Complete Genome of a Novel Lytic Vibrio parahaemolyticus Phage VPp1 and Characterization of Its Endolysin for Antibacterial Activities

2018 ◽  
Vol 81 (7) ◽  
pp. 1117-1125 ◽  
Author(s):  
MENGZHE LI ◽  
YANQIU JIN ◽  
HONG LIN ◽  
JINGXUE WANG ◽  
XIUPING JIANG
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Foodborne Pathogen ◽  
Antibacterial Activities ◽  
Nucleotide Metabolism ◽  
Open Reading Frames ◽  
Bacterial Cells ◽  
Control Groups ◽  
Double Stranded Dna ◽  
Reading Frames

ABSTRACT Vibrio parahaemolyticus is an important foodborne pathogen that is generally transmitted via raw or undercooked seafood. Endolysins originating from bacteriophages offer a new way to control bacterial pathogens. The objectives of this study were to sequence a novel lytic V. parahaemolyticus phage VPp1 and determine the antibacterial activities of the recombinant endolysin (LysVPp1) derived from this phage. The complete VPp1 genome contained a double-stranded DNA of 50,431 bp with a total G+C content of 41.35%. The genome was predicted to encode 67 open reading frames (ORFs), which were organized as nucleotide metabolism, replication, structure, packaging, lysis, and some additional functions. Two tRNAs were encoded to carry anticodons UGG and CCA. Among the functional proteins, ORF33 was deduced to encode endolysin, whereas no holin/antiholin or Rz/Rz1 lysis gene equivalents were found in the VPp1 genome. ORF33 was cloned and expressed. The endolysin LysVPp1 could lyse 9 of 12 V. parahaemolyticus strains, showing its relatively broader host spectrum than phage VPp1, which lysed only 3 of 12 V. parahaemolyticus strains. Furthermore, for EDTA-pretreated bacterial cells, the optical density of the LysVPp1 treatment group decreased by 0.4 at 450 nm, compared with less than 0.1 in control groups, demonstrating enhanced hydrolytic properties. These results contribute to the potential for development of novel enzybiotics for controlling V. parahaemolyticus.

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 Genetic Characterization of DNA Region Containing the trh and ure Genes of Vibrio parahaemolyticus

2000 ◽  
Vol 68 (10) ◽  
pp. 5742-5748 ◽  
Author(s):  
Kwon-Sam Park ◽  
Tetsuya Iida ◽  
Yoshiharu Yamaichi ◽  
Tomohito Oyagi ◽  
Koichiro Yamamoto ◽  
...  
Keyword(s):  
Vibrio Parahaemolyticus ◽  
Open Reading Frames ◽  
The Other ◽  
Close Proximity ◽  
Mutant Strains ◽  
Thermostable Direct Hemolysin ◽  
Urease Production ◽  
Reading Frames ◽  
Type Nickel

ABSTRACT We have demonstrated that possession of the gene for thermostable direct hemolysin-related hemolysin (trh) coincides with the presence of the urease gene among clinical Vibrio parahaemolyticus strains and that the location of the two genes are in close proximity on the chromosome. Here, we cloned and sequenced the 15,754-bp DNA region containing the trh gene and the gene cluster for urease production from the chromosome of clinicalV. parahaemolyticus (TH3996). We found 16 open reading frames (ORFs) and a lower G+C content (41%) compared with the total genome of this bacterium (46 to 47%). The ure cluster consisted of eight genes, namely, ureDABCEFG andureR. ureR was located 5.2 kb upstream of the other seven genes in the opposite direction. The genetic organization and sequences of the ure genes resembled those found in Proteus mirabilis. Between ureR and the other uregenes, there were five ORFs, which are homologous with the nickel transport operon (nik) of Escherichia coli. We disrupted each of the ureR, ureC, andnikD genes in TH3996 by homologous recombination and analyzed the phenotype of the mutants. In the presence of urea these mutant strains had dramatically less urease activity than the strain they were derived from. Disruption of ureR,nikD, or ureC, however, had no effect on TRH production. The DNA region containing the trh,nik, and ure genes was found in onlytrh-positive strains and not in Kanagawa phenomenon-positive and environmental V. parahaemolyticusstrains. At the end of the region, an insertion sequence-like element existed. These results suggest that the DNA region was introduced intoV. parahaemolyticus in the past through a mechanism mediated by insertion sequences. This is the first reported case that the genes for an ATP-binding cassette-type nickel transport system, which may play a role in nickel transport through bacterial cytoplasmic membrane, are located adjacent to the ure cluster on the genome of an organism.

scholarly journals The Characteristics and Genome Analysis of vB_AviM_AVP, the First Phage Infecting Aerococcus viridans

Viruses ◽  
2019 ◽  
Vol 11 (2) ◽  
pp. 104 ◽  
Author(s):  
Hengyu Xi ◽  
Jiaxin Dai ◽  
Yigang Tong ◽  
Mengjun Cheng ◽  
Feiyang Zhao ◽  
...  
Keyword(s):  
Opportunistic Pathogen ◽  
Nucleotide Metabolism ◽  
Open Reading Frames ◽  
Gene Products ◽  
New Class ◽  
Aerococcus Viridans ◽  
Double Stranded Dna ◽  
The Family ◽  
Reading Frames ◽  
Human And Animal Diseases

Aerococcus viridans is an opportunistic pathogen that is clinically associated with various human and animal diseases. In this study, the first identified A. viridans phage, vB_AviM_AVP (abbreviated as AVP), was isolated and studied. AVP belongs to the family Myoviridae. AVP harbors a double-stranded DNA genome with a length of 133,806 bp and a G + C content of 34.51%. The genome sequence of AVP showed low similarity (<1% identity) to those of other phages, bacteria, or other organisms in the database. Among 165 predicted open reading frames (ORFs), there were only 69 gene products exhibiting similarity (≤65% identity) to proteins of known functions in the database. In addition, the other 36 gene products did not match any viral or prokaryotic sequences in any publicly available database. On the basis of the putative functions of the ORFs, the genome of AVP was divided into three modules: nucleotide metabolism and replication, structural components, and lysis. A phylogenetic analysis of the terminase large subunits and capsid proteins indicated that AVP represents a novel branch of phages. The observed characteristics of AVP indicate that it represents a new class of phages.

scholarly journals Genomic Characterization of Ralstonia solanacearum Phage φRSB1, a T7-Like Wide-Host-Range Phage

2008 ◽  
Vol 191 (1) ◽  
pp. 422-427 ◽  
Author(s):  
Takeru Kawasaki ◽  
Mio Shimizu ◽  
Hideki Satsuma ◽  
Akiko Fujiwara ◽  
Makoto Fujie ◽  
...  
Keyword(s):  
Host Range ◽  
Ralstonia Solanacearum ◽  
Open Reading Frames ◽  
Phytopathogenic Bacterium ◽  
Strong Activity ◽  
Double Stranded Dna ◽  
Wide Host Range ◽  
Genomic Characterization ◽  
Reading Frames

ABSTRACT φRSΒ1 is a wide-host-range, T7-like bacteriophage that infects and efficiently lyses the phytopathogenic bacterium Ralstonia solanacearum. The φRSB1 genome comprises 43,079 bp of double-stranded DNA (61.7% G+C) with 325-bp terminal repeats and contains 47 open reading frames. Strong activity of tandem early promoters and wide specificity of phage promoters of φRSB1 were demonstrated.

scholarly journals Genomic characterization of three novel Pseudomonas phages within the subfamily of Autographivirinae isolated from organic waste

2020 ◽  
Author(s):  
Jacob B Jørgensen ◽  
Amaru M Djuurhus ◽  
Alexander B. Carstens ◽  
Witold Kot ◽  
Cindy E. Morris ◽  
...  
Keyword(s):  
Pseudomonas Syringae ◽  
Organic Waste ◽  
New Genus ◽  
Open Reading Frames ◽  
Genomic Comparison ◽  
Double Stranded Dna ◽  
The Family ◽  
Genomic Characterization ◽  
Reading Frames

AbstractThree phages targeting Pseudomonas syringae GAW0113 have been isolated from organic waste samples: Pseudomonas phage Bertil, Misse and Strit. The phages have double-stranded DNA genomes ranging from 41342 to 41374 bp in size comprising 50 to 51 open reading frames. The three phages genomes are highly similar and genomic comparison analyses shows that they all belong to the Autographivirinae subfamily of the family Podoviridae. The phages are however only distantly related to other members of this family, and have limited gene synteny with type-phages of other genera within Autographivirinae, suggesting that the newly isolated phages could represent a new genus.

scholarly journals Isolation and complete genome sequencing of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamily Autographivirinae

2020 ◽  
Author(s):  
Julie Stenberg Pedersen ◽  
Alexander Byth Carstens ◽  
Amaru Miranda Djurhuus ◽  
Witold Kot ◽  
Lars Hestbjerg Hansen
Keyword(s):  
Soft Rot ◽  
Open Reading Frames ◽  
Novel Genus ◽  
The Past ◽  
Isolation And Characterization ◽  
Double Stranded Dna ◽  
Plant Disease Control ◽  
Phage T7 ◽  
Reading Frames

AbstractPectobacterium carotovorum is the causative agent of bacterial soft rot on various plant species. The use of phages for plant disease control have gained increased awareness over the past years. We here describe the isolation and characterization of Pectobacterium phage Jarilo, representing a novel genus of bacteriophages within the subfamily Autographivirinae. Jarilo possesses a double-stranded DNA genome of 40557 bp with a G+C% content of 50.08% and 50 predicted open reading frames (ORFs). Gene synteny and products seem to be somewhat conserved between Pectobacterium phage Jarilo and Enterobacteria phage T7, but limited nucleotide similarity is found between Jarilo and other phages within the subfamily Autographivirinae. We propose Pectobacterium phage Jarilo as the first member of a new genus of bacteriophages within the subfamily Autographivirinae.

scholarly journals Isolation and Characterization of the First Freshwater Cyanophage Infecting Pseudanabaena

2020 ◽  
Vol 94 (17) ◽  
Author(s):  
Dong Zhang ◽  
Fang You ◽  
Yiliang He ◽  
Shu Harn Te ◽  
Karina Yew-Hoong Gin
Keyword(s):  
Large Subunit ◽  
Open Reading Frames ◽  
Aquatic Environments ◽  
Narrow Host Range ◽  
Metabolic Genes ◽  
Isolation And Characterization ◽  
Double Stranded Dna ◽  
Short Latent Period ◽  
Reading Frames

ABSTRACT Cyanobacteria are the major primary producers in both freshwater and marine environments. However, the majority of freshwater cyanophages remain unknown due to the limited number of cyanophage isolates. In this study, we present a novel lytic freshwater cyanophage, PA-SR01, which was isolated from the Singapore Serangoon Reservoir. To our knowledge, this is the first isolate of a cyanophage that has been found to infect the cyanobacterium Pseudanabaena. PA-SR01 has a narrow host range, a short latent period, and is chloroform sensitive. Distinct from the majority of cyanophage isolates, PA-SR01 has a tailless morphology. It is a double-stranded DNA virus with a 137,012-bp genome. Functional annotation for the predicted open reading frames (ORFs) of the PA-SR01 genome identified genes with putative functions related to DNA metabolism, structural proteins, lysis, host-derived metabolic genes, and DNA packaging. Out of 166 predicted ORFs, only 17 ORFs have homology with genes with known function. Phylogenetic analysis of the major capsid protein and terminase large subunit further suggests that phage PA-SR01 is evolutionary distinct from known cyanophages. Metagenomics sequence recruitment onto the PA-SR01 genome indicates that PA-SR01 represents a new evolutionary lineage of phage which shares considerable genetic similarities with phage sequences in aquatic environments and could play key ecological roles. IMPORTANCE This study presents the isolation of the very first freshwater cyanophage, PA-SR01, that infects Pseudanabaena, and fills an important knowledge gap on freshwater cyanophages as well as cyanophages infecting Pseudanabaena.

scholarly journals Genome Sequence and Characterization of theTsukamurellaBacteriophage TPA2

2010 ◽  
Vol 77 (4) ◽  
pp. 1389-1398 ◽  
Author(s):  
Steve Petrovski ◽  
Robert J. Seviour ◽  
Daniel Tillett
Keyword(s):  
Activated Sludge ◽  
Genome Sequence ◽  
Genetic Recombination ◽  
Mycolic Acid ◽  
Open Reading Frames ◽  
The Novel ◽  
Double Stranded Dna ◽  
Phage Evolution ◽  
Reading Frames

ABSTRACTThe formation of stable foam in activated sludge plants is a global problem for which control is difficult. These foams are often stabilized by hydrophobic mycolic acid-synthesizingActinobacteria, among which areTsukamurellaspp. This paper describes the isolation from activated sludge of the novel double-stranded DNA phage TPA2. This polyvalentSiphoviridaefamily phage is lytic for mostTsukamurellaspecies. Whole-genome sequencing reveals that the TPA2 genome is circularly permuted (61,440 bp) and that 70% of its sequence is novel. We have identified 78 putative open reading frames, 95 pairs of inverted repeats, and 6 palindromes. The TPA2 genome has a modular gene structure that shares some similarity to those ofMycobacteriumphages. A number of the genes display a mosaic architecture, suggesting that the TPA2 genome has evolved at least in part from genetic recombination events. The genome sequence reveals many novel genes that should inform any future discussion onTsukamurellaphage evolution.

scholarly journals First Description of a Temperate Bacteriophage (vB_FhiM_KIRK) of Francisella hispaniensis Strain 3523

Viruses ◽  
2021 ◽  
Vol 13 (2) ◽  
pp. 327
Author(s):  
Kristin Köppen ◽  
Grisna I. Prensa ◽  
Kerstin Rydzewski ◽  
Hana Tlapák ◽  
Gudrun Holland ◽  
...  
Keyword(s):  
Open Reading Frames ◽  
Dna Transformation ◽  
Bacterial Cells ◽  
Lysis Activity ◽  
Mean Width ◽  
Prophage Sequence ◽  
Radiation Induced ◽  
Myoviridae Family ◽  
Reading Frames

Here we present the characterization of a Francisella bacteriophage (vB_FhiM_KIRK) including the morphology, the genome sequence and the induction of the prophage. The prophage sequence (FhaGI-1) has previously been identified in F. hispaniensis strain 3523. UV radiation induced the prophage to assemble phage particles consisting of an icosahedral head (~52 nm in diameter), a tail of up to 97 nm in length and a mean width of 9 nm. The double stranded genome of vB_FhiM_KIRK contains 51 open reading frames and is 34,259 bp in length. The genotypic and phylogenetic analysis indicated that this phage seems to belong to the Myoviridae family of bacteriophages. Under the conditions tested here, host cell (Francisella hispaniensis 3523) lysis activity of KIRK was very low, and the phage particles seem to be defective for infecting new bacterial cells. Nevertheless, recombinant KIRK DNA was able to integrate site-specifically into the genome of different Francisella species after DNA transformation.

scholarly journals The Characterization of a Novel Phage, pPa_SNUABM_DT01, Infecting Pseudomonas aeruginosa

2021 ◽  
Vol 9 (10) ◽  
pp. 2040
Author(s):  
Jun Kwon ◽  
Sang Wha Kim ◽  
Sang Guen Kim ◽  
Jeong Woo Kang ◽  
Won Joon Jung ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Otitis Externa ◽  
Phage Genome ◽  
Novel Species ◽  
Major Complication ◽  
Open Reading Frames ◽  
Bacterial Cells ◽  
Genome Comparisons ◽  
Reading Frames

The bacterial genus Pseudomonas is a common causative agent of infections in veterinary medicine. In this study, we focused on Pseudomonas aeruginosa canine otitis externa isolates. Due to prolonged antibiotic treatment of otitis externa, antibiotic resistance is common and has become a major complication. Many alternatives to antibiotics have been studied, with bacteriophages emerging as the most promising alternatives. Here, we isolated and characterized a novel phage, pPa_SNUABM_DT01, by investigating its morphology, growth, lysis kinetics, and genomic characteristics. Phages have a vigorous capacity to eliminate bacterial cells through bacterial lysis. This capacity is dependent on the multiplicity of infection (MOI), but even at low MOIs, the phage successfully inhibited bacterial regrowth. The phage genome was 265,520 bp in size and comprised 312 putative open reading frames (ORFs). Comparative genome analysis demonstrated that the phage is a novel species in Myoviridae. The nucleotide similarity was moderately high compared with the Pseudomonas virus, Noxifer. However, a phylogenetic analysis and a dot plot indicated that pPa_SNUABM_DT01 is not closely related to the Phikzvirus or Noxifervirus genus but, instead, belongs to a novel one. The genome comparisons also indicate that the phage, pPa_SNUABM_DT01, could be a novel genus.

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