scholarly journals Characterization and Genome Analysis of Staphylococcus aureus Podovirus CSA13 and Its Anti-Biofilm Capacity

Viruses ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 54 ◽  
Author(s):  
Yoyeon Cha ◽  
Jihwan Chun ◽  
Bokyung Son ◽  
Sangryeol Ryu
Keyword(s):  
Staphylococcus Aureus ◽  
Biocontrol Agent ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Experimental Setting ◽  
Human Pathogens ◽  
Bacteriophage Therapy ◽  
Chromosomal Structure ◽  
Inhibition Effect ◽  
Reading Frames

Staphylococcus aureus is one of the notable human pathogens that can be easily encountered in both dietary and clinical surroundings. Among various countermeasures, bacteriophage therapy is recognized as an alternative method for resolving the issue of antibiotic resistance. In the current study, bacteriophage CSA13 was isolated from a chicken, and subsequently, its morphology, physiology, and genomics were characterized. This Podoviridae phage displayed an extended host inhibition effect of up to 23 hours of persistence. Its broad host spectrum included methicillin susceptible S. aureus (MSSA), methicillin resistant S. aureus (MRSA), local S. aureus isolates, as well as non-aureus staphylococci strains. Moreover, phage CSA13 could successfully remove over 78% and 93% of MSSA and MRSA biofilms in an experimental setting, respectively. Genomic analysis revealed a 17,034 bp chromosome containing 18 predicted open reading frames (ORFs) without tRNAs, representing a typical chromosomal structure of the staphylococcal Podoviridae family. The results presented here suggest that phage CSA13 can be applicable as an effective biocontrol agent against S. aureus.

scholarly journals Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment

2009 ◽  
Vol 75 (24) ◽  
pp. 7663-7673 ◽  
Author(s):  
Pilar García ◽  
Beatriz Martínez ◽  
José María Obeso ◽  
Rob Lavigne ◽  
Rudi Lurz ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Dna Recombination ◽  
Point Mutations ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Functional Genomic Analysis ◽  
Replication Point ◽  
Terminal Amino ◽  
Functional Analyses ◽  
Reading Frames

ABSTRACT The genomes of the two lytic mutant Staphylococcus aureus bacteriophages, vB_SauS-phiIPLA35 (phiIPLA35) and vB_SauS-phiIPLA88 (phiIPLA88), isolated from milk have been analyzed. Their genomes are 45,344 bp and 42,526 bp long, respectively, and contain 62 and 61 open reading frames (ORFS). Enzymatic analyses and sequencing revealed that the phiIPLA35 DNA molecule has 3′-protruding cohesive ends (cos) 10 bp long, whereas phiIPLA88 DNA is 4.5% terminally redundant and most likely is packaged by a headful mechanism. N-terminal amino acid sequencing, mass spectrometry, bioinformatic analyses, and functional analyses enabled the assignment of putative functions to 58 gene products, including DNA packaging proteins, morphogenetic proteins, lysis components, and proteins necessary for DNA recombination, modification, and replication. Point mutations in their lysogeny control-associated genes explain their strictly lytic behavior. Muralytic activity associated with other structural components has been detected in virions of both phages. Comparative analysis of phiIPLA35 and phiIPLA88 genome structures shows that they resemble those of φ12 and φ11, respectively, both representatives of large genomic groupings within the S. aureus-infecting phages.

scholarly journals Molecular and Genomic Analysis of Genes Encoding Surface-Anchored Proteins from Clostridium difficile

2001 ◽  
Vol 69 (5) ◽  
pp. 3442-3446 ◽  
Author(s):  
Tuomo Karjalainen ◽  
Anne-Judith Waligora-Dupriet ◽  
Marina Cerquetti ◽  
Patrizia Spigaglia ◽  
Andrea Maggioni ◽  
...  
Keyword(s):  
Clostridium Difficile ◽  
Genetic Locus ◽  
Domain Architecture ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Precursor Protein ◽  
Precursor Proteins ◽  
Genes Encoding ◽  
The One ◽  
Reading Frames

ABSTRACT The gene slpA, encoding the S-layer precursor protein in the virulent Clostridium difficile strains C253 and 79–685, was identified. The precursor protein carries a C-terminal highly conserved anchoring domain, similar to the one found in the Cwp66 adhesin (previously characterized in strain 79–685), an SLH domain, and a variable N-terminal domain mediating cell adherence. The genes encoding the S-layer precursor proteins and the Cwp66 adhesin are present in a genetic locus carrying 17 open reading frames, 11 of which encode a similar two-domain architecture, likely to include surface-anchored proteins.

scholarly journals Integrative and Sequence Characteristics of a Novel Genetic Element, ICE6013, in Staphylococcus aureus

2009 ◽  
Vol 191 (19) ◽  
pp. 5964-5975 ◽  
Author(s):  
Davida S. Smyth ◽  
D. Ashley Robinson
Keyword(s):  
Staphylococcus Aureus ◽  
Integration Site ◽  
Open Reading Frames ◽  
Bacterial Conjugation ◽  
Genetic Element ◽  
Direct Repeats ◽  
New Family ◽  
Integrative Conjugative Element ◽  
Sequence Characteristics ◽  
Reading Frames

ABSTRACT A survey of chromosomal variation in the ST239 clonal group of methicillin-resistant Staphylococcus aureus (MRSA) revealed a novel genetic element, ICE6013. The element is 13,354 bp in length, excluding a 6,551-bp Tn552 insertion. ICE6013 is flanked by 3-bp direct repeats and is demarcated by 8-bp imperfect inverted repeats. The element was present in 6 of 15 genome-sequenced S. aureus strains, and it was detected using genetic markers in 19 of 44 diverse MRSA and methicillin-susceptible strains and in all 111 ST239 strains tested. Low integration site specificity was discerned. Multiple chromosomal copies and the presence of extrachromosomal circular forms of ICE6013 were detected in various strains. The circular forms included 3-bp coupling sequences, located between the 8-bp ends of the element, that corresponded to the 3-bp direct repeats flanking the chromosomal forms. ICE6013 is predicted to encode 15 open reading frames, including an IS30-like DDE transposase in place of a Tyr/Ser recombinase and homologs of gram-positive bacterial conjugation components. Further sequence analyses indicated that ICE6013 is more closely related to ICEBs1 from Bacillus subtilis than to the only other potential integrative conjugative element known from S. aureus, Tn5801. Evidence of recombination between ICE6013 elements is also presented. In summary, ICE6013 is the first member of a new family of active, integrative genetic elements that are widely dispersed within S. aureus strains.

scholarly journals Characterization and Genomic Analysis of Phage asccφ28, a Phage of the Family Podoviridae Infecting Lactococcus lactis

2008 ◽  
Vol 74 (11) ◽  
pp. 3453-3460 ◽  
Author(s):  
Steven E. Kotsonis ◽  
Ian B. Powell ◽  
Christopher J. Pillidge ◽  
Gaëtan K. Y. Limsowtin ◽  
Alan J. Hillier ◽  
...  
Keyword(s):  
Lactococcus Lactis ◽  
Dna Hybridization ◽  
Burst Size ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Full Genome Sequence ◽  
The Family ◽  
Reading Frames ◽  
Dairy Fermentation

ABSTRACT Bacteriophage asccφ28 infects dairy fermentation strains of Lactococcus lactis. This report describes characterization of asccφ28 and its full genome sequence. Phage asccφ28 has a prolate head, whiskers, and a short tail (C2 morphotype). This morphology and DNA hybridization to L. lactis phage P369 DNA showed that asccφ28 belongs to the P034 phage species, a group rarely encountered in the dairy industry. The burst size of asccφ28 was found to be 121 ± 18 PFU per infected bacterial cell after a latent period of 44 min. The linear genome (18,762 bp) contains 28 possible open reading frames (ORFs) comprising 90% of the total genome. The ORFs are arranged bidirectionally in recognizable functional modules. The genome contains 577 bp inverted terminal repeats (ITRs) and putatively eight promoters and four terminators. The presence of ITRs, a phage-encoded DNA polymerase, and a terminal protein that binds to the DNA, along with BLAST and morphology data, show that asccφ28 more closely resembles streptococcal phage Cp-1 and the φ29-like phages that infect Bacillus subtilis than it resembles common lactococcal phages. The sequence of this phage is the first published sequence of a P034 species phage genome.

scholarly journals A New Class of Genetic Element, Staphylococcus Cassette Chromosome mec, Encodes Methicillin Resistance in Staphylococcus aureus

2000 ◽  
Vol 44 (6) ◽  
pp. 1549-1555 ◽  
Author(s):  
Y. Katayama ◽  
T. Ito ◽  
K. Hiramatsu
Keyword(s):  
Staphylococcus Aureus ◽  
Methicillin Resistance ◽  
Open Reading Frames ◽  
Multicopy Plasmid ◽  
Sequence Determination ◽  
New Class ◽  
New Family ◽  
Partial Homology ◽  
Reading Frames

ABSTRACT We have previously shown that the methicillin-resistance genemecA of Staphylococcus aureus strain N315 is localized within a large (52-kb) DNA cassette (designated the staphylococcal cassette chromosome mec[SCCmec]) inserted in the chromosome. By sequence determination of the entire DNA, we identified two novel genes (designated cassette chromosome recombinase genes [ccrAand ccrB]) encoding polypeptides having a partial homology to recombinases of the invertase/resolvase family. The open reading frames were found to catalyze precise excision of the SCCmec from the methicillin-resistant S. aureuschromosome and site-specific as well as orientation-specific integration of the SCCmec into the S. aureuschromosome when introduced into the cells as a recombinant multicopy plasmid. We propose that SCCmec driven by a novel set of recombinases represents a new family of staphylococcal genomic elements.

scholarly journals Classification of the gifted natural product producerStreptomyces roseofacienssp. nov. by polyphasic taxonomy

2018 ◽  
Author(s):  
Lizah T. van der Aart ◽  
Imen Nouinoui ◽  
Alexander Kloosterman ◽  
José Mariano Ingual ◽  
Joost Willemse ◽  
...  
Keyword(s):  
Genomic Analysis ◽  
Lateral Wall ◽  
Gene Clusters ◽  
Housekeeping Gene ◽  
Distinct Species ◽  
Open Reading Frames ◽  
Morphological Properties ◽  
Biosynthetic Gene Clusters ◽  
Reading Frames

ABSTRACTA novel verticillate strain of streptomycetes,Streptomycesstrain MBT76T, was isolated from the QinLing mountains, which harbours more than 40 biosynthetic gene clusters for natural products. Here we present full taxonomic classification of strain MBT76T, and show that it has chemotaxonomic, genomic and morphological properties consistent with its classification in the genusStreptomyces. Strain MBT76Tis part of the cluster of Streptoverticillates, a group within the genusStreptomycesthat has characteristic whorl-forming spores produced in chains along the lateral wall of the hyphae. Multi-locus sequence analysis based on five housekeeping gene alleles showed that MBT76Tis closely related toStreptomyces hiroshimensis. Average Nucleotide Identification (ANI) and Genome to Genome Distance Calculation (GGDC) of the genomes of strain MBT76TandS. hiroshimensisseparated them into distinct species. Strain MBT76Trepresents a novel species of the genusStreptomycesfor which we propose the nameStreptomyces roseofacienssp. nov. The type strain is MBT76T(=NCCB 100637T=DSM 106196T). The whole genome of MBT76Thas 7974 predicted open reading frames and a total genome size of 8.64 Mb. Further genomic analysis showed that verticillate streptomycetes lack the sporulation genessgE, and our data suggest that this is a useful genetic marker for the spore-chain morphology of the verticillates.

scholarly journals Genomic Characteristics and Evolutionary Analysis of a Rare GI.1 Norovirus Isolate From Beijing, China

2021 ◽  
Author(s):  
Weishan Zhang ◽  
Wei Zhang ◽  
Xinling Hu ◽  
Xintong Zhou ◽  
Guobao Tian ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Large Scale ◽  
Genomic Analysis ◽  
Open Reading Frames ◽  
Whole Genome Sequence ◽  
Evolutionary Analysis ◽  
And Control ◽  
Beijing China ◽  
Strain Genome ◽  
Reading Frames

Abstract Noroviruses are one of the main pathogens of acute gastroenteritis, causing frequent outbreaks worldwide every year that seriously affect human health. The GII.4 genotype causes most norovirus (NoV) infections and large-scale outbreaks. By contrast, the GI genotype is relatively rare. In this study, the whole genome sequence of a newly isolated ZD strain from a patient in Beijing, China, was sequenced and analyzed. The ZD strain genome consisted of 7,597 nucleotides and contained three open reading frames. Whole-genomic analysis indicated the strain was a GI.1 genotype, and no recombination site was detected in the genome. The histo-blood group antigen (HBGA)binding site associated with invasion of the GI genotype did not change, implying relatively conservative evolution. Phylogenetic analysis indicated the VP1 sequence of GI.1 strains could be divided into three clusters according to time of appearance: older (1968-2011), earlier (2011-2015), and new (2017-2018). Each cluster showed distinctive amino acid substitution characteristics, and the number of substitutions increased with time. The isolated ZD strain was in the new cluster. This study is the first to conduct a phylogenetic analysis of a GI genotype NoV isolated from Beijing. The results improve understanding of NoV diversity in China and can be a reference for further study of nondominant epidemic strains of NoVs as well as epidemic prevention and control.

scholarly journals Transcriptional and Translational Landscape of Equine Torovirus

2018 ◽  
Vol 92 (17) ◽  
Author(s):  
Hazel Stewart ◽  
Katherine Brown ◽  
Adam M. Dinan ◽  
Nerea Irigoyen ◽  
Eric J. Snijder ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Rna Synthesis ◽  
Gastrointestinal Disease ◽  
Ribosome Profiling ◽  
Amino Acid Sequences ◽  
Open Reading Frames ◽  
Comparative Genomic ◽  
Human Pathogens ◽  
Content Type ◽  
Reading Frames

ABSTRACT The genus Torovirus (subfamily Torovirinae, family Coronaviridae, order Nidovirales) encompasses a range of species that infect domestic ungulates, including cattle, sheep, goats, pigs, and horses, causing an acute self-limiting gastroenteritis. Using the prototype species equine torovirus (EToV), we performed parallel RNA sequencing (RNA-seq) and ribosome profiling (Ribo-seq) to analyze the relative expression levels of the known torovirus proteins and transcripts, chimeric sequences produced via discontinuous RNA synthesis (a characteristic of the nidovirus replication cycle), and changes in host transcription and translation as a result of EToV infection. RNA sequencing confirmed that EToV utilizes a unique combination of discontinuous and nondiscontinuous RNA synthesis to produce its subgenomic RNAs (sgRNAs); indeed, we identified transcripts arising from both mechanisms that would result in sgRNAs encoding the nucleocapsid. Our ribosome profiling analysis revealed that ribosomes efficiently translate two novel CUG-initiated open reading frames (ORFs), located within the so-called 5′ untranslated region. We have termed the resulting proteins U1 and U2. Comparative genomic analysis confirmed that these ORFs are conserved across all available torovirus sequences, and the inferred amino acid sequences are subject to purifying selection, indicating that U1 and U2 are functionally relevant. This study provides the first high-resolution analysis of transcription and translation in this neglected group of livestock pathogens. IMPORTANCE Toroviruses infect cattle, goats, pigs, and horses worldwide and can cause gastrointestinal disease. There is no treatment or vaccine, and their ability to spill over into humans has not been assessed. These viruses are related to important human pathogens, including severe acute respiratory syndrome (SARS) coronavirus, and they share some common features; however, the mechanism that they use to produce sgRNA molecules differs. Here, we performed deep sequencing to determine how equine torovirus produces sgRNAs. In doing so, we also identified two previously unknown open reading frames “hidden” within the genome. Together these results highlight the similarities and differences between this domestic animal virus and related pathogens of humans and livestock.

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