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 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 The Moraxella catarrhalis Immunoglobulin D-Binding Protein MID Has Conserved Sequences and Is Regulated by a Mechanism Corresponding to Phase Variation

2003 ◽  
Vol 185 (7) ◽  
pp. 2285-2295 ◽  
Author(s):  
Andrea Möllenkvist ◽  
Therése Nordström ◽  
Christer Halldén ◽  
Jens Jørgen Christensen ◽  
Arne Forsgren ◽  
...  
Keyword(s):  
Moraxella Catarrhalis ◽  
Point Mutations ◽  
Phase Variation ◽  
The United States ◽  
Open Reading Frames ◽  
Peptide Sequence ◽  
Transcriptional Level ◽  
Signal Peptide Sequence ◽  
Immunoglobulin D ◽  
Reading Frames

ABSTRACT The prevalence of the Moraxella catarrhalis immunoglobulin D (IgD)-binding outer membrane protein MID and its gene was determined in 91 clinical isolates and in 7 culture collection strains. Eighty-four percent of the clinical Moraxella strains expressed MID-dependent IgD binding. The mid gene was detected in all strains as revealed by homology of the signal peptide sequence and a conserved area in the 3′ end of the gene. When MID proteins from five different strains were compared, an identity of 65.3 to 85.0% and a similarity of 71.2 to 89.1% were detected. Gene analyses showed several amino acid repeat motifs in the open reading frames, and MID could be called a putative autotransport protein. Interestingly, homopolymeric {polyguanine [poly(G)]} tracts were detected at the 5′ ends within the open reading frames. By flow cytometry, using human IgD and fluorescein isothiocyanate-conjugated anti-IgD polyclonal antibodies, most strains showed two peaks: one high- and one low-intensity peak. All isolates expressing high levels of MID had 1, 2, or 3 triplets of G's in their poly(G) tracts, while strains not expressing MID had 4, 7, 8, or 10 G’s in their poly(G) tracts or point mutations causing a putative preterminated translation. Northern blot analysis revealed that the mid gene was regulated at the transcriptional level. Experiments with nonclumping variants of M. catarrhalis proved that bacteria lost their MID expression by removing a G in their poly(G) tracts. Moraxella strains isolated from the nasopharynx or from blood and sputum specimens expressed MID at approximately the same frequency. In addition, no variation was observed between strains of different geographical origins (Australia, Europe, Japan, or the United States). MID and the mid gene were found solely in M. catarrhalis, whereas related Neisseria and Moraxella species did not express MID. Taken together, MID appears to be a conserved protein that can be found in essentially all M. catarrhalis strains. Furthermore, MID is governed by poly(G) tracts when bacteria undergo phase variation.

scholarly journals Analysis of the genome of Spodoptera frugiperda nucleopolyhedrovirus (SfMNPV-19) and of the high genomic heterogeneity in group II nucleopolyhedroviruses

2008 ◽  
Vol 89 (5) ◽  
pp. 1202-1211 ◽  
Author(s):  
José Luiz Caldas Wolff ◽  
Fernando Hercos Valicente ◽  
Renata Martins ◽  
Juliana Velasco de Castro Oliveira ◽  
Paolo Marinho de Andrade Zanotto
Keyword(s):  
Spodoptera Frugiperda ◽  
Point Mutations ◽  
Open Reading Frames ◽  
Temporal Organization ◽  
Agrotis Segetum ◽  
Gene Gain ◽  
Physical Maps ◽  
Polyadenylation Sites ◽  
Group Ii ◽  
Reading Frames

The genome of the most virulent among 22 Brazilian geographical isolates of Spodoptera frugiperda nucleopolyhedrovirus, isolate 19 (SfMNPV-19), was completely sequenced and shown to comprise 132 565 bp and 141 open reading frames (ORFs). A total of 11 ORFs with no homology to genes in the GenBank database were found. Of those, four had typical baculovirus promoter motifs and polyadenylation sites. Computer-simulated restriction enzyme cleavage patterns of SfMNPV-19 were compared with published physical maps of other SfMNPV isolates. Differences were observed in terms of the restriction profiles and genome size. Comparison of SfMNPV-19 with the sequence of the SfMNPV isolate 3AP2 indicated that they differed due to a 1427 bp deletion, as well as by a series of smaller deletions and point mutations. The majority of genes of SfMNPV-19 were conserved in the closely related Spodoptera exigua NPV (SeMNPV) and Agrotis segetum NPV (AgseMNPV-A), but a few regions experienced major changes and rearrangements. Synthenic maps for the genomes of group II NPVs revealed that gene collinearity was observed only within certain clusters. Analysis of the dynamics of gene gain and loss along the phylogenetic tree of the NPVs showed that group II had only five defining genes and supported the hypothesis that these viruses form ten highly divergent ancient lineages. Crucially, more than 60 % of the gene gain events followed a power-law relation to genetic distance among baculoviruses, indicative of temporal organization in the gene accretion process.

scholarly journals Genetic and Biochemical Characterization of a Novel Monoterpene ɛ-Lactone Hydrolase from Rhodococcus erythropolis DCL14

2001 ◽  
Vol 67 (2) ◽  
pp. 733-741 ◽  
Author(s):  
Cécile J. B van der Vlugt-Bergmans ◽  
Mariët J. van der Werf
Keyword(s):  
Ring Opening ◽  
Biochemical Characterization ◽  
Rhodococcus Erythropolis ◽  
Open Reading Frames ◽  
Apparent Homogeneity ◽  
Terminal Amino ◽  
Acyl Coenzyme A ◽  
Reading Frames

ABSTRACT A monoterpene ɛ-lactone hydrolase (MLH) from Rhodococcus erythropolis DCL14, catalyzing the ring opening of lactones which are formed during degradation of several monocyclic monoterpenes, including carvone and menthol, was purified to apparent homogeneity. It is a monomeric enzyme of 31 kDa that is active with (4R)-4-isopropenyl-7-methyl-2-oxo-oxepanone and (6R)-6-isopropenyl-3-methyl-2-oxo-oxepanone, lactones derived from (4R)-dihydrocarvone, and 7-isopropyl-4-methyl-2-oxo-oxepanone, the lactone derived from menthone. Both enantiomers of 4-, 5-, 6-, and 7-methyl-2-oxo-oxepanone were converted at equal rates, suggesting that the enzyme is not stereoselective. Maximal enzyme activity was measured at pH 9.5 and 30°C. Determination of the N-terminal amino acid sequence of purified MLH enabled cloning of the corresponding gene by a combination of PCR and colony screening. The gene, designated mlhB(monoterpene lactone hydrolysis), showed up to 43% similarity to members of the GDXG family of lipolytic enzymes. Sequencing of the adjacent regions revealed two other open reading frames, one encoding a protein with similarity to the short-chain dehydrogenase reductase family and the second encoding a protein with similarity to acyl coenzyme A dehydrogenases. Both enzymes are possibly also involved in the monoterpene degradation pathways of this microorganism.

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 Multiplexed functional genomic analysis of 5’ untranslated region mutations across the spectrum of prostate cancer

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yiting Lim ◽  
Sonali Arora ◽  
Samantha L. Schuster ◽  
Lukas Corey ◽  
Matthew Fitzgibbon ◽  
...  
Keyword(s):  
Gene Expression ◽  
Prostate Cancer ◽  
Point Mutations ◽  
Genomic Analysis ◽  
Mrna Translation ◽  
Specific Gene ◽  
Functional Genomic Analysis ◽  
A Genome ◽  
Functional Consequences ◽  
Wide Scale

AbstractThe functional consequences of genetic variants within 5’ untranslated regions (UTRs) on a genome-wide scale are poorly understood in disease. Here we develop a high-throughput multi-layer functional genomics method called PLUMAGE (Pooled full-length UTR Multiplex Assay on Gene Expression) to quantify the molecular consequences of somatic 5’ UTR mutations in human prostate cancer. We show that 5’ UTR mutations can control transcript levels and mRNA translation rates through the creation of DNA binding elements or RNA-based cis-regulatory motifs. We discover that point mutations can simultaneously impact transcript and translation levels of the same gene. We provide evidence that functional 5’ UTR mutations in the MAP kinase signaling pathway can upregulate pathway-specific gene expression and are associated with clinical outcomes. Our study reveals the diverse mechanisms by which the mutational landscape of 5’ UTRs can co-opt gene expression and demonstrates that single nucleotide alterations within 5’ UTRs are functional in cancer.

scholarly journals Large-Scale Functional Genomic Analysis of Sporulation and Meiosis in Saccharomyces cerevisiae

Genetics ◽  
2003 ◽  
Vol 163 (1) ◽  
pp. 47-54 ◽  
Author(s):  
Akon H Enyenihi ◽  
William S Saunders
Keyword(s):  
Saccharomyces Cerevisiae ◽  
Large Scale ◽  
Single Gene ◽  
Genomic Analysis ◽  
Essential Genes ◽  
Open Reading Frames ◽  
Functional Genomic Analysis ◽  
Phenotypic Screen ◽  
Mutant Bank ◽  
Late Stages

Abstract We have used a single-gene deletion mutant bank to identify the genes required for meiosis and sporulation among 4323 nonessential Saccharomyces cerevisiae annotated open reading frames (ORFs). Three hundred thirty-four sporulation-essential genes were identified, including 78 novel ORFs and 115 known genes without previously described sporulation defects in the comprehensive Saccharomyces Genome (SGD) or Yeast Proteome (YPD) phenotype databases. We have further divided the uncharacterized sporulation-essential genes into early, middle, and late stages of meiosis according to their requirement for IME1 induction and nuclear division. We believe this represents a nearly complete identification of the genes uniquely required for this complex cellular pathway. The set of genes identified in this phenotypic screen shows only limited overlap with those identified by expression-based studies.

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