Bacteriophage最新文献

{"title":"Life In Science.","authors":"Robert L Sinsheimer","doi":"10.1080/21597081.2014.997143","DOIUrl":"10.1080/21597081.2014.997143","url":null,"abstract":"As a boy in the 1920s and 30s, I was always interested in science. It was an era in which chemists were developing new materials, physicists were developing new instruments and discovering new particles, and engineers were creating new devices (such as radios, airplanes, and refrigerators). As my senior thesis in high school, I researched and wrote a paper on the possibility of transmutation of the elements and of atomic energy. (I did not envision a bomb!) Two high school teachers, one in mathematics and one in chemistry, intrigued and guided my interests, influcening me to enroll at the Massachusetts Institute of Technology (MIT). It was a serious, high-intensity school. During my sophomore year, MIT launched a new program in physical and chemical biology that instantly seized my imagination. After four years’ time out for World War II, (radar research and development) I started work research on nucleic acids in 1946. The nature and mode of action of the gene was mysterious and clearly central to biology. The work of Avery, McLeod, and McCarty (1) with Pneumococcus strongly suggested that the genes were DNA. Uber’s work upon ultraviolet-induced mutation suggested that damage to DNA had genetic effects (2). But the structure of DNA and its biochemistry were essentially unknown. The ultraviolet absorption bands of DNA were broad. We sought to narrow them (so as to be able to produce more specific effects) by taking spectra at low temperatures (liquid nitrogen and liquid hydrogen) (3), but the effects were small. However, upon ultraviolet irradiation of uracil, I discovered a reversible photochemical (4) effect at the same time that Renato Dulbecco discovered a photochemical effect on phage (5). Upon completing my PhD, I obtained a position as Associate Professor of Biophysics at Iowa State (a position earlier held by Uber). To pursue this line of research further it seemed desirable to use deoxynucleotides rather than the purine and pyrimidine bases. At that time the only techniques to isolate deoxynucleotides had yields of about 1%. I developed the technique to obtain 100% yield of nucleotides from DNA (6), and then quantitated and characterized their ultraviolet absorption. I also isolated all of the possible dinucleotides (7). This permitted me to show that (a) the methylcytosine was always adjacent to guanine, and (b) the molar equalities of A and T and of G and C demonstrated by Chargaff (8) could not arise from a sequential order but more likely required two strands of complementary sequence. But I had no proof, only surmise. At this time I realized that if I was to advance further with DNA I needed a biological system in which DNA was active. Bacteriophage, as elucidated by Max Delbruck, was such a system. (Max, at my invitation, had earlier visited at Iowa State to present a series of excellent lectures on bacteriophage.) I was able to take a six month leave of absence from Iowa State, and Max arranged a stipend for me to come to Caltech ","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"5 1","pages":"e997143"},"PeriodicalIF":0.0,"publicationDate":"2015-01-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1080/21597081.2014.997143","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34066291","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":"Niche-dependent genetic diversity in Antarctic metaviromes.","authors":"Olivier Zablocki,&nbsp;Lonnie van Zyl,&nbsp;Evelien M Adriaenssens,&nbsp;Enrico Rubagotti,&nbsp;Marla Tuffin,&nbsp;Stephen C Cary,&nbsp;Don Cowan","doi":"10.4161/21597081.2014.980125","DOIUrl":"https://doi.org/10.4161/21597081.2014.980125","url":null,"abstract":"<p><p>The metaviromes from 2 different Antarctic terrestrial soil niches have been analyzed. Both hypoliths (microbial assemblages beneath transluscent rocks) and surrounding open soils showed a high level diversity of tailed phages, viruses of algae and amoeba, and virophage sequences. Comparisons of other global metaviromes with the Antarctic libraries showed a niche-dependent clustering pattern, unrelated to the geographical origin of a given metavirome. Within the Antarctic open soil metavirome, a putative circularly permuted, ∼42kb dsDNA virus genome was annotated, showing features of a temperate phage possessing a variety of conserved protein domains with no significant taxonomic affiliations in current databases.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 4","pages":"e980125"},"PeriodicalIF":0.0,"publicationDate":"2014-12-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/21597081.2014.980125","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34147502","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":"Metagenomic ventures into outer sequence space.","authors":"Bas E Dutilh","doi":"10.4161/21597081.2014.979664","DOIUrl":"https://doi.org/10.4161/21597081.2014.979664","url":null,"abstract":"<p><p>Sequencing DNA or RNA directly from the environment often results in many sequencing reads that have no homologs in the database. These are referred to as \"unknowns,\" and reflect the vast unexplored microbial sequence space of our biosphere, also known as \"biological dark matter.\" However, unknowns also exist because metagenomic datasets are not optimally mined. There is a pressure on researchers to publish and move on, and the unknown sequences are often left for what they are, and conclusions drawn based on reads with annotated homologs. This can cause abundant and widespread genomes to be overlooked, such as the recently discovered human gut bacteriophage crAssphage. The unknowns may be enriched for bacteriophage sequences, the most abundant and genetically diverse component of the biosphere and of sequence space. However, it remains an open question, what is the actual size of biological sequence space? The de novo assembly of shotgun metagenomes is the most powerful tool to address this question.</p>","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"4 4","pages":"e979664"},"PeriodicalIF":0.0,"publicationDate":"2014-12-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.4161/21597081.2014.979664","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34079998","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":"Mycobacteriophage cell binding proteins for the capture of mycobacteria","authors":"D. Arutyunov, U. Singh, Amr M. El-Hawiet, H. Seckler, Sanaz Nikjah, M. Joe, Yu Bai, T. Lowary, John S. Klassen, S. Evoy, C. Szymanski","doi":"10.4161/21597073.2014.960346","DOIUrl":"https://doi.org/10.4161/21597073.2014.960346","url":null,"abstract":"Slow growing Mycobacterium avium subsp. paratuberculosis (MAP) causes a deadly condition in cattle known as Johne's disease where asymptomatic carriers are the major source of disease transmission. MAP was also shown to be associated with chronic Crohn's disease in humans. Mycobacterium smegmatis is a model mycobacterium that can cause opportunistic infections in a number of human tissues and, rarely, a respiratory disease. Currently, there are no rapid, culture-independent, reliable and inexpensive tests for the diagnostics of MAP or M. smegmatis infections. Bacteriophages are viruses producing a number of proteins that effectively and specifically recognize the cell envelopes of their bacterial hosts. We demonstrate that the mycobacterial phage L5 minor tail protein Gp6 and lysin Gp10 are useful tools for the rapid capture of mycobacteria. Immobilized Gp10 was able to bind both MAP and M. smegmatis cells whereas Gp6 was M. smegmatis specific. Neither of the 2 proteins was able to capture E. coli, salmonella, campylobacter or Mycobacterium marinum cells. Gp6 was detected previously as a component of the phage particle and shows no homology to proteins with known function. Therefore, electrospray ionization mass spectrometry was used to determine whether recombinant Gp6 could bind to a number of chemically synthesized fragments of mycobacterial surface glycans. These findings demonstrate that mycobacteriophage proteins could be used as a pathogen capturing platform that can potentially improve the effectiveness of existing diagnostic methods.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"11 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89519879","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 remediation of bacterial pathogens in aquaculture: a review of the technology","authors":"G. Richards","doi":"10.4161/21597081.2014.975540","DOIUrl":"https://doi.org/10.4161/21597081.2014.975540","url":null,"abstract":"Bacteriophages have been proposed as an alternative to antibiotic usage and several studies on their application in aquaculture have been reported. This review highlights progress to date on phage therapies for the following fish and shellfish diseases and associated pathogens: hemorrhagic septicemia (Aeromonas hydrophila) in loaches, furunculosis (Aeromonas salmonicida) in trout and salmon, edwardsiellosis (Edwardsiella tarda) in eel, columnaris disease (Flavobacterium columnare) in catfish, rainbow trout fry syndrome or cold water disease (Flavobacterium psychrophilum) in trout and salmon, lactococcosis (Lactococcus spp.) in yellowtail, ulcerative skin lesions (Pseudomonas aeruginosa) in freshwater catfish, bacterial hemorrhagic ascites disease (Pseudomonas plecoglossicida) in ayu fish, streptococcosis (Streptococcus iniae) in flounder, and luminescent vibriosis (Vibrio harveyi) in shrimp. Information is reviewed on phage specificity, host resistance, routes of administration, and dosing of fish and shellfish. Limitations in phage research are described and recommended guidelines are provided for conducting future phage studies involving fish and shellfish.","PeriodicalId":8686,"journal":{"name":"Bacteriophage","volume":"84 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2014-10-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91049712","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":"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":"12 11","pages":""},"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":"74 1","pages":""},"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":"4 ","pages":"e32187"},"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":"4 ","pages":"e32129"},"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":"4 ","pages":"e29009"},"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}