BacteriophagePub Date : 2014-07-08eCollection Date: 2014-01-01DOI: 10.4161/bact.29866
Katherine R Hargreaves, Andrew M Kropinski, Martha Rj Clokie
{"title":"Bacteriophage behavioral ecology: How phages alter their bacterial host's habits.","authors":"Katherine R Hargreaves, Andrew M Kropinski, Martha Rj Clokie","doi":"10.4161/bact.29866","DOIUrl":"10.4161/bact.29866","url":null,"abstract":"<p><p>Bacteriophages have an essential gene kit that enables their invasion, replication, and production. In addition to this \"core\" genome, they can carry \"accessory\" genes that dramatically impact bacterial biology, and presumably boost their own success. The content of phage genomes continue to surprise us by revealing new ways that viruses impact bacterial biology. The genome of a <i>Clostridium difficile</i> myovirus, phiCDHM1, contains homologs of three bacterial accessory gene regulator (<i>agr</i>) genes. The <i>agr</i> system is a type of quorum sensing (QS), via which the phage may modify <i>C. difficile</i> interactions with its environment. Although their mechanism of action is unknown, mutants in bacterial versions of these genes impact sporulation and virulence. To explore how phage QS genes may influence <i>C. difficile</i> biology, we examine the main categories of bacterial behavior that phages have been shown to influence and discuss how interactions via QS could influence behavior at a wider level.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 ","pages":"e29866"},"PeriodicalIF":0.0,"publicationDate":"2014-07-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://ftp.ncbi.nlm.nih.gov/pub/pmc/oa_pdf/ab/61/bact-4-e29866.PMC4124054.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32570675","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}
BacteriophagePub Date : 2014-05-29eCollection Date: 2014-01-01DOI: 10.4161/bact.29399
Konstantin Severinov, Leonid Minakhin, Shun-Ichi Sekine, Anna Lopatina, Shigeyuki Yokoyama
{"title":"Molecular basis of RNA polymerase promoter specificity switch revealed through studies of <i>Thermus</i> bacteriophage transcription regulator.","authors":"Konstantin Severinov, Leonid Minakhin, Shun-Ichi Sekine, Anna Lopatina, Shigeyuki Yokoyama","doi":"10.4161/bact.29399","DOIUrl":"https://doi.org/10.4161/bact.29399","url":null,"abstract":"<p><p>Transcription initiation is the central point of gene expression regulation. Understanding of molecular mechanism of transcription regulation requires, ultimately, the structural understanding of consequences of transcription factors binding to DNA-dependent RNA polymerase (RNAP), the enzyme of transcription. We recently determined a structure of a complex between transcription factor gp39 encoded by a <i>Thermus</i> bacteriophage and <i>Thermus</i> RNAP holoenzyme. In this addendum to the original publication, we highlight structural insights that explain the ability of gp39 to act as an RNAP specificity switch which inhibits transcription initiation from a major class of bacterial promoters, while allowing transcription from a minor promoter class to continue.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 ","pages":"e29399"},"PeriodicalIF":0.0,"publicationDate":"2014-05-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.29399","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32570262","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}
BacteriophagePub Date : 2014-04-25eCollection Date: 2014-01-01DOI: 10.4161/bact.29011
Christopher R Cox, Nicholas R Saichek, Herbert P Schweizer, Kent J Voorhees
{"title":"Rapid <i>Burkholderia pseudomallei</i> identification and antibiotic resistance determination by bacteriophage amplification and MALDI-TOF MS.","authors":"Christopher R Cox, Nicholas R Saichek, Herbert P Schweizer, Kent J Voorhees","doi":"10.4161/bact.29011","DOIUrl":"https://doi.org/10.4161/bact.29011","url":null,"abstract":"<p><p>Phage amplification detected by MALDI-TOF MS was investigated for rapid and simultaneous <i>Burkholderia pseudomallei</i> identification and ceftazidime resistance determination. <i>B. pseudomallei</i> ceftazidime susceptible and resistant Δ<i>purM</i> mutant strains Bp82 and Bp82.3 were infected with broadly targeting <i>B. pseudomallei</i> phage ϕX216 and production of the m/z 37.6 kDa phage capsid protein observed by MALDI-TOF MS over the course of 3 h infections. This allowed for repoducible phage-based bacterial ID within 2 h of the onset of infection. MALDI-TOF MS-measured time to detection correlated with in silico modeling, which predicted an approximate 2 h detection time. Ceftazidime susceptible strain Bp82, while detectable in the absence of the drug, owing to the reliance of phage amplification on a viable host, was not detectable when 10 μg/mL ceftazidime was added at the onset of infection. In contrast, resistant strain Bp82.3 was detected in the same 2 h timeframe both with and without the addition of ceftazidime.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 ","pages":"e29011"},"PeriodicalIF":0.0,"publicationDate":"2014-04-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.29011","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32524328","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}
BacteriophagePub Date : 2014-04-02eCollection Date: 2014-01-01DOI: 10.4161/bact.28732
Andrew D Millard, Ian Hands-Portman, Katrin Zwirglmaier
{"title":"Morphotypes of virus-like particles in two hydrothermal vent fields on the East Scotia Ridge, Antarctica.","authors":"Andrew D Millard, Ian Hands-Portman, Katrin Zwirglmaier","doi":"10.4161/bact.28732","DOIUrl":"https://doi.org/10.4161/bact.28732","url":null,"abstract":"<p><p>Viruses from extreme environments are still largely unexplored and may harbor unseen genetic potential. Here, we present a first glance at the morphological diversity of virus like particles (VLPs) from an environment that is extreme in more than one respect: two recently discovered hydrothermal vent fields on the East Scotia Ridge in the Southern Ocean near Antarctica. They are the southernmost hydrothermal sites found to date and have been shown to present a new biogeographic province, containing several new macrofaunal species and associated microbial organisms. Transmission electron microscopy revealed a range of tailed and untailed VLPs of various morphologies as well as an unusual long rod-shaped VLP with three long filaments. Based on its distant similarity with several known archaeal viruses, we hypothesize that this presents a new viral morphology that most likely infects an archaeon. Notably absent in the samples we analyzed were lemon- or spindle-shaped VLPs that have previously been described in other hydrothermal vent settings.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 ","pages":"e28732"},"PeriodicalIF":0.0,"publicationDate":"2014-04-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28732","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32570261","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}
BacteriophagePub Date : 2014-03-11eCollection Date: 2014-01-01DOI: 10.4161/bact.28507
Hitoshi Mitsunobu, Bin Zhu, Seung-Joo Lee, Stanley Tabor, Charles C Richardson
{"title":"Flap endonuclease of bacteriophage T7: Possible roles in RNA primer removal, recombination and host DNA breakdown.","authors":"Hitoshi Mitsunobu, Bin Zhu, Seung-Joo Lee, Stanley Tabor, Charles C Richardson","doi":"10.4161/bact.28507","DOIUrl":"https://doi.org/10.4161/bact.28507","url":null,"abstract":"<p><p>Gene 6 protein of bacteriophage T7 has 5'-3'-exonuclease activity specific for duplex DNA. We have found that gene 6 protein also has flap endonuclease activity. The flap endonuclease activity is considerably weaker than the exonuclease activity. Unlike the human homolog of gene 6 protein, the flap endonuclease activity of gene 6 protein is dependent on the length of the 5'-flap. This dependency of activity on the length of the 5'-flap may result from the structured helical gateway region of gene 6 protein which differs from that of human flap endonuclease 1. The flap endonuclease activity provides a mechanism by which RNA-terminated Okazaki fragments, displaced by the lagging strand DNA polymerase, are processed. 3'-extensions generated during degradation of duplex DNA by the exonuclease activity of gene 6 protein are inhibitory to further degradation of the 5'-terminus by the exonuclease activity of gene 6 protein. The single-stranded DNA binding protein of T7 overcomes this inhibition.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 ","pages":"e28507"},"PeriodicalIF":0.0,"publicationDate":"2014-03-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.28507","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32570260","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}
BacteriophagePub Date : 2014-03-06eCollection Date: 2014-01-01DOI: 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, Olivia McAuliffe, R Paul Ross, Colin Hill, Jim O'Mahony, 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":"4 ","pages":"e28451"},"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}
BacteriophagePub Date : 2014-01-01DOI: 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":"4 1","pages":"e26691"},"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}
BacteriophagePub Date : 2014-01-01Epub Date: 2014-02-27DOI: 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, Agnieszka Piotrowicz, Barbara Owczarek, Katarzyna Hodyra, Paulina Miernikiewicz, Dorota Lecion, Marek Harhala, Andrzej Górski, 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":"4 1","pages":"e28364"},"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}
BacteriophagePub Date : 2014-01-01Epub Date: 2014-02-07DOI: 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":"4 1","pages":"e28137"},"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}
BacteriophagePub Date : 2014-01-01Epub Date: 2014-03-11DOI: 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, Ruth Kiro, Shahar Molshanski-Mor, Rotem Edgar, 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":"4 1","pages":"e28491"},"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}