scholarly journals Are Bordetella bronchiseptica Siphoviruses (Genus Vojvodinavirus) Appropriate for Phage Therapy—Bacterial Allies or Foes?

Viruses ◽  
2021 ◽  
Vol 13 (9) ◽  
pp. 1732
Author(s):  
Aleksandra Petrovic Fabijan ◽  
Verica Aleksic Sabo ◽  
Damir Gavric ◽  
Zsolt Doffkay ◽  
Gábor Rakhely ◽  
...  
Keyword(s):  
Bacterial Growth ◽  
Genomic Analysis ◽  
Bordetella Bronchiseptica ◽  
Host Bacterium ◽  
Flagellar Motility ◽  
Beta Lactam ◽  
Bacterial Host ◽  
Bacterial Dna ◽  
Phage Dna ◽  
Complete Genomic

Bordetella bronchiseptica is a respiratory animal pathogen that shows growing resistance to commonly used antibiotics, which has necessitated the examination of new antimicrobials, including bacteriophages. In this study, we examined the previously isolated and partially characterized B. bronchiseptica siphoviruses of the genus Vojvodinavirus (LK3, CN1, CN2, FP1 and MW2) for their ability to inhibit bacterial growth and biofilm, and we examined other therapeutically important properties through genomic analysis and lysogeny experiments. The phages inhibited bacterial growth at a low multiplicity of infection (MOI = 0.001) of up to 85% and at MOI = 1 for >99%. Similarly, depending on the phages and MOIs, biofilm formation inhibition ranged from 65 to 95%. The removal of biofilm by the phages was less efficient but still considerably high (40–75%). Complete genomic sequencing of Bordetella phage LK3 (59,831 bp; G + C 64.01%; 79 ORFs) showed integrase and repressor protein presence, indicating phage potential to lysogenize bacteria. Lysogeny experiments confirmed the presence of phage DNA in bacterial DNA upon infection using PCR, which showed that the LK3 phage forms more or less stable lysogens depending on the bacterial host. Bacterial infection with the LK3 phage enhanced biofilm production, sheep blood hemolysis, flagellar motility, and beta-lactam resistance. The examined phages showed considerable anti-B. bronchiseptica activity, but they are inappropriate for therapy because of their temperate nature and lysogenic conversion of the host bacterium.

scholarly journals A Salmonella Phage-P22 Mutant Defective in Abortive Transduction

Genetics ◽  
1997 ◽  
Vol 145 (1) ◽  
pp. 17-27 ◽  
Author(s):  
Nicholas R Benson ◽  
John Roth
Keyword(s):  
Protein S ◽  
Lytic Infection ◽  
Genetic Element ◽  
Bacterial Dna ◽  
Phage Mutant ◽  
Viral Particles ◽  
Phage Dna ◽  
Phage P22 ◽  
Mutant Locus ◽  
Salmonella Phage

In the course of a lytic infection the Salmonella phage P22 occasionally encapsulates bacterial DNA instead of phage DNA. Thus, phage lysates include two classes of viral particles. Phage particles carrying bacterial DNA are referred to as transducing particles and deliver this DNA to a host as efficiently as particles carrying phage DNA. Once injected, the transduced DNA can either recombine with the recipient chromosome to form a “complete” transductant, or it can establish itself as an expressible, nonreplicating genetic element and form an “abortive” transductant. In this work, we describe a P22-phage mutant with reduced ability to form abortive transductants. The mutation responsible for this phenotype, called tdx-1, was found as one of two mutations contributing to the high-transducing phenotype of the P22-mutant HT12/4. In addition, the tdx-1 mutation is lethal when combined with an erf-am mutation. The tdx-1 mutation has been mapped to a region of the P22 genome that encodes several injected proteins and may involve more than one mutant locus. The phenotypes of the tdx-1 mutation suggest that the Tdx protein(s) normally assist in the circularization of the P22 genome and also contribute to the formation of DNA circles thought to be required for abortive transduction.

Complete genomic analysis of multidrug-resistance Pseudomonas aeruginosa Guangzhou-Pae617, the host of megaplasmid pBM413

2018 ◽  
Vol 117 ◽  
pp. 265-269 ◽  
Author(s):  
Junyan Liu ◽  
Lin Li ◽  
Brian M. Peters ◽  
Bing Li ◽  
Dingqiang Chen ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Multidrug Resistance ◽  
Genomic Analysis ◽  
Complete Genomic

Complete genomic analysis of a Bangladeshi G1P[8] rotavirus strain detected in 2003 reveals a close evolutionary relationship with contemporary human Wa-like strains

2010 ◽  
Vol 10 (6) ◽  
pp. 746-754 ◽  
Author(s):  
Mustafizur Rahman ◽  
Jelle Matthijnssens ◽  
Farjana Saiada ◽  
Zahid Hassan ◽  
Elisabeth Heylen ◽  
...  
Keyword(s):  
Evolutionary Relationship ◽  
Genomic Analysis ◽  
Complete Genomic

Development of T7 phage and T7 phage containing apurinic sites in an exonuclease III, endonuclease IV double mutant of Escherichia coli

1992 ◽  
Vol 70 (7) ◽  
pp. 605-608 ◽  
Author(s):  
Giselle Sanchez ◽  
Margaret D. Mamet-Bratley
Keyword(s):  
Escherichia Coli ◽  
Dna Repair ◽  
Dna Synthesis ◽  
Double Mutant ◽  
Bacteriophage T7 ◽  
Bacterial Dna ◽  
Exonuclease Iii ◽  
Repair Enzymes ◽  
Phage Dna ◽  
T7 Phage

The development of bacteriophage T7 was examined in an Escherichia coli double mutant defective for the two major apurinic, apyrimidinic endonucleases (exonuclease III and endonuclease IV, xth nfo). In cells infected with phages containing apurinic sites, the defect in repair enzymes led to a decrease of phage survival and a total absence of bacterial DNA degradation and of phage DNA synthesis. These results directly demonstrate the toxic action of apurinic sites on bacteriophage T7 at the intracellular level and its alleviation by DNA repair. In addition, untreated T7 phage unexpectedly displayed reduced plating efficiency and decreased DNA synthesis in the xth nfo double mutant.Key words: apurinic sites, DNA repair, T7 phage.

scholarly journals Genetic association testing using the GENESIS R/Bioconductor package

2019 ◽  
Author(s):  
Stephanie M Gogarten ◽  
Tamar Sofer ◽  
Han Chen ◽  
Chaoyu Yu ◽  
Jennifer A Brody ◽  
...  
Keyword(s):  
Data Storage ◽  
Genomic Analysis ◽  
Supplementary Information ◽  
Storage And Retrieval ◽  
Association Testing ◽  
Link Functions ◽  
Efficient Storage ◽  
Genetic Association Testing ◽  
Analysis Workflow ◽  
Complete Genomic

Abstract Summary The Genomic Data Storage (GDS) format provides efficient storage and retrieval of genotypes measured by microarrays and sequencing. We developed GENESIS to perform various single- and aggregate-variant association tests using genotype data stored in GDS format. GENESIS implements highly flexible mixed models, allowing for different link functions, multiple variance components and phenotypic heteroskedasticity. GENESIS integrates cohesively with other R/Bioconductor packages to build a complete genomic analysis workflow entirely within the R environment. Availability and implementation https://bioconductor.org/packages/GENESIS; vignettes included. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Coevolution ofaah: Adps-Like Gene with the Host Bacterium Revealed by Comparative Genomic Analysis

2012 ◽  
Vol 2012 ◽  
pp. 1-9 ◽  
Author(s):  
Liyan Ping ◽  
Matthias Platzer ◽  
Gaiping Wen ◽  
Nicolas Delaroque
Keyword(s):  
Stop Codon ◽  
Sequence Similarity ◽  
General Pattern ◽  
Genomic Analysis ◽  
Dna Binding Proteins ◽  
Comparative Genomic Analysis ◽  
Comparative Genomic ◽  
Host Bacterium ◽  
High Sequence Similarity ◽  
Lepidopteran Larvae

A protein named AAH was isolated from the bacteriumMicrobacterium arborescensSE14, a gut commensal of the lepidopteran larvae. It showed not only a high sequence similarity to Dps-like proteins (DNA-binding proteins from starved cell) but also reversible hydrolase activity. A comparative genomic analysis was performed to gain more insights into its evolution. The GC profile of theaahgene indicated that it was evolved from a low GC ancestor. Its stop codon usage was also different from the general pattern of Actinobacterial genomes. The phylogeny ofdps-like proteins showed strong correlation with the phylogeny of host bacteria. A conserved genomic synteny was identified in some taxonomically related Actinobacteria, suggesting that the ancestor genes had incorporated into the genome before the divergence of Micrococcineae from other families. Theaahgene had evolved new function but still retained the typical dodecameric structure.

scholarly journals Characterization and genomic analysis of two Staphylococcus aureus bacteriophages isolated from poultry/livestock farms

2013 ◽  
Vol 94 (11) ◽  
pp. 2569-2576 ◽  
Author(s):  
Hyunjin Yoon ◽  
Jiae Yun ◽  
Jeong-A Lim ◽  
Eunjung Roh ◽  
Kyu-Seok Jung ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Host Range ◽  
Genomic Analysis ◽  
Enzyme Treatment ◽  
Comparative Genomic ◽  
The Family ◽  
Phage Dna ◽  
Host Range Determination ◽  
Range Determination ◽  
Livestock Farms

Staphylococcus aureus is one of the most important pathogens, causing various diseases in humans and animals. As methicillin-resistant S. aureus (MRSA) has become increasingly prevalent, controlling this pathogen with standard antibiotic treatment has become challenging. Bacteriophages (phages) have attracted interest as alternative antibacterial agents to control MRSA. In this study, we isolated six S. aureus phages from soils of poultry/livestock farms. Based on the results of host range determination with 150 S. aureus strains and restriction enzyme treatment of phage DNA, two phages, designated SP5 and SP6, were selected for further characterization and genome sequencing. Both SP5 and SP6 were classified as members of the family Siphoviridae. The genome of SP5 comprises 43 305 bp and contains 63 ORFs, while the SP6 genome comprises 42 902 bp and contains 61 ORFs. Although they have different host spectra, the phage genomes exhibit high nucleotide similarity to each other. Adsorption assay results suggested that the host range determinants of the two phages are involved in both adsorption and infection. Comparative genomic analyses of the two phages provided evidence that the lysogenic/lytic control module and tail proteins may be important for host specificity.

scholarly journals Maturation of Pseudo-nucleus Compartment in P. aeruginosa, Infected with Giant PhiKZ Phage

2020 ◽  
Author(s):  
Yana Danilova ◽  
Viktoria V. Belousova ◽  
Andrey V. Moiseenko ◽  
Innokentii E. Vishnyakov ◽  
Maria V. Yakunina ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Electron Tomography ◽  
Analytical Electron Microscopy ◽  
The Other ◽  
Bacterial Dna ◽  
Short Intervals ◽  
Bacteriophage Infection ◽  
Phage Dna ◽  
Analytical Electron ◽  
Bacterial Cytoplasm

Bacteria develop various defense mechanisms against stresses, including the bacteriophage infection. The giant phiKZ phage infection induced the appearance of a pseudo-nucleus inside the bacterial cytoplasm. Here, we used FISH, electron tomography and analytical electron microscopy to study the morphology of this unique nucleus-like shell and to demonstrate the distribution of phiKZ and bacterial DNA in infected P. aeruginosa cells. The maturation of the pseudo-nucleus was traced in short intervals for 40 min after infection. This study was accompanied by the identification of phiKZ and bacterial DNA by real-time RCR. We demonstrated that phage DNA that isolated from the cytoplasm during all infection stages were compacted within the pseudo-nucleus in a specific structure. Bacterial DNA was diminished in the course of infection, but did not completely degrade until at least 40 min after phage application. The content of the total phage DNA, on the other hand, increased. EDX analysis confirmed these results and revealed that, during the infection, Sulfur content in the bacterial cytoplasm increased, which suggests the increase of DNA-binding Met-reach proteins synthesis, which could protect bacterial DNA from stress.

scholarly journals DBSCAN-SWA: an integrated tool for rapid prophage detection and annotation

2020 ◽  
Author(s):  
Rui Gan ◽  
Fengxia Zhou ◽  
Yu Si ◽  
Han Yang ◽  
Chuangeng Chen ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Bacterial Infections ◽  
Software Tool ◽  
High Specificity ◽  
Bacterial Genomes ◽  
Bacterial Host ◽  
Accurate Identification ◽  
Bacterial Dna ◽  
Intracellular Form ◽  
User Friendly

AbstractSummaryAs an intracellular form of a bacteriophage in the bacterial host genome, a prophage is usually integrated into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). Phage therapy has been widely applied, for example, using phages to kill bacteria to treat pathogenic and resistant bacterial infections. Therefore, it is necessary to develop effective tools for the fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions of bacterial genomes. DBSCAN-SWA runs faster than any previous tool. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%) and PHASTER (82%) for raw DNA sequences. DBSCAN-SWA also provides user-friendly visualizations including a circular prophage viewer and interactive DataTables.Availability and implementationDBSCAN-SWA is implemented in Python3 and is freely available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.

Sign in / Sign up

Export Citation Format

Share Document