1591-603. [PMID: 26439675 DOI: 10.1111/1462-2920.13077] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/25/2015] [Accepted: 09/28/2015] [Indexed: 12/12/2022]
Abstract
Bacteria employ bacteriocins for interference competition in microbial ecosystems. Colicin Ib (ColIb), a pore-forming bacteriocin, confers a significant fitness benefit to Salmonella enterica serovar Typhimurium (S. Tm) in competition against commensal Escherichia coli in the gut. ColIb is released from S. Tm into the environment, where it kills susceptible competitors. However, colicin-specific release proteins, as they are known for other colicins, have not been identified in case of ColIb. Thus, its release mechanism has remained unclear. In the current study, we have established a new link between ColIb release and lysis activity of temperate, lambdoid phages. By the use of phage-cured S. Tm mutant strains, we show that the presence of temperate phages and their lysis genes is necessary and sufficient for release of active ColIb into the culture supernatant. Furthermore, phage-mediated lysis significantly enhanced S. Tm fitness in competition against a ColIb-susceptible competitor. Finally, transduction with the lambdoid phage 933W rescued the defect of E. coli strain MG1655 with respect to ColIb release. In conclusion, ColIb is released from bacteria in the course of phage lysis. Our data reveal a new mechanism for colicin release and point out a novel function of temperate phages in enhancing colicin-dependent bacterial fitness.
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Affiliation(s)
- Lubov P Nedialkova
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Maja Sidstedt
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Martin B Koeppel
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.,German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Stefanie Spriewald
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany
| | - Diana Ring
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.,German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
| | - Roman G Gerlach
- Wernigerode Branch, Robert Koch Institute, Project Group 5, Burgstr. 37, 38855, Wernigerode, Germany
| | - Lionello Bossi
- CNRS, Centre de Genetique Moleculaire, Gif-sur-Yvette Cedex, 91198, France
| | - Bärbel Stecher
- Max-von-Pettenkofer Institute, LMU Munich, Pettenkoferstr. 9a, 80336, Munich, Germany.,German Center for Infection Research (DZIF), partner site LMU Munich, Munich, Germany
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Dynamics of Mycobacteriophage-Mycobacterial Host Interaction: Evidence for Secondary Mechanisms for Host Lethality. Appl Environ Microbiol 2015; 82:124-33. [PMID: 26475112 DOI: 10.1128/aem.02700-15] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2015] [Accepted: 10/12/2015] [Indexed: 12/15/2022] Open
Abstract
Mycobacteriophages infect mycobacteria, resulting in their death. Therefore, the possibility of using them as therapeutic agents against the deadly mycobacterial disease tuberculosis (TB) is of great interest. To obtain better insight into the dynamics of mycobacterial inactivation by mycobacteriophages, this study was initiated using mycobacteriophage D29 and Mycobacterium smegmatis as the phage-host system. Here, we implemented a goal-oriented iterative cycle of experiments on one hand and mathematical modeling combined with Monte Carlo simulations on the other. This integrative approach lends valuable insight into the detailed kinetics of bacterium-phage interactions. We measured time-dependent changes in host viability during the growth of phage D29 in M. smegmatis at different multiplicities of infection (MOI). The predictions emerging out of theoretical analyses were further examined using biochemical and cell biological assays. In a phage-host interaction system where multiple rounds of infection are allowed to take place, cell counts drop more rapidly than expected if cell lysis is considered the only mechanism for cell death. The phenomenon could be explained by considering a secondary factor for cell death in addition to lysis. Further investigations reveal that phage infection leads to the increased production of superoxide radicals, which appears to be the secondary factor. Therefore, mycobacteriophage D29 can function as an effective antimycobacterial agent, the killing potential of which may be amplified through secondary mechanisms.
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Dang VT, Howard-Varona C, Schwenck S, Sullivan MB. Variably lytic infection dynamics of large Bacteroidetes podovirus phi38:1 against two Cellulophaga baltica host strains. Environ Microbiol 2015; 17:4659-71. [PMID: 26248067 DOI: 10.1111/1462-2920.13009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 07/10/2015] [Accepted: 08/02/2015] [Indexed: 01/21/2023]
Abstract
Bacterial viruses (phages) influence global biogeochemical cycles by modulating bacterial mortality, metabolic output and evolution. However, our understanding of phage infections is limited by few methods and environmentally relevant model systems. Prior work showed that Cellulophaga baltica phage ϕ38:1 infects its original host lytically, and an alternative host either delayed lytically or lysogenically. Here we investigate these infections through traditional and marker-based approaches, and introduce geneELISA for high-throughput examination of phage-host interactions. All methods confirmed the lytic, original host infection (70-80 min latent period; approximately eight phages produced per cell), but alternative host assays were more challenging. A 4.5 h experiment detected no phage production by plaque assay, whereas phageFISH and geneELISA revealed phage genome replication and a latent period ≥ 150 min. Longer experiments (26 h) suggested an 11 h latent period and a burst size of 871 by plaque assay, whereas phageFISH identified cell lysis starting at < 5 h and lasting to 11 h, but for only 7% to 21.5% of infected cells, respectively, and with ∼ 39 phages produced per cell. These findings help resolve the nature of the alternative host infection as delayed lytic and offer solutions to methodological challenges for studying inefficient phage-host interactions.
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Affiliation(s)
- Vinh T Dang
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | | | - Sarah Schwenck
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA
| | - Matthew B Sullivan
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA.,Department of Molecular and Cellular Biology, University of Arizona, Tucson, AZ, USA
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HK022 Nun Requires Arginine-Rich Motif Residues Distinct from λ N. J Bacteriol 2015; 197:3573-82. [PMID: 26350130 DOI: 10.1128/jb.00466-15] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2015] [Accepted: 08/24/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Bacteriophage λ N protein binds boxB RNA hairpins in the nut (N utilization) sites of immediate early λ transcripts and interacts with host factors to suppress transcriptional termination at downstream terminators. In opposition to λ N, the Nun protein of HK022 binds the boxBs of coinfecting λ transcripts, interacts with a similar or identical set of host factors, and terminates transcription to suppress λ replication. Comparison of N-boxB and Nun-boxB nuclear magnetic resonance (NMR) structural models suggests similar interactions, though limited mutagenesis of Nun is available. Here, libraries of Nun's arginine-rich motif (ARM) were screened for the ability to exclude λ coinfection, and mutants were assayed for Nun termination with a boxB plasmid reporter system. Several Nun ARM residues appear to be immutable: Asp26, Arg28, Arg29, Arg32, Trp33, and Arg36. Asp26 and Trp33 appear to be unable to contact boxB and are not found at equivalent positions in λ N ARM. To understand if the requirement of Asp26, Trp33, and Arg36 indicated differences between HK022 Nun termination and λ N antitermination complexes, the same Nun libraries were fused to the activation domain of λ N and screened for clones able to complement N-deficient λ. Mutants were assayed for N antitermination. Surprisingly, Asp26 and Trp33 were still essential when Nun ARM was fused to N. Docking suggests that Nun ARM contacts a hydrophobic surface of the NusG carboxy-terminal domain containing residues necessary for Nun function. These findings indicate that Nun ARM relies on distinct contacts in its ternary complex and illustrate how protein-RNA recognition can evolve new regulatory functions. IMPORTANCE λ N protein interacts with host factors to allow λ nut-containing transcripts to elongate past termination signals. A competing bacteriophage, HK022, expresses Nun protein, which causes termination of λ nut transcripts. λ N and HK022 Nun use similar arginine-rich motifs (ARMs) to bind the same boxB RNAs in nut transcripts. Screening libraries of Nun ARM mutants, both in HK022 Nun and in a λ N fusion, revealed amino acids essential to Nun that could bind one or more host factors. Docking suggests that NusG, which is present in both Nun termination and N antitermination, is a plausible partner. These findings could help understand how transcription elongation is regulated and illustrate how subtle differences allow ARMs to evolve new regulatory functions.
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