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 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 Isolation and Characterization of Salmonella Jumbo-Phage pSal-SNUABM-04

Viruses ◽  
2020 ◽  
Vol 13 (1) ◽  
pp. 27
Author(s):  
Jun Kwon ◽  
Sang Guen Kim ◽  
Hyoun Joong Kim ◽  
Sib Sankar Giri ◽  
Sang Wha Kim ◽  
...  
Keyword(s):  
Morphological Traits ◽  
Open Reading Frames ◽  
Genome Comparison ◽  
The Novel ◽  
Promising Alternative ◽  
Isolation And Characterization ◽  
Global Issue ◽  
Reading Frames ◽  
Predicted Function

The increasing emergence of antimicrobial resistance has become a global issue. Therefore, many researchers have attempted to develop alternative antibiotics. One promising alternative is bacteriophage. In this study, we focused on a jumbo-phage infecting Salmonella isolated from exotic pet markets. Using a Salmonella strain isolated from reptiles as a host, we isolated and characterized the novel jumbo-bacteriophage pSal-SNUABM-04. This phage was investigated in terms of its morphology, host infectivity, growth and lysis kinetics, and genome. The phage was classified as Myoviridae based on its morphological traits and showed a comparatively wide host range. The lysis efficacy test showed that the phage can inhibit bacterial growth in the planktonic state. Genetic analysis revealed that the phage possesses a 239,626-base pair genome with 280 putative open reading frames, 76 of which have a predicted function and 195 of which have none. By genome comparison with other jumbo phages, the phage was designated as a novel member of Machinavirus composed of Erwnina phages.

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.

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 Isolation and Characterization of Genes Responsible for Naphthalene Degradation from Thermophilic Naphthalene Degrader, Geobacillus sp. JF8

2019 ◽  
Vol 8 (1) ◽  
pp. 44 ◽  
Author(s):  
Daisuke Miyazawa ◽  
Le Thi Ha Thanh ◽  
Akio Tani ◽  
Masaki Shintani ◽  
Nguyen Hoang Loc ◽  
...  
Keyword(s):  
Amino Acid ◽  
Thermophilic Bacterium ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Pcr Analysis ◽  
Naphthalene Degradation ◽  
Isolation And Characterization ◽  
Dihydrodiol Dehydrogenase ◽  
Reading Frames

Geobacillus sp. JF8 is a thermophilic biphenyl and naphthalene degrader. To identify the naphthalene degradation genes, cis-naphthalene dihydrodiol dehydrogenase was purified from naphthalene-grown cells, and its N-terminal amino acid sequence was determined. Using a DNA probe encoding the N-terminal region of the dehydrogenase, a 10-kb DNA fragment was isolated. Upstream of nahB, a gene for dehydrogenase, there were two open reading frames which were designated as nahAc and nahAd, respectively. The products of nahAc and nahAd were predicted to be alpha and beta subunit of ring-hydroxylating dioxygenases, respectively. Phylogenetic analysis of amino acid sequences of NahB indicated that it did not belong to the cis-dihydrodiol dehydrogenase group that includes those of classical naphthalene degradation pathways. Downstream of nahB, four open reading frames were found, and their products were predicted as meta-cleavage product hydrolase, monooxygenase, dehydrogenase, and gentisate 1,2-dioxygenase, respectively. A reverse transcriptase-PCR analysis showed that transcription of nahAcAd was induced by naphthalene. These findings indicate that we successfully identified genes involved in the upper pathway of naphthalene degradation from a thermophilic bacterium.

Isolation and Characterization of a Novel n-Alkane-Degrading Strain, Acinetobacter haemolyticus AR-46

2007 ◽  
Vol 62 (3-4) ◽  
pp. 285-295 ◽  
Author(s):  
Zoltán Bihari ◽  
Aladár Pettkó-Szandtner ◽  
Gyula Csanádi ◽  
Margit Balázs ◽  
Péter Bartos ◽  
...  
Keyword(s):  
Hydrophobic Surface ◽  
Open Reading Frames ◽  
Substrate Uptake ◽  
Alkane Hydroxylase ◽  
Detailed Report ◽  
Isolation And Characterization ◽  
Acinetobacter Spp ◽  
Acinetobacter Haemolyticus ◽  
Reading Frames

Abstract Strain AR-46, isolated and identified as Acinetobacter haemolyticus, evolutionally distant from the known hydrocarbon-degrading Acinetobacter spp., proved to have excellent longchain n-alkane-degrading ability. This is the first detailed report on an n-alkane-utilizing strain belonging to this species. The preferred substrate is n-hexadecane, with an optimal temperature of 37 °C under aerobic conditions. Five complete and two partial open reading frames were sequenced and correlated with the early steps of monoterminal oxidation-initiated n-alkane mineralization. The encoded protein sequences and the arrangement of these genes displayed high similarity to those found in Acinetobacter sp. M-1, but AR-46 seemed to have only one alkane hydroxylase gene, with a completely different induction profile. Unique behaviour was also observed in n-alkane bioavailability. Substrate uptake occurred through the hydrophobic surface of n-alkane droplet-adhered cells possessing long, thick fimbriae, which were presumed to play a major role in n-alkane solubilization. A majority of the cells was in detached form, with thick, but short fimbriae. These free cells were permanently hydrophilic, unlike the cells of other Acinetobacter strains.

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 Isolation and characterization of Israeli acute paralysis virus, a dicistrovirus affecting honeybees in Israel: evidence for diversity due to intra- and inter-species recombination

2007 ◽  
Vol 88 (12) ◽  
pp. 3428-3438 ◽  
Author(s):  
Eyal Maori ◽  
Shai Lavi ◽  
Rita Mozes-Koch ◽  
Yulia Gantman ◽  
Yuval Peretz ◽  
...  
Keyword(s):  
Information Exchange ◽  
Open Reading Frames ◽  
Stem Loop ◽  
Israeli Acute Paralysis Virus ◽  
Isolation And Characterization ◽  
Kashmir Bee Virus ◽  
Acute Bee Paralysis Virus ◽  
Paralysis Virus ◽  
Reading Frames

We report the isolation, purification, genome-sequencing and characterization of a picorna-like virus from dead bees in Israel. Sequence analysis indicated that IAPV (Israeli acute paralysis virus) is a distinct dicistrovirus. It is most homologous to Kashmir bee virus and acute bee paralysis virus. The virus carries a 9487 nt RNA genome in positive orientation, with two open reading frames separated by an intergenic region, and its coat comprises four major proteins, the sizes of which suggest alternate processing of the polyprotein. IAPV virions also carry shorter, defective-interfering (DI)-like RNAs. Some of these RNAs are recombinants of different segments of IAPV RNA, some are recombinants of IAPV RNA and RNA from another dicistrovirus, and yet others are recombinants of IAPV and non-viral RNAs. In several of the DI-like RNAs, a sense-oriented fragment has recombined with its complement, forming hairpins and stem–loop structures. In previous reports, we have shown that potyviral and IAPV sequences are integrated into the genome of their respective hosts. The dynamics of information exchange between virus and host and the possible resistance-engendering mechanisms are discussed.

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.

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