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

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.Staphylococcus aureus is a commensal of the human nose and a common cause of both hospital-and community-acquired infection. It is becoming increasingly virulent and resistant to antibiotics due to the horizontal transfer of mobile genetic elements (MGE) encoding virulence and resistance genes (17). S. aureus can be classified into approximately 10 dominant lineages, each with unique surface protein profiles and each capable of causing disease (18). In addition, approximately 15% of any S. aureus genome consists of MGE, such as bacteriophage, transposons, plasmids, and pathogenicity islands (17, 18). These elements may be transferred horizontally between isolates at high frequency, both in the laboratory and in vivo (19,21). However, this is not reflected in the epidemiological spread of resistance and virulence genes among naturally occurring S. aureus strains. For example, the transfer of vanA to S. aureus from vancomycin-resistant enterococci has been exceedingly slow (only four cases) given the high incidence of patients harboring both vancomycin-resistant enterococci and S. aureus and treated with vancomycin (30). Another example is that over more than 40 years, only some S. aureus lineages have acquired SCCmec elements (12, 25) despite the widespread use of methicillin-type antibiotics. Another example is that virulence genes in S. aureus carried on MGE include the Panto...

Staphylococcus aureus host specificity: comparative genomics of human versus animal isolates by multi-strain microarray

“…This confirmed our earlier hypothesis that each lineage has a unique sau1hsdS gene that encodes Sau1 restriction-modification specificity, which then contributes to the relatively independent evolution of each lineage (see Discussion) (Waldron & Lindsay, 2006). Sequencing revealed that sau1hsdS1 genes of ST151 (CC151), ST771 (CC133) and ST130 (CC130) have similar conserved regions to the human isolates, mainly at the short 59 end known otherwise as the proximal conserved region, but had novel variable regions predicted to code the binding region to specific DNA sequences (data not shown).…”

“…These sequenced strains are all from humans and correspond to lineages CC1, CC5, CC8 and CC30. The microarray was also designed to include spots corresponding to putative target recognition domain (TRD) regions of sau1hsd1 that show major sequence variation, as described by Waldron & Lindsay (2006). PCR products were printed in duplicate on GAPS slides (Corning).…”

“…It can be argued that a tree, or any other simplified representation of relatedness, is insufficient to show true relatedness of S. aureus isolates that are phylogenetically very diverse and have evolved through frequent horizontal transfer or point mutation at multiple sites throughout the chromosome. Our current understanding of S. aureus population structure suggests each lineage has evolved relatively independently of the other lineages due to restricted horizontal transfer controlled by the Sau1 restriction-modification system, but that infrequent horizontal transfer occurs between lineages (Waldron & Lindsay, 2006). Fig.…”

“…We have recently reported a restriction-modification system in S. aureus, Sau1 (or SauI1) that controls MGE transfer between isolates of different lineages (Waldron & Lindsay, 2006). Sau1 encodes a restriction enzyme that recognizes un-modified foreign DNA and digests it, reducing the frequency of horizontal transfer of MGE, which is likely to contribute to the independent evolution of lineages.…”

“…The emergence of increasingly virulent strains of S. aureus in humans is also being reported, such as the community-acquired (CA-)MRSA that produces PantonValentine leukocidin (PVL) toxin. PVL (encoded by PVluk) and other known toxins such as toxic shock syndrome toxin (tst) and enterotoxin A (eta) are encoded on MGEs such as bacteriophage and S. aureus pathogenicity islands (SaPI), and also transfer horizontally between S. aureus isolates, leading to the emergence of new clones with novel clinical implications (Lindsay & Holden, 2006;Waldron & Lindsay, 2006). The biggest concern is the potential transfer of vancomycin resistance (vanA) from vancomycin-resistant enterococci (VRE) to human S. aureus; since VRE are found in the agricultural setting (Witte, 2000), this is a potential locale for the emergence of fully vancomycinresistant S. aureus (VRSA), which would be a major catastrophe for human healthcare.…”