1887

Abstract

ADEP, a molecule of the acyl depsipeptide family, has an antibiotic activity with a unique mode of action. ADEP binding to the ubiquitous protease ClpP alters the structure of the enzyme. Access of protein to the ClpP proteolytic chamber is therefore facilitated and its cohort regulatory ATPases (ClpA, ClpC, ClpX) are not required. The consequent uncontrolled protein degradation in the cell appears to kill the ADEP-treated bacteria. ADEP is produced by . Most sequenced genomes of have five genes, organized as two distinct bicistronic operons, and , and a single gene. We investigated whether the different Clp proteases are all sensitive to ADEP. We report that ClpP1 is a target of ADEP whereas ClpP3 is largely insensitive. In wild-type , expression is constitutively repressed and the reason for the maintenance of this operon in has been elusive. ClpP activity is indispensable for survival of actinomycetes; we therefore tested whether the operon, encoding an ADEP-insensitive Clp protease, contributes to a mechanism of ADEP resistance by target substitution. We report that in , inactivation of ClpP1ClpP2 production or protease activity is indeed a mode of resistance to ADEP although it is neither the only nor the most frequent mode of resistance. The ABC transporter SclAB (orthologous to the multidrug resistance pump SCO4959–SCO4960) is also able to confer ADEP resistance, and analysis of strains with deletions indicates that there are also other mechanisms of ADEP resistance.

Funding
This study was supported by the:
  • Institut Pasteur
  • Centre National de Recherche Scientifique
  • IRA-IB
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2011-08-01
2024-04-27
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References

  1. Bellier A., Mazodier P. ( 2004). ClgR, a novel regulator of clp and lon expression in Streptomyces . J Bacteriol 186:3238–3248 [View Article][PubMed]
    [Google Scholar]
  2. Bellier A., Gominet M., Mazodier P. ( 2006). Post-translational control of the Streptomyces lividans ClgR regulon by ClpP. Microbiology 152:1021–1027 [View Article][PubMed]
    [Google Scholar]
  3. Bentley S. D., Chater K. F., Cerdeño-Tárraga A. M., Challis G. L., Thomson N. R., James K. D., Harris D. E., Quail M. A., Kieser H. et al. ( 2002). Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147 [View Article][PubMed]
    [Google Scholar]
  4. Bradford M. M. ( 1976). A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Biochem 72:248–254 [View Article][PubMed]
    [Google Scholar]
  5. Brötz-Oesterhelt H., Beyer D., Kroll H. P., Endermann R., Ladel C., Schroeder W., Hinzen B., Raddatz S., Paulsen H. et al. ( 2005). Dysregulation of bacterial proteolytic machinery by a new class of antibiotics. Nat Med 11:1082–1087 [View Article][PubMed]
    [Google Scholar]
  6. de Crécy-Lagard V., Servant-Moisson P., Viala J., Grandvalet C., Mazodier P. ( 1999). Alteration of the synthesis of the Clp ATP-dependent protease affects morphological and physiological differentiation in Streptomyces . Mol Microbiol 32:505–517 [View Article][PubMed]
    [Google Scholar]
  7. Floriano B., Bibb M. ( 1996). afsR is a pleiotropic but conditionally required regulatory gene for antibiotic production in Streptomyces coelicolor A3(2). Mol Microbiol 21:385–396 [View Article][PubMed]
    [Google Scholar]
  8. Gottesman S. ( 1999). Regulation by proteolysis: developmental switches. Curr Opin Microbiol 2:142–147 [View Article][PubMed]
    [Google Scholar]
  9. Gottesman S., Maurizi M. R. ( 1992). Regulation by proteolysis: energy-dependent proteases and their targets. Microbiol Rev 56:592–621[PubMed]
    [Google Scholar]
  10. Gottesman S., Wickner S., Maurizi M. R. ( 1997). Protein quality control: triage by chaperones and proteases. Genes Dev 11:815–823 [View Article][PubMed]
    [Google Scholar]
  11. Grimaud R., Kessel M., Beuron F., Steven A. C., Maurizi M. R. ( 1998). Enzymatic and structural similarities between the Escherichia coli ATP-dependent proteases, ClpXP and ClpAP. J Biol Chem 273:12476–12481 [View Article][PubMed]
    [Google Scholar]
  12. Hinzen B., Raddatz S., Paulsen H., Lampe T., Schumacher A., Häbich D., Hellwig V., Benet-Buchholz J., Endermann R. et al. ( 2006). Medicinal chemistry optimization of acyldepsipeptides of the enopeptin class antibiotics. ChemMedChem 1:689–693 [View Article][PubMed]
    [Google Scholar]
  13. Hopwood D. A., Bibb M. J., Chater K. F. et al. ( 1985). Genetic Manipulation of Streptomyces. A Laboratory Manual Norwich, UK: John Innes Foundation;
    [Google Scholar]
  14. Jenkins G., Cundliffe E. ( 1991). Cloning and characterization of two genes from Streptomyces lividans that confer inducible resistance to lincomycin and macrolide antibiotics. Gene 108:55–62 [View Article][PubMed]
    [Google Scholar]
  15. Kieser T., Bibb M., Buttner K., Chater K., Hopwood D. A. ( 2000). Practical Streptomyces Genetics Norwich, UK: John Innes Foundation;
    [Google Scholar]
  16. Kim M. S., Hahn M. Y., Cho Y., Cho S. N., Roe J. H. ( 2009). Positive and negative feedback regulatory loops of thiol-oxidative stress response mediated by an unstable isoform of σR in actinomycetes. Mol Microbiol 73:815–825 [View Article][PubMed]
    [Google Scholar]
  17. Kirstein J., Hoffmann A., Lilie H., Schmidt R., Rübsamen-Waigmann H., Brötz-Oesterhelt H., Mogk A., Turgay K. ( 2009). The antibiotic ADEP reprogrammes ClpP, switching it from a regulated to an uncontrolled protease. EMBO Mol Med 1:37–49 [View Article][PubMed]
    [Google Scholar]
  18. Laemmli U. K. ( 1970). Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Nature 227:680–685 [View Article][PubMed]
    [Google Scholar]
  19. Lee B. G., Park E. Y., Lee K. E., Jeon H., Sung K. H., Paulsen H., Rübsamen-Schaeff H., Brötz-Oesterhelt H., Song H. K. ( 2010a). Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism. Nat Struct Mol Biol 17:471–478 [View Article][PubMed]
    [Google Scholar]
  20. Lee M. E., Baker T. A., Sauer R. T. ( 2010b). Control of substrate gating and translocation into ClpP by channel residues and ClpX binding. J Mol Biol 399:707–718 [View Article][PubMed]
    [Google Scholar]
  21. MacNeil D. J. ( 1988). Characterization of a unique methyl-specific restriction system in Streptomyces avermitilis . J Bacteriol 170:5607–5612[PubMed]
    [Google Scholar]
  22. Maurizi M. R., Clark W. P., Katayama Y., Rudikoff S., Pumphrey J., Bowers B., Gottesman S. ( 1990a). Sequence and structure of ClpP, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli . J Biol Chem 265:12536–12545[PubMed]
    [Google Scholar]
  23. Maurizi M. R., Clark W. P., Kim S. H., Gottesman S. ( 1990b). ClpP represents a unique family of serine proteases. J Biol Chem 265:12546–12552[PubMed]
    [Google Scholar]
  24. Mazodier P., Petter R., Thompson C. ( 1989). Intergeneric conjugation between Escherichia coli and Streptomyces species. J Bacteriol 171:3583–3585[PubMed]
    [Google Scholar]
  25. Motamedi H., Shafiee A., Cai S. J. ( 1995). Integrative vectors for heterologous gene expression in Streptomyces spp. Gene 160:25–31 [View Article][PubMed]
    [Google Scholar]
  26. Mullis K. B., Faloona F. A. ( 1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Methods Enzymol 155:335–350 [View Article][PubMed]
    [Google Scholar]
  27. Murad F. ( 2003). Etude de la résistance aux macrolides chez Streptomyces ambofaciens et Streptomyces lividans PhD thesis, Université Paris Sud XI:
    [Google Scholar]
  28. Murakami T., Holt T. G., Thompson C. J. ( 1989). Thiostrepton-induced gene expression in Streptomyces lividans . J Bacteriol 171:1459–1466[PubMed]
    [Google Scholar]
  29. Paget M. S., Kang J. G., Roe J. H., Buttner M. J. ( 1998). σR, an RNA polymerase sigma factor that modulates expression of the thioredoxin system in response to oxidative stress in Streptomyces coelicolor A3(2). EMBO J 17:5776–5782 [View Article][PubMed]
    [Google Scholar]
  30. Pernodet J. L., Fish S., Blondelet-Rouault M. H., Cundliffe E. ( 1996). The macrolide-lincosamide-streptogramin B resistance phenotypes characterized by using a specifically deleted, antibiotic-sensitive strain of Streptomyces lividans . Antimicrob Agents Chemother 40:581–585[PubMed]
    [Google Scholar]
  31. Saiki R. K., Gelfand D. H., Stoffel S., Scharf S. J., Higuchi R., Horn G. T., Mullis K. B., Erlich H. A. ( 1988). Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 239:487–491 [View Article][PubMed]
    [Google Scholar]
  32. Sassetti C. M., Boyd D. H., Rubin E. J. ( 2003). Genes required for mycobacterial growth defined by high density mutagenesis. Mol Microbiol 48:77–84 [View Article][PubMed]
    [Google Scholar]
  33. Stanne T. M., Pojidaeva E., Andersson F. I., Clarke A. K. ( 2007). Distinctive types of ATP-dependent Clp proteases in cyanobacteria. J Biol Chem 282:14394–14402 [View Article][PubMed]
    [Google Scholar]
  34. Vecchione J. J., Sello J. K. ( 2009). A novel tryptophanyl-tRNA synthetase gene confers high-level resistance to indolmycin. Antimicrob Agents Chemother 53:3972–3980 [View Article][PubMed]
    [Google Scholar]
  35. Ventura M., Zhang Z., Cronin M., Canchaya C., Kenny J. G., Fitzgerald G. F., van Sinderen D. ( 2005). The ClgR protein regulates transcription of the clpP operon in Bifidobacterium breve UCC 2003. J Bacteriol 187:8411–8426 [View Article][PubMed]
    [Google Scholar]
  36. Viala J., Mazodier P. ( 2002). ClpP-dependent degradation of PopR allows tightly regulated expression of the clpP3 clpP4 operon in Streptomyces lividans . Mol Microbiol 44:633–643 [View Article][PubMed]
    [Google Scholar]
  37. Viala J., Mazodier P. ( 2003). The ATPase ClpX is conditionally involved in the morphological differentiation of Streptomyces lividans . Mol Genet Genomics 268:563–569[PubMed]
    [Google Scholar]
  38. Viala J., Rapoport G., Mazodier P. ( 2000). The clpP multigenic family in Streptomyces lividans: conditional expression of the clpP3 clpP4 operon is controlled by PopR, a novel transcriptional activator. Mol Microbiol 38:602–612 [View Article][PubMed]
    [Google Scholar]
  39. Wehmeier U. F. ( 1995). New multifunctional Escherichia coli–Streptomyces shuttle vectors allowing blue–white screening on XGal plates. Gene 165:149–150 [View Article][PubMed]
    [Google Scholar]
  40. Xia D., Esser L., Singh S. K., Guo F., Maurizi M. R. ( 2004). Crystallographic investigation of peptide binding sites in the N-domain of the ClpA chaperone. J Struct Biol 146:166–179 [View Article][PubMed]
    [Google Scholar]
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