Bacteriophage最新文献

{"title":"Distinguishing direct binding interactions from allosteric effects in the protease–HK97 prohead I δ domain complex by amide H/D exchange mass spectrometry","authors":"S. Krishnamurthy, D. Veesler, R. Khayat, J. Snijder, R. Huang, Ajr Heck, Jeremi Johnson, GS Anand","doi":"10.4161/21597073.2014.959816","DOIUrl":"https://doi.org/10.4161/21597073.2014.959816","url":null,"abstract":"A major question in mapping protein-ligand or protein-protein interactions in solution is to distinguish direct-binding interactions from long-range conformational changes at allosteric sites. We describe here the applicability of amide hydrogen deuterium exchange mass spectrometry (HDXMS) in addressing this important question using the bacteriophage HK97 capsid proteins’ interactions with their processing protease. HK97 is a lambda-like dsDNA bacteriophage that is ideal for studies of particle assembly and maturation. Its capsid precursor protein is composed of two main regions, the scaffolding protein (δ-domain, residues 2-103), and the coat subunit (residues 104-385), which spontaneously forms a mixture of hexamers and pentamers upon association. Activation of the viral protease, which occurs after particle assembly, is initiated by the protease mediated digestion of the scaffolding domains to yield Prohead-2. This irreversible step is obligatory for activation of the virus maturation pathway. Here we provide an “addendum” to our previous study of Prohead I and Prohead I+pro (a transient complex of Prohead I and the protease) where we investigated the interactions between the δ domain and the packaged protease using HDXMS. Our results revealed two sites on the δ domain: one set of contiguous peptides that showed decreased exchange at the protease binding site at early time points of deuterium labeling and another separate set of continuous peptides that showed decreased exchange at later time points. Even though this cannot reveal the time scales of molecular processes governing binding and allostery, we believe this differential pattern of exchange across deuteration times can allow spatial distinction between binding sites and long range conformational changes with allosteric implications. This partitioning can be discerned from the lag between noncontiguous regions on a protein showing maximal changes in deuterium exchange and highlights a powerful application of HDXMS in distinguishing direct binding in transient protein-protein interactions from allosteric changes.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91418654","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evidence for horizontal gene transfer between Chlamydophila pneumoniae and Chlamydia phage","authors":"A. Rosenwald, B. Murray, Theodore Toth, R. Madupu, A. Kyrillos, Gaurav S. Arora","doi":"10.4161/21597073.2014.965076","DOIUrl":"https://doi.org/10.4161/21597073.2014.965076","url":null,"abstract":"Chlamydia-infecting bacteriophages, members of the Microviridae family, specifically the Gokushovirinae subfamily, are small (4.5–5 kb) single-stranded circles with 8–10 open-reading frames similar to E. coli phage φX174. Using sequence information found in GenBank, we examined related genes in Chlamydophila pneumoniae and Chlamydia-infecting bacteriophages. The 5 completely sequenced C. pneumoniae strains contain a gene orthologous to a phage gene annotated as the putative replication initiation protein (PRIP, also called VP4), which is not found in any other members of the Chlamydiaceae family sequenced to date. The C. pneumoniae strain infecting koalas, LPCoLN, in addition contains another region orthologous to phage sequences derived from the minor capsid protein gene, VP3. Phylogenetically, the phage PRIP sequences are more diverse than the bacterial PRIP sequences; nevertheless, the bacterial sequences and the phage sequences each cluster together in their own clade. Finally, we found evidence for another Microviridae phage-related gene, the major capsid protein gene, VP1 in a number of other bacterial species and 2 eukaryotes, the woodland strawberry and a nematode. Thus, we find considerable evidence for DNA sequences related to genes found in bacteriophages of the Microviridae family not only in a variety of prokaryotic but also eukaryotic species.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-10-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85502927","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bacteriophage HK022 Nun protein arrests transcription by blocking lateral mobility of RNA polymerase during transcription elongation.","authors":"Christal L Vitiello,&nbsp;Max E Gottesman","doi":"10.4161/bact.32187","DOIUrl":"https://doi.org/10.4161/bact.32187","url":null,"abstract":"<p><p>Coliphage HK022 excludes phage λ by subverting the λ antitermination system and arresting transcription on the λ chromosome. The 12 kDa HK022 Nun protein binds to λ nascent transcript through its N-terminal Arginine Rich Motif (ARM), blocking access by λ N and arresting transcription via a C-terminal interaction with RNA polymerase. In a purified in vitro system, we recently demonstrated that Nun arrests transcription by restricting lateral movement of transcription elongation complex (TEC) along the DNA register, thereby freezing the translocation state. We will discuss some of the key experiments that led to this conclusion, as well as present additional results that further support it.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-07-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.32187","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32570676","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}

{"title":"Inactivation of <i>Streptomyces</i> phage ɸC31 by 405 nm light: Requirement for exogenous photosensitizers?","authors":"Rachael M Tomb,&nbsp;Michelle Maclean,&nbsp;Paul R Herron,&nbsp;Paul A Hoskisson,&nbsp;Scott J MacGregor,&nbsp;John G Anderson","doi":"10.4161/bact.32129","DOIUrl":"https://doi.org/10.4161/bact.32129","url":null,"abstract":"<p><p>Exposure to narrowband violet-blue light around 405 nm wavelength can induce lethal oxidative damage to bacteria and fungi, however effects on viruses are unknown. As photosensitive porphyrin molecules are involved in the microbicidal inactivation mechanism, and since porphyrins are absent in viruses, then any damaging effects of 405 nm light on viruses might appear unlikely. This study used the bacteriophage ɸC31, as a surrogate for non-enveloped double-stranded DNA viruses, to establish whether 405 nm light can induce virucidal effects. Exposure of ɸC31 suspended in minimal media, nutrient-rich media, and porphyrin solution, demonstrated differing sensitivity of the phage. Significant reductions in phage titer occurred when exposed in nutrient-rich media, with ~3-, 5- and 7-log₁₀ reductions achieved after exposure to doses of 0.3, 0.5 and 1.4 kJ/cm², respectively. When suspended in minimal media a 0.3-log₁₀ reduction (<i>P</i> = 0.012) occurred after exposure to 306 J/cm²: much lower than the 2.7- and > 2.5-log₁₀ reductions achieved with the same dose in nutrient-rich, and porphyrin-supplemented media, suggesting inactivation is accelerated by the photo-activation of light-sensitive components in the media. This study provides the first evidence of the interaction of narrowband 405 nm light with viruses, and demonstrates that viral susceptibility to 405 nm light can be significantly enhanced by involvement of exogenous photosensitive components. The reduced susceptibility of viruses in minimal media, compared with that of other microorganisms, provides further evidence that the antimicrobial action of 405 nm light is predominantly due to the photo-excitation of endogenous photosensitive molecules such as porphyrins within susceptible microorganisms.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.32129","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32566670","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}

{"title":"Life in Science: Abraham Eisenstark.","authors":"Abraham Eisenstark","doi":"10.4161/bact.29009","DOIUrl":"https://doi.org/10.4161/bact.29009","url":null,"abstract":"The Influence of Books and Movies addiction to microbiology came early in my boyhood through books and film. First there was the novel Arrowsmith by sinclair Lewis. in the movie adaptation, actor ronald coleman dealt with bubonic plague and quickly became my scientific hero. throughout the years, my paperback copy of this novel has been loaned to many students. next, i became fascinated by paul muni in The Story of Louis Pasteur. then there was Microbe Hunters by paul DeKruif, and Rats, Lice and History by hans Zinsser. Later came a 1940 biographical film, Dr. Ehrlich’s Magic Bullet starring edward g robinson. in addition to these items from popular culture, i was inspired by books from the Life in Science","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2014-07-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/bact.29009","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32567287","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}

{"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":null,"pages":null},"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}

{"title":"Molecular basis of RNA polymerase promoter specificity switch revealed through studies of <i>Thermus</i> bacteriophage transcription regulator.","authors":"Konstantin Severinov,&nbsp;Leonid Minakhin,&nbsp;Shun-Ichi Sekine,&nbsp;Anna Lopatina,&nbsp;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":null,"pages":null},"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}

{"title":"Rapid <i>Burkholderia pseudomallei</i> identification and antibiotic resistance determination by bacteriophage amplification and MALDI-TOF MS.","authors":"Christopher R Cox,&nbsp;Nicholas R Saichek,&nbsp;Herbert P Schweizer,&nbsp;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":null,"pages":null},"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}

{"title":"Morphotypes of virus-like particles in two hydrothermal vent fields on the East Scotia Ridge, Antarctica.","authors":"Andrew D Millard,&nbsp;Ian Hands-Portman,&nbsp;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":null,"pages":null},"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}

{"title":"Flap endonuclease of bacteriophage T7: Possible roles in RNA primer removal, recombination and host DNA breakdown.","authors":"Hitoshi Mitsunobu,&nbsp;Bin Zhu,&nbsp;Seung-Joo Lee,&nbsp;Stanley Tabor,&nbsp;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":null,"pages":null},"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}