scholarly journals Sau1: a Novel Lineage-Specific Type I Restriction-Modification System That Blocks Horizontal Gene Transfer into Staphylococcus aureus and between S. aureus Isolates of Different Lineages

2006 ◽  
Vol 188 (15) ◽  
pp. 5578-5585 ◽  
Author(s):  
Denise E. Waldron ◽  
Jodi A. Lindsay
Keyword(s):  
Staphylococcus Aureus ◽  
Resistance Genes ◽  
Genetic Manipulation ◽  
Type I ◽  
Sequence Specificity ◽  
Modification System ◽  
Major Mechanism ◽  
Restriction Modification System ◽  
Resistance Transfer ◽  
Restriction Modification

ABSTRACT The Sau1 type I restriction-modification system is found on the chromosome of all nine sequenced strains of Staphylococcus aureus and includes a single hsdR (restriction) gene and two copies of hsdM (modification) and hsdS (sequence specificity) genes. The strain S. aureus RN4220 is a vital intermediate for laboratory S. aureus manipulation, as it can accept plasmid DNA from Escherichia coli. We show that it carries a mutation in the sau1hsdR gene and that complementation restored a nontransformable phenotype. Sau1 was also responsible for reduced conjugative transfer from enterococci, a model of vancomycin resistance transfer. This may explain why only four vancomycin-resistant S. aureus strains have been identified despite substantial selective pressure in the clinical setting. Using a multistrain S. aureus microarray, we show that the two copies of sequence specificity genes (sau1hsdS1 and sau1hsdS2) vary substantially between isolates and that the variation corresponds to the 10 dominant S. aureus lineages. Thus, RN4220 complemented with sau1hsdR was resistant to bacteriophage lysis but only if the phage was grown on S. aureus of a different lineage. Similarly, it could be transduced with DNA from its own lineage but not with the phage grown on different S. aureus lineages. Therefore, we propose that Sau1 is the major mechanism for blocking transfer of resistance genes and other mobile genetic elements into S. aureus isolates from other species, as well as for controlling the spread of resistance genes between isolates of different S. aureus lineages. Blocking Sau1 should also allow genetic manipulation of clinical strains of S. aureus.

scholarly journals Inactivation of the SauI Type I Restriction-Modification System Is Not Sufficient To Generate Staphylococcus aureus Strains Capable of Efficiently Accepting Foreign DNA

2009 ◽  
Vol 75 (10) ◽  
pp. 3034-3038 ◽  
Author(s):  
Helena Veiga ◽  
Mariana G. Pinho
Keyword(s):  
Staphylococcus Aureus ◽  
Genetic Manipulation ◽  
Type I ◽  
Modification System ◽  
Single Strain ◽  
Pathogenic Organism ◽  
Restriction Modification System ◽  
High Transformation ◽  
Foreign Dna ◽  
Restriction Modification

ABSTRACT Genetic manipulation of Staphylococcus aureus is limited by the availability of only a single strain, RN4220, that is capable of easily accepting foreign DNA. Inactivation of the hsdR gene of the SauI type I restriction-modification system was shown previously to be responsible for the high transformation efficiency of RN4220 (D. E. Waldron and J. A. Lindsay, J Bacteriol. 188:5578-5585, 2006). However, deletion of this gene in three different S. aureus strains was not sufficient to make them readily transformable, which would be remarkably useful for genetic studies of this pathogenic organism. These results indicate that another unknown factor(s) is required for the transformable phenotype in S. aureus.

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

2019 ◽  
Vol 116 (40) ◽  
pp. 20135-20140 ◽  
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.

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

PLoS ONE ◽  
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.

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

2021 ◽  
Author(s):  
Meredith B. Finn ◽  
Kathryn M. Ramsey ◽  
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

AbstractStreptococcus 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 transformation 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 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.

scholarly journals Diversification of the restriction–modification system of Streptococcus pyogenes through its acquisition of mobile elements

2020 ◽  
Author(s):  
Atsushi Ota ◽  
Yukiko Nishiuchi ◽  
Noriko Nakanishi ◽  
Yoshio Iijima ◽  
Tomotada Iwamoto ◽  
...  
Keyword(s):  
Streptococcus Pyogenes ◽  
Complete Genome ◽  
Type I ◽  
Sequence Specificity ◽  
Type Ii ◽  
Genome Sequences ◽  
Modification System ◽  
Dna Sequence Specificity ◽  
Restriction Modification System ◽  
Restriction Modification

ABSTRACTRestriction–modification (RM) systems are typically regarded as “primitive immune systems” in bacteria. The roles of methylation in gene regulation, segregation, and mismatch repair are increasingly recognized. To analyze methyltransferase (MTase) diversity in Streptococcus pyogenes, we compared the RM system distribution in eight new complete genome sequences obtained here and in the database-deposited complete genome sequences of 51 strains. The MTase gene distribution showed that type I MTases often change DNA sequence specificity via switching target recognition domains between strains. The type II MTases in the included strains fell into two groups: a prophage-dominant one and a CRISPR-dominant one. Some highly variable type II MTases were found in the prophage region, suggesting that MTases acquired from phage DNA can generate methylome diversity. Additionally, to investigate the possible contribution of DNA methylation to phenotype, we compared the methylomes and transcriptomes from the four most closely related strains, the results of which suggest that phage-derived methylases possibly regulate the methylome, and, hence, regulate expression levels in S. pyogenes. Our findings will benefit further experimental work on the relationship between virulence genes and pathogenicity in S. pyogenes.

scholarly journals Complete Genome Sequence of Brevibacterium linens SMQ-1335

2016 ◽  
Vol 4 (6) ◽  
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.

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

2019 ◽  
Vol 15 (6) ◽  
pp. e1007841 ◽  
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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