scholarly journals To Defend or Not To Defend: That’s the Question

mSphere ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Sriram Varahan ◽  
Lynn E. Hancock
Keyword(s):  
Antibiotic Resistance Genes ◽  
Adaptive Immune System ◽  
Opportunistic Pathogen ◽  
Modification System ◽  
Content Type ◽  
Adaptive Immune ◽  
Restriction Modification System ◽  
Short Palindromic Repeat ◽  
Evolution Of Resistance ◽  
Restriction Modification

ABSTRACT Enterococcus faecalis is an opportunistic pathogen and is one of the leading causes of nosocomial infections. E. faecalis harbors a number of antibiotic resistance genes, and most of these are present on mobile genetic elements (MGEs) that can be disseminated within the species, as well as to other members of the human microflora. In an article by Price and colleagues [V. J. Price et al., mSphere 1(3):e00064-16, 2016, http://dx.doi.org/10.1128/mSphere.00064-16 ], the authors demonstrated how E. faecalis uses a restriction-modification system along with a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas to function as a bacterial innate and adaptive immune system to regulate the influx of MGEs. The absence of these systems in high-risk hospital-adapted lineages of E. faecalis, including the prototypical V583 strain, appears to allow the ready acquisition of new traits that aid in the adaptation to new environmental stresses, including the evolution of resistance to many of our best antibiotics.

scholarly journals The EcoKI Type I Restriction-Modification System in Escherichia coli Affects but Is Not an Absolute Barrier for Conjugation

2014 ◽  
Vol 197 (2) ◽  
pp. 337-342 ◽  
Author(s):  
Louise Roer ◽  
Frank M. Aarestrup ◽  
Henrik Hasman
Keyword(s):  
Escherichia Coli ◽  
Rapid Evolution ◽  
Type I ◽  
Modification System ◽  
Major Barrier ◽  
Exogenous Dna ◽  
Content Type ◽  
Restriction Modification System ◽  
K 12 ◽  
Restriction Modification

The rapid evolution of bacteria is crucial to their survival and is caused by exchange, transfer, and uptake of DNA, among other things. Conjugation is one of the main mechanisms by which bacteria share their DNA, and it is thought to be controlled by varied bacterial immune systems. Contradictory results about restriction-modification systems based on phenotypic studies have been presented as reasons for a barrier to conjugation with and other means of uptake of exogenous DNA. In this study, we show that inactivation of the R.EcoKI restriction enzyme in strainEscherichia coliK-12 strain MG1655 increases the conjugational transfer of plasmid pOLA52, which carriers two EcoKI recognition sites. Interestingly, the results were not absolute, and uptake of unmethylated pOLA52 was still observed in the wild-type strain (with an intacthsdRgene) but at a reduction of 85% compared to the uptake of the mutant recipient with a disruptedhsdRgene. This leads to the conclusion that EcoKI restriction-modification affects the uptake of DNA by conjugation but is not a major barrier to plasmid transfer.

scholarly journals Deletion of the Zinc Transporter Lipoprotein AdcAII Causes Hyperencapsulation of Streptococcus pneumoniae Associated with Distinct Alleles of the Type I Restriction-Modification System

mBio ◽  
2020 ◽  
Vol 11 (2) ◽  
Author(s):  
Claire Durmort ◽  
Giuseppe Ercoli ◽  
Elisa Ramos-Sevillano ◽  
Suneeta Chimalapati ◽  
Richard D. Haigh ◽  
...  
Keyword(s):  
Streptococcus Pneumoniae ◽  
Mouse Models ◽  
Zinc Uptake ◽  
Invasive Infection ◽  
Type I ◽  
Modification System ◽  
Content Type ◽  
Restriction Modification System ◽  
Capsule Thickness ◽  
Restriction Modification

ABSTRACT The capsule is the dominant Streptococcus pneumoniae virulence factor, yet how variation in capsule thickness is regulated is poorly understood. Here, we describe an unexpected relationship between mutation of adcAII, which encodes a zinc uptake lipoprotein, and capsule thickness. Partial deletion of adcAII in three of five capsular serotypes frequently resulted in a mucoid phenotype that biochemical analysis and electron microscopy of the D39 adcAII mutants confirmed was caused by markedly increased capsule thickness. Compared to D39, the hyperencapsulated ΔadcAII mutant strain was more resistant to complement-mediated neutrophil killing and was hypervirulent in mouse models of invasive infection. Transcriptome analysis of D39 and the ΔadcAII mutant identified major differences in transcription of the Sp_0505-0508 locus, which encodes an SpnD39III (ST5556II) type I restriction-modification system and allelic variation of which correlates with capsule thickness. A PCR assay demonstrated close linkage of the SpnD39IIIC and F alleles with the hyperencapsulated ΔadcAII strains. However, transformation of ΔadcAII with fixed SpnD39III alleles associated with normal capsule thickness did not revert the hyperencapsulated phenotype. Half of hyperencapsulated ΔadcAII strains contained the same single nucleotide polymorphism in the capsule locus gene cps2E, which is required for the initiation of capsule synthesis. These results provide further evidence for the importance of the SpnD39III (ST5556II) type I restriction-modification system for modulating capsule thickness and identified an unexpected linkage between capsule thickness and mutation of ΔadcAII. Further investigation will be needed to characterize how mutation of adcAII affects SpnD39III (ST5556II) allele dominance and results in the hyperencapsulated phenotype. IMPORTANCE The Streptococcus pneumoniae capsule affects multiple interactions with the host including contributing to colonization and immune evasion. During infection, the capsule thickness varies, but the mechanisms regulating this are poorly understood. We have identified an unsuspected relationship between mutation of adcAII, a gene that encodes a zinc uptake lipoprotein, and capsule thickness. Mutation of adcAII resulted in a striking hyperencapsulated phenotype, increased resistance to complement-mediated neutrophil killing, and increased S. pneumoniae virulence in mouse models of infection. Transcriptome and PCR analysis linked the hyperencapsulated phenotype of the ΔadcAII strain to specific alleles of the SpnD39III (ST5556II) type I restriction-modification system, a system which has previously been shown to affect capsule thickness. Our data provide further evidence for the importance of the SpnD39III (ST5556II) type I restriction-modification system for modulating capsule thickness and identify an unexpected link between capsule thickness and ΔadcAII, further investigation of which could further characterize mechanisms of capsule regulation.

scholarly journals Genome analysis of lactic acid bacterial strains selected as potential starters for traditional Slovakian bryndza cheese

2018 ◽  
Vol 366 (Supplement_1) ◽  
pp. i3-i9
Author(s):  
Barbora Markusková ◽  
Aneta Lichvariková ◽  
Tomáš Szemes ◽  
Janka Koreňová ◽  
Tomáš Kuchta ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Lactic Acid ◽  
Biogenic Amines ◽  
Antibiotic Resistance Genes ◽  
Bacterial Strains ◽  
Modification System ◽  
Restriction Modification System ◽  
Lactobacillus Paraplantarum ◽  
Genes Encoding ◽  
Restriction Modification

ABSTRACT Genomes of 21 strains of lactic acid bacteria isolated from Slovakian traditional cheeses were sequenced on an Illumina MiSeq platform. Subsequently, they were analysed regarding taxonomic classification, presence of genes encoding defence systems, antibiotic resistance and production of biogenic amines. Thirteen strains were found to carry genes encoding at least one bacteriocin, 18 carried genes encoding at least one restriction–modification system, all strains carried 1–6 prophages and 9 strains had CRISPR-Cas systems. CRISPR-Cas type II-A was the most common, containing 0–24 spacers. Only 10% spacers were found to be homological to known bacteriophage or plasmid sequences in databases. Two Enterococcus faecium strains and a Lactococcus lactis strain carried antibiotic resistance genes. Genes encoding for ornithine decarboxylase were detected in four strains and genes encoding for agmatine deiminase were detected in four strains. Lactobacillus paraplantarum 251 L appeared to be the most interesting strain, as it contained genes encoding for two bacteriocins, a restriction–modification system, two CRISPR-Cas systems, four prophages and no genes connected with antibiotic resistance or production of biogenic amines.

scholarly journals A Novel Restriction-Modification System Is Responsible for Temperature-Dependent Phage Resistance in Listeria monocytogenes ECII

2012 ◽  
Vol 78 (6) ◽  
pp. 1995-2004 ◽  
Author(s):  
Jae-Won Kim ◽  
Vikrant Dutta ◽  
Driss Elhanafi ◽  
Sangmi Lee ◽  
Jason A. Osborne ◽  
...  
Keyword(s):  
Listeria Monocytogenes ◽  
Low Temperatures ◽  
Phage Resistance ◽  
Type Ii ◽  
Temperature Dependent ◽  
Epidemic Clone ◽  
Modification System ◽  
Content Type ◽  
Restriction Modification System ◽  
Restriction Modification

ABSTRACTListeria monocytogenesepidemic clone II (ECII) strains are unusual in being completely resistant to phage when grown at low temperatures (≤30°C). In the current study we constructed and characterized amariner-based mutant (J46C) of the ECII strain H7550-CdSthat lacked temperature-dependent resistance to phage. The transposon was localized in LMOh7858_2753 (open reading frame [ORF] 2753), a member of a 12-ORF genomic island unique to ECII strains. ORF 2753 and ORF 2754 exhibited homologies to restriction endonucleases and methyltransferases associated with type II restriction-modification (RM) systems.In silico-based predictions of the recognition site for this putative RM system were supported by resistance of DNA from ECII strains to digestion by BfuI, a type II restriction enzyme specific for GTATCC (N6/5). Similarly to J46C, a mutant harboring an in-frame deletion of ORF 2753 was susceptible to phage regardless of temperature of growth (25°C or 37°C). Genetic complementation restored phage resistance in 25°C-grown cells of ORF 2753 mutants. Reverse transcription (RT) and quantitative real-time PCR data suggested enhanced transcription of ORF 2753 at low temperatures (≤25°C) compared to 37°C. In contrast, available transcriptional data suggested that the putative methyltransferase (ORF 2754) was constitutively expressed at all tested temperatures (4 to 37°C). Thus, temperature-dependent resistance ofL. monocytogenesECII to phage is mediated by temperature-dependent expression of the restriction endonuclease associated with a novel RM system (LmoH7) unique to this epidemic clone.

scholarly journals Complete Genome Sequence of Microbacterium foliorum NRRL B-24224, a Host for Bacteriophage Discovery

2019 ◽  
Vol 8 (5) ◽  
Author(s):  
Daniel A. Russell ◽  
Rebecca A. Garlena ◽  
Graham F. Hatfull
Keyword(s):  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Type Strain ◽  
Modification System ◽  
Content Type ◽  
Restriction Modification System ◽  
Restriction Modification

We report the complete annotated genome sequence of Microbacterium foliorum NRRL B-24224, a type strain isolated from the phyllosphere of grasses and a commonly used host for bacteriophage discovery. The genome contains no identifiable prophage or CRISPR or restriction-modification system, which suggests that it may continue to be a fruitful host for phage discovery.

scholarly journals Extreme C-to-A Hypermutation at a Site of Cytosine-N4 Methylation

mBio ◽  
2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Joshua L. Cherry
Keyword(s):  
Mutation Rate ◽  
Raw Material ◽  
Modification System ◽  
Content Type ◽  
Restriction Modification System ◽  
Naturally Occurring ◽  
Type Gene ◽  
A Site ◽  
Restriction Modification ◽  
Shed Light

ABSTRACT Methylation of cytosine in DNA at position C5 increases the rate of C→T mutations in bacteria and eukaryotes. Methylation at the N4 position, employed by some restriction-modification systems, is not known to increase the mutation rate. Here, I report that a Salmonella enterica Type III restriction-modification system that includes a cytosine-N4 methyltransferase causes an enormous increase in the rate of mutation of the methylated cytosines, which occur at the overlined C in the motif CACC̅GT. Mutations consist mainly of C→A transversions, the rate of which is increased ∼500-fold by the restriction-modification system. The rate of C→T transitions is also increased and somewhat exceeds that at C5-methylated cytosines in Dcm sites. Two other Salmonella N4 methyltransferases investigated do not have such dramatic effects, although in one case there is a modest increase in C→A mutations along with an increase in C→T mutations. The sensitivity of the C→A rate to orientation with respect to both DNA replication and transcription is higher at hypermutable sites than at other cytosines, suggesting a fundamental mechanistic difference between hypermutation and ordinary mutation. IMPORTANCE Mutation produces the raw material for adaptive evolution but also imposes a burden because most mutations are deleterious. The rate of mutation at a particular site is affected by a variety of factors. In both prokaryotes and eukaryotes, methylation of C at the C5 position, a naturally occurring DNA modification, greatly increases the rate of C→T mutation. A distinct C modification that occurs in prokaryotes, methylation at N4, is not known to increase mutation rate. Here, I report that a bacterial restriction-modification system, found in some Salmonella bacteria, increases the rate of C→A mutation by a factor of 500 at sites that it methylates at N4. This rate increase is much greater than that caused by C5 methylation. Although fewer than 1 in 1,600 positions analyzed are methylation sites, over 10% of all mutations occur at these sites. Like other examples of extremely high mutation rate, whether naturally occurring or the result of laboratory mutation, this phenomenon may shed light on the mechanism of mutation in general.

Cloning the KpnI restriction-modification system in Escherichia coli

Gene ◽  
1991 ◽  
Vol 97 (1) ◽  
pp. 97-102 ◽  
Author(s):  
Alan W. Hammond ◽  
Gary F. Gerard ◽  
Deb K. Chatterjee
Keyword(s):  
Escherichia Coli ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals A putative mobile genetic element carrying a novel type IIF restriction-modification system (PluTI)

2010 ◽  
Vol 38 (9) ◽  
pp. 3019-3030 ◽  
Author(s):  
Feroz Khan ◽  
Yoshikazu Furuta ◽  
Mikihiko Kawai ◽  
Katarzyna H. Kaminska ◽  
Ken Ishikawa ◽  
...  
Keyword(s):  
Mobile Genetic Element ◽  
Genetic Element ◽  
Modification System ◽  
Restriction Modification System ◽  
Restriction Modification

scholarly journals CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis

mSphere ◽  
2016 ◽  
Vol 1 (3) ◽  
Author(s):  
Valerie J. Price ◽  
Wenwen Huo ◽  
Ardalan Sharifi ◽  
Kelli L. Palmer
Keyword(s):  
Antibiotic Resistance ◽  
High Risk ◽  
Enterococcus Faecalis ◽  
Resistance Genes ◽  
Treatment Options ◽  
Antibiotic Resistance Genes ◽  
Multidrug Resistant ◽  
Content Type ◽  
New Genes ◽  
Restriction Modification

ABSTRACT Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics. Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis. IMPORTANCE Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.

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