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 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 Characterization of Porcine Endogenous Retrovirus γ pro-pol Nucleotide Sequences

2002 ◽  
Vol 76 (22) ◽  
pp. 11738-11743 ◽  
Author(s):  
Nikolai Klymiuk ◽  
Mathias Müller ◽  
Gottfried Brem ◽  
Bernhard Aigner
Keyword(s):  
Endogenous Retrovirus ◽  
Open Reading Frames ◽  
The Novel ◽  
Infectious Risk ◽  
Porcine Endogenous Retrovirus ◽  
Pig Genome ◽  
Reading Frames ◽  
Selection Of

ABSTRACT Endogenous retroviral sequences in the pig genome (PERV) represent a potential infectious risk in xenotransplantation. All known infectious PERV have been asssigned to the PERV γ1 family, consisting of the subfamilies A, B, and C. The aim of the study was the concise examination of PERV γ by the analysis of the retroviral pro-pol sequences. The analysis of 52 pro-pol clones amplified in this study revealed eight PERV γ families. In addition to four already-described families (γ1, γ4, γ5, γ6), four novel families (γ7, γ8, γ9, γ10) were identified. Quantitative analysis of the novel PERV γ sequences in selected breeds revealed variations in the endogenous retroviral load. Open reading frames (ORF) in the amplified proviral fragment were only found for PERV γ1. In addition, novel ORF-containing PERV γ1 clones consisting of hybrid sequences were revealed. Sequence comparison from published full-length PERV γ1 clones of the PERV subfamilies A, B, and C resulted in a lack of strict correlation of the classification of pro-pol and env. The results indicated the occurrence of causative recombination events between retroviral genomes. Thus, our study on PERV γ provides new data for the evaluation and selection of pigs intended to be used in xenotransplantation.

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 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 Isolation and Characterization of a Novel Klebsiella pneumoniae N4-like Bacteriophage KP8

Viruses ◽  
2019 ◽  
Vol 11 (12) ◽  
pp. 1115 ◽  
Author(s):  
Vera Morozova ◽  
Igor Babkin ◽  
Yuliya Kozlova ◽  
Ivan Baykov ◽  
Olga Bokovaya ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
New Genus ◽  
Wide Spectrum ◽  
Biological Properties ◽  
Open Reading Frames ◽  
Gene Encoding ◽  
Isolation And Characterization ◽  
Distinct Branch ◽  
Reading Frames

Klebsiella pneumoniae is a common pathogen, associated with a wide spectrum of infections, and clinical isolates of K. pneumoniae often possess multiple antibiotic resistances. Here, we describe a novel lytic N4-like bacteriophage KP8, specific to K. pneumoniae, including its genome, partial structural proteome, biological properties, and proposed taxonomy. Electron microscopy revealed that KP8 belongs to the Podoviridae family. The size of the KP8 genome was 73,679 bp, and it comprised 97 putative open reading frames. Comparative genome analysis revealed that the KP8 genome possessed the highest similarity to the genomes of Enquatrovirus and Gamaleyavirus phages, which are N4-like podoviruses. In addition, the KP8 genome showed gene synteny typical of the N4-like podoviruses and contained the gene encoding a large virion-encapsulated RNA polymerase. Phylogenetic analysis of the KP8 genome revealed that the KP8 genome formed a distinct branch within the clade, which included the members of Enquatrovirus and Gamaleyavirus genera besides KP8. The average evolutionary divergences KP8/Enquatrovirus and KP8/Gamaleyavirus were 0.466 and 0.447 substitutions per site (substitutes/site), respectively, similar to that between Enquatrovirus and Gamaleyavirus genera (0.468 substitutes/site). The obtained data suggested that Klebsiella phage KP8 differs from other similar phages and may represent a new genus within the N4-like phages.

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 Identification and Characterization of an Active Plasmid Partition Mechanism for the Novel Lactococcus lactisPlasmid pCI2000

2000 ◽  
Vol 182 (1) ◽  
pp. 30-37 ◽  
Author(s):  
Karen Kearney ◽  
Gerald F. Fitzgerald ◽  
Jos F. M. L. Seegers
Keyword(s):  
Open Reading Frames ◽  
Gram Negative Bacteria ◽  
The Novel ◽  
Replication Proteins ◽  
Gram Positive Bacteria ◽  
Plasmid Partition ◽  
Replication Region ◽  
Identification And Characterization ◽  
Reading Frames

ABSTRACT The replication region of the lactococcal plasmid pCI2000 was subcloned and analyzed. The nucleotide sequence of one 5.6-kbEcoRI fragment which was capable of supporting replication when cloned on a replication probe vector revealed the presence of seven putative open reading frames (ORFs). One ORF exhibited significant homology to several replication proteins from plasmids considered to replicate via a theta mode. Deletion analysis showed that this ORF, designated repA, is indeed required for replication. The results also suggest that the origin of replication is located outside repA. Upstream and divergently transcribed from repA, an ORF that showed significant (48 to 64%) homology to a number of proteins that are required for faithful segregation of chromosomal or plasmid DNA of gram-negative bacteria was identified. Gene interruption and transcomplementation experiments showed that this ORF, designated parA, is required for stable inheritance of pCI2000 and is active in trans. This is the first example of such a partitioning mechanism for plasmids in gram-positive bacteria.

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