Temperate bacteriophages play an important role in the pathogenicity of Staphylococcus aureus, for instance, by mediating the horizontal gene transfer of virulence factors. Here we established a classification scheme for staphylococcal prophages of the major Siphoviridae family based on integrase gene polymorphism. Seventy-one published genome sequences of staphylococcal phages were clustered into distinct integrase groups which were related to the chromosomal integration site and to the encoded virulence gene content. Analysis of three marker modules (lysogeny, tail, and lysis) for phage functional units revealed that these phages exhibit different degrees of genome mosaicism. The prevalence of prophages in a representative S. aureus strain collection consisting of 386 isolates of diverse origin was determined. By linking the phage content to dominant S. aureus clonal complexes we could show that the distribution of bacteriophages varied remarkably between lineages, indicating restriction-based barriers. A comparison of colonizing and invasive S. aureus strain populations revealed that hlb-converting phages were significantly more frequent in colonizing strains.Staphylococcus aureus asymptomatically colonizes the anterior nares of humans but also causes a wide spectrum of acute and chronic diseases. Most of the dissimilarity between S. aureus strains is due to the presence of mobile genetic elements such as plasmids, bacteriophages, pathogenicity islands, transposons, and insertion sequences (2,14,19,23). Many virulence factors are encoded on such mobile elements (3,6,17,26,27,35). In particular, bacteriophages play an important role in the pathogenicity of S. aureus either by carrying accessory virulence factors such as Panton-Valentine leukocidin (PVL) (encoded by the luk-PV operon), staphylokinase (encoded by sak), enterotoxin A (encoded by sea), and exfoliative toxin A (encoded by eta) or by interrupting chromosomal virulence genes such as those for ␤-hemolysin (hlb) and lipase (geh) upon insertion. Additionally, phages are the primary vehicle of lateral gene transfer between S. aureus strains, providing the species with the potential for broad genetic variation. We could show that phages increase the genome plasticity of S. aureus during infection, facilitating the adaptation of the pathogen to various host conditions (11,12).Despite the obvious importance of phages for the biology of S. aureus, epidemiological data on the prevalence of phages in this species are limited (28, 33). More than 80 genome sequences of staphylococcal bacteriophages and prophages are available in the public genome databases. Most published S. aureus phages belong to the Siphoviridae family of temperate, tailed bacterial viruses. Traditionally, S. aureus phages were characterized according to their lytic activity, morphology, and serological properties (1, 28). Today, the temperate phages in clinical S. aureus isolates can by identified with a multiplex PCR strategy, which is based on sequence differences between viral genes codin...

The repressor CodY is reported to inhibit metabolic genes mainly involved in nitrogen metabolism. We analyzed codY mutants from three unrelated Staphylococcus aureus strains (Newman, UAMS-1, and RN1HG). The mutants grew more slowly than their parent strains in a chemically defined medium. However, only codY mutants were able to grow in medium lacking threonine. An excess of isoleucine resulted in growth inhibition in the wild type but not in the codY mutants, indicating that isoleucine plays a role in CodY-dependent repression. Prototypic CodY-repressed genes including the virulence regulator agr are repressed after up-shift with isoleucine. The CodY-dependent repression of agr is consistent with the concomitant influence of CodY on typical agr-regulated genes such as cap, spa, fnbA, and coa. However, some of these virulence genes (e.g., cap, fnbA, and spa) were also regulated by CodY in an agr-negative background. Microarray analysis revealed that the large majority of CodY-repressed genes were involved in amino acid metabolism; CodY-activated genes were mainly involved in nucleotide metabolism or virulence. In summary, CodY in S. aureus not only acts as a repressor for genes involved in nitrogen metabolism but also contributes to virulence gene regulation by supporting as well as substituting for agr function.Staphylococcus aureus asymptomatically colonizes the nares of healthy individuals but also causes a variety of infections in humans. Regulatory loci are necessary for the adaptation of the organism to the different nutrient limitations and stress conditions encountered in vivo. This allows the pathogen to survive and/or multiply in different compartments during colonization and infection processes. However, knowledge of the environmental conditions encountered in vivo is still incomplete, and the interaction of regulatory circuits leading to metabolic adaptation and differential expression of virulence factors remains poorly understood. The in vitro expression of most virulence factors is tightly related to the growth phase. For instance protein A (encoded by spa), fibronectin-binding proteins (encoded by fnbA and fnbB), and coagulase (encoded by coa) are expressed during the exponential growth phase, whereas most secreted proteins (e.g., hemolysins, enterotoxins, and proteases) and the capsule (enzymes encoded by the capA-capP operon) are expressed mainly during the postexponential phase (22, 37). In many bacteria, the transition to postexponential growth is accompanied by a profound reprogramming of gene expression. Several underlying mechanisms are thought to be involved in such a transition. Quorum sensing allows the bacteria to detect their own density. Basically, bacteria secrete small diffusible molecules (autoinducers) which are also effectors of their own synthesis. Upon passing a critical concentration threshold, the autoinducers activate specific transcriptional regulators, leading to the differential expression of target genes. The agr locus of S. aureus is a prototypic quorum-sensing system m...

The two-component system SaeRS of Staphylococcus aureus is closely involved in the regulation of major virulence factors. However, little is known about the signals leading to saeRS activation. A total of four overlapping transcripts (T1 to T4) from three different transcription starting points are expressed in the sae operon. We used a ␤-galactosidase reporter assay to characterize the putative promoter regions within the saeRS upstream region. The main transcript T2 is probably generated by endoribonucleolytic processing of the T1 transcript. Only two distinct promoter elements (P1 and P3) could be detected within the saeRS upstream region. The P3 promoter, upstream of saeRS, generates the T3 transcript, includes a cis-acting enhancer element and is repressed by saeRS. The most distal P1 promoter is strongly autoregulated, activated by agr, and repressed by sigma factor B. In strain Newman a mutation within the histidine kinase SaeS leads to a constitutively activated sae system. Evaluation of different external signals revealed that the P1 promoter in strain ISP479R and strain UAMS-1 is inhibited by low pH and high NaCl concentrations but activated by hydrogen peroxide. The most prominent induction of P1 was observed at subinhibitory concentrations of ␣-defensins in various S. aureus strains, with the exception of strain ISP479R and strain COL. P1 was not activated by the antimicrobial peptides LL37 and daptomycin. In summary, the results indicate that the sensor molecule SaeS is activated by alteration within the membrane allowing the pathogen to react to phagocytosis related effector molecules.Staphylococcus aureus asymptomatically colonizes the noses of healthy individuals but also causes a variety of infections in humans. Polymorphonuclear neutrophils (PMNs) provide an effective line of defense against infections. However, S. aureus has developed a variety of mechanisms to avoid being killed by PMNs, including the expression of a number of immune modulators and toxins (for a review, see reference 8). The expression of most virulence and adherence factors is directly or indirectly influenced by diverse regulators such as agr, the alternative sigma factor B (SigB), sarA homologues or sae (for reviews, see references 4, 6, 17, and 32). Within this network sae appears to be a central downstream regulator that controls the expression of major virulence genes such as hla (coding for alpha-hemolysin), coa (coding for coagulase), or fnbA (coding for fibronectin-binding protein A) (11,33,39). Microarray analysis and proteomics have revealed that most of the genes activated by sae are involved in bacterial adhesion, immune modulation, or toxicity (25,29,38). In addition, the importance of gene regulation by sae in vivo was shown in several animal models (3,15,16,29,43).The sae locus consists of four open reading frames, two of which (saeR and saeS) show strong sequence homology to response regulators and to histidine kinases (HKs) of bacterial two-component regulators (10). Two additional open reading frames, saeP ...