scholarly journals Genome, Integration, and Transduction of a Novel Temperate Phage of Helicobacter pylori

2012 ◽  
Vol 86 (16) ◽  
pp. 8781-8792 ◽  
Author(s):  
Cheng-Hung Luo ◽  
Pei-Yu Chiou ◽  
Chiou-Ying Yang ◽  
Nien-Tsung Lin
Keyword(s):  
Helicobacter Pylori ◽  
Open Reading Frames ◽  
Clinical Strain ◽  
Host Chromosome ◽  
Content Type ◽  
Double Stranded Dna ◽  
Genome Integration ◽  
H Pylori ◽  
Generalized Transduction ◽  
Reading Frames

Helicobacter pyloriis a common human pathogen that has been identified to be carcinogenic. This study isolated the temperate bacteriophage 1961P from the lysate of a clinical strain ofH. pyloriisolated in Taiwan. The bacteriophage has an icosahedral head and a short tail, typical of thePodoviridaefamily. Its double-stranded DNA genome is 26,836 bp long and has 33 open reading frames. Only 9 of the predicted proteins have homologs of known functions, while the remaining 24 are only similar to unknown proteins encoded byHelicobacterprophages and remnants. Analysis of sequences proximal to the phage-host junctions suggests that 1961P may integrate into the host chromosome via a mechanism similar to that of bacteriophage lambda. In addition, 1961P is capable of generalized transduction. To the best of our knowledge, this is the first report of the isolation, characterization, genome analysis, integration, and transduction of aHelicobacter pyloriphage.

scholarly journals Isolation and Characterization of Gardnerella Phage vB_Gva_AB1, a Bacteriophage Infecting a Clinical Strain of Gardnerella vaginalis

2021 ◽  
Vol 10 (12) ◽  
Author(s):  
Alexia Bordigoni ◽  
Sonia Bouchard ◽  
Christelle Desnues
Keyword(s):  
Bacterial Vaginosis ◽  
Gc Content ◽  
Open Reading Frames ◽  
Gardnerella Vaginalis ◽  
Clinical Strain ◽  
Content Type ◽  
Isolation And Characterization ◽  
Double Stranded Dna ◽  
Reading Frames

ABSTRACT Gardnerella vaginalis is the presumed causative agent of bacterial vaginosis. Here, we describe the complete genome sequence of Gardnerella phage vB_Gva_AB1, induced from a vaginal bacterial strain from a woman suffering with bacterial vaginosis. The phage double-stranded DNA (dsDNA) genome is 50,268 bp long with a GC content of 39.55% and contains 62 predicted open reading frames.

scholarly journals Bacteriophages LIMElight and LIMEzero of Pantoea agglomerans, Belonging to the “phiKMV-Like Viruses”

2011 ◽  
Vol 77 (10) ◽  
pp. 3443-3450 ◽  
Author(s):  
Evelien M. Adriaenssens ◽  
Pieter-Jan Ceyssens ◽  
Vincent Dunon ◽  
Hans-Wolfgang Ackermann ◽  
Johan Van Vaerenbergh ◽  
...  
Keyword(s):  
Soil Samples ◽  
Pantoea Agglomerans ◽  
Open Reading Frames ◽  
Human Pathogen ◽  
Content Type ◽  
Host Diversity ◽  
Double Stranded Dna ◽  
Opportunistic Human Pathogen ◽  
Reading Frames

ABSTRACTPantoea agglomeransis a common soil bacterium used in the biocontrol of fungi and bacteria but is also an opportunistic human pathogen. It has been described extensively in this context, but knowledge of bacteriophages infecting this species is limited. Bacteriophages LIMEzero and LIMElight ofP. agglomeransare lytic phages, isolated from soil samples, belonging to thePodoviridaeand are the firstPantoeaphages of this family to be described. The double-stranded DNA (dsDNA) genomes (43,032 bp and 44,546 bp, respectively) encode 57 and 55 open reading frames (ORFs). Based on the presence of an RNA polymerase in their genomes and their overall genome architecture, these phages should be classified in the subfamily of theAutographivirinae, within the genus of the “phiKMV-like viruses.” Phylogenetic analysis of all the sequenced members of theAutographivirinaesupports the classification of phages LIMElight and LIMEzero as members of the “phiKMV-like viruses” and corroborates the subdivision into the different genera. These data expand the knowledge ofPantoeaphages and illustrate the wide host diversity of phages within the “phiKMV-like viruses.”

scholarly journals Characterization of Two Virulent Phages of Lactobacillus plantarum

2012 ◽  
Vol 78 (24) ◽  
pp. 8719-8734 ◽  
Author(s):  
Mariángeles Briggiler Marcó ◽  
Josiane E. Garneau ◽  
Denise Tremblay ◽  
Andrea Quiberoni ◽  
Sylvain Moineau
Keyword(s):  
Lactobacillus Plantarum ◽  
Corn Silage ◽  
Open Reading Frames ◽  
High Identity ◽  
Content Type ◽  
Defense Systems ◽  
Double Stranded Dna ◽  
Type Phage ◽  
Reading Frames

ABSTRACTWe characterized twoLactobacillus plantarumvirulent siphophages, ATCC 8014-B1 (B1) and ATCC 8014-B2 (B2), previously isolated from corn silage and anaerobic sewage sludge, respectively. Phage B2 infected two of the eightL. plantarumstrains tested, while phage B1 infected three. Phage adsorption was highly variable depending on the strain used. Phage defense systems were found in at least twoL. plantarumstrains, LMG9211 and WCSF1. The linear double-stranded DNA genome of thepac-type phage B1 had 38,002 bp, a G+C content of 47.6%, and 60 open reading frames (ORFs). Surprisingly, the phage B1 genome has 97% identity with that ofPediococcus damnosusphage clP1 and 77% identity with that ofL. plantarumphage JL-1; these phages were isolated from sewage and cucumber fermentation, respectively. The double-stranded DNA (dsDNA) genome of thecos-type phage B2 had 80,618 bp, a G+C content of 36.9%, and 127 ORFs with similarities to those ofBacillusandLactobacillusstrains as well as phages. Some phage B2 genes were similar to ORFs fromL. plantarumphage LP65 of theMyoviridaefamily. Additionally, 6 tRNAs were found in the phage B2 genome. Protein analysis revealed 13 (phage B1) and 9 (phage B2) structural proteins. To our knowledge, this is the first report describing such high identity between phage genomes infecting different genera of lactic acid bacteria.

scholarly journals Genome Sequence of a T4-like Phage, Escherichia Phage vB_EcoM-Sa45lw, Infecting Shiga Toxin-Producing Escherichia coli Strains

2019 ◽  
Vol 8 (32) ◽  
Author(s):  
Yen-Te Liao ◽  
Yujie Zhang ◽  
Alexandra Salvador ◽  
Vivian C. H. Wu
Keyword(s):  
Escherichia Coli ◽  
Surface Water ◽  
Genome Size ◽  
Shiga Toxin ◽  
Open Reading Frames ◽  
Content Type ◽  
E Coli ◽  
Double Stranded Dna ◽  
A Genome ◽  
Reading Frames

Escherichia phage vB_EcoM-Sa45lw, a new member of the T4-like phages, was isolated from surface water in a produce-growing area. The phage, containing double-stranded DNA with a genome size of 167,353 bp and 282 predicted open reading frames (ORFs), is able to infect generic Escherichia coli and Shiga toxin-producing E. coli O45 and O157 strains.

scholarly journals Complete Genome Sequence of Salmonella Bacteriophage SS3e

2012 ◽  
Vol 86 (18) ◽  
pp. 10253-10254 ◽  
Author(s):  
Sung-Hun Kim ◽  
Jeong-Hyun Park ◽  
Bok-Kwon Lee ◽  
Hyuk-Joon Kwon ◽  
Ji-Hyun Shin ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Sequence Analysis ◽  
Genomic Sequence ◽  
Enterobacter Cloacae ◽  
Open Reading Frames ◽  
Lytic Bacteriophage ◽  
Content Type ◽  
Double Stranded Dna ◽  
Genomic Sequence Analysis ◽  
Reading Frames

ASalmonellalytic bacteriophage, SS3e, was isolated, and its genome was sequenced completely. This phage is able to lyse not only variousSalmonellaserovars but alsoEscherichia coli,Shigella sonnei,Enterobacter cloacae, andSerratia marcescens, indicating a broad host specificity. Genomic sequence analysis of SS3e revealed a linear double-stranded DNA sequence of 40,793 bp harboring 58 open reading frames, which is highly similar toSalmonellaphages SETP13 and MB78.

scholarly journals Genome Sequence of the Broad-Host-Range Pseudomonas Phage Φ-S1

2012 ◽  
Vol 86 (18) ◽  
pp. 10239-10239 ◽  
Author(s):  
Sanna Sillankorva ◽  
Andrew M. Kropinski ◽  
Joana Azeredo
Keyword(s):  
Host Range ◽  
Genome Sequence ◽  
Open Reading Frames ◽  
Broad Host Range ◽  
Content Type ◽  
Double Stranded Dna ◽  
The Family ◽  
Reading Frames

The broad-host-range lyticPseudomonasphage Φ-S1 possess a 40,192 bp double-stranded DNA (dsDNA) genome of 47 open reading frames (ORFs) and belongs to the familyPodoviridae, subfamilyAutographivirinae, genusT7likevirus.

scholarly journals A Virulent Phage Infecting Lactococcus garvieae, with Homology to Lactococcus lactis Phages

2015 ◽  
Vol 81 (24) ◽  
pp. 8358-8365 ◽  
Author(s):  
Giovanni Eraclio ◽  
Denise M. Tremblay ◽  
Alexia Lacelle-Côté ◽  
Simon J. Labrie ◽  
Maria Grazia Fortina ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Common Ancestor ◽  
Burst Size ◽  
Open Reading Frames ◽  
Content Type ◽  
Virulent Phage ◽  
Lactococcus Garvieae ◽  
Double Stranded Dna ◽  
Compost Soil ◽  
Reading Frames

ABSTRACTA new virulent phage belonging to theSiphoviridaefamily and able to infectLactococcus garvieaestrains was isolated from compost soil. Phage GE1 has a prolate capsid (56 by 38 nm) and a long noncontractile tail (123 nm). It had a burst size of 139 and a latent period of 31 min. Its host range was limited to only twoL. garvieaestrains out of 73 tested. Phage GE1 has a double-stranded DNA genome of 24,847 bp containing 48 predicted open reading frames (ORFs). Putative functions could be assigned to only 14 ORFs, and significant matches in public databases were found for only 17 ORFs, indicating that GE1 is a novel phage and its genome contains several new viral genes and encodes several new viral proteins. Of these 17 ORFs, 16 were homologous to deduced proteins of virulent phages infecting the dairy bacteriumLactococcus lactis, including previously characterized prolate-headed phages. Comparative genome analysis confirmed the relatedness ofL. garvieaephage GE1 toL. lactisphages c2 (22,172 bp) and Q54 (26,537 bp), although its genome organization was closer to that of phage c2. Phage GE1 did not infect any of the 58L. lactisstrains tested. This study suggests that phages infecting different lactococcal species may have a common ancestor.

scholarly journals Complete Genome Sequence of Acinetobacter baumannii Phage BS46

2020 ◽  
Vol 9 (22) ◽  
Author(s):  
Anastasia V. Popova ◽  
Mikhail M. Shneider ◽  
Yulia V. Mikhailova ◽  
Andrey A. Shelenkov ◽  
Dmitry A. Shagin ◽  
...  
Keyword(s):  
Complete Genome Sequence ◽  
Complete Genome ◽  
Open Reading Frames ◽  
Capsular Polysaccharides ◽  
Bacterial Host ◽  
Gene Encoding ◽  
Content Type ◽  
Double Stranded Dna ◽  
A Genome ◽  
Reading Frames

ABSTRACT Acinetobacter myovirus BS46 was isolated from sewage by J. S. Soothill in 1991. We have sequenced the genome of BS46 and found it to be almost unique. BS46 contains double-stranded DNA with a genome size of 94,068 bp and 176 predicted open reading frames. The gene encoding the tailspike that presumably possesses depolymerase activity toward the capsular polysaccharides of the bacterial host was identified.

scholarly journals Systematic Identification of Selective Essential Genes in Helicobacter pylori by Genome Prioritization and Allelic Replacement Mutagenesis

2001 ◽  
Vol 183 (4) ◽  
pp. 1259-1268 ◽  
Author(s):  
Alison F. Chalker ◽  
Heather W. Minehart ◽  
Nicky J. Hughes ◽  
Kristin K. Koretke ◽  
Michael A. Lonetto ◽  
...  
Keyword(s):  
Helicobacter Pylori ◽  
Essential Genes ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Allelic Replacement ◽  
Genomic Approach ◽  
H Pylori ◽  
Systematic Identification ◽  
Reading Frames

ABSTRACT A comparative genomic approach was used to identifyHelicobacter pylori 26695 open reading frames (ORFs) which are conserved in H. pylori J99 but highly diverged in other eubacteria. A survey of selected pathways of central intermediary metabolism was also carried out, and genes with a potentially selective role in H. pylori were identified. Forty-five ORFs identified in these two analyses were screened using a rapid vector-free allelic replacement mutagenesis technique, and 33 were shown to be essential in vitro. Notably, 13 ORFs gave essentiality results which are unexpected in view of their known or proposed functions, and phylogenetic analysis was used to investigate the annotation of 7 such ORFs which are highly diverged. We propose that the products of a number of these H. pylori-specific essential genes may be suitable targets for novel anti-H. pylori therapies.

scholarly journals Acid-Adaptive Genes of Helicobacter pylori

2003 ◽  
Vol 71 (10) ◽  
pp. 5921-5939 ◽  
Author(s):  
Yi Wen ◽  
Elizabeth A. Marcus ◽  
Uday Matrubutham ◽  
Martin A. Gleeson ◽  
David R. Scott ◽  
...  
Keyword(s):  
Gene Expression ◽  
Helicobacter Pylori ◽  
Cell Envelope ◽  
Open Reading Frames ◽  
Ph Optimum ◽  
Transcriptional Regulatory ◽  
Adaptive Mechanisms ◽  
H Pylori ◽  
Reading Frames ◽  
External Ph

ABSTRACT Helicobacter pylori is the only neutralophile that has been able to colonize the human stomach by using a variety of acid-adaptive mechanisms. One of the adaptive mechanisms is increased buffering due to expression of an acid-activated inner membrane urea channel, UreI, and a neutral pH-optimum intrabacterial urease. To delineate other possible adaptive mechanisms, changes in gene expression in response to acid exposure were examined using genomic microarrays of H. pylori exposed to different levels of external pH (7.4, 6.2, 5.5, and 4.5) for 30 min in the absence and presence of 5 mM urea. Gene expression was correlated with intrabacterial pH measured using 2′,7′-bis-(2-carboxyethyl)-5-carboxyfluorescein and compared to that observed with exposure to 42°C for 30 min. Microarrays containing the 1,534 open reading frames of H. pylori strain 26695 were hybridized with cDNAs from control (pH 7.4; labeled with Cy3) and acidic (labeled with Cy5) conditions. The intrabacterial pH was 8.1 at pH 7.4, fell to 5.3 at pH 4.5, and rose to 6.2 with urea. About 200 genes were up-regulated and ∼100 genes were down-regulated at pH 4.5 in the absence of urea, and about half that number changed in the presence of urea. These genes included pH-homeostatic, transcriptional regulatory, motility, cell envelope, and pathogenicity genes. The up-regulation of some pH-homeostatic genes was confirmed by real-time PCR. There was little overlap with the genes induced by temperature stress. These results suggest that H. pylori has evolved multifaceted acid-adaptive mechanisms enabling it to colonize the stomach that may be novel targets for eliminating infection.

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