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Bacteriophages

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https://www.readbyqxmd.com/read/29331608/allosteric-effects-in-bacteriophage-hk97-procapsids-revealed-directly-from-covariance-analysis-of-cryo-em-data
#1
Nan Xu, David Veesler, Peter C Doerschuk, John E Johnson
The information content of cryo EM data sets exceeds that of the electron scattering potential (cryo EM) density initially derived for structure determination. Previously we demonstrated the power of data variance analysis for characterizing regions of cryo EM density that displayed functionally important variance anomalies associated with maturation cleavage events in Nudaurelia Omega Capensis Virus and the presence or absence of a maturation protease in bacteriophage HK97 procapsids. Here we extend the analysis in two ways...
January 10, 2018: Journal of Structural Biology
https://www.readbyqxmd.com/read/29330592/genomic-characterization-of-key-bacteriophages-to-formulate-the-potential-biocontrol-agent-to-combat-enteric-pathogenic-bacteria
#2
Krupa M Parmar, Nishant A Dafale, Hitesh Tikariha, Hemant J Purohit
Combating bacterial pathogens has become a global concern especially when the antibiotics and chemical agents are failing to control the spread due to its resistance. Bacteriophages act as a safe biocontrol agent by selectively lysing the bacterial pathogens without affecting the natural beneficial microflora. The present study describes the screening of prominent enteric pathogens NDK1, NDK2, NDK3, and NDK4 (Escherichia, Klebsiella, Enterobacter, and Serratia) mostly observed in domestic wastewater; against which KNP1, KNP2, KNP3, and KNP4 phages were isolated...
January 12, 2018: Archives of Microbiology
https://www.readbyqxmd.com/read/29330023/unraveling-the-differential-structural-stability-and-dynamics-features-of-t7-endolysin-partially-folded-conformations
#3
Meenakshi Sharma, Dinesh Kumar, Krishna Mohan Poluri
BACKGROUND: Characterization of partially collapsed protein conformations at atomic level is a daunting task due to their inherent flexibility and conformational heterogeneity. T7 bacteriophage endolysin (T7L) is a single-domain amidase that facilitates the lysis of Gram-negative bacteria. T7L exhibits a pH-dependent structural transition from native state to partially folded (PF) conformation. In the pH range 5-3, T7L PF states display differential ANS binding characteristics. METHODS: CD, fluorescence, NMR spectroscopy and lysis assays were used to investigate the structure-stability- dynamics relationships of T7L PF conformations...
January 9, 2018: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/29327679/natural-and-artificial-strategies-to-control-the-conjugative-transmission-of-plasmids
#4
María Getino, Fernando de la Cruz
Conjugative plasmids are the main carriers of transmissible antibiotic resistance (AbR) genes. For that reason, strategies to control plasmid transmission have been proposed as potential solutions to prevent AbR dissemination. Natural mechanisms that bacteria employ as defense barriers against invading genomes, such as restriction-modification or CRISPR-Cas systems, could be exploited to control conjugation. Besides, conjugative plasmids themselves display mechanisms to minimize their associated burden or to compete with related or unrelated plasmids...
January 2018: Microbiology Spectrum
https://www.readbyqxmd.com/read/29327434/a-fast-and-reliable-method-for-monitoring-of-prophage-activating-chemicals
#5
Juan Xu, Bärbel Kiesel, René Kallies, Feng-Lei Jiang, Yi Liu, Thomas Maskow
Bacteriophages, that is viruses that infect bacteria, either lyse bacteria directly or integrate their genome into the bacterial genome as so-called prophages, where they remain at a silent state. Both phages and bacteria are able to survive in this state. However, prophages can be reactivated with the introduction of chemicals, followed by the release of a high number of phage particles, which could infect other bacteria, thus harming ecosystems by a viral bloom. The basics for a fast, automatable analytical method for the detection of prophage-activating chemicals are developed and successfully tested here...
January 12, 2018: Microbial Biotechnology
https://www.readbyqxmd.com/read/29327410/genomic-insights-into-the-acidobacteria-reveal-strategies-for-their-success-in-terrestrial-environments
#6
Stephanie A Eichorst, Daniela Trojan, Simon Roux, Craig Herbold, Thomas Rattei, Dagmar Woebken
Members of the phylum Acidobacteria are abundant and ubiquitous across soils. We performed the largest (to date) comparative genome analysis spanning subdivisions 1, 3, 4, 6, 8, and 23 (n=24) with the goal to identify features to help explain their prevalence in soils and understand their ecophysiology. In contrast to earlier studies, our analysis revealed that bacteriophage integration events along with transposable and mobile elements influenced the structure and plasticity of these genomes. Low- and high-affinity respiratory oxygen reductases were detected in multiple genomes, suggesting the capacity for growing across different oxygen gradients...
January 12, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29327235/complete-genome-sequence-of-a-phage-hyperparasite-of-candidatus-xenohaliotis-californiensis-rickettsiales-a-pathogen-of-haliotis-spp-gasteropoda
#7
Roberto Flores, Jorge Cáceres-Martínez, Miguel Ángel Del Río-Portilla, Alexei F Licea-Navarro, Ricardo Gonzales-Sánchez, Abraham Guerrero
Bacteriophages are recognized as major mortality agents of microbes, among them intracellular marine rickettsiales-like bacteria. Recently, a phage hyperparasite of Candidatus Xenohaliotis californiensis (CXc) has been described. This bacterium is considered the causal agent of Withering Syndrome (WS) which is a chronic and potentially lethal disease of abalone species from California, USA and the peninsula of Baja California, Mexico. This hyperparasite which infects CXc could be used as a biocontrol agent for WS...
January 11, 2018: Archives of Virology
https://www.readbyqxmd.com/read/29326207/complete-genome-sequence-of-bacteriophage-st11ph5-which-infects-uropathogenic-escherichia-coli-strain-up11
#8
Alla K Golomidova, Eugene E Kulikov, Vladislav V Babenko, Elena S Kostryukova, Andrey V Letarov
Bacteriophage St11Ph5 was isolated from a sewage sample on a particularly phage-resistant uropathogenic Escherichia coli (UPEC) up11 host strain. It appeared to be closely related to bacteriophage G7C, isolated from horse feces; however, it carries a highly divergent host recognition module.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29326201/eight-genome-sequences-of-cluster-be1-phages-that-infect-streptomyces-species
#9
Lee E Hughes, Christopher D Shaffer, Vassie C Ware, Issac Aguayo, Rahat M Aziz, Swapan Bhuiyan, Isaac S Bindert, Canyon K Calovich-Benne, Jordyn Chapman, Richard Donegan-Quick, Amal Farooq, Cynthia Garcia, Lee H Graham, Baylee Y Green, Margaret A Kenna, Emily R Kneeream, Christian E Laing, Catherine M Mageeney, Sandra N Meridew, Abigail R Mikolon, Ryann E Morgan, Subhayu Nayek, Idowu D Olugbade, Kim C Pike, Lauren E Schlegel, Taylor C Shishido, Tara Suresh, Nikita Suri, Kathleen Weston Hafer, Rebecca A Garlena, Daniel A Russell, Steven G Cresawn, Welkin H Pope, Deborah Jacobs-Sera, Graham F Hatfull
Cluster BE1 Streptomyces bacteriophages belong to the Siphoviridae, with genome sizes over 130 kbp, and they contain direct terminal repeats of approximately 11 kbp. Eight newly isolated closely related cluster BE1 phages contain 43 to 48 tRNAs, one transfer-messenger RNA (tmRNA), and 216 to 236 predicted open reading frames (ORFs), but few of their genes are shared with other phages, including those infecting Streptomyces species.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29326200/complete-genome-sequence-of-a-bacteriophage-pvco-5-that-infects-vibrio-coralliilyticus-which-causes-bacillary-necrosis-in-pacific-oyster-crassostrea-gigas-larvae
#10
Hyoun Joong Kim, Jin Woo Jun, Sib Sankar Giri, Cheng Chi, Saekil Yun, Sang Guen Kim, Sang Wha Kim, Jeong Woo Kang, Se Jin Han, Se Chang Park
We report here the complete genome sequence of the Vibrio coralliilyticus-specific phage pVco-5, a double-stranded DNA virus isolated from an oyster hatchery tank. Vibrio coralliilyticus causes bacillary necrosis in marine bivalve larvae; hence, phage pVco-5 could be used to prevent V. coralliilyticus infections in these larvae.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29326199/genome-sequences-of-four-cluster-p-mycobacteriophages
#11
Erin L Doyle, Christy L Fillman, Nathan S Reyna, Deborah M Tobiason, Daniel E Westholm, Jonathan L Askins, Brittany P Backus, Ashlynn C Baker, Harrison S Ballard, Paul J Bisesi, Logan Bond, Deanna Byrnes, Hannah Carlstedt, Kinnon S Dodson, Megan J Fallert, Kyla J Foster, Daniel N Games, Tristan R Grams, Nancy A Guild, Autumn Hurd, Nicholas Iwata, Cassidy R Kepler, Lucinda R Krenzke, Kelly Luekens, Jackie Lewis, Cali McEntee, Justin C McGee, Noah Nalley, Ruth C Plymale, Jade Prochaska, Reid G Rogers, Jessica B Schipper, Kelsey Snyder, Kali Uhrich, Chelsey D Vermillion, Sarah K Vickers, Meredyth D Wenta, Tyler Z Yates, Chas F Young, Ty H Stoner, Welkin H Pope, Deborah Jacobs-Sera, Rebecca A Garlena, Daniel A Russell, Steven G Cresawn, Graham F Hatfull
Four bacteriophages infecting Mycobacterium smegmatis mc2155 (three belonging to subcluster P1 and one belonging to subcluster P2) were isolated from soil and sequenced. All four phages are similar in the left arm of their genomes, but the P2 phage differs in the right arm. All four genomes contain features of temperate phages.
January 11, 2018: Genome Announcements
https://www.readbyqxmd.com/read/29320875/characterization-of-bacteriophages-and-their-carriage-in-staphylococcus-aureus-isolated-from-broilers-in-poland
#12
A Marek, E Pyzik, D Stępień-Pyśniak, R Urban-Chmiel, A Nowaczek
1. The objective of this study was the isolation and morphological characterisation of temperate bacteriophages induced from Staphylococcus aureus strains isolated from clinical samples from broiler chickens and turkeys. 2. Eighty-five S. aureus strains were tested for susceptibility to oxacillin in order to determine which were multi-resistant. A total of 24 strains showed resistance to methicillin. 3. Thirty-one bacteriophages that were lytic against S. aureus strains were isolated and the host range of the bacteriophages was evaluated...
January 11, 2018: British Poultry Science
https://www.readbyqxmd.com/read/29320762/corrected-and-republished-from-identification-of-peptidoglycan-hydrolase-constructs-with-synergistic-staphylolytic-activity-in-cow-s-milk
#13
Carolin T Verbree, Steven M Dätwyler, Susanne Meile, Fritz Eichenseher, David M Donovan, Martin J Loessner, Mathias Schmelcher
Peptidoglycan hydrolases (PGHs) have been suggested as novel therapeutics for the treatment of bovine mastitis. However, activity in the presence of cow's milk is an important requirement for drugs administered into the bovine udder. We have used a microtiter plate-based protocol to screen a library of >170 recombinant PGHs, including engineered bacteriophage endolysins, for enzymes with activity against Staphylococcus aureus in milk. Eight suitable PGH constructs were identified by this approach, and their efficacies against S...
January 1, 2018: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/29318984/a-brief-history-of-shigella
#14
Keith A Lampel, Samuel B Formal, Anthony T Maurelli
The history of Shigella, the causative agent of bacillary dysentery, is a long and fascinating one. This brief historical account starts with descriptions of the disease and its impact on human health from ancient time to the present. Our story of the bacterium starts just before the identification of the dysentery bacillus by Kiyoshi Shiga in 1898 and follows the scientific discoveries and principal scientists who contributed to the elucidation of Shigella pathogenesis in the first 100 years. Over the past century, Shigella has proved to be an outstanding model of an invasive bacterial pathogen and has served as a paradigm for the study of other bacterial pathogens...
January 2018: EcoSal Plus
https://www.readbyqxmd.com/read/29318247/forced-phage-uncorking-viral-dna-ejection-triggered-by-a-mechanically-sensitive-switch
#15
Miklós S Z Kellermayer, Zsuzsanna Vörös, Gabriella Csík, Levente Herényi
The foremost event of bacteriophage infection is the ejection of genomic material into the host bacterium after virus binding to surface receptor sites. How ejection is triggered is yet unknown. Here we show, in single mature T7 phage particles, that tapping the capsid wall with an oscillating atomic-force-microscope cantilever triggers rapid DNA ejection via the tail complex. The triggering rate increases exponentially as a function of force, following transition-state theory, across an activation barrier of 23 kcal mol-1 at 1...
January 10, 2018: Nanoscale
https://www.readbyqxmd.com/read/29316743/studies-on-lytic-tailed-bacillus-cereus-specific-phage-for-usein-a-ferromagnetoelastic-biosensor-as-a-novel-recognition-element
#16
In Young Choi, JooHyeon Park, Kwang-Pyo Kim, Jun-Hyun Oh, Mi-Kyung Park
This study investigated the feasibility of the lytic, tailed Bacillus cereus-specific phage for use in a ferromagnetoelastic (FME) biosensor as a novel recognition element. The phage was immobilized at various concentrations through a direct adsorption or a combination of 11-MUA and EDC/NHS. The effects of time and temperature on its lytic properties were investigated through the exposure of B. cereus (4 and 8 logCFU/ml) to the phage (8 logPFU/ml) for various incubation periods at 22°C and at various temperatures for 30 and 60 min...
January 11, 2018: Journal of Microbiology and Biotechnology
https://www.readbyqxmd.com/read/29315249/bacteriophage-%C3%AE-sa012-has-a-broad-host-range-against-staphylococcus-aureus-and-effective-lytic-capacity-in-a-mouse-mastitis-model
#17
Hidetomo Iwano, Yusuke Inoue, Takuji Takasago, Hironori Kobayashi, Takaaki Furusawa, Kotomi Taniguchi, Jumpei Fujiki, Hiroshi Yokota, Masaru Usui, Yasunori Tanji, Katsuro Hagiwara, Hidetoshi Higuchi, Yutaka Tamura
Bovine mastitis is an inflammation of the mammary gland caused by bacterial infection in dairy cattle. It is the most costly disease in the dairy industry because of the high use of antibiotics. Staphylococcus aureus is one of the major causative agents of bovine mastitis and antimicrobial resistance. Therefore, new strategies to control bacterial infection are required in the dairy industry. One potential strategy is bacteriophage (phage) therapy. In the present study, we examined the host range of previously isolated S...
January 9, 2018: Biology
https://www.readbyqxmd.com/read/29314266/fluorescence-detected-linear-dichroism-spectroscopy-a-selective-and-sensitive-probe-for-fluorophores-in-flow-oriented-systems
#18
Alan M Wemyss, Nikola P Chmel, Daniela P Lobo, John A Sutherland, Timothy R Dafforn, Alison Rodger
Fluorescence detection typically enhances sensitivity and selectivity for fluorescent analytes. The potential for combining fluorescence detection with flow orientation of the sample in the normal configuration of linear dichroism experiments is explored in this work by measuring the fluorescence emitted from flow-orientated DNA-bound ligands and M13 bacteriophage. Data for ethidium bromide, Hoechst 33258, and 4,6-diamidino-2-phenyindole are presented. The theoretical basis of the technique is also presented for instruments running in both the fixed direct-current mode, which is the normal operation mode of circular dichroism spectropolarimeters, and also in fixed high-tension voltage mode...
January 3, 2018: Chirality
https://www.readbyqxmd.com/read/29311716/discovering-viral-genomes-in-human-metagenomic-data-by-predicting-unknown-protein-families
#19
Mauricio Barrientos-Somarribas, David N Messina, Christian Pou, Fredrik Lysholm, Annelie Bjerkner, Tobias Allander, Björn Andersson, Erik L L Sonnhammer
Massive amounts of metagenomics data are currently being produced, and in all such projects a sizeable fraction of the resulting data shows no or little homology to known sequences. It is likely that this fraction contains novel viruses, but identification is challenging since they frequently lack homology to known viruses. To overcome this problem, we developed a strategy to detect ORFan protein families in shotgun metagenomics data, using similarity-based clustering and a set of filters to extract bona fide protein families...
January 8, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29311700/phage-host-population-dynamics-promotes-prophage-acquisition-in-bacteria-with-innate-immunity
#20
Maroš Pleška, Moritz Lang, Dominik Refardt, Bruce R Levin, Călin C Guet
Temperate bacteriophages integrate in bacterial genomes as prophages and represent an important source of genetic variation for bacterial evolution, frequently transmitting fitness-augmenting genes such as toxins responsible for virulence of major pathogens. However, only a fraction of bacteriophage infections are lysogenic and lead to prophage acquisition, whereas the majority are lytic and kill the infected bacteria. Unless able to discriminate lytic from lysogenic infections, mechanisms of immunity to bacteriophages are expected to act as a double-edged sword and increase the odds of survival at the cost of depriving bacteria of potentially beneficial prophages...
January 8, 2018: Nature Ecology & Evolution
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