Characterization of a restriction modification system from the commensal Escherichia coli strain A0 34/86 (O83:K24:H31)

Weiserová, Marie; Ryu, Junichi

doi:10.1186/1471-2180-8-106

Cited by 5 publications

(5 citation statements)

References 41 publications

(50 reference statements)

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“…The letters (a-c) indicate significant differences between various temperatures at the same storage periods at p < 0.05 infection [49]. E. coli O157:H7 has type I restrictionmodification system [50,51]. Most enzymes do not digest DNA due to the modification of cytosine [49,52,53].…”

Section: Discussionmentioning

confidence: 99%

Isolation and characterization of a novel Escherichia coli O157:H7-specific phage as a biocontrol agent

Lee

Choi

Park

et al. 2020

J Environ Health Sci Engineer

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Purpose Escherichia coli O157:H7 is one of the major foodborne pathogens of global public concern. Bacteriophages (phages) have emerged as a promising alternative to antibiotics for controlling pathogenic bacteria. Here, a lytic E. coli O157:H7-specific phage (KFS-EC) was isolated, identified, and characterized to evaluate its potential as a biocontrol agent for E. coli O157:H7. Methods KFS-EC was isolated from slaughterhouse in Korea. Morphological analysis, genomic analysis and several physiological tests were performed to identify and characterize the KFS-EC. Results A specificity test indicated KFS-EC was strictly specific to E. coli O157:H7 strains among 60 bacterial strains tested. Morphological and phylogenetic analyses confirmed that KFS-EC belongs to the Rb49virus genus, Tevenvirinae subfamily, and the Myoviridae family of phages. KFS-EC genome consists of 164,725 bp and a total of 270 coding sequence features, of which 114 open reading frames (ORFs) were identified as phage functional genes. KFS-EC does not contain genes encoding lysogenic property and pathogenicity, which ensure its safe application. KFS-EC was relatively stable (~1 log decrease) under stressed conditions such as temperatures (20 °C-50 °C), pHs (3-11), organic solvents (ethanol and chloroform), and biocides (0.1% citric acid, 1% citric acid, and 0.1% peracetic acid). KFS-EC was able to inhibit E. coli O157:H7 efficiently at a multiplicity of infection (MOI) of 0.01 for 8 h with greater inhibitory effect and durability and was stable at 4 °C and 22 °C over a 12-week storage period. Conclusions Our results suggest that KFS-EC could be used as a biocontrol agent to E. coli O157:H7.

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Section: Discussionmentioning

confidence: 99%

Isolation and characterization of a novel Escherichia coli O157:H7-specific phage as a biocontrol agent

Lee

Choi

Park

et al. 2020

J Environ Health Sci Engineer

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“…Many bacteria are equipped with a restriction endonuclease that recognizes one specific DNA sequence, usually a palindromic tetramer (e.g. GGCC), hexamer, or octamer; these bacteria are also equipped with a modification enzyme that methylates the recognition sequence and thereby protects the cell's DNA from its own restriction enzyme (Weiserová & Ryu, 2008). Thus, bacteria that share the same restriction–modification system can more easily share a phage or a plasmid, whereas bacteria with different restriction–modification systems will effectively digest the DNA of one another's vectors (Jeltsch, 2003; Budroni et al ., 2011).…”

Section: Donor–recipient Similarities Required For Genetic Transfermentioning

confidence: 99%

Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches

2011

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Horizontal genetic transfer (HGT) has played an important role in bacterial evolution at least since the origins of the bacterial divisions, and HGT still facilitates the origins of bacterial diversity, including diversity based on antibiotic resistance. Adaptive HGT is aided by unique features of genetic exchange in bacteria such as the promiscuity of genetic exchange and the shortness of segments transferred. Genetic exchange rates are limited by the genetic and ecological similarity of organisms. Adaptive transfer of genes is limited to those that can be transferred as a functional unit, provide a niche-transcending adaptation, and are compatible with the architecture and physiology of other organisms. Horizontally transferred adaptations may bring about fitness costs, and natural selection may ameliorate these costs. The origins of ecological diversity can be analyzed by comparing the genomes of recently divergent, ecologically distinct populations, which can be discovered as sequence clusters. Such genome comparisons demonstrate the importance of HGT in ecological diversification. Newly divergent populations cannot be discovered as sequence clusters when their ecological differences are coded by plasmids, as is often the case for antibiotic resistance; the discovery of such populations requires a screen for plasmid-coded functions. This paper reviews the features of bacterial genetics that allow HGT, the similarities between organisms that foster HGT between them, the limits to the kinds of adaptations that can be transferred, and amelioration of fitness costs associated with HGT; the paper also reviews approaches to discover the origins of new, ecologically distinct bacterial populations and the role that HGT plays in their founding.

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“…This locus encodes the target specificity gene hsdS , methyltransferase gene hsdM , and restriction gene hsdR that encode the HsdS, HsdM, and HsdR subunits. The subunits assemble into a heteromeric enzyme complex that functions to specifically methylate the bacterial genomic DNA and destroy foreign DNA [ 25 ]. The HsdS subunit has two different DNA target recognition domains (designated as TRD 1 and TRD 2) which direct recognition of specific sequence motifs that are then methylated by the HsdM subunit [ 22 , 23 ].…”

Section: Introductionmentioning

confidence: 99%

Comparative Analysis of Streptococcus pneumoniae Type I Restriction-Modification Loci: Variation in hsdS Gene Target Recognition Domains

Oliver

Swords

2020

Pathogens

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Streptococcus pneumoniae (pneumococcus) is a respiratory commensal pathogen that causes a range of infections, particularly in young children and the elderly. Pneumococci undergo spontaneous phase variation in colony opacity phenotype, in which DNA rearrangements within the Type I restriction-modification (R-M) system specificity gene hsdS can potentially generate up to six different hsdS alleles with differential DNA methylation activity, resulting in changes in gene expression. To gain a broader perspective of this system, we performed bioinformatic analyses of Type I R-M loci from 18 published pneumococcal genomes, and one R-M locus sequenced for this study, to compare genetic content, organization, and homology. All 19 loci encoded the genes hsdR, hsdM, hsdS, and at least one hsdS pseudogene, but differed in gene order, gene orientation, and hsdS target recognition domain (TRD) content. We determined the coding sequences of 87 hsdS TRDs and excluded seven from further analysis due to the presence of premature stop codons. Comparative analyses revealed that the TRD 1.1, 1.2, and 2.1 protein sequences had single amino acid substitutions, and TRD 2.2 and 2.3 each had seven differences. The results of this study indicate that variability exists among the gene content and arrangements within Type I R-M loci may provide an additional level of divergence between pneumococcal strains, such that phase variation-mediated control of virulence factors may vary significantly between individual strains. These findings are consistent with presently available transcript profile data.

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Characterization of a restriction modification system from the commensal Escherichia coli strain A0 34/86 (O83:K24:H31)

Cited by 5 publications

References 41 publications

Isolation and characterization of a novel Escherichia coli O157:H7-specific phage as a biocontrol agent

Isolation and characterization of a novel Escherichia coli O157:H7-specific phage as a biocontrol agent

Origins of bacterial diversity through horizontal genetic transfer and adaptation to new ecological niches

Comparative Analysis of Streptococcus pneumoniae Type I Restriction-Modification Loci: Variation in hsdS Gene Target Recognition Domains

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