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Journal of Bacteriology, December 2002, p. 6559-6565, Vol. 184, No. 23
0021-9193/02/$04.00+0 DOI: 10.1128/JB.184.23.6559-6565.2002
Copyright © 2002, American Society for Microbiology. All Rights Reserved.
Area de Microbiología, Facultad de Ciencias Biológicas y Ambientales, Universidad de León, 24071 León, Spain
Received 28 June 2002/ Accepted 10 September 2002
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S. clavuligerus is an excellent model for the study of the relationships between the regulatory mechanisms controlling the biosynthesis of the different secondary metabolites produced by these microorganisms. Formation of clavulanic acid is controlled by a LysR-type regulatory protein encoded by the claR gene. Formation of both clavulanic acid and cephamycin C in S. clavuligerus is controlled by the positive autoregulatory protein CcaR (25, 32). Mutant strains with disruption in ccaR do not express the claR gene (26), although this control is not exerted directly by the CcaR regulatory protein and appears to involve a cascade mechanism (32). The control of the formation of cephamycin C and/or clavulanic acid by CcaR or ClaR is exerted at the transcription level (1, 25).
However, the ccaR::aph S. clavuligerus mutant, with disruption in ccaR, was found to produce traces of antibiotic activity in some media, and we decided to characterize and purify this antibiotic compound in order to understand its response to the CcaR regulator. The compound produced was found to be holomycin. The availability of a complete set of S. clavuligerus mutants blocked in the different steps of the clavulanic acid pathway allowed us to establish that whereas mutants blocked in the early steps of the clavulanic pathway are holomycin nonproducers, mutants blocked in the late steps of the clavulanic acid pathway synthesize very large amounts of holomycin. No enzymes or genes for holomycin biosynthesis have been described yet, but from the structure of holomycin, a putative enzyme activity in the holomycin pathway would be the formation of holomycin from deacetyl-holomycin (holothin). In this paper, we describe the formation of holomycin and holomycin synthase activities in several mutants of S. clavuligerus with disruptions in different genes involved in clavulanic acid production.
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TABLE 1. Strains used in this work
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Purification of holomycin and holothin. Holomycin was purified initially from a 2-liter culture of an S. clavuligerus ccaR::aph strain grown for 48 h in TSB medium by the procedure described by Kenig and Reading (10). The purified compound (8 mg) was used for chemical characterization. Additional batches of holomycin were purified from cultures of an S. clavuligerus cyp::aph strain. Holothin (11 mg) was obtained by hydrolysis of holomycin (20 mg) in 2N HCl by the method described by Gaeumann et al. (9). Chemical hydrolysis of pure, ninhydrin-negative, holomycin (Rf, 0.5) was followed by the detection of the ninhydrin-positive holothin (Rf, 0.45) when the hydrolysis mixture was applied to a Silica Gel 60 thin-layer chromatography plate and developed in chloroform-methanol (9:1). The compound with an Rf of 0.45 was converted by treatment with acetic anhydride (9) into a compound chromatographically identical to pure holomycin, confirming that the substance was holothin. Holothin was further purified by preparative high-performance liquid chromatography (HPLC) with a µBondapack C18 (30 by 7.8 mm) column (Waters).
Holomycin synthase assay. Holomycin synthase activity was assayed in a final volume of 50 µl of 50 mM Tris-HCl buffer (pH 8.0). The reaction mixture contained dialyzed cell extracts (2 to 50 µg), acetyl coenzyme A (acetyl-CoA) (0.5 mM), and holothin (0.5 mM) and was incubated at 30°C for 10 min. The reaction was stopped by adding 30 µl of methanol. Formation of holomycin was quantified by HPLC with a Nucleosil C18 (30 by 4 mm) column (Scharlau) with methanol (40%) at a flow rate of 1 ml/min. Both holothin (retardation time [Rt], 4.7 min) and holomycin (Rt, 6.7 min) were detected at 360 nm. The pyrrothin compounds give peaks that are concentration dependent, with a standard plot for holothin of y = 0.293x + 0.163 and with a standard plot for holomycin of y = 0.261x - 0.182, where x corresponds to peak area and y corresponds to the pyrrothin compound concentration. The plots have correlation coefficients of 0.9982 and 0.9987 for holothin and holomycin, respectively.
A unit of enzyme is defined as the enzyme activity producing 1 µmol of holomycin per min.
Chemical characterization of holomycin. The mass spectrum of holomycin was determined by A. Rumbero (Universidad Autónoma, Madrid, Spain). The solid-phase infrared (IR) spectrum was obtained with a Perkin-Elmer 2000 FTIR. The UV spectrum was obtained with a Hitachi-2000 spectrophotometer.
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The concentrated supernatant of a 48-h culture of the ccaR::aph S. clavuligerus strain grown in TSB medium was treated for 15 min at 22°C with a narrow-spectrum penicillinase (Difco) or with the broad-spectrum cephalosporinase from Enterobacter cloacae P99. The bioactivity of the sample remained unaffected by the penicillinase or cephalosporinase treatment, indicating that the compound responsible is not cephamycin C or a ß-lactam antibiotic. Samples of pure penicillin G and cephamycin C treated in parallel under the same conditions completely lost their bioactivities. No ß-lactamase inhibitory activity characteristic of clavulanic acid was detected in the sample.
The bioactive compound produced by the S. clavuligerus ccaR::aph strain was found to be extractable with n-butanol and was active against Micrococcus luteus, Bacillus sp. strain ATCC 27860, E. coli E22-31, Klebsiella pneumoniae 29665, or Alcaligenes faecalis. In addition, the broth from cultures of the S. clavuligerus ccaR::aph strain grown in defined SA medium or GSPG medium was found to be slightly yellow, suggesting that the compound produced by this mutant might be holomycin. When butanol extracts were chromatographed on Silica Gel 60 plates with chloroform-methanol (9:1) as the solvent system, a large bioactive spot was found at an Rf of 0.5, which agrees with the Rf of pure holomycin in this solvent system (20). Therefore, we proceeded to purify the bioactive compound from an S. clavuligerus ccaR::aph culture supernatant.
The UV spectrum of the purified compound in methanol showed peaks at 246, 300, and 384 nm, which are characteristic of the pyrroline ring. Moreover the IR spectrum was very similar to that of a pure preparation of holomycin provided by M. Okanishi (Fig. 1A) (21). The mass spectrum of the purified compound gave m/e peaks of 214 (M+) and 172 (M+-CH2CO), as well as peaks of 72 (C2H2SN) and 143 (C4H5SNO2), which correspond to fragmentation of the S-S linkage and the peptide linkage internal to the holomycin ring (Fig. 1B), indicating a compound with a mass of 213.98, which corresponds to the holomycin structure (Fig. 1B, inset).
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FIG. 1. (A) IR spectra of a pure sample of holomycin (solid line) and the compound purified from cultures in TSB medium of the S. clavuligerus ccaR::aph strain (dotted lane). (B) Mass spectra of the purified compound and chemical structure of holomycin.
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FIG. 2. (A) Pathway of clavulanic acid biosynthesis indicating the known intermediates and the genes encoding the different enzymes. (B) Organization of the clavulanic acid gene cluster. The disrupted genes in the mutant strains used in this work are indicated by black arrows.
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The wild-type S. clavuligerus strain produces only traces of holomycin. Culture broth from the S. clavuligerus wild-type strain 27064, grown as indicated above, showed an uniform production of holomycin of about 11 µg per mg of DNA, close to its detection limits, which is less than 20% of the holomycin produced by ccaR::aph S. clavuligerus at 48 h of culture (Fig. 3A).
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FIG. 3. Production of holomycin in SA medium by the wild-type S. clavuligerus strain ATCC 27064 ( ) and the following clavulanic acid-nonproducing strains: (A) S. clavuligerus ccaR::aph (); (B) S. clavuligerus claR::aph ( ) and S. clavuligerus car::aph ( ); (C) S. clavuligerus cyp::aph ( ), S. clavuligerus ORF12::aph ( ), and S. clavuligerus ORF15::aph ( ).
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Also the S. clavuligerus ORF6::apr strain and the S. clavuligerus ccaR::aph ORF6::apr double mutant strain showed a holomycin-negative phenotype. ORF6 encodes an ornithine acetyltransferase of unknown function in clavulanic acid biosynthesis, and the S. clavuligerus ORF6::apr strain is able to produce clavulanic acid, as well as probably the intermediates that trigger holomycin biosynthesis, although at levels lower than those of the wild-type strain. Therefore, holomycin production in this strain might be below the limits of detection. Moreover, in the S. clavuligerus ccaR::aph ORF6::apr double mutant strain, the mutations in ORF6 reverse the positive effect exerted by the ccaR mutation on holomycin formation
High levels of holomycin are produced by mutants blocked in the late steps of the clavulanic acid pathway. The S. clavuligerus car::aph and claR::aph strains showed a steady pattern of production, reaching holomycin levels of around 200 and 450 µg per mg of DNA at 96 h (Fig. 3B). Consistently, holomycin formation by the S. clavuligerus claR::aph strain was detected earlier than in the parental strain in several experiments. Both S. clavuligerus car::aph and claR::aph strains produced holomycin at levels 7- and 16-fold higher, respectively, than those of the S. clavuligerus ccaR::aph strain, in which holomycin was first detected and purified. A third group of clavulanic acid-nonproducing mutants, with the genotypes cyp::aph, ORF12::aph, and ORF15::aph (14, 16), showed very high levels of holomycin production, which reached up to 1,200 µg of holomycin per mg of DNA, or about 112-fold in relation to the wild-type strain and 45-fold in relation to the S. clavuligerus ccaR::aph strain at 96 h. The production of holomycin by the S. clavuligerus ORF15::aph strain reached levels similar to those of the S. clavuligerus cyp::aph strain at late times during the fermentation.
Effect of arginine addition on holomycin formation by the wild type and the clavulanic acid-nonproducing mutants. In early studies designed to examine the effect of arginine addition on clavulanic acid formation, we observed a slightly yellow color in the culture broths of S. clavuligerus ccaR::aph cells. Therefore, a systematic study on the effect of addition of arginine (10 mM) to SA medium on the formation of holomycin by the clavulanic acid-nonproducing mutants was performed. The S. clavuligerus ccaR::aph, claR::aph, and cyp::aph strains produced consistently more holomycin in the presence of arginine, with increases ranging from 2- to 10-fold, depending on the strain and time of the culture. The arginine stimulatory effect was stronger at early times during the fermentation (24 to 48 h), and 24 to 48 h was the only time in which any effect was observed in the ORF15::aph strain. This result is probably due to an arginine precursor effect that favors accumulation of clavulanic acid intermediates (see Discussion).
Complementation of the cyp and ORF15 mutants reverses production of high levels of holomycin. In order to determine whether the mutations in the clavulanic acid genes were responsible for the increasing production of holomycin, two disrupted mutants, S. clavuligerus cyp::aph and ORF15::aph strains, were transformed with control plasmids pULVK99 and pIJ699, and the mutations were complemented with plasmids containing ORF15 (pIJ699-ORF15) or the cyp gene (pVK99-cyp), in which those genes are expressed from the tipAp promoter (Fig. 4, inset) or their own promoter, respectively. These results showed (Fig. 4) that holomycin overproduction was clearly reduced (to 29% at 96 h) in the complemented S. clavuligerus ORF::15(pIJ699-ORF15) transformant. Similar results were observed in the S. clavuligerus cyp::aph(pVK99-cyp) transformant (not shown). The incomplete lack of reversion to nonproduction observed in the complemented ORF::15(pIJ699-ORF15) strain may be due to the presence of thiostrepton (4 µg/ml) in the cultures, which positively affects the biosynthesis of holomycin in both the control strain and the complemented strain (compare with Fig. 3).
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FIG. 4. Formation of holomycin by the disrupted S. clavuligerus mutant ORF15::aph(pIJ699) () strain and the S. clavuligerus ORF15::aph(pIJ699-ORF15) ( ) complemented strain. (Inset) Physical map of plasmid pIJ699-ORF15 used in the complementation studies. tsr and aph correspond to the thiostrepton and kanamycin resistance genes, respectively. Ter, terminator (from pIJ699). PtipA, tipA gene promoter. The restriction sites for HindIII (H), ApaI (A), SalI (S), and KpnI (K) are shown.
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Holomycin synthase activity was assayed with holothin as the acceptor substrate and either acetylglutamic acid, acetylornithine, acetylarginine, or acetyl-CoA at a concentration of 0.5 or 1 mM as the acetyl group donor. Formation of holomycin from holothin was monitored by HPLC under the conditions indicated above (Fig. 5). Only acetyl-CoA was used as acetyl donor in the reaction, and no holomycin was formed with other acetylated compounds as acetyl donors. The reaction was linear for up to 20 min for enzyme activities in the order of 0.1 to 0.8 mU/µg of protein under the standard assay conditions; therefore, all of the enzyme preparations were diluted appropriately before holomycin synthase activity was measured. As shown in Fig. 5, the reaction is irreversible, and the entire amount of holothin in the sample is converted to holomycin if enough reaction time is allowed (Fig. 5D).
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FIG. 5. Conversion of holothin into holomycin. (A) Holothin consumed ( ) and holomycin formed () during the reaction. (B to D) Holomycin (Rt, 6.7 min) and holothin (Rt, 4.7 min) present in the reaction at 0 min (B), 30 min (C), and 60 min (D), as measured by HPLC. The holothin peak is shaded. The level of holomycin synthase activity in the reaction was 0.7 mU/µg of protein.
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TABLE 2. Holomycin synthase activity in different strains of S. clavuligerusa
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There are no studies on the holomycin biosynthetic pathway, but tentatively, the compound is formed from two cysteine molecules (8) or perhaps from the condensation of cysteine and 2-amino-ethanethiol, compounds clearly unrelated to clavulanic acid, clavulanic biosynthesis intermediates, or clavulanic acid precursors.
The high level of production of holomycin by the mutant strains studied in this work suggests a role, probably regulatory, of an intermediate of the clavulanic acid (e.g., clavaminic acid or other intermediates between proclavaminic acid and clavaminic acid) in the formation of holomycin. Indeed, mutants blocked in early genes of the pathway, such as the mutants blocked in the ceaS or bls genes, showed a holomycin-negative phenotype (i.e., are unable to produce holomycin). The wild-type S. clavuligerus strain 27064, which produces low levels of clavulanic acid and does not accumulate a high enough concentration of the putative intermediate to trigger holomycin biosynthesis, is also a low holomycin producer. The stimulatory effect of arginine on holomycin production by all of the strains tested might be interpreted in the same sense. Arginine stimulates the biosynthesis of clavulanic acid in S. clavuligerus (30) as a limiting precursor of the C5 fragment of the ß-lactamase inhibitor, but in mutants with mutations in the genes car, cyp, and claR blocked in late steps of the pathway, this stimulation by arginine of the first part of the pathway results in even higher accumulation of clavaminic acid or other intermediates of the middle steps of the pathway.
The role of cla-ORF6 is especially intriguing. This gene encodes a relatively unspecific N-acetyltransferase, homologous to the argJ gene, and the proteins encoded by both genes possess ornithine-n-acetyltransferase activity (7, 11, 28). Despite producing clavulanic acid at 40% of the wild-type level, this mutant is totally unable to form holomycin under any of the conditions tested, thus excluding that clavulanic acid itself is an inducer of the holomycin pathway. There is a good correlation between the holomycin synthase activity and the level of holomycin produced by the different mutants blocked in clavulanic acid biosynthesis. The acetylation catalyzed by this enzyme is essential for antibiotic activity, since the deacetylated compound holothin is 100-fold less active than holomycin against Bacillus and Micrococcus strains (9). Dithiopyrrolone compounds, which include holomycin, have been described as having potential antitumor activity (33). The use of the mutant strains described in this work and the higher level of production of holomycin in the presence of arginine are extremely useful tools to increase the yield of this antibiotic.
We acknowledge M. Okanishi for providing a sample of pure holomycin and R. Pérez-Redondo and C. A. Townsend for the gifts of the S. clavuligerus ceaS::aph strain and Streptomyces sp. strain RLF3, respectively. We thank A. Rumbero for help with interpretation of the IR and MS spectra of holomycin.
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