scholarly journals Genomic Analysis of the Polyvalent Bacteriophage FP01

2019 ◽  
Author(s):  
Ignacio Vasquez ◽  
Julio Retamales ◽  
Barbara Parra ◽  
James Robeson ◽  
Javier Santander
Keyword(s):  
Escherichia Coli ◽  
Potential Application ◽  
Complete Genome ◽  
Phylogenetic Analyses ◽  
Genomic Analysis ◽  
Host Factors ◽  
Coding Sequences ◽  
Double Stranded Dna ◽  
Host Infection ◽  
Lysogenic Phage

Recently the polyvalent bacteriophage FP01, isolated from wastewater in Valparaiso, Chile, was described to have lytic activity across species against Escherichia coli and Salmonella enterica serovars. Due to it polyvalent nature the bacteriophage FP01 could have potential application in food and agri-industry. Also, fundamental aspects of polyvalent bacteriophage biology are not well known. In this study we sequenced and describe the complete genome of the polyvalent phage FP01 (MH745368) using the nanopore technology. The bacteriophage FP01 genome has a 44,900 bp, double-stranded DNA with an average G+C content of 49.41% and 90 coding sequences (CDSs). We found that the phage FP01 critically depends on host factors for replication and transcription. Also, it has a critical lysogenic repressor pseudogene. Phylogenetic analyses indicated that the phage FP01 is closely related to phages lambda and P22. These results suggest that the phage FP01 could be a lytic variant of a lysogenic phage or acquired genes from lysogenic phages during host infection.

Genomic Analysis of a Novel Active Prophage of Hafnia Paralvei

2021 ◽  
Author(s):  
Lingting Pan ◽  
Dengfeng Li ◽  
Wei Lin ◽  
Wencai Liu ◽  
Weinan Qin ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Phylogenetic Analysis ◽  
Mitomycin C ◽  
Complete Genome ◽  
Genomic Analysis ◽  
Evolutionary Status ◽  
Conserved Sequences ◽  
Double Stranded Dna ◽  
Reading Frames

Abstract Relatively little is known about the prophages in Enterobacterales bacteria except Escherichia coli. A novel phage, Hafnia phage yong2, was induced from Hafnia paralvei by mitomycin C. The phage has an elliptical head of approximately 45 × 38 nm, a long noncontractile tail of approximately 157 × 4 nm. The complete genome of Hafnia phage yong2 is a 39,546 bp double-stranded DNA with a G+C content of 49.9%, containing 59 opening reading frames (ORFs), and having at least one fixed terminus (GGGGCAGCGACA) with R=107>100. In phylogenetic analysis, Hafnia phage yong2 clustered with 4 predicted Hafnia prophages and 1 predicted Enterobacteriaceae prophage. The prophages cluster and Drexlerviridae family together formed two distinct subclades nested within a clade, suggesting the existence of a novel class of prophages with conserved sequences and unique evolutionary status not yet studied before in Hafniaceae and Enterobacteriaceae bacteria.

scholarly journals Complete Genome Sequence of a Lytic Siphoviridae Bacteriophage Infecting Several Serovars of Salmonella enterica

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Rubina Paradiso ◽  
Serena Lombardi ◽  
Maria Grazia Iodice ◽  
Marita Georgia Riccardi ◽  
Massimiliano Orsini ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Salmonella Enterica ◽  
Complete Genome ◽  
Water Buffalo ◽  
Southern Italy ◽  
Lytic Activity ◽  
Coding Sequences ◽  
Double Stranded Dna

The bacteriophage 100268_sal2 was isolated from water buffalo feces in southern Italy, exhibiting lytic activity against several subspecies of Salmonella enterica . This bacteriophage belongs to the Siphoviridae family and has a 125,114-bp double-stranded DNA (ds-DNA) genome containing 188 coding sequences (CDSs).

scholarly journals Complete Genome Sequences of Two Salmonella Viruses, VSe11 and VSe102 (Family Myoviridae, Subfamily Ounavirinae), with a Very High Degree of Similarity

2018 ◽  
Vol 6 (21) ◽  
Author(s):  
Nikolay V. Volozhantsev ◽  
Egor A. Denisenko ◽  
Angelina A. Kislichkina ◽  
Vera P. Myakinina ◽  
Valentina M. Krasilnikova ◽  
...  
Keyword(s):  
Broad Spectrum ◽  
Complete Genome ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Content Type ◽  
Double Stranded Dna ◽  
Poultry Farms ◽  
High Degree ◽  
Degree Of Similarity ◽  
Very High

ABSTRACT Two lytic double-stranded DNA bacteriophages, VSe11 and VSe102, infecting broad-spectrum Salmonella enterica were isolated from the sewage of two different poultry farms. The phage genomes comprise 86,360 bp and 86,365 bp, respectively, with a G+C content of 39.0%, and both contain 129 putative coding sequences.

scholarly journals The Complete Genome of the Atypical Enteropathogenic Escherichia coli Archetype Isolate E110019 Highlights a Role for Plasmids in Dissemination of the Type III Secreted Effector EspT

2019 ◽  
Vol 87 (10) ◽  
Author(s):  
Tracy H. Hazen ◽  
David A. Rasko
Keyword(s):  
Escherichia Coli ◽  
Complete Genome ◽  
Genomic Analysis ◽  
Host Cells ◽  
Comparative Genomic ◽  
Content Type ◽  
E Coli ◽  
Type Iii ◽  
Severe Diarrhea ◽  
Typical Epec

ABSTRACT Enteropathogenic Escherichia coli (EPEC) is a leading cause of moderate to severe diarrhea among young children in developing countries, and EPEC isolates can be subdivided into two groups. Typical EPEC (tEPEC) bacteria are characterized by the presence of both the locus of enterocyte effacement (LEE) and the plasmid-encoded bundle-forming pilus (BFP), which are involved in adherence and translocation of type III effectors into the host cells. Atypical EPEC (aEPEC) bacteria also contain the LEE but lack the BFP. In the current report, we describe the complete genome of outbreak-associated aEPEC isolate E110019, which carries four plasmids. Comparative genomic analysis demonstrated that the type III secreted effector EspT gene, an autotransporter gene, a hemolysin gene, and putative fimbrial genes are all carried on plasmids. Further investigation of 65 espT-containing E. coli genomes demonstrated that different espT alleles are associated with multiple plasmids that differ in their overall gene content from the E110019 espT-containing plasmid. EspT has been previously described with respect to its role in the ability of E110019 to invade host cells. While other type III secreted effectors of E. coli have been identified on insertion elements and prophages of the chromosome, we demonstrated in the current study that the espT gene is located on multiple unique plasmids. These findings highlight a role of plasmids in dissemination of a unique E. coli type III secreted effector that is involved in host invasion and severe diarrheal illness.

scholarly journals Complete Genome Sequence of the Escherichia coli Phage Ayreon

2018 ◽  
Vol 6 (2) ◽  
Author(s):  
Marnix Vlot ◽  
Franklin L. Nobrega ◽  
Che F. A. Wong ◽  
Yue Liu ◽  
Stan J. J. Brouns
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Temperate Phage ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Double Stranded Dna ◽  
Escherichia Coli Phage

ABSTRACT We report the whole-genome sequence of a new Escherichia coli temperate phage, Ayreon, comprising a linear double-stranded DNA (dsDNA) genome of 44,708 bp.

scholarly journals Baculovirus: Molecular Insights on Their Diversity and Conservation

2011 ◽  
Vol 2011 ◽  
pp. 1-15 ◽  
Author(s):  
Solange Ana Belen Miele ◽  
Matías Javier Garavaglia ◽  
Mariano Nicolás Belaich ◽  
Pablo Daniel Ghiringhelli
Keyword(s):  
Phylogenetic Analyses ◽  
Core Gene ◽  
Gene Sequences ◽  
Genome Sequences ◽  
Coding Sequences ◽  
Large Group ◽  
Double Stranded Dna ◽  
Core Genes ◽  
Insect Viruses

The Baculoviridae is a large group of insect viruses containing circular double-stranded DNA genomes of 80 to 180 kbp. In this study, genome sequences from 57 baculoviruses were analyzed to reevaluate the number and identity of core genes and to understand the distribution of the remaining coding sequences. Thirty one core genes with orthologs in all genomes were identified along with other 895 genes differing in their degrees of representation among reported genomes. Many of these latter genes are common to well-defined lineages, whereas others are unique to one or a few of the viruses. Phylogenetic analyses based on core gene sequences and the gene composition of the genomes supported the current division of the Baculoviridae into 4 genera: Alphabaculovirus, Betabaculovirus, Gammabaculovirus, and Deltabaculovirus.

scholarly journals Escherichia coli O157:H7 Typing Phage V7 Is a T4-Like Virus

2012 ◽  
Vol 86 (18) ◽  
pp. 10246-10246 ◽  
Author(s):  
Andrew M. Kropinski ◽  
Erika J. Lingohr ◽  
Dianne M. Moyles ◽  
Andrew Chibeu ◽  
Amanda Mazzocco ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Escherichia Coli O157 ◽  
Content Type ◽  
Typing Phage ◽  
Double Stranded Dna

The complete genome sequence of theEscherichia coliO157:H7 typing phage V7 was determined. Its double-stranded DNA genome is 166,452 bp long, encoding 273 proteins and including 11 tRNAs. This virus belongs to the genus T4-like viruses within the subfamilyTevenvirinae, familyMyoviridae.

scholarly journals The complete genome and comparative analysis of the phage phiC120 infecting multidrug-resistant Escherichia coli and Salmonella strains

2021 ◽  
Vol 11 (2) ◽  
Author(s):  
Luis Amarillas ◽  
Claudia Villicaña ◽  
Luis Lightbourn-Rojas ◽  
Arturo González-Robles ◽  
Josefina León-Félix
Keyword(s):  
Escherichia Coli ◽  
Comparative Analysis ◽  
Foodborne Pathogens ◽  
Complete Genome ◽  
Multidrug Resistant ◽  
Open Reading Frames ◽  
E Coli ◽  
Protein Levels ◽  
Double Stranded Dna ◽  
Genes Encoding

Abstract Phages infecting Salmonella and Escherichia coli are promising agents for therapeutics and biological control of these foodborne pathogens, in particular those strains with resistance to several antibiotics. In an effort to assess the potential of the phage phiC120, a virulent phage isolated from horse feces in Mexico, we characterized its morphology, host range and complete genome. Herein, we showed that phiC120 possesses strong lytic activity against several multidrug-resistant E. coli O157: H7 and Salmonella strains, and its morphology indicated that is a member of Myoviridae family. The phiC120 genome is double-stranded DNA and consists of 186,570 bp in length with a 37.6% G + C content. A total of 281 putative open reading frames (ORFs) and two tRNAs were found, where 150 ORFs encoded hypothetical proteins with unknown function. Comparative analysis showed that phiC120 shared high similarity at nucleotide and protein levels with coliphages RB69 and phiE142. Detailed phiC120 analysis revealed that ORF 94 encodes a putative depolymerase, meanwhile genes encoding factors associated with lysogeny, toxins, and antibiotic resistance were absent; however, ORF 95 encodes a putative protein with potential allergenic and pro-inflammatory properties, making needed further studies to guarantee the safety of phiC120 for human use. The characterization of phiC120 expands our knowledge about the biology of coliphages and provides novel insights supporting its potential for the development of phage-based applications to control unwanted bacteria.

scholarly journals Sequence Analysis of a Jumbo Bacteriophage, Xoo-sp14, That Infects Xanthomonas oryzae pv. oryzae

2020 ◽  
Vol 9 (48) ◽  
Author(s):  
Amina Nazir ◽  
Zhaoxia Dong ◽  
Jin Liu ◽  
Xianglilan Zhang ◽  
Rana Adnan Tahir ◽  
...  
Keyword(s):  
Sequence Analysis ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Xanthomonas Oryzae ◽  
Protein Coding ◽  
Coding Sequences ◽  
Content Type ◽  
Dsdna Molecule ◽  
Double Stranded Dna

ABSTRACT A jumbo bacteriophage, Xoo-sp14, infecting Xanthomonas oryzae pv. oryzae was isolated from rice fields in China. Here, we report the complete genome sequence of this phage, revealing that it had a linear double-stranded DNA (dsDNA) molecule 232,104 bp long, with a G+C content of 58%. It has 251 annotated protein-coding sequences.

scholarly journals Complete Genome of Staphylococcus aureus Phage SA11

2012 ◽  
Vol 86 (18) ◽  
pp. 10232-10232 ◽  
Author(s):  
Min Soo Kim ◽  
Heejoon Myung
Keyword(s):  
Staphylococcus Aureus ◽  
Microscopic Observation ◽  
Complete Genome ◽  
Genomic Analysis ◽  
Electron Microscopic Observation ◽  
Whole Genome ◽  
Lytic Bacteriophage ◽  
Electron Microscopic ◽  
Content Type ◽  
Double Stranded Dna

A novel lytic bacteriophage, SA11, infectingStaphylococcus aureuswas isolated, and the whole genome was sequenced. It belongs to the siphoviridae based on electron microscopic observation. It has a linear double-stranded DNA genome of 136,326 bp. Genomic analysis showed that it is distantly related toStaphylococcusphages A5W, K, ISP, Sb-1, and G1.

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