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Journal of Bacteriology, December 2006, p. 8079-8086, Vol. 188, No. 23
0021-9193/06/$08.00+0     doi:10.1128/JB.00858-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

Microevolution of Cytochrome bd Oxidase in Staphylococci and Its Implication in Resistance to Respiratory Toxins Released by Pseudomonas

Lalitha Voggu,¹ Steffen Schlag,¹ Raja Biswas,¹ Ralf Rosenstein,¹ Christian Rausch,² and Friedrich Götz^1*

Microbial Genetics, University of Tübingen, 72076 Tübingen, Germany,¹ Algorithms in Bioinformatics, Wilhelm Schickard Institut für Informatik, Eberhard Karls Universität Tübingen, Sand 14, 72076 Tübingen, Germany²

Received 15 June 2006/ Accepted 24 June 2006

Top Abstract Introduction Materials and Methods Results Discussion References

 
Pseudomonas aeruginosa and Staphylococcus aureus are opportunistic pathogens and frequently coinfect the lungs of cystic fibrosis patients. P. aeruginosa secretes an arsenal of small respiratory inhibitors, like pyocyanin, hydrogen cyanide, or quinoline N-oxides, that may act against the commensal flora as well as host cells. Here, we show that with respect to their susceptibility to these respiratory inhibitors, staphylococcal species can be divided into two groups: the sensitive group, comprised of pathogenic species such as S. aureus and S. epidermidis, and the resistant group, represented by nonpathogenic species such as S. carnosus, S. piscifermentans, and S. gallinarum. The resistance in the latter group of species was due to cydAB genes that encode a pyocyanin- and cyanide-insensitive cytochrome bd quinol oxidase. By exchanging cydB in S. aureus with the S. carnosus-specific cydB, we could demonstrate that CydB determines resistance. The resistant or sensitive phenotype was based on structural alterations in CydB, which is part of CydAB, the cytochrome bd quinol oxidase. CydB represents a prime example of both microevolution and the asymmetric pattern of evolutionary change.

Top Abstract Introduction Materials and Methods Results Discussion References

 
A number of bacterial infections result from the colonization of more than one microorganism (12). Pseudomonas aeruginosa and Staphylococcus aureus are associated with diseases such as chronic lung infections in cystic fibrosis patients and peritoneal infections in patients undergoing dialysis (20). P. aeruginosa is an opportunistic pathogen that produces an arsenal of virulence factors that may act against the commensal flora as well as host cells. These virulence factors include a number of secreted and surface-associated molecules such as pilus adhesins (25), phospholipase (40), proteases (7, 36), ADP-ribosylating enzymes (37), and rhamnolipid biosurfactants (10, 29). Also among the secreted molecules are enzymes such as LasA, a staphylolytic endopeptidase (23), as well as small respiratory inhibitors like pyocyanin (19), hydrogen cyanide (5), and a mixture of quinoline N-oxides (28). Although it is thought that the antistaphylococcal activity in Pseudomonas supernatants is due mainly to LasA, our knowledge of the compounds and their antistaphylococcal activities is still fragmentary.

As most studies have focused primarily on monoculture infections, little is known about how and whether the Pseudomonas and staphylococcal strains interact with each other. Here, we show that P. aeruginosa exhibits an antagonistic relationship with S. aureus and other pathogenic staphylococci through its secreted respiratory inhibitors pyocyanin and cyanide. The nonpathogenic staphylococcal species resist these respiratory toxins released by P. aeruginosa due to cydAB genes that encode a pyocyanin- and cyanide-insensitive cytochrome bd quinol oxidase that oxidizes ubiquinol and reduces oxygen as part of the electron transport chain (6).

Top Abstract Introduction Materials and Methods Results Discussion References

 
Transposon mutagenesis and selection of mutants. Staphylococcus carnosus TM300, harboring plasmid pTV1ts, was grown overnight at 30°C in basic medium (BM) containing 5 µg ml^–1 erythromycin and 10 µg ml^–1 chloramphenicol. The culture was subsequently diluted 1:1,000 in BM broth containing 2.5 µg ml^–1 erythromycin and was incubated twice at 40°C for 12 h. Appropriate dilutions of the bacterial suspension were spread onto BM agar containing 2.5 µg ml^–1 erythromycin and incubated at 37°C. Erythromycin-resistant and chloramphenicol-sensitive mutants were further screened on BM agar plates containing 30% (vol/vol) filter-sterilized culture supernatant of P. aeruginosa PAO1 and monitored for impaired growth. Tn917-specific primers were used to sequence genomic DNA upstream and downstream from the transposon insertion sites.

Construction of the S. aureus cydAB deletion mutant. Primers SAcydA up F (5'-TACATTGCTAGCAAATGAATCCATTCTTAGG-3'; introduced restriction site is underlined) and SAcyd up R (5'-TATCATAAGCTTCGCAGAATGATTGTCCACC-3') were used to amplify the upstream flanking region of cydAB from the chromosomal DNA of S. aureus SA113. The PCR product was cloned into the NheI/HindIII sites of pBT2, creating plasmid pBT2-F1. Primers SAcydB downF (5'-TACATTGGATCCTTGAGACGATACCCCAAC-3') and SAcydB down R (5'-TATCATGAATTCCCAGTCATTATGAAGGTAAAC-3') were used to PCR amplify the downstream flanking region of cydB. The PCR product was cloned into the BamHI/EcoRI sites of pBT2-F1, yielding pBT2-F1-F2. The erythromycin cassette (ermB) from pEC2 was ligated into the HindIII/BamHI sites of pBT2-F1-F2, generating pBT2-KO1. All recombinant plasmids were introduced into Escherichia coli DH5. Plasmids were introduced into staphylococci via electroporation (2). Allelic replacement of wild-type cydAB genes by ermB was carried out as described previously by Brückner (4). The sequence of the altered genes of the resulting strain S. aureus cydAB::ermB was confirmed by PCR and DNA sequence analyses.

Construction of cydAB_Sa and cydAB_Sc expression plasmids. Primers SAcydA F (5'-TACATTGGATCCAAAAGGTGATGTTTTTAAATG-3') and SAcydB R (5'-TATCATCTGCAGTTATGATTTCTTTCCTTC-3') were used to amplify the cydAB genes from S. aureus SA113 genomic DNA. The PCR product after digestion with BamHI at one end was ligated to BamHI/SmaI-digested pCX19, resulting in plasmid pCXcydAB_Sa. Expression of S. aureus cydAB (cydAB_Sa) genes was induced by the addition of 0.5% xylose to cultures at an optical density at 578 nm (OD₅₇₈) of 0.5. S. carnosus TM300 cydAB (cydAB_Sc) genes with their native promoter were amplified by PCR from genomic DNA using the primers SCcydA F (5'-TACATTAGTACTCTTTATTAAAAGTGA-3') and SCcydB R (5'-TTATTGCTGCAGTTAATAATGACCTTCTTC-3'). The resulting PCR product was cloned into ScaI/PstI sites of pCX19, generating plasmid pCcydAB_Sc; the recombinant plasmid lacked the xylR regulation gene. This plasmid was used to complement S. carnosus cydAB mutants. Ligation mixtures were transferred into staphylococci by protoplast transformation (15).

Exchanging cydB of S. aureus with cydB of S. carnosus. The primer pair SaCydApromF (5'-ATTATAAGATCTCACAATTTCATAGCGC-3') and SaCydABR (5'-TGAACCTGGTACCAACAATACCGTGCC-3') was used to amplify cydA and the first part of the cydB gene (including the first 81 amino acids) of S. aureus. The PCR product obtained was restricted with BglII/KpnI and ligated with plasmid pRB473 precut with BamHI/KpnI. The plasmid obtained was designated pRBcydA. S. carnosus cydB was amplified from codon 81 using the primer pair ScCydBF (5'-GTATTACTGGTACCAGGGTCTATTGGATTG-3') and SchiscydBR (5'-TACATTGAGCTCTTAATAATGACCTTCTTCAC-3'). The amplicon obtained was restricted with KpnI/SacI and ligated into pRBcydA precut with the same enzymes. The plasmid generated was named as pRBcydA_SaB_Sc. Primers SaCydABR and ScCydBF were designed to anneal to the overlapping sequence of the cydB of both S. aureus and S. carnosus, and a KpnI site was generated by a single nucleotide exchange without altering the amino acid sequence.

Measurement of oxygen uptake. S. aureus clones were precultivated aerobically in the presence of xylose to induce the plasmid-encoded cydAB genes. Cells were pelleted from a culture grown in BM broth for 12 h, washed, and resuspended in 33 mM potassium phosphate buffer (pH 7.0) to a final volume of 1.5 ml (OD₅₇₈ of 50) at 25°C. The washed cell suspensions were analyzed for oxygen consumption using a Clark-type oxygen electrode. Respiration was initiated by the addition of 50 mM succinate as an electron donor to the cell suspension. After 30 to 40% of the oxygen was consumed, i.e., approximately 5 min after the addition of succinate, freshly prepared sodium cyanide solution (1.5 mM) was added.

Purification and analysis of pyocyanin. Pyocyanin was isolated as described previously (8). For isolation of pyocyanin, P. aeruginosa was cultivated in various media: tryptic soy (TS) broth, pyocyanogenic medium (succinate minimal medium with 0.1 mM potassium phosphate buffer), and apyocyanogenic medium (succinate minimal medium with 4 mM potassium phosphate buffer) (3). Purified pyocyanin was analyzed by reverse-phase high-performance liquid chromatography (HPLC) using a Hypersil ODS C₁₈ column (5 µm, Grom. 125 by 4.6 mm) with a solvent flow rate of 350 µl min^–1. The flow consisted of 2 min of 8% acetonitrile-25 mM ammonium acetate followed by a 25-min linear gradient to 80% acetonitrile-25 mM ammonium acetate. Pyocyanin was detected at 313 nm.

Agar disk diffusion assay. P. aeruginosa strains PAO1 and SH1 were incubated in TS agar medium at 37°C for 24 h. Cells were pelleted by centrifugation, and the culture supernatant was filtered through 0.22-µm-pore-size filters and stored at 4°C. Staphylococcal cells (100 µl of a culture grown overnight at 37°C in TS broth medium) were mixed with 4 ml of TS soft agar (TS broth plus 0.75% agar) and poured onto TS agar plates. Sterile filter disks spotted with 25 µl of P. aeruginosa culture supernatant were placed on top of the soft agar. Plates were incubated at 37°C and photographed after 12 h.

CydAB partial purification. Cell pellets obtained from a 1-liter culture were resuspended in 30 ml digestion buffer (30% raffinose, 25 mM Tris-HCl [pH 7.5], 145 mM NaCl) containing 200 µg/ml lysostaphin, 5 µg DNase, and 1 mM phenylmethylsulfonyl fluoride. The protoplasts obtained after incubation at 37°C were broken by two passages through a French pressure cell. All further steps were carried out at 4°C. Unbroken cells were removed by centrifugation at 11,200 x g for 10 min. Membranes were pelleted at 100,000 x g for 1 h, resuspended in 50 mM Tris-HCl (pH 7.5) containing 2% sodium cholate, and stirred for 1 h before centrifugation at 100,000 x g for 1 h. The pellet obtained was resuspended in 100 mM Tris-HCl (pH 7.5), and dodecyl maltoside was added to a final concentration of 1.5% (wt/vol). The suspension was stirred for 1 h before centrifugation at 45,000 x g for 30 min.

Heme staining. The partially purified CydAB proteins were subjected to native polyacrylamide gel electrophoresis without boiling and stained for heme-dependent peroxidase activity (31). Briefly, the gel was incubated in 10% trichloroacetic acid for 30 min at 25°C. The gel was rinsed with water before it was incubated in the dark for 1 to 2 h in the heme stain. This stain contained 3 parts of 6.3 mM 3,3',5,5'-tetramethylbenzidine dissolved in methanol and 7 parts of 0.25 M sodium acetate, pH 5.0. The gel was developed for 10 to 20 min by adding 60 mM H₂O₂. Finally, the gel was placed into a stop solution containing 30% isopropyl alcohol and 0.25 M sodium acetate, pH 5.0. Lastly, the gel was photographed.

Phylogenetic analysis of CydA and CydB proteins. CydA and CydB protein sequences of S. aureus, S. carnosus, S. epidermidis, S. haemolyticus, S. piscifermentans, Bacillus subtilis, Corynebacterium glutamicum, Chromobacterium violaceum, Escherichia coli, Listeria monocytogenes F2365, Mycobacterium tuberculosis, and Pseudomonas aeruginosa were obtained from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database. The sequences were aligned using the program MUSCLE (13, 14). We calculated a distance-based tree with the neighbor-joining (NJ) method (33) using protdist and neighbor from the PHYLIP package (J. Felsenstein, University of Washington) and a character-based (maximum-likelihood [ML]) tree using IQPNNI (38). To estimate the significance of the NJ tree, a 1,000-fold bootstrap analysis was carried out using PHYLIP's seqboot. The tree was visualized with SplitsTree4 (21); the same program was used to calculate the majority-rule consensus of the 1,000 bootstrap trees.

For comparison, pairwise global sequence similarities of subsets were computed with the program stretcher of the EMBOSS program package (32).

Top Abstract Introduction Materials and Methods Results Discussion References

 
Distribution of resistance/sensitive phenotype in various staphylococcal species. While studying the antagonistic activity of P. aeruginosa against S. aureus and other staphylococcal species, we found that stationary-phase culture supernatants of P. aeruginosa PAO1 and another clinical isolate, SH1, inhibited the growth of all S. aureus and S. epidermidis strains tested, including their clinical isolates, as well as species representatives of S. haemolyticus, S. saprophyticus, S. hyicus, S. muscae, and S. lugdunensis. However, the growth of apathogenic staphylococcal species such as S. carnosus, S. piscifermentans, S. simulans, S. lentus, and S. gallinarum was not inhibited. S. carnosus was resistant even when a 10-fold excess of P. aeruginosa culture supernatant was used. The resistance of S. carnosus and the susceptibility of S. aureus and S. epidermidis are illustrated by the agar disk diffusion assay (Fig. 1A).

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FIG. 1. (A) Agar disk diffusion assay with wild-type (WT) S. carnosus (17) and its cydA::Tn917 mutant, wild-type S. aureus SA113, S. aureus harboring pCcydABSc, and wild-type S. epidermidis. Filter disks were impregnated with 25 µl filter-sterilized culture supernatant of P. aeruginosa. (B) Gene organization of the S. carnosus cydAB region with the Tn917 insertion site. (C) Relevant part of plasmid pCcydABSc encoding cydABSc under the control of its native promoter. (D) Relevant part of plasmid pCXcydABSa encoding cydABSa under the control of a xylose-inducible promoter.

Role of cydAB in resistance to P. aeruginosa culture supernatants. In order to identify the gene locus responsible for the resistance to the P. aeruginosa culture supernatant, S. carnosus was mutagenized with transposon Tn917. Around 1,500 mutants were screened on BM agar plates containing 30% (vol/vol) filter-sterilized culture supernatant of P. aeruginosa PAO1 and monitored for impaired growth. Six sensitive mutants were identified; an agar disk diffusion assay of one representative mutant (cydA::Tn917) is shown in Fig. 1A. The analysis of chromosomal sequences flanking the Tn917 insertion site revealed that all the insertions were in the cydAB genes, which encode the two subunits of the cytochrome bd-type quinol oxidase. Three of the Tn917 mutations were located within cydA, two were in the cydA promoter region, and one was within cydB. One mutant with the Tn917 insertion in cydA, cydA::Tn917 (Fig. 1B), was chosen for further studies. The mutant could be complemented with vector pCcydAB_Sc (Fig. 1C), containing the entire S. carnosus cydAB operon (cydAB_Sc genes) with its native promoter. These data indicate that in S. carnosus, CydAB_Sc confers resistance to secreted toxins of P. aeruginosa, which produces various toxic compounds such as cyanide (5), pyocyanin (27), and quinolone signal molecules (11) as secondary metabolites.

CydAB_Sc is essential for growth of S. carnosus in the presence of cyanide. Normally, the respiration of bacteria expressing cytochrome bd quinol oxidase is cyanide insensitive (1); therefore, we investigated whether the growth of S. carnosus, S. carnosus cydA::Tn917, and S. carnosus cydA::Tn917(pCcydAB_Sc) is affected by cyanide. In the presence of 1.5 mM sodium cyanide, S. carnosus and the complemented mutant, S. carnosus cydA::Tn917(pCcydAB_Sc), grew at a slow but constant rate. In contrast, the growth of the S. carnosus cydA::Tn917 mutant was almost completely inhibited (Fig. 2). In the absence of cyanide, wild-type S. carnosus and the cydA::Tn917 mutant grew equally well.

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FIG. 2. Growth of S. carnosus cydA::Tn917 is completely inhibited by 1.5 mM cyanide. , S. carnosus cydA::Tn917; •, wild-type S. carnosus; , S. carnosus cydA::Tn917(pCcydABSc). Open symbols indicate growth in presence of 1.5 mM sodium cyanide. Closed symbols indicate growth in the absence of cyanide. The arrow indicates the time point of the addition of 1.5 mM sodium cyanide (CN) to the growing cultures.

CydAB_Sc imparts resistance to P. aeruginosa culture supernatants in S. aureus. When transformed with pCcydAB_Sc, S. aureus SA113 became almost as resistant to the P. aeruginosa culture supernatant as the S. carnosus wild type (Fig. 1A). Based on this result, we expected that S. aureus strains would lack the cydAB genes. Surprisingly, all S. aureus and S. epidermidis genomes available so far encode homologous cydAB genes at the same locus as that in S. carnosus (sequence similarities of the encoded proteins of 82% for CydA and 65% for CydB). In order to evaluate the role of cydAB genes in S. aureus, we replaced the genes with an erythromycin cassette (Fig. 3A) and also complemented this mutant with the recombinant plasmid pCXcydAB_Sa, which was constructed by cloning the cydAB_Sa genes in the xylose-inducible vector pCX19 (Fig. 1D). S. aureus was also transformed with pCcydAB_Sc. S. aureus cydAB::ermB and S. aureus cydAB::ermB(pCXcydAB_Sa) were sensitive to P. aeruginosa culture supernatant (Fig. 3A), cyanide (Fig. 3B), and pyocyanin (Fig. 3C), indicating that the cydAB_Sa genes were unable to confer resistance. However, S. aureus cells expressing CydAB_Sc became resistant to cyanide and pyocyanin (Fig. 3B and C) and to P. aeruginosa culture supernatant (Fig. 1A). Therefore, only the S. carnosus cydAB genes impart resistance. In order to determine whether insufficient expression of the cydAB genes in S. aureus is responsible for its susceptibility, the CydAB complex was partially purified from various S. aureus and S. carnosus clones and monitored for CydAB production by using zymograms stained for heme-dependent peroxidase activity. The S. aureus wild type produced low levels of CydAB but clearly increased amounts in the presence of pCXcydAB_Sc or pCXcydAB_Sa (see Fig. S1 in the supplemental material).

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FIG. 3. Effect of cyanide and pyocyanin. (A) Deletion of cydAB in S. aureus and susceptibility of S. aureus cydAB to the culture supernatant of P. aeruginosa. (B and C) Susceptibility of S. aureus clones to cyanide (B) and pyocyanin (C). •, S. aureus; , S. aureus cydAB; , S. aureus cydAB(pCXcydABSa); , S. aureus(pCcydABSc). Cells were grown in BM broth to an OD578 of approximately 0.5. Arrows indicate time points of the addition of 1.5 mM sodium cyanide (CN) and 10 µM pyocyanin (PY).

Effect of cyanide on cellular respiration. Cyanide caused an almost immediate cessation of oxygen consumption in S. aureus cydAB::ermB and S. aureus cydAB::ermB(pCXcydAB_Sa) but not in S. aureus(pCcydAB_Sc) (Fig. 4). As expected, the respiration of S. carnosus was insensitive to cyanide, whereas its cydA::Tn917 mutant was sensitive (data not shown). These results showed that only the S. carnosus cytochrome bd quinol oxidase (CydAB_Sc) functions as a cyanide-resistant alternative terminal oxidase.

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FIG. 4. Effect of cyanide on succinate-dependent O2 consumption of S. aureus strains. The oxygen concentration was measured polarographically. Respiration was initiated with 50 mM succinate as a substrate. The dotted line represents oxygen consumption after the addition of succinate (control, without cyanide). Solid lines indicate the effect of sodium cyanide (CN) (1.5 mM) on respiration initiated by succinate. •, S. aureus; , S. aureus cydAB; , S. aureus cydAB(pCXcydABSa); , S. aureus(pCcydABSc).

Pyocyanin is an important antistaphylococcal compound in P. aeruginosa extracts. The antibacterial mechanism of pyocyanin is less clear than that of cyanide. Pyocyanin is secreted into the medium by P. aeruginosa in copious amounts. Pyocyanin was isolated and purified to study its effect on the growth inhibition of S. aureus. The bluish-green pigment, pyocyanin, was produced in phosphate-poor medium (pyocyanogenic medium) and in TS broth but not in phosphate-rich (apyocyanogenic) medium. Purified pyocyanin was analyzed by reverse-phase HPLC (Fig. 5A), and its spectrum revealed the characteristic absorption maxima for pyocyanin (Fig. 5B). S. aureus growth was inhibited by purified pyocyanin and culture supernatants of P. aeruginosa cells grown in TS broth and pyocyanogenic medium but not by supernatants from apyocyanogenic medium (Fig. 5C). These results indicate that pyocyanin, which is active at concentrations that are almost 100-fold lower than those of cyanide, is an important antistaphylococcal compound produced in abundance by P. aeruginosa.

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FIG. 5. (A) HPLC analysis of purified pyocyanin from pyocyanogenic medium. (B) UV spectra of purified pyocyanin obtained from pyocyanogenic medium. mAU, milli-absorption units. (C) Agar disk diffusion assay with S. aureus. Filter disks contain culture supernatant of P. aeruginosa grown in pyocyanogenic medium (plate 1), apyocyanogenic medium (plate 2), purified pyocyanin (plate 3), and chloroform extract from apyocyanogenic culture (plate 4). The retention time for pyocyanin was 6.2 min, and the typical absorption maxima were at 237, 313, and 376 nm.

Sequence alterations in CydB are responsible for the resistant or sensitive phenotype in pathogenic and nonpathogenic staphylococcal species. Unlike CydA, we find no homologues of Staphylococcus-specific CydB in E. coli or B. subtilis. Even within the various staphylococcal species, the primary sequence reveals marked differences at various sites in the CydB sequence (Fig. 6A). The substitution of the C-terminal portion of CydB of S. aureus (from amino acid position 82 to the C terminus) (Fig. 6A, underlined sequence) with the corresponding CydB sequence of S. carnosus conferred enhanced cyanide (1.5 mM) resistance to S. aureus(pRBcydA_SaB_Sc) (Fig. 6B). In the absence of cyanide, the S. aureus parent strain and its transformants grew equally well. This result indicates that the slight differences in sequence and structure of the CydB subunit are responsible for the resistant or sensitive phenotype of the various species mentioned.

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FIG. 6. (A) Multiple sequence alignment of the protein sequences of subunit CydB using ClustalW. Sequences shown are CydBSc (Sc_CydB) and CydBSa (Sa_CydB). Identical amino acid residues are shaded in black, whereas similarly charged amino acids are shaded gray. Amino acids that differ between the two strains are boxed. The part where CydB of S. aureus is exchanged with that of S. carnosus is underlined. (B) Growth of S. aureus and its transformants in the presence of 1.5 mM cyanide. , S. aureus(pRBcydASaBSc); •, wild-type S. aureus; , S. aureus(pCcydABSc). Open symbols indicate growth in the presence of cyanide. Closed symbols indicate growth in the absence of cyanide. The arrow indicates the time point of the addition of 1.5 mM sodium cyanide to the growing cultures.

Phylogenetic analysis of CydA and CydB proteins: CydB represents a prime example of microevolution. CydA is more conserved in staphylococci than CydB. Amino acid sequence identity within the pathogenic and apathogenic species lies in the range of 79 to 96%; the values between the two groups were around 70%. This is in line with the few changes observed in the amino acid sequence alignment (see Fig. S2 in the supplemental material). CydB also appears to be conserved within the pathogenic and apathogenic species. However, the amino acid sequence identity between the two groups is only between 56 and 59%, which represents rather high sequence variation, implying that CydB suffered a higher evolutionary rate than CydA. This is surprising, as cydAB are organized in the same operon, are cotranscribed (start and stop codons are overlapping), and are under the same evolutionary pressure. Indeed, it has been found that the subunits within the cytochrome bd complex vary considerably among different species and that subunit II (CydB equivalent) evolved 1.2 times faster on most of the branches of its phylogeny than subunit I genes (18). The phylogenetic trees of CydA and CydB protein sequences obtained with the NJ method and ML method had the same topologies (ML tree not shown). The mean mutual global sequence similarity of CydA and CydB proteins of the selected nonstaphylococci is very close (54% and 53%, respectively), whereas the homologous proteins from staphylococci resemble each other by 88% versus 81% (similarity), respectively, indicating that staphylococcal CydA proteins are more similar to each other than are CydB proteins of the same genus (Fig. 7). Whereas the subtrees of nonstaphylococcal CydA and CydB were almost superimposable, staphylococcal CydB sequences appear to have more divergence from each other than do staphylococcal CydA sequences. S. carnosus and S. piscifermentans CydB are more distant from the other CydBs of the same genus than they are in the CydA subtree. The mean similarity between CydA of nonstaphylococci and CydA of staphylococci is 46%, whereas the CydB of nonstaphylococcal species and that of staphylococcal species have a mean similarity of only 36%. This again is easily observable on the phylogenetic tree (Fig. 7). CydB represents a prime example of microevolution (evolution on a small scale at the species level). It also represents an interesting example of an asymmetric pattern of evolutionary change.

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FIG. 7. Phylogenetic tree of CydA and CydB proteins of five staphylococcal species and seven other species (for details, see Materials and Methods). Numbers at the edges denote bootstrap support values. (All bootstrap values are >67.8 and at most >90). The evolutionary distance is proportional to the edge length. The tree reveals that CydB sequences of staphylococci are more distantly related to CydB sequences of nonstaphylococci than is the case in the subset of CydA sequences. Furthermore, staphylococcal CydB sequences are mutually more distant than are staphylococcal CydA sequences.

Top Abstract Introduction Materials and Methods Results Discussion References

 
In this study, we found that Pseudomonas aeruginosa exhibits an antagonistic relationship with Staphylococcus via its secreted respiratory inhibitors. The presence of a resistant or sensitive CydAB, the cytochrome bd oxidase, governs the impact of the respiratory inhibitors on the respiration and thereby the viability of staphylococci. Our results indicated that S. aureus produces low levels of CydAB, but even when the cydAB_Sa genes were overexpressed, the corresponding clones did not become pyocyanin or cyanide resistant. Therefore, even though the S. aureus and S. carnosus CydAB proteins have similar structural patterns, only the latter confers resistance. Both S. carnosus and S. aureus CydA proteins have characteristic amino acids found in Escherichia coli and Bacillus subtilis CydA proteins, which also encode two subunits of cytochrome bd-type quinol oxidase (6, 41). In E. coli, CydA, His-19, His-186, and Met-393 provide three of the four axial ligands to the iron of the three hemes in the cytochrome bd complex (35). These amino acid residues are conserved in S. carnosus and S. aureus CydA proteins (His-18, His-183, and Met-393). The 11-amino-acid stretch in E. coli and B. subtilis CydA proteins, thought to constitute part of the ubiquinol binding site (22), is also present in S. carnosus and S. aureus CydA (residues 252 to 262). The CydA heme binding and Q-loop motifs that are conserved in B. subtilis and E. coli, and also in Corynebacterium glutamicum (26) and P. aeruginosa (9), are also found in S. carnosus and S. aureus CydA (see Fig. S2 in the supplemental material). CydA is highly conserved in all the staphylococcal species and also in Escherichia coli and Bacillus subtilis. The S. aureus CydA is not only highly conserved, it is also functional together with the S. carnosus-specific CydB subunit.

Our results indicate that subunit B governs cyanide and pyocyanin resistance. Therefore, we speculate that there was a higher selective pressure on CydB than on CydA, leading to asymmetric evolution. The driving force very likely was the selection of cydB mutants that resist the respiratory toxic compounds produced by Pseudomonas. We assume that the resistant nonpathogenic staphylococcal species share their natural habitat with Pseudomonas species and have therefore evolved a resistant phenotype. Little is known with respect to the habitat of nonpathogenic staphylococcal species. Many of them can be isolated from food or are even used in food fermentation, e.g., S. carnosus, S. xylosus, S. equorum, S. arlettae, S. condimenti, and S. piscifermentans. For a long time, S. carnosus, S. xylosus, and S. equorum have been used as starter cultures for the production of raw fermented sausages and hams (34), and the cheese industry employs S. succinus subsp. casei, S. equorum, and S. xylosus as starter cultures in red smear cheese production. We assume that these staphylococcal species live in an environment that is also occupied by Pseudomonas and that they have learned to resist cyanide and pyocyanin to be able to coexist with Pseudomonas.

The mechanism of resistance of cytochrome bd oxidase to cyanide can be explained by bypassing the electrons to the cyanide-insensitive oxidase (Fig. 8). However, the resistance mechanism for pyocyanin is unclear. It has been described that in vitro pyocyanin oxidizes NADH+H⁺, forming O₂^– and H₂O₂ as by-products, and it was concluded that the production of these reactive oxygen species is responsible for the antibiotic activity of pyocyanin (19). However, it is unlikely that pyocyanin-resistant cytochrome bd quinol oxidase protects NADH-H⁺ from oxidation by pyocyanin. We assume that in vivo pyocyanin interferes with components of the respiratory chain. Since cytochrome bd quinol oxidases oxidize dihydroubiquinol or dihydromenaquinol while reducing oxygen to water, we postulate that pyocyanin very likely becomes reduced to a toxic radical form. This reduction occurs somewhere between the electron flow from the menaquinol pool to cytochrome b and/or from the terminal oxidases (cytochrome aa₃ or cytochrome o) to oxygen, as indicated in Fig. 8.

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FIG. 8. Proposed pathway of electron transport in staphylococci. The meager information available on the respiratory components of staphylococci (16) suggests a branched respiratory system consisting of two alternative and menaquinol-dependent terminal oxidases, a cytochrome bo and a cytochrome aa3 oxidase. NADH-dehydrogenase (DHase) delivers electrons to the menaquinone pool. From there, the electrons are transferred either to cytochrome b (Cyt b) or to the alternative electron acceptor, cytochrome bd quinol oxidase. Cytochrome b transfers the electrons to one of two terminal oxidases, cytochrome o or cytochrome aa3. These terminal oxidases transfer the electrons to oxygen and are cyanide sensitive. Quinoline N-oxides interfere with electron transfer by inhibiting the oxidation of cytochrome b1 and the reduction of cytochrome a2. Pyocyanin also interferes with electron transfer, but it is not known whether it inhibits the electron transfer from the menaquinone pool to cytochrome b or from the two terminal oxidases to oxygen or whether it is involved in both steps. We showed that the bypass pathway through cytochrome bd quinoline oxidase is resistant to pyocyanin, cyanide, and also quinoline oxides in apathogenic staphylococci. Due to the low molecular weight, hydrophobic alkyl-hydroxyquinoline N-oxides (28) are also called the Pseudomonas quinolone signal molecules. These quinoline N-oxides are known to inhibit the growth of S. aureus and other gram-positive organisms. They inhibit the oxidation of cytochrome b and the reduction of cytochrome c in general. In S. aureus, they inhibit the oxidation of cytochrome b1 and the reduction of cytochrome a2 (24). The scheme is necessarily incomplete, since not all of the components of the respiratory chain of S. aureus and other staphylococci have been identified. CN, sodium cyanide.

It is intriguing that S. aureus and other pathogenic staphylococcal species have not evolved a cyanide- and pyocyanin-resistant respiration. Our hypothesis is that in their evolution, they have been so much adapted to their hosts (animals and humans) that they either have not gained or have lost the ability to resist the respiratory toxins released by Pseudomonas species. Probably, there was no real selective pressure, as pathogenic Staphylococcus and Pseudomonas species do not interact frequently during infection. For example, in the course of lung infection in cystic fibrosis patients, S. aureus infection frequently comes first and is later followed by P. aeruginosa infection. But even when they infect the same organ, they must not necessarily reside at the same site. The persistence of S. aureus in cystic fibrosis has previously been associated with the isolation of a subpopulation of S. aureus with small-colony variant (SCV) phenotypes (30, 39). Our preliminary studies reveal that S. aureus SCVs are indeed resistant towards pyocyanin and cyanide. A detailed study involving S. aureus SCVs and their susceptibility is in progress.

The apathogenic species representatives have evolved a higher tolerance, suggesting that they share their biotope more frequently with Pseudomonas species than with pathogenic staphylococci. It should be noted that Pseudomonas species that live in soil, such as P. fluorescence and P. aureofaciens, also produce these phenazine compounds. We don't know whether pathogenic staphylococcal species have developed backwards from an originally cyanide-resistant cytochrome bd-type quinol oxidase to a sensitive one or whether the originally sensitive bd-type quinol oxidases in nonpathogenic staphylococci have evolved to resistant ones. We favor the latter evolutionary pathway, as there is selective pressure as a driving force.

 
We thank Leo Eberl (Institute of Plant Biology, University of Zürich), Larry Gallagher (Genome Sciences, University of Washington), and Jeffery A. Hobden (Immunology and Microbiology, Wayne State University) for providing us with P. aeruginosa strains. We thank Rüdiger Hampp (Botanical Institute, University of Tübingen) for support in oxygen consumption assays.

This work was supported by the DFG, Graduate College, Infection Biology, GKI 685, and the BMBF PathoGenoMik (031U213B).

 
* Corresponding author. Mailing address: Mikrobielle Genetik, Universität Tübingen, Auf der Morgenstelle 28, D-72076 Tübingen, Germany. Phone: (49) 7071 2974636. Fax: (49) 7071 295039. E-mail: friedrich.goetz{at}uni-tuebingen.de.

Supplemental material for this article may be found at http://jb.asm.org/.

Top Abstract Introduction Materials and Methods Results Discussion References

 

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Journal of Bacteriology, December 2006, p. 8079-8086, Vol. 188, No. 23
0021-9193/06/$08.00+0     doi:10.1128/JB.00858-06
Copyright © 2006, American Society for Microbiology. All Rights Reserved.

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