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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":"4 1","pages":"e28520"},"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":" ","pages":"e28365"},"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":" ","pages":"e28265"},"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":"4 1","pages":"e27943"},"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":"4 1","pages":"e27517"},"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
The XXIIIrd Phage/Virus Assembly Meeting. 第二十三届噬菌体/病毒大会。
Bacteriophage Pub Date : 2014-01-01 DOI: 10.4161/bact.27272
Philip Serwer
{"title":"The XXIIIrd Phage/Virus Assembly Meeting.","authors":"Philip Serwer","doi":"10.4161/bact.27272","DOIUrl":"https://doi.org/10.4161/bact.27272","url":null,"abstract":"<p><p>The XXIIIrd Phage/Virus Assembly (PVA) meeting returned to its birthplace in Lake Arrowhead, CA on September 8-13, 2013 (Fig. 1). The original meeting occurred in 1968, organized by Bob Edgar (Caltech, Pasadena, CA USA), Fred Eiserling (University of California, Los Angeles, Los Angeles, CA USA) and Bill Wood (Caltech, Pasadena, CA USA). The organizers of the 2013 meeting were Bill Gelbart (University of California, Los Angeles, Los Angeles, CA USA) and Jack Johnson (Scripps Research Institute, La Jolla, CA USA). This meeting specializes in an egalitarian format. Students are distinguished from senior faculty primarily by the signs of age. With the exception of historically based introductory talks, all talks were allotted the same time and freedom. This tradition began when the meeting was phage-only and has been continued now that all viruses are included. Many were the animated conversations about basic questions. New and international participants were present, a sign that the field has significant attraction, as it should, based on details below. The meeting was also characterized by a sense of humor and generally good times, a chance to both enjoy the science and forget the funding malaise to which many participants are exposed. I will present some of the meeting content, without attempting to be comprehensive.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 1","pages":"e27272"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.27272","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32093590","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: 1
Bacteriophage as instructional organisms in introductory biology labs. 噬菌体在生物学导论实验室中的指导作用。
Bacteriophage Pub Date : 2014-01-01 DOI: 10.4161/bact.27336
Paul Hyman
{"title":"Bacteriophage as instructional organisms in introductory biology labs.","authors":"Paul Hyman","doi":"10.4161/bact.27336","DOIUrl":"https://doi.org/10.4161/bact.27336","url":null,"abstract":"<p><p>Designing lab exercises for introductory biology classes requires balancing the need for students to obtain results with a desire to provide unpredictable outcomes to better approximate actual research. Bacteriophage are particularly well suited for this as many species are well-understood but, with their hosts, represent a relatively complex interacting system. I have designed a seven week series of lab exercises that allow students to select bacteriophage resistant mutant hosts, isolate and sequence the corresponding receptor gene to identify the specific bacterial mutation from a large number of potential mutations. I also examined the possibility of collecting useful mutant strains for other studies. After two semesters, the lab series is working well with over 90% of students successfully isolating mutant bacteria and about half identifying the specific mutation. Here I discuss the advantages of using bacteriophage in an introductory class, the specific labs in this series and future plans.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 1","pages":"e27336"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.27336","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32076353","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: 2
Molecular architecture of tailed double-stranded DNA phages. 尾部双链DNA噬菌体的分子结构。
Bacteriophage Pub Date : 2014-01-01 Epub Date: 2014-02-21 DOI: 10.4161/bact.28281
Andrei Fokine, Michael G Rossmann
{"title":"Molecular architecture of tailed double-stranded DNA phages.","authors":"Andrei Fokine,&nbsp;Michael G Rossmann","doi":"10.4161/bact.28281","DOIUrl":"https://doi.org/10.4161/bact.28281","url":null,"abstract":"<p><p>The tailed double-stranded DNA bacteriophages, or <i>Caudovirales</i>, constitute ~96% of all the known phages. Although these phages come in a great variety of sizes and morphology, their virions are mainly constructed of similar molecular building blocks via similar assembly pathways. Here we review the structure of tailed double-stranded DNA bacteriophages at a molecular level, emphasizing the structural similarity and common evolutionary origin of proteins that constitute these virions.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":" ","pages":"e28281"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28281","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40299382","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: 189
Identification of the ssDNA-binding protein of bacteriophage T5: Implications for T5 replication. 噬菌体T5的ssdna结合蛋白的鉴定:对T5复制的意义。
Bacteriophage Pub Date : 2013-10-01 Epub Date: 2013-12-09 DOI: 10.4161/bact.27304
Sebastiaan Werten
{"title":"Identification of the ssDNA-binding protein of bacteriophage T5: Implications for T5 replication.","authors":"Sebastiaan Werten","doi":"10.4161/bact.27304","DOIUrl":"https://doi.org/10.4161/bact.27304","url":null,"abstract":"<p><p>In a recent study, we identified and characterized the long-elusive replicative single-stranded DNA-binding protein of bacteriophage T5, which we showed is related to the eukaryotic transcription coactivator PC4. Here, we provide an extended discussion of these data, report several additional observations and consider implications for the recombination-dependent replication mechanism of the T5 genus, which is still poorly understood.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"3 4","pages":"e27304"},"PeriodicalIF":0.0,"publicationDate":"2013-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.27304","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32078279","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: 8
Identification and characterization of ϕH111-1: A novel myovirus with broad activity against clinical isolates of Burkholderia cenocepacia. 一种新型肌病毒的鉴定和特性:对临床分离的结核杆菌具有广泛活性。
Bacteriophage Pub Date : 2013-10-01 DOI: 10.4161/bact.26649
Karlene H Lynch, Yongjie Liang, Leo Eberl, David S Wishart, Jonathan J Dennis
{"title":"Identification and characterization of ϕH111-1: A novel myovirus with broad activity against clinical isolates of <i>Burkholderia cenocepacia.</i>","authors":"Karlene H Lynch,&nbsp;Yongjie Liang,&nbsp;Leo Eberl,&nbsp;David S Wishart,&nbsp;Jonathan J Dennis","doi":"10.4161/bact.26649","DOIUrl":"https://doi.org/10.4161/bact.26649","url":null,"abstract":"<p><p>Characterization of prophages in sequenced bacterial genomes is important for virulence assessment, evolutionary analysis, and phage application development. The objective of this study was to identify complete, inducible prophages in the cystic fibrosis (CF) clinical isolate <i>Burkholderia cenocepacia</i> H111. Using the prophage-finding program PHAge Search Tool (PHAST), we identified three putative intact prophages in the H111 sequence. Virions were readily isolated from H111 culture supernatants following extended incubation. Using shotgun cloning and sequencing, one of these virions (designated ϕH111-1 [vB_BceM_ϕH111-1]) was identified as the infective particle of a PHAST-detected intact prophage. ϕH111-1 has an extremely broad host range with respect to <i>B. cenocepacia</i> strains and is predicted to use lipopolysaccharide (LPS) as a receptor. Bioinformatics analysis indicates that the prophage is 42,972 base pairs in length, encodes 54 proteins, and shows relatedness to the virion morphogenesis modules of <i>Aca</i>ML1 and \"Vhmllikevirus\" myoviruses. As ϕH111-1 is active against a broad panel of clinical strains and encodes no putative virulence factors, it may be therapeutically effective for <i>Burkholderia</i> infections.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"3 4","pages":"e26649"},"PeriodicalIF":0.0,"publicationDate":"2013-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.26649","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"31893988","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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