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Journal of Bacteriology, July 2007, p. 5119-5129, Vol. 189, No. 14
0021-9193/07/$08.00+0     doi:10.1128/JB.00274-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

Only One of Four Oligopeptide Transport Systems Mediates Nitrogen Nutrition in Staphylococcus aureus

Aurelia Hiron, Elise Borezée-Durant,^,* Jean-Christophe Piard, and Vincent Juillard

Unité Bactéries Lactiques et pathogènes Opportunistes, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas cedex, France

Received 19 February 2007/ Accepted 1 May 2007

Top ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION REFERENCES

 
Oligopeptides internalized by oligopeptide permease (Opp) transporters play key roles in bacterial nutrition, signaling, and virulence. To date, two opp operons, opp-1 and opp-2, have been identified in Staphylococcus aureus. Systematic in silico analysis of 11 different S. aureus genomes revealed the existence of two new opp operons, opp-3 and opp-4, plus an opp-5A gene encoding a putative peptide-binding protein. With the exception of opp-4, the opp operons were present in all S. aureus strains. Within a single strain, the different opp operons displayed little sequence similarity and distinct genetic organization. Transcriptional studies showed that opp-1, opp-2, opp-3, and opp-4 operons were polycistronic and that opp-5A is monocistronic. We designed a minimal chemically defined medium for S. aureus RN6390 and showed that all opp genes were expressed but at different levels. Where tested, OppA protein production paralleled transcriptional profiles. opp-3, which encodes proteins most similar to known peptide transport proteins, displayed the highest expression level and was the only transporter to be regulated by specific amino acids, tyrosine and phenylalanine. Defined deletion mutants in one or several peptide permeases were constructed and tested for their capacity to grow in peptide-containing medium. Among the four putative Opp systems, Opp-3 was the only system able to provide oligopeptides for growth, ranging in length from 3 to 8 amino acids. Dipeptides were imported exclusively by DtpT, a proton-driven di- and tripeptide permease. These data provide a first complete inventory of the peptide transport systems opp and dtpT of S. aureus. Among them, the newly identified Opp-3 appears to be the main Opp system supplying the cell with peptides as nutritional sources.

Top ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION REFERENCES

 
Oligopeptide permeases (Opp) have been identified in numerous gram-negative and -positive bacteria. These transport systems belong to the superfamily of highly conserved ATP-binding cassette transporters (44). Typically, Opp importers comprise a complex of five proteins. The oligopeptide-binding protein OppA is responsible for the capture of peptides from the external medium. OppA is a periplasmic protein in gram-negative bacteria, whereas it is a lipoprotein in gram-positive bacteria. Two integral transmembrane proteins, OppB and OppC, form a channel through the membrane used for peptide translocation. Two membrane-bound cytoplasmic ATP-binding proteins, OppD and OppF, provide energy for peptide transport.

At a genetic level, the five opp genes encoding the transporter are usually organized in an operon, oppABCDF. However, gene organization can vary, or one of the opp genes may be absent (19). Moreover, the number of peptide-binding protein-encoding genes associated with the opp operon is variable from one system to another. The opp operons of Listeria monocytogenes or Lactococcus lactis contain a single copy of oppA (6, 46), whereas two, three, and five distinct oppA genes are associated with the opp operons of Escherichia coli (34), Streptococcus thermophilus (16), and Borrelia burgdorferi (24), respectively.

Opp systems are generally regulated at the transcriptional level. Particular intracellular pools of amino acids, e.g., leucine and alanine in E. coli (2) or branched-chain amino acids in L. lactis (20), regulate oppA expression. Environmental changes have also been shown to influence opp expression. For example, transcription of oppA genes is induced by a temperature down-shift in L. monocytogenes (6) and Bacillus subtilis (7); expression of the E. coli opp operon is up-regulated under anaerobic conditions (2).

A variety of roles have been described for the bacterial Opp systems. The most obvious one is to supply bacteria with essential amino acids, as demonstrated for lactic acid bacteria (15, 25). Duplication of OppA and/or Opp homologues could be explained as a means of increasing peptide transport efficiency and thereby optimizing nutritional function. Besides nutrition, Opp systems might also be involved in various functions such as cell wall turnover in E. coli (34) or peptide-mediated signaling in B. subtilis and Enterococcus faecalis (28). Opp systems also play a role in virulence of some gram-positive pathogenic bacteria by transporting a specific peptide (called a pheromone) that activates a pleiotropic virulence regulon, as demonstrated in the case of Bacillus thuringiensis (18, 43), or by stimulating adherence of pathogenic streptococci to human cells (10, 40).

In Staphylococcus aureus, two putative oligopeptide transport systems, Opp-1 and Opp-2 were suggested to play a role in different infection models (5, 9, 29). S. aureus is a remarkably versatile pathogen, responsible for a broad spectrum of human diseases ranging from superficial skin abscesses to serious infections such as pneumonia, endocarditis, and severe sepsis. This bacterium is one of the main agents of nosocomial and food-borne infections, suggesting its great potential for adaptation. Numerous studies have focused on the identification of virulence genes in S. aureus. However, no detailed analysis of the opp genes of S. aureus has been carried out. We initiated a systematic analysis of these transporters. Our results indicate that S. aureus encodes four distinct putative Opp systems, which differ from one another on the basis of their (i) genetic organization, (ii) amino acid sequence, (iii) regulation of expression, and (iv) physiological roles.

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Bioinformatic procedures. DNA sequence analysis was performed from the genomes of the S. aureus strains JH1 and JH9 (unfinished sequences; accession numbers for JH1, NZ_AAPK00000000 and AAPK00000000; accession numbers for JH9, NZ_AAPL00000000 and AAPL00000000,), NCTC8325 (CP000253 and NC_007795), N315 (25), Mu50 (25), COL (17), MRSA252 (22), MSSA476 (22), MW2 (4), USA300 (13), and RF122 (AJ938182 and NC_007622). Percentages of identity between nucleotide or amino acid sequences were determined using the FASTA sequence comparison program (35) and the AliBee-multiple alignment method (33), respectively. Putative promoter sequences were identified using the BPROM prediction of bacterial promoter program (http://www.softberry.com). Putative terminators of transcription were determined using the RNA secondary structure prediction program (http://www.genebee.msu.su).

Bacterial strain and growth conditions. S. aureus RN6390 (36), a derivative of the clinical strain NCTC8325, was grown aerobically with shaking at 37°C in chemically defined medium (CDM) (45), supplemented with biotin (0.1 mg liter^–1) and calcium panthotenate (2 mg liter^–1). Cultures in CDM were performed either in complete CDM (CM), containing 18 amino acids in their free form, or in minimal CDM (MM) containing 9 amino acids (Glu, Leu, Cys, Met, Gly, Val, Thr, Arg, and Lys). MM medium, designed by studying RN6390 auxotrophy, ensured bacterial growth up to an optical density at 600 nm (OD₆₀₀) of 2. When required, MM was supplemented with 1% (wt/vol) pancreatic enzyme digest of casein (Bacto Tryptone; Difco Laboratories). Cultures in all CDMs were inoculated with cells grown overnight in CM and washed twice in 50 mM phosphate buffer (pH 6.8). For peptide utilization experiments, CM was depleted of the essential amino acid glutamic acid that was supplied in a peptide at a glutamic acid final concentration of 3.5 mM. All peptides were from a commercial source (Sigma, St. Louis, MO).

Construction of peptide transport mutants in S. aureus RN6390. Peptide transport mutants of S. aureus RN6390 were obtained by single or successive gene deletions. In a first step, a recombination cassette was cloned in E. coli using an overlap PCR technique (12, 30). Briefly, two fragments (called boxes A and B, corresponding to upstream and downstream regions of the fragment to be deleted, respectively) were amplified by PCR from RN6390 chromosomal DNA using external primers that incorporate terminal BamHI restriction sites and internal primers that contain 16 complementary nucleotides between boxes A and B (12, 30). Nucleotide primers used for PCR amplification are listed in Table 1. PCR products were purified by agarose gel electrophoresis, quantified, mixed at equal concentrations, and used as a template for a second round of PCR using only the two external primers (overlap PCR). The hybrid PCR product (joining boxes A and B and termed boxAB), which corresponds to the recombination cassette, was cloned into the pCR-Blunt II-TOPO vector (Invitrogen), resulting in plasmid pTOPO::boxAB. The BamHI-boxAB fragment was then purified and cloned into the temperature-sensitive shuttle vector pMAD (3). The resulting plasmid pMAD::boxAB was introduced into S. aureus RN4220 by electroporation, and erythromycin-resistant transformants were selected at 30°C, the permissive temperature for plasmid replication. S. aureus RN6390 was then transformed with pMAD::boxAB purified from RN4220 transformant. Deletion of the chromosomal region was subsequently obtained by double-crossover events as previously described (39). Chromosomal deletions were checked by PCR and Southern blotting of BclI-digested genomic DNA from mutant and wild-type strains with probes specific for boxes A or B.

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TABLE 1. Primers used for deletion of opp-like operons and the dtpT gene of S. aureus RN6390

Production of anti-OppA antibodies. The opp-1A, opp-3A, and opp-4A genes (deprived of signal sequence codons) were amplified by PCR from chromosomal DNA of S. aureus RN6390 using the following primers: opp-1A, 5'-CACCAATAAAGGTTTAGAGGAGAAAAAAG-3' and 5'-TTATTTATACTGCATTTCATTGAATGG-3'; opp-3A, 5'-CACCAATGACGATGGTATTTATTCAGATAAAGG-3' and 5'-TTATTTTTTCTTCTTACCTGTTTC-3'; opp-4A, 5'-CACCAGCAGTAATAAAGATGAAGGAGTAAAAG-3' and 5'-CTAAGCTTCTTTAGTTAAATTATATAAAC-3'. Amplification products were cloned in E. coli BL21(DE3) (Invitrogen) using the bacterial expression vector pET100/D-TOPO (Invitrogen) containing a His₆ tag.

Production of the Opp-1A, Opp-3A, and Opp-4A His₆-tagged proteins was carried out as follows. Cells were grown to an OD₆₀₀ of 0.5 in Luria-Bertani medium containing ampicillin (50 µg ml^–1) at 37°C. Expression of oppA-His₆ recombinant genes was induced for 2 h with isopropyl-ß-D-thiogalactopyranoside (1 mM). Cells were harvested by centrifugation; resuspended (OD₆₀₀ of 50) in 50 mM NaH₂PO₄, 300 mM NaCl, and 10 mM imidazole; and broken using a cell disrupter system (Constant Systems Ltd). Cell debris was removed by centrifugation, and the supernatant was loaded on a His-select nickel affinity resin column (QIAGEN). The His₆-tagged proteins were eluted with an imidazole gradient (20 to 250 mM). Eluted fractions were subjected to sodium dodecyl sulfate (SDS)-polyacrylamide gel electrophoresis (26) and analyzed by Western blotting using monoclonal anti-polyhistidine antibody (Sigma, St. Louis, MO). The OppA-His₆ containing fractions were dialyzed against 50 mM NaH₂PO₄ and 300 mM NaCl and used for custom antibody production in guinea pigs (Centre de Production Animale, Olivet, France). Antisera were tested for their specificity and efficiency using known amounts of purified OppA-His₆ proteins. All were highly specific and produced signals with comparable intensities when used at the same dilution.

Preparation of S. aureus protein extracts and Western blot analyses. Total cell protein extracts were prepared essentially as described previously (39). Briefly, S. aureus cells were harvested by centrifugation, precipitated with 10% (vol/vol) trichloroacetic acid, washed in 80% (vol/vol) acetone, incubated for 90 min at 37°C in the presence of lysostaphin (100 µg ml^–1), and lysed with 2% (vol/vol) SDS. Protein concentration was evaluated using a detergent-compatible assay (Bio-Rad). For each sample, 20 µg of total cell protein extract was loaded and separated on SDS-polyacrylamide gel electrophoresis gels and electrotransferred on Immobilon-FL transfer membrane (Millipore). Opp-1A, Opp-3A, and Opp-4A were detected using corresponding polyclonal guinea pig antibodies (dilution, 1:10,000). Immunodetection was carried out with Alexa Fluor 488 anti-guinea pig immunoglobulin G (Invitrogen), followed by visualization (at 540 nm) using a Fluorimager 595 (Amersham Biosciences). Fluorescence signal was quantified using the Image Quant program (version 5.2; Molecular Dynamics). Each experiment was performed three times with independent protein extracts.

RNA isolation and RT-PCR amplification. Total RNA was extracted from S. aureus RN6390 grown in CDM. Cells were sedimented by centrifugation and resuspended in 500 µl of cold TE buffer (10 mM Tris, 1 mM EDTA, pH 8). Cell suspension was transferred to a microcentrifuge tube containing 0.5 g of glass beads (0.1 mm in diameter), 30 µl of 3 M sodium acetate (pH 5.2), 500 µl of water-saturated phenol-chloroform (5:1), and 30 µl of 10% (vol/vol) SDS. Cells were disrupted using a Fast Prep FP120 system (Bio101 Thermo Electron Corp.). After removal of nonsoluble material (centrifugation at 13,000 x g for 15 min at 4°C), RNA was extracted with 1 volume of phenol-chloroform (5:1) and washed in 1 volume of chloroform. Total RNA was purified using a High Pure RNA Isolation kit (Roche). RNA concentration was evaluated by measuring the OD₂₆₀. Extracts were adjusted to 0.5 µg µl^–1 and tested for DNA contamination by PCR prior to reverse transcription (RT). Annealing of 2 µg of total RNA with random nonamers (CyScribe cDNA Post labeling Kit; Amersham Biosciences) was performed for 10 min at 20°C after denaturation of RNA secondary structures (5 min at 70°C). cDNA synthesis by RT was accomplished at 42°C for 2 h with PowerScript Reverse Transcriptase and Ultrapure deoxynucleoside triphosphate mix (Clontech/Takara Bioscience), followed by enzyme inactivation (15 min at 70°C). For limit dilution (LD) RT-PCR, serial dilutions (1:1, 1:10, 1:100, 1:500, and 1:1000) of cDNA were performed, followed by amplification of each dilution by PCR using the oligonucleotides listed in Table 2. PCR (30 cycles) was performed as follows: 94°C for 30 s, 50°C for 30 s, and 72°C for 1 to 3 min using a Taq Core Kit (Qbiogene). Transcripts of the hu gene were used as internal controls (15). Results were quantified when needed using Image Quant software. Each experiment was performed three times.

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TABLE 2. Oligonucleotide primers used for RT-PCR

RP-HPLC analyses. Peptide consumption during growth of RN6390 and mutant derivatives was done in MM supplemented with peptides and was evaluated by reverse-phase high-performance liquid chromatography (RP-HPLC). Cells were removed from stationary phase culture medium by centrifugation. Supernatant was supplemented with trifluoroacetic acid (1%, vol/vol), centrifuged, and filtered through 0.22-µm-pore-size filters (Millipore). Peptide separation was carried out at 40°C using an RP18 X-Terra column (250 by 4.6 mm; Waters) at a flow rate of 1 ml min^–1. Solvent A was 0.115% (vol/vol) trifluoroacetic, and solvent B was 0.1% (vol/vol) trifluoroacetic acid plus 60% (vol/vol) acetonitrile in MilliQ water. A 5-min isocratic phase in solvent A was followed by a linear gradient of solvent B (0 to 60% within 40 min). Eluted peptides were detected by UV detection at the OD₂₁₄.

Top ABSTRACT INTRODUCTION MATERIALS AND METHODS RESULTS DISCUSSION REFERENCES

 
S. aureus harbors four distinct putative oligopeptide permease systems. Computational analysis of the 11 available genomic DNA sequences of S. aureus strains revealed the presence of four distinct putative opp operons (Fig. 1). The opp-1ABCDF (genes SAOUHSC_02767 to SAOUHSC_02763) and opp-2BCDF (SAOUHSC_01380 to SAOUHSC_01377) operons have already been identified in S. aureus RN6390, a derivative of the NCTC8325 sequenced strain (9). By sequence homology searches using the opp-1 sequence of NCTC8325, we found two additional adjacent opp operons, opp-3 (genes SAOUHSC_00923 to SAOUHSC_00927) organized as oppBCDFA, and opp-4 (genes SAOUHSC_00928 to SAOUHSC_00932) organized as oppADFBC and located 212 bp downstream of opp-3. An additional isolated oppA-like gene (gene SAOUHSC_00201) encoding a putative oligopeptide binding protein, Opp-5A, was also identified in all strains. Organization of these opp systems is poorly conserved from one system to another. This is also the case for their amino acid sequence. For example, four putative OppA proteins of NCTC8325 share about 28% identity (Table 3), while transmembrane proteins, or ATPase proteins, each share between 27 and 35% identity. All the OppA proteins carry the typical signature of bacterial extracellular solute-binding proteins, and all OppD and OppF proteins carry the ABC transporter signature sequence (42, 44).

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FIG. 1. Genetic and transcriptional organization of the S. aureus NCTC8325 opp systems. The opp genes were designated according to their homology with characterized bacterial opp genes. Gene numbers were adapted from the genomic DNA sequence annotation of S. aureus NCTC8325 (accession numbers CP000253 and NC_007795). Open reading frames adjacent to the represented loci are present on the opposite strand. Double arrows indicate the amplification products obtained during RT-PCR experiments (see Results). Primers for transcriptional analysis are listed in Table 2. P, putative promoter sequence; T, putative terminator of transcription.

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TABLE 3. Identity (%) between the OppA proteins of S. aureus NCTC8325

Each opp cluster is highly conserved between strains of S. aureus, with identity in most cases greater than 99% at the nucleotide level. One exception is opp-4, which is interrupted by a transposase gene in opp-4A of S. aureus MRSA252 (the most genetically diverse human strain) and absent from strain RF122 (isolated from bovine mastitis). Surprisingly, the RF122 genome appears to have a duplication of the opp-3 cluster: an opp cluster located 169 nucleotides downstream of opp-3 displays the same genetic organization and encodes proteins closely related to Opp-3 proteins. Nevertheless, two stop codons are present in the oppA gene of this additional opp cluster, leading to a nonfunctional OppA protein. Finally, one of the 11 sequenced strains of S. aureus, USA300 (a highly virulent isolate), contains a fifth oppABCDF operon in a novel mobile genetic element termed ACME that is absent from other sequenced S. aureus strains (13).

A search for homologs of S. aureus Opp proteins revealed that opp-1, opp-2, opp-3, and opp-5A are highly conserved in Staphylococcus epidermidis, the second clinically important staphylococcal species (Table 4). Moreover, Opp-3 is also detected in all other sequenced staphylococcal species, namely Staphylococcus haemolyticus and Staphylococcus saprophyticus. Interestingly, Opp systems that have been shown to be implicated in bacterial nutrition in L. lactis, L. monocytogenes, and Streptococcus agalactiae are most similar to the S. aureus Opp-3 system (6, 27, 40) (Table 4).

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TABLE 4. Identity between Opp proteins of S. aureus NCTC8325 and those from other gram-positive bacteria

All Opp systems are expressed during growth in CDM. Expression of the different opp genes of S. aureus RN6390 was analyzed in exponential MM cultures by semiquantitative RT-PCR using specific opp primers. All oppA genes were expressed (Fig. 2A), and similar results were also obtained for the expression of other opp genes (data not shown). Their expression levels depended on the opp system under study. Under our experimental conditions and assuming that messenger stabilities are comparable, the opp-3A gene was apparently the most highly expressed oppA. To verify these observations, we evaluated the production of the three binding proteins Opp-1A, Opp-3A, and Opp-4A by Western-blot analyses using specific antibodies. The expression level depended on the protein (Fig. 2B), with a predominant production of Opp-3A. These results correlated with the observed levels of opp-1A, opp-3A, and opp-4A transcripts.

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FIG. 2. Expression of opp genes and production of OppA proteins in S. aureus RN6390 grown in MM. Proteins and RNA were extracted in exponential growth phase (OD600 of 0.5). (A) opp transcription analyzed by RT-PCR. cDNA dilutions used for transcript quantification were 1:1, 1:10, 1:100, and 1:1,000. hu transcript was used as an internal standard. (B) OppA production analyzed by Western blotting. Opp-1A, Opp-3A, and Opp-4A proteins were detected at their expected sizes of 58, 59, and 62 kDa, respectively.

We performed further RT-PCR transcriptional analysis on total RNA extracted from S. aureus RN6390 cells grown in MM to examine operon expression (Fig. 1). Results indicated that genes SAOUHSC_02770 to SAOUHSC_02762, comprising the opp-1 genes, are organized in an operon and are transcribed polycistronically. This would be expected from examination of the opp-1ABCDF cluster in S. aureus NCTC8325 as (i) transcriptional signals upstream and downstream of opp genes were not found, and (ii) codirectional ORFs are present upstream and downstream of the opp genes (Fig. 1). According to S. aureus NCTC8325 genome annotation, SAOUHSC_02770 was referenced as the diaminopimelate epimerase DapF, SAOUHSC_02769 as the Zn-dependent alcohol deshydrogenase AdhP, SAOUHSC_02768 as a conserved hypothetical protein of unknown function, and SAOUHSC_02762 as AraJ, an arabinose efflux permease.

Transcriptional coupling of SAOUHSC_01376 and opp-2BCDF was consistent with the absence of a transcriptional terminator downstream of opp-2F (Fig. 1). Cotranscription of SAOUHSC_01382 with opp-2BCDF, despite a putative promoter sequence upstream of opp-2B, presumably results from the absence of a terminator downstream of SAOUHSC_01382.

The opp-3BCDFA cluster contained a putative promoter sequence in front of opp-3B and a transcriptional terminator downstream of opp-3A (–14.6 kcal mol^–1). These features are in agreement with a polycistronic transcription of the opp-3 genes and the lack of evidence for cotranscription of opp-3 and opp-4 (no RT-PCR product could be obtained between opp3A and opp4A genes).

In the case of opp-4, RT-PCR results indicated transcriptional coupling of opp-4ADFBC, despite the presence of a terminator structure in the noncoding region between opp-4A and opp-4D (–16.8 kcal mol^–1). No consensus promoter was predicted in front of opp-4A, which might explain the weak expression levels for opp-4A.

No transcriptional terminators were detected in the noncoding regions downstream of clusters containing opp-1, opp-2, opp-4, and opp-5A. However, downstream open reading frames were all divergently transcribed, thus circumscribing the opp transcriptional units.

Expression of opp-3 but not other operons is modulated by aromatic amino acids. Previous results revealed that the S. aureus opp operons were not equally expressed during growth in CDM, suggesting specific transcriptional regulatory mechanisms. In several bacteria, opp expression is known to be regulated by nitrogen sources, including specific amino acids (1, 2, 20). Therefore, the possible effect of free amino acids on production of S. aureus Opp transporters was investigated. Two complementary approaches were developed. Oligopeptide-binding protein production was estimated by Western blot experiments in exponential phase cultures, either in MM supplemented with one of the nine nonessential amino acids (Pro, Ala, Ile, Phe, Trp, Tyr, Ser, Asn, and His) or in CM depleted of one of these amino acids. The external amino acid pool affected the protein production of Opp-3A only: addition of Tyr to MM and removal of Phe from CM significantly (P < 0.001) increased (about sixfold) Opp-3A production (Fig. 3A).

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FIG. 3. Regulation of Opp-3A by the amino acid content of the medium. Proteins and RNA were extracted in exponential phase of growth (OD600 of 0.5). (A) Opp-3A production analyzed by Western blotting. Opp-3A was detected at the expected size of 59 kDa. MM+Y, MM supplemented with Tyr; CM-F, CM depleted of Phe. (B) opp-3A transcription analyzed by RT-PCR. cDNA dilutions used for transcript quantification were 1:1, 1:10, 1:100, and 1:1,000. hu transcript was used as an internal standard. a, MM; b, MM+Y; c, CM; d, CM-F. (C) Quantification of opp-3A transcripts. Values are the means of three independent experiments with standard deviations. Transcripts were quantified using the 1:100 dilution samples. For each experiment, the amount of opp-3A transcript was given as a ratio to that of hu. (D) Quantification of Opp-3A production. Proteins were extracted in exponential growth phase in MM (OD600 of 0.5). Values are the means of five independent determinations with standard deviations. MM+Y, MM supplemented with Tyr; MM+Y+F, MM supplemented with Tyr and Phe; MM+Y+FV, MM supplemented with Tyr and the dipeptide Phe-Val.

To ascertain the effects of the amino acids Tyr and Phe, a semiquantitative transcriptional analysis (LD RT-PCR) was performed on all opp systems using the primers listed in Table 2. RNA was extracted from mid-exponential cultures in MM supplemented or not with Tyr and in CM depleted or not of Phe. Only expression of opp-3 was affected by the presence of Tyr in MM or by the removal of Phe from CM (Fig. 3B). Amounts of opp-3A mRNA were 5-fold higher in cells grown in Tyr-supplemented MM than in MM and 2.5-fold higher in Phe-deprived CM than in CM (Fig. 3C). Similar results were obtained using opp-3C primers (data not shown), in agreement with the cotranscription of the opp-3BCDFA genes.

These results indicate that Tyr and Phe exert opposite effects on opp-3 expression. Surprisingly, addition of Phe to MM did not affect the production of Opp-3A (data not shown). A possible explanation is that only Tyr affects opp-3 expression, whereas Phe acts as a competitor, preventing the action of Tyr. To evaluate this hypothesis, we compared Opp-3A production in MM supplemented with Tyr or with both Tyr and Phe. In the presence of Phe, stimulation of Opp-3A production by Tyr was significantly reduced (Fig. 3D), which therefore supports the hypothesis of a competitive effect of Phe on Tyr induction. Phe might impair Tyr entry into the cell (competition for transport by the same amino acid permease) or prevent its binding to an intracellular target. To further discriminate between these hypotheses, Opp-3A production was compared in MM containing Tyr and supplemented with Phe brought either in its free form or in a dipeptide form. The inhibitory effect of Phe was in the same range under either condition (Fig. 3D), thus favoring the hypothesis that Phe is likely to compete with Tyr for an intracellular target.

Altogether, these results indicate that opp-3 operon transcription is influenced by the aromatic amino acids Tyr and Phe and suggest that the two amino acids might compete for an intracellular target.

Depletion of Opp-3, but not other Opp proteins, prevents growth of S. aureus in peptide-containing CDM. As all Opp systems were expressed during growth in CDM, this medium was suitable to evaluate involvement of Opp systems in nitrogen nutrition. This was estimated by replacing an essential amino acid by a peptide containing the amino acid. As expected, removal of Glu and Gln from the complete CDM prevented growth of S. aureus RN6390. Glu (or Gln)-containing peptides from 2 to 8 amino acid residues were able to sustain growth. In contrast, no growth could be detected when medium was supplemented with peptides containing 9 amino acid residues or more (Fig. 4). These results suggest that (i) at least one of the Opp systems was able to fulfill the amino acid requirement of the strain and (ii) S. aureus was unable to use peptides larger than octapeptides for nutrient purposes.

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FIG. 4. Peptide utilization by wild-type and opp mutant strains of S. aureus. Growth yield was calculated as the percentage of population (final OD) reached in peptide-containing medium compared to CM in the stationary phase of growth. QILQWQWL, EQVIR, and PQRF peptides were not tested on the opp-1 opp-2 opp-4 (opp-124) mutant strain. wt, wild type.

To determine which of the systems is involved in nutrient uptake, the different opp operons were deleted by double-crossover events, resulting in the opp-1, opp-2, opp-3, and opp-4 mutant strains. Combinations of deletions were also constructed, and the opp-1 opp-2 opp-4 triple mutant strain was also obtained. Growth of each mutant was similar to that of the parental strain in complete CDM (data not shown). Deletion of opp-1, opp-2, or opp-4 alone or in combination did not affect the ability of S. aureus RN6390 to use tested peptides as nutrients, regardless of the peptide length. In contrast, deletion of opp-3 fully impaired the use of 4-mer to 8-mer peptides as a source of Glu/Gln (Fig. 4).

Interestingly, all dipeptides and most tripeptides were able to sustain growth of the opp mutants, regardless of the inactivated system. As a di- or tripeptide permease-like gene (dtpT) is present in all S. aureus genomes (SAOUHSC_00738 of S. aureus NCTC8325), this transporter is very likely involved in di- and tripeptide uptake. To evaluate the respective roles of DtpT and Opp in nutrient di- and tripeptide utilization, dtpT, opp-3 dtpT, opp-1 opp-2 opp-4 dtpT, and opp-1 opp-2 opp-3 opp-4 dtpT mutant strains were constructed, and their ability to utilize di- or tripeptides for growth was evaluated. The mutant strain dtpT did not grow when Glu/Gln was provided in a dipeptide form, indicating that DtpT only is responsible for the use of dipeptides (Fig. 5). Of the four tripeptides tested, Pro-His-Glu was imported exclusively by Opp-3, Lys-Glu-Gly and Gly-Gly-Gln were used by DtpT only, and Ser-Glu-Gly was imported by both systems, as only the double deletion opp-3 dtpT impaired the growth (Fig. 5).

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FIG. 5. Di- and tripeptide utilization by opp-3 and dtpT mutants of S. aureus. Growth yield was calculated as the percentage of population (final OD) reached in peptide-containing medium compared to CM in the stationary phase of growth. wt, wild type.

To complete this study with a larger range of peptides, dtpT and combined opp dtpT mutant strains were grown in MM supplemented with a pancreatic digest of caseins containing a large mix of peptides. All strains grew equally well, as the casein digest also contained a large amount of free amino acids. A control RT-PCR experiment indicated that the four opp systems of the wild-type strain were expressed (data not shown). The peptide content of the medium from stationary phase cultures was analyzed by RP-HPLC. No difference in peptide content was detectable between medium from the dtpT mutant and opp-1 opp-2 opp-4 dtpT mutant strains (data not shown). Chromatograms could be superimposed, suggesting that the peptide contents were qualitatively and quantitatively comparable. In contrast, several peaks were detected in growth medium of the opp-3 dtpT mutant (Fig. 6). Moreover, some of the common peaks were present in larger amounts in the opp-3 dtpT culture medium. This situation most probably corresponded to coeluting peptides, of which one accumulated with the opp-3 dtpT mutant only. Similar profiles were obtained with the opp-1 opp-2 opp-3 opp-4 dtpT mutant strain (data not shown). Altogether, these results indicate a prevalent role of Opp-3 in oligopeptide utilization during growth of S. aureus RN6390. Among the 4 putative Opp systems of S. aureus, only Opp3 is involved in nutrition, transporting efficiently tri- to octapeptides with overlapping substrate specificity with DtpT concerning some tripeptides.

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FIG. 6. Peptide content of the growth medium of S. aureus dtpT and opp-3 dtpT mutants. Cells were grown in CM supplemented with casein-derived peptides to the stationary phase, and peptide content of the external medium was analyzed by RP-HPLC. From bottom to top, the strains are the dtpT and opp-3 dtpT mutants. Arrows highlight main peaks that were detected at higher levels or only in the culture medium of the opp-3 dtpT mutant.

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Genome analysis of 11 S. aureus strains revealed the presence of three putative complete Opp systems, Opp-1, Opp-3, and Opp-4, of which two, Opp-3 and Opp-4, are described for the first time. Each of them comprises a peptide-binding protein, two integral membrane proteins, and two ATPases. They all have the signatures of oligopeptide/dipeptide/nickel transport systems. In addition, the 11 sequenced S. aureus strains express a particular opp operon, opp-2BCDF, which lacks the substrate-binding protein. This system could act as an exporter, as export systems usually do not require a substrate-binding component needed for uptake (21). However, as Opp-2 is classified as an importer in the ABCISSE database (41), it is also possible that it recruits one of the four OppA proteins for peptide binding. Several Opp systems recruit peptide-binding protein(s) encoded by isolated genes located in another region of the genome (16, 34). In the case of Opp-2, a candidate partner is encoded by the orphan gene opp-5A. This suggestion is not supported by previous studies, as (i) in other cases, at least one oppA copy was also present within the operon, which is not observed with S. aureus opp-2; (ii) with the exception of the closely related species S. epidermidis, the unusual structure of the opp-2 operon in S. aureus has not been reported in other bacterial genomes; and (iii) isolated peptide-binding proteins utilizing an Opp complex share significant homologies with the OppA protein encoded by the opp operon (16, 34). This is clearly not the case for Opp-5A, which revealed weak homologies with Opp-1A, Opp-3A, and Opp-4A (26, 30, and 29% identity, respectively). The roles of the atypical Opp-2 system and Opp-5A binding-protein thus remain to be determined.

Within a given strain, the opp operons display specific genetic organization and low degrees of sequence similarity. In contrast, each of the opp operons is highly conserved in all S. aureus strains, with the exception of opp-4, which is absent in RF122, altered in MRSA252, and missing from the S. epidermidis genome. These features and the low expression level of opp-4 observed under different conditions suggest that this system might be involved in biological processes specific to certain staphylococci.

S. aureus is predicted to possess four distinct potential Opp systems. This multiplicity raises questions as to whether they have overlapping or distinct functions. One of the demonstrated roles of bacterial Opp systems is to provide peptides as nutrients. This study demonstrates that Opp-3 only is responsible for this nutritional function. Interestingly, Opp-3 is closer to bacterial Opp permeases involved in nutrient uptake than the other staphylococcal Opp systems (Table 1). The best documented nutritional oligopeptide transport system is by far the lactococcal Opp system. It transports peptides from 4 to up to 35 residues with little amino acid sequence specificity (14). Despite a more restricted capability in terms of peptide length (from 3 to 8 residues), the Opt system of L. lactis also seems to be characterized by broad substrate specificity (27), a feature that seems to be common to Opp systems involved in bacterial nutrition. From the results presented here, Opp-3 from S. aureus is capable of using peptides comprising 3 to 8 amino acid residues having unrelated sequence or biochemical features, which is in agreement with its nutritional function. In terms of preferences for peptide utilization, the staphylococcal Opp-3 system appears closer to Opt from L. lactis or Opp from S. agalactiae than to Opp or Ami from L. lactis and S. thermophilus, respectively (14, 16, 27, 40). These results are in concordance with sequence similarities (Table 4).

Opp-3 is the sole Opp system of S. aureus ensuring a nutritional function under the tested conditions. It is also the only staphylococcal Opp system whose expression was modulated by amino acids. In bacteria, nitrogen sources are known to regulate opp expression (31). For instance, E. coli K-12 opp expression is regulated by leucine, via the global regulator Lrp (8). Similarly, another global regulator, CodY, represses L. lactis opp expression in response to the intracellular pool of branched-chain amino acids (20). Nevertheless, regulation of opp genes by aromatic amino acids (as is the case for S. aureus opp-3) was not previously described. Aromatic amino acid regulation was previously demonstrated for other genes. The best documented case is the tyrR regulon of E. coli (37). TyrR is a transcriptional regulator that interacts with aromatic amino acids and binds to a specific DNA sequence. No TyrR homologue was found in the S. aureus genomes, thus making a regulatory pathway via TyrR unlikely in S. aureus. However, by using the dedicated program iMoMi (for interactive motif mining) (38), a putative regulatory binding motif was detected. It consisted of a 14-nucleotide repeated sequence located at –219 and –236 nucleotides upstream of the opp-3B start codon. This putative regulatory sequence was detected upstream of only one other gene among all available S. aureus genomes. The gene, SAOUHSC_02729 of S. aureus NCTC8325, encodes a putative amino acid transporter whose expression was also induced by Tyr, as revealed by LD RT-PCR analyses (data not shown). These preliminary data suggest a regulatory network implicating aromatic amino acids, oligopeptides, and amino acid transporter(s).

What are the roles of the other Opp systems? Opp-1, Opp-2, and Opp-4 are not involved in nutrient supply of S. aureus, at least under our experimental conditions. We cannot exclude the possibility that they can import nutritional peptides under different conditions, especially in the case of Opp-4, which was weakly expressed under all conditions tested. Alternatively, some of them could also be involved in the uptake of substrates other than peptides. Interestingly, Opp-1A is 35% identical to NikA from E. coli which has been experimentally shown to transport nickel (11, 32), whereas similarities to confirmed oligopeptide-binding proteins are lower (e.g., 22% with AmiA3 from S. thermophilus and 24% with OppA from L. lactis). S. aureus Opp-1A is also 39% identical to Gbs1577 of S. agalactiae, a binding protein of a putative peptide transporter that appeared not to be required for nitrogen nutrition and revealed similarity with Ni²⁺ permeases (40). Transcriptional analysis of the opp-1 region showed that additional genes were coexpressed with the opp-1 genes, in correlation with their genomic organization. The corresponding proteins could be linked to the Opp-1 function. One of them (SAOUHSC_02770) encodes a protein homologous to DapF, a central enzyme in the biosynthesis pathways of both lysine and cell wall peptidoglycan in some bacterial species (23, 47). This could make sense as the E. coli Opp system has been shown to be involved in peptidoglycan turnover (34). Peptide uptake systems are also involved in other cellular functions, and the Opp-1 and Opp-2 systems have been suggested to play a role in virulence in different animal models (5, 9, 29). Nevertheless, the exact contribution of these systems in the course of infection is unknown and remains to be elucidated.

 
We are grateful to A. Gruss and D. Lechardeur for critical reading of the manuscript, N. Pons for technical assistance in computer analysis, and E. Guedon for helpful discussions.

A.H. received a fellowship from the Ministère de l'Education Nationale, de l'Enseignement Supérieur et de la Recherche.

 
* Corresponding author. Mailing address: Unité Bactéries Lactiques et pathogènes Opportunistes, Institut National de la Recherche Agronomique, Domaine de Vilvert, 78352 Jouy en Josas cedex, France. Phone: 33 134 652 395. Fax: 33 134 652 065. E-mail: elise.durant{at}jouy.inra.fr

Published ahead of print on 11 May 2007.

A. H. and E.B.-D. contributed equally to this work.

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