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

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.

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

Journal of Bacteriology ◽

10.1128/jb.02418-14 ◽

2014 ◽

Vol 197 (2) ◽

pp. 337-342 ◽

Cited By ~ 27

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.

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Complete Genome Sequence of Brevibacterium linens SMQ-1335

Genome Announcements ◽

10.1128/genomea.01242-16 ◽

2016 ◽

Vol 4 (6) ◽

Cited By ~ 1

Author(s):

Alessandra G. de Melo ◽

Simon J. Labrie ◽

Jeannot Dumaresq ◽

Richard J. Roberts ◽

Denise M. Tremblay ◽

...

Keyword(s):

Complete Genome Sequence ◽

Open Reading Frames ◽

Type I ◽

Industrial Strain ◽

Modification System ◽

Brevibacterium Linens ◽

Restriction Modification System ◽

New Type ◽

Restriction Modification ◽

Reading Frames

Brevibacterium linens is one of the main bacteria found in the smear of surface-ripened cheeses. The genome of the industrial strain SMQ-1335 was sequenced using PacBio. It has 4,209,935 bp, a 62.6% G+C content, 3,848 open reading frames, and 61 structural RNAs. A new type I restriction-modification system was identified.

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DNA methylation from a Type I restriction modification system influences gene expression and virulence in Streptococcus pyogenes

PLoS Pathogens ◽

10.1371/journal.ppat.1007841 ◽

2019 ◽

Vol 15 (6) ◽

pp. e1007841 ◽

Cited By ~ 9

Author(s):

Taylor M. Nye ◽

Kristin M. Jacob ◽

Elena K. Holley ◽

Juan M. Nevarez ◽

Suzanne Dawid ◽

...

Keyword(s):

Gene Expression ◽

Dna Methylation ◽

Streptococcus Pyogenes ◽

Type I ◽

Modification System ◽

Restriction Modification System ◽

Restriction Modification

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Unstable chromosome rearrangements in Staphylococcus aureus cause phenotype switching associated with persistent infections

Proceedings of the National Academy of Sciences ◽

10.1073/pnas.1904861116 ◽

2019 ◽

Vol 116 (40) ◽

pp. 20135-20140 ◽

Cited By ~ 17

Author(s):

Romain Guérillot ◽

Xenia Kostoulias ◽

Liam Donovan ◽

Lucy Li ◽

Glen P. Carter ◽

...

Keyword(s):

Staphylococcus Aureus ◽

Genetic Basis ◽

Host Cells ◽

Type I ◽

Modification System ◽

Persistent Infections ◽

Restriction Modification System ◽

Long Read ◽

Small Colony ◽

Restriction Modification

Staphylococcus aureus small-colony variants (SCVs) are associated with unusually chronic and persistent infections despite active antibiotic treatment. The molecular basis for this clinically important phenomenon is poorly understood, hampered by the instability of the SCV phenotype. Here we investigated the genetic basis for an unstable S. aureus SCV that arose spontaneously while studying rifampicin resistance. This SCV showed no nucleotide differences across its genome compared with a normal-colony variant (NCV) revertant, yet the SCV presented the hallmarks of S. aureus linked to persistent infection: down-regulation of virulence genes and reduced hemolysis and neutrophil chemotaxis, while exhibiting increased survival in blood and ability to invade host cells. Further genome analysis revealed chromosome structural variation uniquely associated with the SCV. These variations included an asymmetric inversion across half of the S. aureus chromosome via recombination between type I restriction modification system (T1RMS) genes, and the activation of a conserved prophage harboring the immune evasion cluster (IEC). Phenotypic reversion to the wild-type–like NCV state correlated with reversal of the chromosomal inversion (CI) and with prophage stabilization. Further analysis of 29 complete S. aureus genomes showed strong signatures of recombination between hsdMS genes, suggesting that analogous CI has repeatedly occurred during S. aureus evolution. Using qPCR and long-read amplicon deep sequencing, we detected subpopulations with T1RMS rearrangements causing CIs and prophage activation across major S. aureus lineages. Here, we have discovered a previously unrecognized and widespread mechanism of reversible genomic instability in S. aureus associated with SCV generation and persistent infections.

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

mSphere ◽

10.1128/msphere.00127-16 ◽

2016 ◽

Vol 1 (3) ◽

Cited By ~ 2

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.

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Plasmid R16 ArdA Protein Preferentially Targets Restriction Activity of the Type I Restriction-Modification System EcoKI

Journal of Bacteriology ◽

10.1128/jb.185.6.2022-2025.2003 ◽

2003 ◽

Vol 185 (6) ◽

pp. 2022-2025 ◽

Cited By ~ 17

Author(s):

Angela T. Thomas ◽

William J. Brammar ◽

Brian M. Wilkins

Keyword(s):

Type I ◽

Bacterial Conjugation ◽

Modification System ◽

Restriction Modification System ◽

Modification Activity ◽

Restriction Modification

ABSTRACT The ArdA antirestriction protein of the IncB plasmid R16 selectively inhibited the restriction activity of EcoKI, leaving significant levels of modification activity under conditions in which restriction was almost completely prevented. The results are consistent with the hypothesis that ArdA functions in bacterial conjugation to allow an unmodified plasmid to evade restriction in the recipient bacterium and yet acquire cognate modification.

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Improved transformation efficiency of group A Streptococcus by inactivation of a type I restriction modification system

PLoS ONE ◽

10.1371/journal.pone.0248201 ◽

2021 ◽

Vol 16 (4) ◽

pp. e0248201

Author(s):

Meredith B. Finn ◽

Kathryn M. Ramsey ◽

Hunter J. Tolliver ◽

Simon L. Dove ◽

Michael R. Wessels

Keyword(s):

Genetic Transformation ◽

Parent Strain ◽

Transformation Efficiency ◽

Genetic Manipulation ◽

Spontaneous Mutation ◽

Type I ◽

Modification System ◽

Restriction Modification System ◽

Group A ◽

Restriction Modification

Streptococcus pyogenes or group A Streptococcus (GAS) is a leading cause of bacterial pharyngitis, skin and soft tissue infections, life-threatening invasive infections, and the post-infectious autoimmune syndromes of acute rheumatic fever and post-streptococcal glomerulonephritis. Genetic manipulation of this important pathogen is complicated by resistance of the organism to genetic transformation. Very low transformation efficiency is attributed to recognition and degradation of introduced foreign DNA by a type I restriction-modification system encoded by the hsdRSM locus. DNA sequence analysis of this locus in ten GAS strains that had been previously transformed with an unrelated plasmid revealed that six of the ten harbored a spontaneous mutation in hsdR, S, or M. The mutations were all different, and at least five of the six were predicted to result in loss of function of the respective hsd gene product. The unexpected occurrence of such mutations in previously transformed isolates suggested that the process of transformation selects for spontaneous inactivating mutations in the Hsd system. We investigated the possibility of exploiting the increased transformability of hsd mutants by constructing a deletion mutation in hsdM in GAS strain 854, a clinical isolate representative of the globally dominant M1T1 clonal group. Mutant strain 854ΔhsdM exhibited a 5-fold increase in electrotransformation efficiency compared to the wild type parent strain and no obvious change in growth or off-target gene expression. We conclude that genetic transformation of GAS selects for spontaneous mutants in the hsdRSM restriction modification system. We propose that use of a defined hsdM mutant as a parent strain for genetic manipulation of GAS will enhance transformation efficiency and reduce the likelihood of selecting spontaneous hsd mutants with uncharacterized genotypes.

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Characterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci

mSphere ◽

10.1128/msphere.00799-21 ◽

2021 ◽

Author(s):

Sruti DebRoy ◽

William C. Shropshire ◽

Chau Nguyen Tran ◽

Haiping Hao ◽

Marc Gohel ◽

...

Keyword(s):

Dna Methylation ◽

Epigenetic Modification ◽

Type I ◽

Whole Genome ◽

Group A Streptococci ◽

Modification System ◽

Restriction Modification System ◽

Group A ◽

Restriction Modification

The advent of whole-genome approaches capable of detecting DNA methylation has markedly expanded appreciation of the diverse roles of epigenetic modification in prokaryotic physiology. For example, recent studies have suggested that DNA methylation impacts gene expression in some streptococci.

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