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Genome analysis of the staphylococcal temperate phage DW2 and functional studies on the endolysin and tail hydrolase. 葡萄球菌温带噬菌体DW2的基因组分析及内溶素和尾水解酶的功能研究。
Bacteriophage Pub Date : 2014-03-06 eCollection Date: 2014-01-01 DOI: 10.4161/bact.28451
Ruth Keary, Olivia McAuliffe, R Paul Ross, Colin Hill, Jim O'Mahony, Aidan Coffey
{"title":"Genome analysis of the staphylococcal temperate phage DW2 and functional studies on the endolysin and tail hydrolase.","authors":"Ruth Keary,&nbsp;Olivia McAuliffe,&nbsp;R Paul Ross,&nbsp;Colin Hill,&nbsp;Jim O'Mahony,&nbsp;Aidan Coffey","doi":"10.4161/bact.28451","DOIUrl":"https://doi.org/10.4161/bact.28451","url":null,"abstract":"<p><p>This study describes the genome of temperate <i>Siphoviridae</i> phage DW2, which is routinely propagated on <i>Staphylococcus aureus</i> DPC5246. The 41941 bp genome revealed an open reading frame (ORF1) which has a high level of homology with members of the resolvase subfamily of site-specific serine recombinase, involved in chromosomal integration and excision. In contrast, the majority of staphylococcal phages reported to date encode tyrosine recombinases. Two putative genes encoded by phage DW2 (ORF15 and ORF24) were highly homologous to the NWMN0273 and NWMN0280 genes encoding virulence factors carried on the genome of ϕNM4, a prophage in the genome of <i>S. aureus</i> Newman. Phage DW2 also encodes proteins highly homologous to two well-characterized <i>Staphylococcus aureus</i> pathogenicity island derepressors encoded by the staphylococcal helper phage 80α indicating that it may similarly act as a helper phage for mobility of pathogenicity islands in <i>S. aureus</i>. This study also focused on the enzybiotic potential of phage DW2. The structure of the putative endolysin and tail hydrolase were investigated and used as the basis for a cloning strategy to create recombinant peptidoglycan hydrolyzing proteins. After overexpression in <i>E. coli,</i> four of these proteins (LysDW2, THDW2, CHAP<sub>E1-153</sub>, and CHAP<sub>E1-163</sub>) were demonstrated to have hydrolytic activity against peptidoglycan of <i>S. aureus</i> and thus represent novel candidates for exploitation as enzybiotics.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28451","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32570259","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 18
Life in Science: William C Summers. 科学生活:威廉·C·萨默斯。
Bacteriophage Pub Date : 2014-01-01 DOI: 10.4161/bact.26691
William C Summers
{"title":"Life in Science: William C Summers.","authors":"William C Summers","doi":"10.4161/bact.26691","DOIUrl":"https://doi.org/10.4161/bact.26691","url":null,"abstract":"","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.26691","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32076351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Molecular imaging of T4 phage in mammalian tissues and cells. 哺乳动物组织和细胞中T4噬菌体的分子成像。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-02-27 DOI: 10.4161/bact.28364
Zuzanna Kaźmierczak, Agnieszka Piotrowicz, Barbara Owczarek, Katarzyna Hodyra, Paulina Miernikiewicz, Dorota Lecion, Marek Harhala, Andrzej Górski, Krystyna Dąbrowska
{"title":"Molecular imaging of T4 phage in mammalian tissues and cells.","authors":"Zuzanna Kaźmierczak,&nbsp;Agnieszka Piotrowicz,&nbsp;Barbara Owczarek,&nbsp;Katarzyna Hodyra,&nbsp;Paulina Miernikiewicz,&nbsp;Dorota Lecion,&nbsp;Marek Harhala,&nbsp;Andrzej Górski,&nbsp;Krystyna Dąbrowska","doi":"10.4161/bact.28364","DOIUrl":"https://doi.org/10.4161/bact.28364","url":null,"abstract":"<p><p>Advances in phage therapy encourage scientific interest in interactions of phages with human and animal organisms. This has created a need for developing tools that facilitate studies of phage circulation and deposition in tissues and cells. Here we propose a new green fluorescent protein (GFP)-based method for T4 phage molecular imaging in living systems. The method employs decoration of a phage capsid with GFP fused to the N-terminus of Hoc protein by in vivo phage display. Fluorescent phages were positively assessed as regards their applicability for detection inside living mammalian cells (by phagocytosis) and tissues (filtering and retention by lymph nodes and spleen). Molecular imaging provides innovative techniques that have brought substantial progress in life sciences. We propose it as a useful tool for studies of phage biology.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28364","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32195795","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 33
Application of bacteriophages for detection of foodborne pathogens. 应用噬菌体检测食源性病原体。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-02-07 DOI: 10.4161/bact.28137
Mathias Schmelcher, Martin J Loessner
{"title":"Application of bacteriophages for detection of foodborne pathogens.","authors":"Mathias Schmelcher, Martin J Loessner","doi":"10.4161/bact.28137","DOIUrl":"10.4161/bact.28137","url":null,"abstract":"<p><p>Bacterial contamination of food products presents a challenge for the food industry and poses a high risk for the consumer. Despite increasing awareness and improved hygiene measures, foodborne pathogens remain a threat for public health, and novel methods for detection of these organisms are needed. Bacteriophages represent ideal tools for diagnostic assays because of their high target cell specificity, inherent signal-amplifying properties, easy and inexpensive production, and robustness. Every stage of the phage lytic multiplication cycle, from the initial recognition of the host cell to the final lysis event, may be harnessed in several ways for the purpose of bacterial detection. Besides intact phage particles, phage-derived affinity molecules such as cell wall binding domains and receptor binding proteins can serve for this purpose. This review provides an overview of existing phage-based technologies for detection of foodborne pathogens, and highlights the most recent developments in this field, with particular emphasis on phage-based biosensors.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3919822/pdf/bact-4-e28137.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32121215","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Different approaches for using bacteriophages against antibiotic-resistant bacteria. 利用噬菌体对抗耐药细菌的不同方法。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-03-11 DOI: 10.4161/bact.28491
Ido Yosef, Ruth Kiro, Shahar Molshanski-Mor, Rotem Edgar, Udi Qimron
{"title":"Different approaches for using bacteriophages against antibiotic-resistant bacteria.","authors":"Ido Yosef,&nbsp;Ruth Kiro,&nbsp;Shahar Molshanski-Mor,&nbsp;Rotem Edgar,&nbsp;Udi Qimron","doi":"10.4161/bact.28491","DOIUrl":"https://doi.org/10.4161/bact.28491","url":null,"abstract":"<p><p>Bacterial resistance to antibiotics is an emerging threat requiring urgent solutions. Ever since their discovery, lytic bacteriophages have been suggested as therapeutic agents, but their application faces various obstacles: sequestration of the phage by the spleen and liver, antibodies against the phage, narrow host range, poor accessibility to the infected tissue, and bacterial resistance. Variations on bacteriophage use have been suggested, such as temperate phages as gene-delivery vehicles into pathogens. This approach, which is proposed to sensitize pathogens residing on hospital surfaces and medical personnel's skin, and its prospects are described in this addendum. Furthermore, phage-encoded products have been proposed as weapons against antibiotic resistance in bacteria. We describe a new phage protein which was identified during basic research into T7 bacteriophages. This protein may serendipitously prove useful for treating antibiotic-resistant pathogens. We believe that further basic research will lead to novel strategies in the fight against antibiotic-resistant bacteria.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28491","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32195796","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 23
The sabotage of the bacterial transcription machinery by a small bacteriophage protein. 一个小的噬菌体蛋白对细菌转录机制的破坏。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-03-12 DOI: 10.4161/bact.28520
Bing Liu, Andrey Shadrin, Carol Sheppard, Vladimir Mekler, Yingqi Xu, Konstantin Severinov, Steve Matthews, Sivaramesh Wigneshweraraj
{"title":"The sabotage of the bacterial transcription machinery by a small bacteriophage protein.","authors":"Bing Liu,&nbsp;Andrey Shadrin,&nbsp;Carol Sheppard,&nbsp;Vladimir Mekler,&nbsp;Yingqi Xu,&nbsp;Konstantin Severinov,&nbsp;Steve Matthews,&nbsp;Sivaramesh Wigneshweraraj","doi":"10.4161/bact.28520","DOIUrl":"https://doi.org/10.4161/bact.28520","url":null,"abstract":"<p><p>Many bacteriophages produce small proteins that specifically interfere with the bacterial host transcription machinery and thus contribute to the acquisition of the bacterial cell by the bacteriophage. We recently described how a small protein, called P7, produced by the Xp10 bacteriophage inhibits bacterial transcription initiation by causing the dissociation of the promoter specificity sigma factor subunit from the host RNA polymerase holoenzyme. In this addendum to the original publication, we present the highlights of that research.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28520","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32236204","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 7
Tradeoffs in bacteriophage life histories. 噬菌体生活史中的权衡。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-02-27 DOI: 10.4161/bact.28365
Eric C Keen
{"title":"Tradeoffs in bacteriophage life histories.","authors":"Eric C Keen","doi":"10.4161/bact.28365","DOIUrl":"10.4161/bact.28365","url":null,"abstract":"<p><p>Viruses are the most abundant biological entities on the planet, yet most classical principles of evolutionary biology and ecology were not developed with viruses in mind. Here, the concept of biological tradeoffs, a fundamental tenet of life history theory, is examined in the context of bacteriophage biology. Specifically, several important parameters of phage life histories-replication, persistence, host range, and adsorption-are evaluated for tradeoffs. Available data indicate that replication rate is strongly negatively correlated with both persistence and host range, suggesting that the well-documented tradeoff in macroorganisms between offspring production and offspring quality also applies to phages. The biological tradeoffs that appear to characterize viruses' life histories have potential importance for viral evolution, ecology, and pathogenesis.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3942329/pdf/bact-4-e28365.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40299381","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tales from a thousand and one phages. 一千零一个噬菌体的故事。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-02-18 DOI: 10.4161/bact.28265
Francisco Rodriguez-Valera, Carolina Megumi Mizuno, Rohit Ghai
{"title":"Tales from a thousand and one phages.","authors":"Francisco Rodriguez-Valera,&nbsp;Carolina Megumi Mizuno,&nbsp;Rohit Ghai","doi":"10.4161/bact.28265","DOIUrl":"https://doi.org/10.4161/bact.28265","url":null,"abstract":"<p><p>The sequencing of marine metagenomic fosmids led to the discovery of several new complete phage genomes. Among the 21 major sequence groups, 10 totally novel groups of marine phages could be identified. Some of these represent the first phages infecting large marine prokaryotic phyla, such as the Verrucomicrobia and the recently described <i>Ca.</i> Actinomarinales. Coming from a single deep photic zone sample the diversity of phages found is astonishing, and the comparison with a metavirome from the same location indicates that only 2% of the real diversity was recovered. In addition to this large macro-diversity, rich micro-diversity was also found, affecting host-recognition modules, mirroring the variation of cell surface components in their host marine microbes.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28265","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40300448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 18
Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and E. coli virulence genes in bacteriophage and prophage nucleotide sequences. 应用ResFinder和VirulenceFinder网络服务，轻松鉴定获得性抗生素耐药性和大肠杆菌噬菌体和前噬菌体核苷酸序列中的毒力基因。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-01-22 DOI: 10.4161/bact.27943
Kortine Annina Kleinheinz, Katrine Grimstrup Joensen, Mette Voldby Larsen
{"title":"Applying the ResFinder and VirulenceFinder web-services for easy identification of acquired antibiotic resistance and <i>E. coli</i> virulence genes in bacteriophage and prophage nucleotide sequences.","authors":"Kortine Annina Kleinheinz,&nbsp;Katrine Grimstrup Joensen,&nbsp;Mette Voldby Larsen","doi":"10.4161/bact.27943","DOIUrl":"https://doi.org/10.4161/bact.27943","url":null,"abstract":"<p><p>Extensive research is currently being conducted on the use of bacteriophages for applications in human medicine, agriculture and food manufacturing. However, phages are important vehicles of horisontal gene transfer and play a significant role in bacterial evolution. As a result, concern has been raised that this increased use and dissemination of phages could result in spread of deleterious genes, e.g., antibiotic resistance and virulence genes. Meanwhile, in the wake of the genomic era, several tools have been developed for characterization of bacterial genomes. Here we describe how two of these tools, ResFinder and VirulenceFinder, can be used to identify acquired antibiotic resistance and virulence genes in phage genomes of interest. The general applicability of the tools is demonstrated on data sets of 1,642 phage genomes and 1,442 predicted prophages.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.27943","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32158608","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 246
Effect of supercoiling on the λ switch. 超线圈对λ开关的影响。
Bacteriophage Pub Date : 2014-01-01 DOI: 10.4161/bact.27517
Kamilla Norregaard, Magnus Andersson, Kim Sneppen, Peter Eigil Nielsen, Stanley Brown, Lene B Oddershede
{"title":"Effect of supercoiling on the λ switch.","authors":"Kamilla Norregaard,&nbsp;Magnus Andersson,&nbsp;Kim Sneppen,&nbsp;Peter Eigil Nielsen,&nbsp;Stanley Brown,&nbsp;Lene B Oddershede","doi":"10.4161/bact.27517","DOIUrl":"https://doi.org/10.4161/bact.27517","url":null,"abstract":"<p><p>The lysogenic state of the λ switch is exceptionally stable, still, it is capable of responding to DNA-damage and rapidly enter the lytic state. We invented an assay where PNA mediated tethering of a plasmid allowed for single molecule investigations of the effect of supercoiling on the efficiency of the epigenetic λ switch. Compared with non-supercoiled DNA, the presence of supercoils enhances the CI-mediated DNA looping probability and renders the transition between the looped and unlooped states steeper, thus increasing the Hill coefficient. Interestingly, the transition occurs exactly at the CI concentration corresponding to the minimum number of CI molecules capable of maintaining the pRM-repressed state. Based on these results we propose that supercoiling maintains the pRM-repressible state as CI concentration decline during induction and thus prevent autoregulation of <i>cI</i> from interfering with induction.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.27517","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31996835","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 5
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