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Friday, July 19, 2019

Lifespan of restriction-modification systems critically affects avoidance of their recognition sites in host genomes.

Avoidance of palindromic recognition sites of Type II restriction-modification (R-M) systems was shown for many R-M systems in dozens of prokaryotic genomes. However the phenomenon has not been investigated systematically for all presently available genomes and annotated R-M systems. We have studied all known recognition sites in thousands of prokaryotic genomes and found factors that influence their avoidance.Only Type II R-M systems consisting of independently acting endonuclease and methyltransferase (called ‘orthodox’ here) cause avoidance of their sites, both palindromic and asymmetric, in corresponding prokaryotic genomes; the avoidance takes place for?~?50 % of 1774 studied cases. It is known that prokaryotes can…

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Sunday, July 7, 2019

Burkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.

Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that…

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Sunday, July 7, 2019

Short communication: Single molecule, real-time sequencing technology revealed species- and strain-specific methylation patterns of 2 Lactobacillus strains.

Pacific Biosciences’ (Menlo Park, CA) single molecule, real-time sequencing technology was reported to have some advantages in generating finished genomes and characterizing the epigenome of bacteria. In the present study, this technology was used to sequence 2 Lactobacillus strains, Lactobacillus casei Zhang and Lactobacillus plantarum P-8. Previously, the former bacterium was sequenced by an Applied Biosystems 3730 DNA analyzer (Grand Island, NY), whereas the latter one was analyzed with Roche 454 (Indianapolis, IN) and Illumina sequencing technologies (San Diego, CA). The results showed that single molecule, real-time sequencing resulted in high-quality, finished genomes for both strains. Interestingly, epigenome analysis indicates…

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Sunday, July 7, 2019

Complete genome sequence of Salmonella enterica subsp. enterica serovar Agona 460004 2-1, associated with a multistate outbreak in the United States.

Within the last several years, Salmonella enterica subsp. enterica serovar Agona has been among the 20 most frequently isolated serovars in clinical cases of salmonellosis. In this report, the complete genome sequence of S. Agona strain 460004 2-1 isolated from unsweetened puffed-rice cereal during a multistate outbreak in 2008 was sequenced using single-molecule real-time DNA sequencing. Copyright © 2015 Hoffmann et al.

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Sunday, July 7, 2019

Complete genome sequence of enteroinvasive Escherichia coli O96:H19 associated with a severe foodborne outbreak.

We present here the complete genome sequence of a strain of enteroinvasive Escherichia coli O96:H19 from a severe foodborne outbreak in a canteen in Italy in 2014. The complete genome may provide important information about the acquired pathogenicity of this strain and the transition between commensal and pathogenic E. coli. Copyright © 2015 Pettengill et al.

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Sunday, July 7, 2019

The functions of DNA methylation by CcrM in Caulobacter crescentus: a global approach.

DNA methylation is involved in a diversity of processes in bacteria, including maintenance of genome integrity and regulation of gene expression. Here, using Caulobacter crescentus as a model, we exploit genome-wide experimental methods to uncover the functions of CcrM, a DNA methyltransferase conserved in most Alphaproteobacteria. Using single molecule sequencing, we provide evidence that most CcrM target motifs (GANTC) switch from a fully methylated to a hemi-methylated state when they are replicated, and back to a fully methylated state at the onset of cell division. We show that DNA methylation by CcrM is not required for the control of the…

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Sunday, July 7, 2019

Methylome diversification through changes in DNA methyltransferase sequence specificity.

Epigenetic modifications such as DNA methylation have large effects on gene expression and genome maintenance. Helicobacter pylori, a human gastric pathogen, has a large number of DNA methyltransferase genes, with different strains having unique repertoires. Previous genome comparisons suggested that these methyltransferases often change DNA sequence specificity through domain movement–the movement between and within genes of coding sequences of target recognition domains. Using single-molecule real-time sequencing technology, which detects N6-methyladenines and N4-methylcytosines with single-base resolution, we studied methylated DNA sites throughout the H. pylori genome for several closely related strains. Overall, the methylome was highly variable among closely related strains.…

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Sunday, July 7, 2019

Complete genome sequences of Salmonella enterica serovar Heidelberg strains associated with a multistate food-borne illness investigation.

Next-generation sequencing is being evaluated for use with food-borne illness investigations, especially when the outbreak strains produce patterns that cannot be discriminated from non-outbreak strains using conventional procedures. Here we report complete genome assemblies of two Salmonella enterica serovar Heidelberg strains with a common pulsed-field gel electrophoresis pattern isolated during an outbreak investigation.

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Sunday, July 7, 2019

Type I restriction enzymes and their relatives.

Type I restriction enzymes (REases) are large pentameric proteins with separate restriction (R), methylation (M) and DNA sequence-recognition (S) subunits. They were the first REases to be discovered and purified, but unlike the enormously useful Type II REases, they have yet to find a place in the enzymatic toolbox of molecular biologists. Type I enzymes have been difficult to characterize, but this is changing as genome analysis reveals their genes, and methylome analysis reveals their recognition sequences. Several Type I REases have been studied in detail and what has been learned about them invites greater attention. In this article, we…

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Sunday, July 7, 2019

First complete genome sequence of Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 13311 (NCTC 74), a reference strain of multidrug resistance, as achieved by use of PacBio Single-Molecule Real-Time technology.

We report the first complete genomic sequence of Salmonella enterica subsp. enterica serovar Typhimurium strain ATCC 13311, the leading food-borne pathogen and a reference strain used in drug resistance studies. De novo assembly with PacBio sequencing completed its chromosome and one plasmid. They will accelerate the investigation into multidrug resistance in Salmonella Typhimurium. Copyright © 2014 Terabayashi et al.

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Sunday, July 7, 2019

Whole-genome assembly of Klebsiella pneumoniae coproducing NDM-1 and OXA-232 carbapenemases using Single-Molecule, Real-Time Sequencing.

The whole-genome sequence of a carbapenem-resistant Klebsiella pneumoniae strain, PittNDM01, which coproduces NDM-1 and OXA-232 carbapenemases, was determined in this study. The use of single-molecule, real-time (SMRT) sequencing provided a closed genome in a single sequencing run. K. pneumoniae PittNDM01 has a single chromosome of 5,348,284 bp and four plasmids: pPKPN1 (283,371 bp), pPKPN2 (103,694 bp), pPKPN3 (70,814 bp), and pPKPN4 (6,141 bp). The contents of the chromosome were similar to that of the K. pneumoniae reference genome strain MGH 78578, with the exception of a large inversion spanning 23.3% of the chromosome. In contrast, three of the four plasmids…

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