Balaban et al. (1, 2) purified the RAP protein from concentrated and boiled S. aureus RN6390B (agr⁺) or RN6911 (agr-null) supernatants by gel filtration chromatography on a Bio-Rad HPLC SEC250 7 × 300 column, using a 1-ml sample for each run. Supernatants of both strains had activity, as demonstrated by Northern blot hybridization with an RNAIII probe, but, surprisingly, all of the activity was in a single 0.5-ml fraction containing only the anomalously eluting 38-kD protein, which was present only in this fraction (2). The activation of agr by RAP in culture supernatants of the agr-null mutant (1) meant that the activating factor was not agr-encoded.

It had previously been observed that a heavily mutagenized derivative of an S. aureus strain (Foggi--our RN833) produced a small peptide that strongly inhibited agr activation in a standard group I S. aureus strain (2). This peptide was found to have the sequence YSPXTNF (1), where X could be cysteine or tryptophan, and a synthetic version was prepared with the sequence YSPWTNF (1). This synthetic linear heptapeptide (Pep) was reported to have inhibitory activity against S. aureus, both in vitro and in vivo, although the in vivo dose used was probably about 1000-fold higher than that of the native staphylococcal peptide isolated from RN833 culture supernatants (1).

We obtained culture supernatants from three strains: RN6390B (standard group I agr⁺), RN6911 (agr-null [5]) and RN6734 (a derivative of RN6390B lysogenic for phage 13). The first two were the same strains from which Balaban et al. (1, 2) isolated the RAP protein. The third was included to confirm the generality of RAP production. The supernatants were concentrated 10-fold by lyophilization, one 3-ml sample was dialyzed, and a second 3-ml sample was boiled, centrifuged, and fractionated on a Bio-Rad SEC250 gel filtration column (7.5 × 300 mm) 1 ml at a time. The fractions from the three separate column runs were combined in order to have larger amounts of protein for the subsequent analyses. The starting material, the dialysate, the retained material, and the gel filtration fractions were then analyzed for agr activating activity, using an agr-P3-blaZ fusion, and separated by PAGE (Fig. 1).

In neither experiments of this type (using different starting cultures) nor in experiments in which the supernatant was concentrated 50-fold, have we been able to detect any activity in fractionated or unfractionated supernatants of the agr-null strain (Figs. 1A and 2A). Nor have we detected any activity in similarly analyzed but unboiled supernatants. The agr⁺ strains had the expected activity (Figs. 1B and 2A), which always eluted as a broad peak centering at an elution time of 10 min, 1 min before the cobalamin standard (MW 1350). A sample of the synthetic thiolactone-containing group I AIP (4) eluted from this column approximately one min later (not shown). All of the detectable agr-activating activity in supernatants of the agr⁺ strains and in the gel filtration fractions passed through a dialysis membrane, although three cycles of dialysis were necessary (Fig. 2C). Each of the active fractions showed multiple protein bands, two of which were in the 30- to 46-kD range and paralleled the activating activity; either of these could correspond to the 38-kD band of Balaban et al. (1, 2) (Fig. 1B). In no case was there a fraction containing only a single protein species. The two bands in the 30- to 45-kD range were retained by the dialysis membrane (Fig. 1C). There was no significant protein band in this region in supernatants of the agr-null strain, although other protein bands were clearly visible (Fig. 1A). This analysis has been repeated five times with similar results (not shown). On the chance that our reporter gene assay was an imperfect reflection of the agr activation process, we assayed culture supernatants by Northern blot hybridization. On the chance that RN6911 had undergone a spontaneous mutation, we included RN7206, a 13 lysogen of RN6911. As shown in Fig. 2B, there was no detectable activity in concentrated culture supernatants of either of the agr-null strains. We conclude, therefore, that supernatants of the agr-null strain contain neither agr activating factor nor detectable thermostable protein in the 30- to 45-kD range, and that the agrD peptide accounts for all of the agr-activating activity in the agr⁺ strain.

To explain the apparent discrepancy between our results and previous results that a significant portion of agr-activating material was retained by a dialysis membrane (2), we note that the dose-response curve with synthetic group I AIP is linear over only a ten-fold concentration range, between 3 and 30 nM (4), and that the AIP concentration in the culture supernatant of our standard agr⁺ strain, RN6390B, is approximately 100 nM. As shown in Fig. 2C, during a single overnight dialysis, ~20% of the activity was retained by the dialysis membrane, two more cycles of dialysis were required to remove the rest, and the activity was quantitatively recovered in the dialysate. Starting with a 10× concentrated sample (at about 1 mM), retention of 20% is equivalent to a retentate concentration of ~200 nM--well above the saturation level for the assay of activity with undiluted material. Because the dialysate was not assayed in the original study (2), the conclusion--based on this retained activity--that the activity is largely nondialysable (2), was incorrect. An ultrafilter with a 3-kD cutoff has been successfully used to separate the peptide from higher molecular weight materials in the supernatants (3); Balaban et al. (1) reported that such a filter retains a significant portion of agr activating activity, consistent with a proteinaceous activating factor. We agree that a significant amount of activity is retained by such filters (not shown); however, in our experience, the concentrated crude culture supernatant rapidly clogs the filter, so that retention cannot be taken as evidence of material with molecular weight greater than that corresponding to the filter cutoff.

We examined the possibility that a linear heptapeptide inhibits agr activation. Because all of the known agr-encoded activating/inhibiting peptides contain a five-membered thiolactone ring (4, 6), the report of an active linear heptapeptide lacking the conserved cysteine (1) suggested that such a peptide might have an origin independent of agr and might represent a mechanism of agr inhibition different from that of the known cross-reacting AIPs (4, 6). To obtain a supply of the native agr-inhibiting peptide produced by strain RN833, we prepared a concentrated postexponential phase supernatant from a culture of this strain as previously described, and confirmed its potent agr-inhibiting activity (Fig. 3). We also prepared a synthetic sample of the linear heptapeptide YSPWTNF by standard peptide synthesis, and then determined its sequence for confirmation. This material had no detectable agr-inhibiting activity in vitro (Fig. 3) or in vivo (not shown) when compared to the potent activity of the native material. Identical results have been obtained independently by Wright and Larrick (J. Larrick, personal communication). This result suggested that the native and synthetic RIP peptides may not be the same and that the native peptide might belong to the AgrD family after all. To test for this, we compared its sensitivity to boiling at pH 8 versus pH 2 with that of the native and synthetic AIPs of agr groups I and II. All of the peptides tested were highly and equally sensitive to boiling at pH 8 but were stable to boiling at pH 2. The data for native RIP and synthetic AIP II are shown in Fig. 4. As determined from these data, the half-life of native RIP at pH 8 and 100°C was about 14 min, and that of AIPII about 23 min. This behavior is expected for a peptide with an essential thiolactone bond, but is not expected for any simple linear peptide. The Pep could not be tested in this manner, because it had no measureable activity.

We next turned our attention to strain RN833, kindly provided by G. Omenn many years ago, which was described as a mutant defective in the production of staphylococcal nuclease obtained by extensive nitrosoguanidine mutagenesis of a standard strain of S. aureus known as the Foggi strain (7). RN833 has been in our strain collection for over 25 years, maintained at 80°C, and has been used as a recipient for DNA-mediated transformation because of its lack of nuclease activity. It is nonhemolytic on sheep blood agar and does not produce S. aureus virulence factors such as -hemolysin, protein A, and coagulase in detectable quantities. We have considered the possibility that it is an S. aureus mutant producing a mutationally altered AgrD peptide that inhibits its own agr activation. Its failure to produce protein A or coagulase make this unlikely because the protein A and coagulase genes are ordinarily down-regulated by agr. Nevertheless, we considered it important to confirm that RNAIII, the agr effector (5), was not produced. Accordingly, we tested for RNAIII production by Northern blot hybridization analysis of whole-cell RNA from RN833 by our standard method. The result, shown in Fig. 5B, lanes 1 and 2, was that RN833 does produce RNAIII, but that the RN833 material has considerably slower mobility than RNAIII produced by agr⁺ S. aureus (Fig. 5B, lanes 3 and 4). Therefore, while it is possible that the phenotype of RN833 is the result of an agr mutation--perhaps one affecting RNAIII structure--it cannot be the result of agr autoinhibition by a mutant peptide, because this would block RNAIII production. We next considered the possibility that RN833 is not S. aureus after all, noting that S. warnerii has been reported to produce an RNAIII variant larger than that of most other staphylococcal strains studied, including several S. aureus strains, S. simulans, S. lugdunensis (8, 9) (which produces a smaller RNAIII), and S. epidermidis (10). Biotyping, kindly performed by the NYU/Tisch Hospital bacteriology laboratory, revealed that RN833 was not S. aureus but was 85% likely to be S. warnerii, and that therefore our stock culture of the nuclease-negative mutant of strain Foggi is, and has always been, a non-S. aureus strain. Using conserved regions of the agr locus, we obtained and sequenced PCR products corresponding to most of the agr locus of RN833. The sequence of the 5' half of the RNAIII region from RN833 closely matched that of S. warnerii (8) (Fig. 5A), and the sequence of the agrD region was typical of other agrD sequences, revealing the putative AIP sequence as YSPCTNFF (Fig. 5C). This is clearly the same peptide as that described by Balaban et al. (1), except that it contains a cysteine residue at the usual position rather than the arbitrarily inserted tryptophan, and, on the basis of its NH₂-terminal amino acid and the position of the conserved COOH-terminal processing site, it would unquestionably be an octapeptide rather than a heptapeptide (Fig. 5C). Our conclusion is that RIP is the native thiolactone-containing AIP of S. warnerii, and that it fits very well into the general picture of AIPs developed in the past few years (see Fig. 6 for a diagram of the agr locus as we currently understand it.).

We are unable to corroborate the finding of soluble agr activation or inhibition activity associated with any staphylococcal product other than the AIPs encoded by agrD and processed to yield the thiolactone derivatives. We have not attempted to determine the possible basis for mouse protection described for the protein(s) tracking on SDS-PAGE with molecular weights between 30 and 46 kD. It is possible that one of these proteins contains an epitope cross reactive with either the AIP or the receptor; alternatively, it is possible that one or another is a protective antigen on its own. It is certain, however, that none is an agr activator. The activity reported for the agr-null strain (1) could conceivably be explained by a mix-up in strains. The inhibitory activity reported for the linear synthetic heptapeptide has been explained by the presence of impurities in the preparation.

R. P. Novick
H. F. Ross
A. M. S. Figueiredo
G. Abramochkin
Skirball Institute for Biomolecular Medicine
New York University School of Medicine
550 First Avenue
New York, NY 10016, USA
E-mail: novick{at}saturn.med.nyu.edu
T. Muir
Rockefeller University
East 65 Street and York Avenue
New York, NY 10021, USA

REFERENCES

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8. K. Tegmark, E. Morfeldt, S. Arvidson, J. Bacteriol. 180, 3181 (1998) [Abstract] .
9. F. Vandenesch, et al., FEMS Microbiol. Lett. 111, 115 (1993) [CrossRef] [Web of Science] [Medline] .
10. W. J. Van Wamel, et al., FEMS Microbiol. Lett. 163, 1 (1998) [Web of Science] [Medline] .
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Response: Novick et al. state that because they were not able to purify the ~38-kD RAP that RAP does not exist, and they therefore conclude that RNAIII synthesis can only be activated by the octapeptide. Below, we demonstrate that Novick et al. applied purification methods different from ours, which perhaps explains their failure to purify RAP. We also show that the NH₂-terminal sequence of RAP highly resembles that of RIP and demonstrate that RAP and RIP use a signal transduction different from the octapeptide to regulate the synthesis of RNAIII.

Novick et al. claim that the synthetic peptide RIP (YSPTNF) synthesized by them was inactive and suggest that it was inactive because it does not contain a thiolactone structure. Their arguments are based on their conclusion that RIP is an octapeptide YSPTNF and that all octapeptides are in need of a thiolactone structure in order to be active. As we demonstrate below, RIP (YSPTNF) is active. We further demonstrate that derivatives of RIP (designed according to the putative NH₂-terminal sequence of RAP) are also active. None of the peptides were synthesized with a thiolactone structure. Both groups agree, however, that inhibition of RNAIII synthesis is of therapeutic potential (1, 2).

The different results between the groups may be explained by different handling of the product. Handling conditions are of primary importance. We do not know how the peptide was synthesized, solubilized, and stored. RIP, as we observed, can degrade (as can any peptide) and can become inactive under certain handling conditions.

Novick et al. also conclude (with 85% certainty) that the bacterial strain RN833 that produces RIP is S. warnerii. They back this by showing that the agr of S. warnerii contains a sequence YSPTNF and conclude that RIP is an octapeptide and is consequently made by S. warnerii.

Our results indicate that the bacteria producing RIP (RN833) may be S. xylosus (as identified by our collaborators with 99% certainty) and that a sequence identical to RIP (YSPTNF) was identified in RN833 (TATTCGCCGTGGACCAATTTTTGA). Discussion of these findings follows.

RAP is sensitive to boiling (3). Therefore, if maximal activity of RAP is desirable, supernatants should not be boiled prior to RAP purification. Separation between the octapeptide and RAP by dialysis can be carried out, but only for a limited amount of time, and must be kept at 4°C. Novick et al. too show (figure 2C) that 20% activity could be retained after an overnight dialysis (at 4°C, we assume). Unfortunately, they could not use the cutoff membranes because their concentrated crude culture supernatant rapidly clogged the filter. If Novick et al. had used Centriprep instead of Centricon (Amicon), their membranes would not have clogged.

Use of -lactamase activity (using the agr-P3-blaZ fusion as a reporter) as a test for RNAIII is not sensitive enough and can lead to experimental artifacts. We therefore tested for RNAIII exclusively by Northern blotting. -Lactamase is naturally produced and secreted by the wild-type strain RN6390B [a common source of RAP in our lab (4)]. If the supernatant of this strain is collected in order to purify RAP from it, and each purification step is tested for its ability to activate RNAIII synthesis in the bacterial strain containing the P3:blaZ fusion by the -lactamase assay, what one actually detects is -lactamase activity in the supernatant of RN6390B rather than the consequent induction of P3 in the bacterial strain containing the P3:blaZ fusion. -Lactamase is sensitive to boiling. If the supernatant is boiled prior to RAP purification, one can assume that most of the enzymes' activity in the supernatant is lost. In theory, one could then use the -lactamase assay that would in fact reflect P3 activity. However, this assay is not sensitive enough for the detection of low levels of P3 activity induced by boiled or purified RAP. If RAP+octapeptide activity is maximal (100%) (RAP activity alone is only 20%), further boiling or purification leads to a further decrease in its activity. If the positive control is still the unpurified material, the activity of purified material becomes negligible and goes undetected by this assay. The inability to detect pure material by the -lactamase assay is not only related to RAP but also to the octapeptide. It is not possible to detect induction of P3 by the octapeptide (HPLC-purified from wild-type supernatants) with the use of the -lactamase assay.

RAP contributes to approximately 20% of the total activity in the supernatant. In the process of purification, some activity is lost. Therefore, to properly detect the active fraction eluting from the HPLC column, the positive control of the assay should be the partially purified material that was used to load the column that only contain RAP. If the positive control always remains the total supernatant (containing RAP and the octapeptide), and if the autoradiogram of the Northern blot is developed just to detect the positive control, the faint bands can go undetected.

To purify RAP, the HPLC column should not be overloaded. In figure 1, A, B, and C, of Novick et al., the gel filtration column was overloaded (as observed in the SDS-PAGE) and RNAIII was detected with the use of the -lactamase assay instead of Northern blotting. In figure 1A of Novick et al., a wild-type autoinduction of RNAIII synthesis by postexponential supernatants contributed 80% by the octapeptide and 20% by RAP. In RN6911 (4) (which does not contain the agr), only RAP contributes to the induction of RNAIII synthesis, the overall activity is relatively low (1) and decreases with further purification steps. Therefore, -lactamase assay should not be used for the detection of RAP in RN6911. If this assay is nevertheless carried out, the proper positive control (supernatant of RN6911, which was applied to the column) should be used. Fraction 9 (a possible elution time of RAP) does in fact contain activity. In figure 1B of Novick et al., the high results obtained using the -lactamase assay may reflect purification of RAP (smaller quantities that probably go undetected) together with the octapeptide. If not boiled, the results might reflect purification of RAP, the octapeptide, as well as -lactamase itself from the supernatant. In figure 1C of Novick et al., no activity is observed because the material applied to the column should not have been boiled or dialyzed for an extended period of time, particularly if no protease inhibitors were added (see comments on figure 2C of Novick et al.).

In figure 2A of Novick et al., RN6390 supernatant contains octapeptide + RAP if boiled. If not boiled, the supernatant also contains -lactamase. Therefore, high results do not necessarily reflect P3 activity, but rather -lactamase in the supernatant. On the other hand, supernatants of RN6911 do not contain the octapeptide but do contain RAP, but its quantity is too low to be properly detected by the -lactamase assay. However, careful inspection of the graph shows that some activity can be detected in the supernatant (about 20% of activity observed in RN6390 supernatants). In figure 2B of Novick et al., the positive control, which was induced by the octapeptide + RAP (lane 8), gives a strong signal. The film should be exposed longer in order to detect possible lower activity in other lanes. In figure 2C of Novick et al., about 20% activity was retained by dialysis (which could not be extended beyond 1 day at 4°C without adding protease inhibitors). Loss of activity after second and third dialysis observed in figure 2C of Novick et al. might be due to the overall length of dialysis time in the absence of protease inhibitors. If activity was lost only due to dialysis, as Novick et al. suggest, after the first dialysis (of 1-ml sample against 100-ml buffer), less than 20% activity would have been retained. We cannot comment on Novick et al.'s observation that 100% activity was recovered in the dialysis buffer. To be tested appropriately, the buffer (100 ml of 10 mM phosphate) would have to be concentrated to the original volume of the sample (1 ml), thus increasing the phosphate concentration from 10 mM to 1 M. No positive control using 1 M phosphate is presented.

What follows is a discussion of one of the protocols that we used for purification of analytical amounts of RAP. Wild-type S. aureus RN6390B (4) cells were grown to the postexponential phase of growth. Growth culture was centrifuged at 6000 × g for 10 min at 4°C. The supernatant was collected and filtered through a 0.22-µm filter to remove residual cells. The supernatant was lyophilized and resuspended in water to 1/10 of the original volume (total 10×). Fifteen milliliters of total 10× was applied to a 10-kD cutoff membrane [Centriprep 10 (Amicon)]. This enabled us to concentrate the material further and to remove material smaller than 10 kD. One milliliter concentrated material greater than 10 kD was washed twice in PBS by resuspending it each time in 15-ml PBS and reconcentrating it on the Centriprep 10, and the material greater than 10 kD collected (>10). Alternatively, postexponential supernatants were precipitated using 75% ammonium sulfate. The precipitate was resuspended in water to 66× and extensively dialyzed through an 8-kD dialysis membrane with PBS. Twenty to 30% of RNAIII upregulating activity was retained in the dialyzed high molecular weight fraction. One hundred microliter material greater than 10 kD was applied to an HPLC gel filtration column (Bio-Sil SEC-125 300 × 7.8 mm, Bio-Rad) in 1 mM PBS, pH 7.2 (0.1 × PBS), at a flow rate of 0.5 ml/min, and 1-ml fractions collected. Fractions were concentrated to 1/10 of their original volume by lyophilization and tested for activation of RNAIII synthesis as described (3). RAP can be further purified by anion exchange chromatography. Specifically, active gel filtration fraction (1 ml) was fractionated by anion exchange chromatography (HPLC SynchroPak Q300, Keystone Scientific, Inc.) in water, pH 7.2. Bound material was eluted by a salt gradient of 0 to 1 M NaCl in water. Pure ~38 kD RAP eluted at 0.75 M NaCl. As demonstrated in Fig. 1, RAP and the octapeptide elute at close but different fractions.

The fraction that activated RNAIII synthesis was collected, separated by SDS- PAGE, and Coommassie-stained, and the protein band of approximately 38 kD (1) was amino acid-sequenced commercially by Edman degradation chemistry. The NH₂-terminal sequence of RAP was determined to be IKKYKPITN (6). This sequence was compared to the S. aureus database, and the sequence of the open reading frame suggests that it is a possible 279-amino acid polypeptide that has a high (76%) sequence identity compared to the Bacillus subtilis ribosomal protein L2 (5). We have not yet been able to express the protein in Escherichia coli or to inactivate the gene (possibly because of its essentiality and its high sequence similarity among bacterial species), and therefore still consider these results preliminary. However, we were struck by the similarity between the NH₂- terminal sequence of RAP and RIP (YKPITN as compared to YSPWTN). Based on our hypothesis (3) that RAP and RIP may bind to the same receptor, one as an agonist and the other as an antagonist, RIP derivatives were synthesized [by Fmoc chemistry (15)] according to the putative NH₂-terminal sequence of RAP. These peptides were tested for their ability to inhibit RNAIII synthesis in vitro and for their ability to prevent cellulitis in vivo. The results of these experiments (see below) indicate that the peptides most successful in inhibiting cellulitis were in fact the peptides that most resembled the NH₂-terminal of RAP and contained the sequence YKPITN. Our results suggest that RAP and RIP may bind to the same receptor, one as an agonist the other as an antagonist.

The pathway by which RAP activates and RIP inhibits RNAIII synthesis was unknown. However, it seemed reasonable to hypothesize that, like other quorum sensing molecules, RAP would activate a classical bacterial two-component system by phosphorylation (7). Wild-type S. aureus cells were incubated with the octapeptide (<3) or with RAP which was purified from the postexponential supernatants of the same strain (8), with RIP (native or synthetic) or RIP derivatives, or with PBS as a control. Cells were assayed for RNAIII synthesis by Northern blotting (3) and for in vivo phosphorylation (9). Figure 2A shows that RAP and the octapeptide activate RNAIII synthesis while RIP inhibits it. As shown in Fig. 2B, RAP specifically phosphorylates a 21-kD protein while RIP inhibits its phosphorylation. We termed this protein TRAP (for target of RAP). The sequence of TRAP (9) revealed that it is a novel 167-amino acid polypeptide. Figure 2, A and B, also shows that, while RAP activates RNAIII synthesis and activates TRAP phosphorylation, the octapeptide activates RNAIII synthesis but inhibits TRAP phosphorylation. Furthermore, while RAP and RIP regulate TRAP phosphorylation in the agr null mutant RN6911, the octapeptide does not, suggesting that the octapeptide inhibits TRAP phosphorylation indirectly by activating the agr system (9). Our results suggest that RAP and the octapeptide regulate RNAIII synthesis by different signal transduction pathways, RAP (and RIP) by the TRAP system, and the octapeptide by the agr system (10).

In bacteria, many important processes are known to be mediated by extracellular signal molecules produced by the bacteria (11). A single bacterial cell can contain many signaling modules that operate in parallel (12) or in series (13), where convergent quorum sensing pathways lead to important cellular functions (14, 18-21). Production of virulence factors is essential for the survival of S. aureus in the host. It is therefore not surprising that more than one pathway would contribute to achieve the important goal of toxin production.

RIP peptides were synthesized by the Fmoc chemistry, as described below. The synthesis was performed with an automatic peptide synthesizer (PS3, Rainin-Protein Technologies, Emeryville, California), and all of the procedures and programming followed the manufacturer's instructions as previously described (15). The peptide was synthesized utilizing 9-fluoroenylmethoxycarbonyl (Fmoc) chemistry and high-capacity (0.7 to 1.1 mmol/g) Knorr resin, Fmoc-2,4-dimethoxy-4'-(carboxymethyloxy)-benzhydrylamine resin with 1% divinylbenzene cross linker (100 to 200 mesh, Advanced Chemtech, Louisville, Kentucky). The first amino acid was allowed to couple for 2 hours and the remainder amino acids (Advanced Chemtech) were coupled for 20 min at room temperature. The peptide was cleaved and deprotected by the addition of 90% trifluoroacetic acid (TFA), 5%, 1,2-ethanediol, and 5% water solution to the resin. The resin was incubated at room temperature for 14 hours and then washed several times with TFA. The peptide was extracted with cold ether. The peptide/TFA solution was reduced to a volume of 1.0 ml with nitrogen gas. After adding 25 ml of ether, the peptide solution was mixed and incubated on dry ice for 5 min. Samples were then centrifuged at 1000g for 5 min, the ether removed, and the extraction with ethyl acetate. Ether (1.5:1 v/v) on dry ice was repeated three times. Finally 1.0 ml of water and 25 ml of ether were added to the peptide followed by another incubation on dry ice and centrifugation. The top layer was removed, the ether evaporated with nitrogen gas, and the peptide resuspended in water and dialyzed. Following dialysis, the peptide was lyophilized and stored at room temperature in a dessicator under vacuum. Proper molar ratios of the amino acids in the peptide were confirmed by amino acid analysis. YSPWTNF was soluble in dimethyl sulfoxide (DMSO).

The peptide RIP (YSPWTNF) was also synthesized by the Fmoc chemistry using FMOC-amino acyl Wang resin followed by reverse phase chromatography (courtesy of M. Booth) at the Molecular Biology Research Facility, William K. Warren Medical Research Institute, University of Oklahoma Health Science Center, Oklahoma City, Oklahoma. The peptide that was synthesized by the Fmoc chemistry, was extensively dialyzed in water and evaporated, and resulted in a yellowish powder. The powder was resuspended in 30% acetic acid, extensively vortexed and sonicated, and was further diluted to a final concentration of 6% acetic acid and 0.083% TFA. Soluble material was applied to a C8 Dynamax 300A HPLC column (Rainin Inc., Woburn, Massachusetts) and eluted by the following gradient: 0 to 21% acetonitrile in 0.083% TFA for 6 min, 21 to 27% acetonitrile in 0.083% for 18 min, followed by 27 to 60% acetonitrile in 0.083% TFA. Peptide was eluted within 21 to 27% acetonitrile gradient. The resulting peptide was white and could be solubilized in water or in DMSO.

The RIP peptides (YSPWTNF) were tested successfully for inhibition of S. aureus sepsis, septic arthritis, keratitis, osteomyelitis and mastitis (16). Our findings substantiate RIP as an effective suppressor of toxin production, that RIP is not strain specific in its inhibitory activity, and that RIP is an effective inhibitor of bacterial pathology at multiple body sites following diverse routes and doses of administration. These findings are strong evidence for the potential value of RIP as a chemotherapeutic agent.

The RIP peptide was tested following preparation by two methods described above, and peptide in each form was found to be effective in suppressing RNAIII synthesis in vitro and suppressed S. aureus in vivo. Similar positive results were obtained for those RIP samples prepared by the Fmoc system (solubilized in DMSO) and for those that were prepared in a similar fashion, then further purified by HPLC (solubilized in water). The material prepared by the Fmoc chemistry and solubilized in DMSO has been demonstrated to be more stable (that is, longer shelf life) than the more purified peptide that was water-soluble. The water-soluble form of RIP could have a greater direct penetration of biological fluids, while the DMSO preparations could release RIP to aqueous fluids in a sustained fashion. Comparisons of the two preparations are needed to determine if the drug's uptake from each formulation differs.

RIP derivatives were designed according to the putative NH₂-terminal sequence of RAP (YKPITN, see above), synthesized by the Fmoc chemistry as described above and tested for their ability to inhibit RNAIII synthesis in vitro and to inhibit S. aureus cellulitis in vivo, as described (1, 25). For the in vitro experiments, 1× culture supernatant of RN833 (native RIP) or 150 µg of synthetic peptides were incubated with 2.5 × 10⁶ wild-type S. aureus cells (RN6390B) for 2 hours at 37°C and RNAIII was determined by Northern blotting, as described (3). As shown in Fig. 3, A and B, native RIP and RIP peptides inhibited RNAIII synthesis.

RIP peptides were tested for their ability to inhibit S. aureus cellulitis in mice. The number of bacteria injected per mouse (3.5 × 10⁸) is beyond the range of protection of 1× native RIP and causes a high mortality rate (1). 3.5 × 10⁸ S. aureus Smith diffuse (SD) were incubated with buffer, with 1× native RIP (8), or with 200 µg of synthetic RIP peptides for 30 min at room temperature, and the mixtures were injected (17). Mice were followed for mortality and for development of lesion. As shown in Table 1, some of the RIP derivatives protected animals 100% from mortality (B1, B3, Q, T), as well as from cellulitis (B1). Although one animal died (1/8) in an animal group treated with the peptide B6, the remaining animals (7/8) were 100% protected also from cellulitis. Our results indicate that in the cellulitis model, peptides containing the sequence YKPITN may even have a greater therapeutic potential than the original YSPWTNF RIP peptide. We do not yet know if the high therapeutic potential of certain RIP derivatives comes from better binding of the peptide to its receptor or from differences in chemical properties and stability of the peptides in vivo. We do know, however, that differences in stability do exist because, for example, peptides that are synthesized by the Fmoc chemistry are as active but have a longer shelf life than the ones further purified by HPLC. RIP derivatives were also tested successfully for their ability to inhibit TRAP phosphorylation (not shown), suggesting that RIP and its derivatives inhibit RNAIII synthesis in a similar way to the native RIP peptide (9). None of the peptides were synthesized with a thiolactone structure, suggesting that they may be distinct from the octapeptides that require the thiolactone structure for their activity.

Table 1. Suppression of S. aureus SD sepsis/cellulitis. 3.5 × 108 CFU S. aureus strain SD were incubated with 200 µg synthetic peptides, 1× native RIP or carrier buffer for 30 min at room temperature and the mixture injected subcutaneously into Balb/C mice (17). Mortality and lesion size 7 days post challenge are indicated. Treatment group No. of mice Death Lesion No lesion n (%) n Mean size (mm2) n (%) B1 YKPITNF 8 0 0 8 (100) B2 YSPITNF 8 4 (50) 4 (1178) 0 B3YKPWTNF 8 0 8 (339) 0 B4 PWTNF 8 3 (37) 5 (953) 0 B5 PITNF 8 1 (12) 7 (1135) 0 B6 YKPITN 8 1 (12) 0 7 (87) Q YSPCTNFF 4 0 4 (520) 0 S YSPCTNF 8 4 (50) 4 (1129) 0 T YSPWTNF 4 0 4 (893) 0 U Native RIP 8 3 (37) 5 (471) 0 H2O Control 8 4 (50) 4 (2159) 0 DMSO Control 8 6 (75) 2 (707) 0 CY Control 7 5 (71) 2 (1296) 0

Interestingly, the identity of the Staphylococcus strain RN833 that produces RIP remains elusive. This strain was originally thought to be a mutated form of S. aureus (3), but has recently been identified as a coagulase negative strain. However, while one commercial Clinical Microbiology Laboratory determined it to be S. warnerii (with 85% certainty) another lab determined it to be S. xylosus (with 99% certainty) and yet another lab recently determined it to be S. hominis. The reason for these discrepancies could be that RN833 may have been mutagenized in 1968 (3) and is therefore no longer a classical strain. In an attempt to resolve the difference, we tested postexponential supernatants of various coagulase negative staphylococci for their ability to inhibit RNAIII synthesis of S. aureus. Figure 4 shows that all supernatants tested inhibited RNAIII synthesis of S. aureus. The actual inhibitory molecules have not yet been purified and therefore their sequences are not known. We also tested other strains of S. xylosus and S. saprophiticus (4) and discovered that not all strains were able to inhibit RNAIII synthesis of S. aureus, suggesting strain variability (not shown). The use of the degenerate sequence of RIP (YSPWTNF), a sequence identical to RIP, was identified in RN833 (TATTCGCCGTGGACCAATTTTTGA), which was not within the agr locus. These results suggest that RIP may be YSPWTNF and not YSPCTNFF, as suggested by Novick et al. Another possibility is that RN833 produces YSPWTNF (encoded by the above locus) as well as YSPCTNFF, encoded by the agr locus. In conclusion, as shown by Balaban et al. (1) and confirmed by Mayville et al. (2), inhibition of RNAIII synthesis by inhibitory peptides can protect animals from infections caused by S. aureus.

Naomi Balaban
Baljit Singh
Department of Pathology
University of California Medical Center
Research Building 3
4645 2nd Avenue
Sacramento, CA 95817, USA
E-mail: nbalaban{at}ucdavis.edu
Tzipora Goldkorn
Department of Internal Medicine
University of California Medical Center
Davis, CA 95616, USA
Avraham Rasooly
Division of Microbiological Studies
U.S. Food and Drug Administration
Washington, DC, USA
Jose V. Torres
Department of Medical Microbiology
and Immunology
School of Medicine
University of California
Davis, CA 95616, USA
Orit Uziel
Department of Human Microbiology
Sackler School of Medicine
Tel Aviv University, Tel Aviv, Israel

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26. We thank B. Menzies for kindly providing us with the Smith diffuse S. aureus strain, H. Matthews for helpful discussion, U. Kuhnt for reviewing the manuscript, M. Booth for the HPLC-purified RIP peptide, and I. Borovok for helpful discussions. Supported by UCDHSRA to N.B.