1887

Abstract

Genetic engineering has been applied to reprogramme non-ribosomal peptide synthetases (NRPSs) to produce novel antibiotics, but little is known about what determines the efficiency of production. We explored module exchanges at nucleotide sequences encoding interpeptide linkers in , a gene encoding a di-modular NRPS subunit that incorporates 3-methylglutamic acid (3mGlu) and kynurenine (Kyn) into daptomycin. Mutations causing amino acid substitutions, deletions or insertions in the inter-module linker had no negative effects on lipopeptide yields. Hybrid DptD subunits were generated by fusing the 3mGlu module to terminal modules from calcium-dependent antibiotic (CDA) or A54145 NRPSs, and recombinants produced daptomycin analogues with Trp or Ile at high efficiencies. A recombinant expressing DptD with a hybrid Kyn module containing a di-domain from a -Asn module caused the production of a new daptomycin analogue containing Asn.

Loading

Article metrics loading...

/content/journal/micro/10.1099/mic.0.2008/020685-0
2008-09-01
2024-12-07
Loading full text...

Full text loading...

/deliver/fulltext/micro/154/9/2872.html?itemId=/content/journal/micro/10.1099/mic.0.2008/020685-0&mimeType=html&fmt=ahah

References

  1. Arbeit R. D., Maki D., Tally F. P., Campanaro E., Eisenstein B. I. 2004; The safety and efficacy of daptomycin for the treatment of complicated skin and skin-structure infections. Clin Infect Dis 38:1673–1681
    [Google Scholar]
  2. Baltz R. H. 2008; Biosynthesis and genetic engineering of lipopeptide antibiotics related to daptomycin. Curr Top Med Chem 8:618–638
    [Google Scholar]
  3. Baltz R. H., Miao V., Wrigley S. W. 2005; Natural products to drugs: daptomycin and related lipopeptide antibiotics. Nat Prod Rep 22:717–741
    [Google Scholar]
  4. Challis G. L., Ravel J., Townsend C. A. 2000; Predictive, structure-based model of amino acid recognition by nonribosomal peptide synthetase adenylation domains. Chem Biol 7:211–224
    [Google Scholar]
  5. Coëffet-Le Gal M.-F., Thurson L., Rich P., Miao V., Baltz R. H. 2006; Complementation of daptomycin dptA and dptD deletion mutations in-trans and production of hybrid lipopeptide antibiotics. Microbiology 152:2993–3001
    [Google Scholar]
  6. Datsenko K. A., Wanner B. 2000; One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 97:6640–6645
    [Google Scholar]
  7. Debono M., Barnhart M., Carrell C. B., Hoffmann J. A., Occolowitz J. L., Abbott B. J., Fukuda D. S., Hamill R. L., Biemann K., Herlihy W. C. 1987; A21978C, a complex of new acidic peptide antibiotics: isolation, chemistry, and mass spectral structure elucidation. J Antibiot 40:761–777
    [Google Scholar]
  8. Doekel S., Marahiel M. A. 2000; Dipeptide formation on engineered hybrid peptide synthetases. Chem Biol 7:373–384
    [Google Scholar]
  9. Eppelmann K., Stachelhaus T., Marahiel M. A. 2002; Exploitation of the selectivity-conferring code of nonribosomal peptide synthetases for the rational design of novel peptide antibiotics. Biochemistry 41:9718–9726
    [Google Scholar]
  10. Fischbach M. A., Walsh C. T. 2006; Assembly-line enzymology for polyketide and nonribosomal peptide antibiotics: logic, machinery, and mechanisms. Chem Rev 106:3468–3496
    [Google Scholar]
  11. Fischbach M. A., Lai J. R., Roche E. D., Walsh C. T., Liu D. R. 2007; Directed evolution can rapidly improve the activity of chimeric assembly-line enzymes. Proc Natl Acad Sci U S A 104:11951–11956
    [Google Scholar]
  12. Fowler V. G., Boucher H. W., Corey G. R., Abrutyn E., Karchmer A. W., Rupp M. E., Levine D. P., Chambers H. F., Tally F. P. other authors 2006; Daptomycin versus standard therapy for bacteremia and endocarditis caused by Staphylococcus aureus . N Engl J Med 355:653–655
    [Google Scholar]
  13. Grünewald J., Sieber S. A., Mahlert C., Linne U., Marahiel M. A. 2004; Synthesis and derivation of daptomycin: a chemoenzymatic route to acidic lipopeptide antibiotics. J Am Chem Soc 126:17025–17031
    [Google Scholar]
  14. Hojati Z., Milne C., Harvey B., Gordon L., Borg M., Flett F., Wilkinson B., Sidebottom P. J., Rudd B. A. M. other authors 2002; Structure, biosynthetic origin, and engineered biosynthesis of calcium-dependent antibiotics from Streptomyces coelicolor . Chem Biol 9:1175–1187
    [Google Scholar]
  15. Hosted T. J., Baltz R. H. 1997; Use of rpsL for dominance selection and gene replacement in Streptomyces roseosporus . J Bacteriol 179:180–186
    [Google Scholar]
  16. Huber F. M., Pieper R. L., Tietz A. J. 1988; The formation of daptomycin by supplying decanoic acid to Streptomyces roseosporus cultures producing the antibiotic complex A21978C. J Biotechnol 7:283–292
    [Google Scholar]
  17. Kohli R. M., Walsh C. T. 2003; Enzymology of acyl chain macrocyclization in natural product biosynthesis. Chem Commun297–307
    [Google Scholar]
  18. Kopp F., Grünewald J., Mahlert C., Marahiel M. A. 2006; Chemoenzymatic design of acidic lipopeptide hybrids: new insights into the structure–activity relationship of daptomycin and A54145. Biochemistry 45:10474–10481
    [Google Scholar]
  19. Miao V., Coëffet-Le Gal M.-F., Brian P., Brost R., Penn J., Whiting A., Martin S., Ford R., Parr R. other authors 2005; Daptomycin biosynthesis in Streptomyces roseosporus : cloning and analysis of the gene cluster and revision of peptide stereochemistry. Microbiology 151:1507–1523
    [Google Scholar]
  20. Miao V., Brost R., Chapple J., She K., Coëffet-Le Gal M.-F., Baltz R. H. 2006a; The lipopeptide antibiotic A54145 biosynthetic gene cluster from Streptomyces roseosporus . J Ind Microbiol Biotechnol 33:129–140
    [Google Scholar]
  21. Miao V., Coëffet-Le Gal M.-F., Nguyen K., Brian P., Penn J., Whiting A., Steele J., Kau D., Martin S. other authors 2006b; Genetic engineering in Streptomyces roseoporus to produce hybrid lipopeptide antibiotics. Chem Biol 13:269–276
    [Google Scholar]
  22. Mootz H. D., Schwarzer D., Marahiel M. A. 2000; Construction of hybrid peptide synthetases by module and domain fusions. Proc Natl Acad Sci U S A 97:5848–5853
    [Google Scholar]
  23. Mootz H. D., Kessler N., Linne U., Eppelmann K., Schwarzer D., Marahiel M. A. 2002; Decreasing the ring size of a cyclic nonribosomal peptide antibiotic by in-frame module deletion in the biosynthetic genes. J Am Chem Soc 124:10980–10981
    [Google Scholar]
  24. Motamedi H., Shafiee A., Cai S. J. 1995; Integrative vectors for heterologous gene expression in Streptomyces spp. Gene 160:25–31
    [Google Scholar]
  25. Nguyen K. T., Kau D., Gu J.-Q., Brian P., Wrigley S. K., Baltz R. H., Miao V. 2006a; A glutamic acid 3-methyltransferase encoded by an accessory gene locus important for daptomycin biosynthesis in Streptomyces roseosporus . Mol Microbiol 61:1294–1307
    [Google Scholar]
  26. Nguyen K. T., Ritz D., Gu J.-Q., Alexander D., Chu M., Miao V., Brian P., Baltz R. H. 2006b; Combinatorial biosynthesis of lipopeptide antibiotics related to daptomycin. Proc Natl Acad Sci U S A 103:17462–17467
    [Google Scholar]
  27. Samel S. A., Schoenafinger G., Knappe T. A., Marahiel M. A., Essen L.-O. 2007; Structural and functional insights into a peptide bond-forming bidomain from a nonribosomal peptide synthetase. Structure 15:781–792
    [Google Scholar]
  28. Shen B., Du L., Sanchez C., Edwards D. J., Chen M., Murrell J. M. 2002; Cloning and characterization of the bleomycin biosynthetic gene cluster from Streptomyces verticillus ATCC15003. J Nat Prod 65:422–431
    [Google Scholar]
  29. Sieber S. A., Marahiel M. A. 2005; Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem Rev 105:715–738
    [Google Scholar]
  30. Stachelhaus T., Walsh C. T. 2000; Mutational analysis of the epimerization domain in the initiation module PheATE of gramicidin S synthetase. Biochemistry 39:5775–5787
    [Google Scholar]
  31. Stachelhaus T., Schneider A., Marahiel M. A. 1995; Rational design of peptide antibiotics by targeted replacement of bacterial and fungal domains. Science 269:69–72
    [Google Scholar]
  32. Stachelhaus T., Hüser A., Marahiel M. A. 1996; Biochemical characterization of the peptidyl carrier protein (PCP), the thiolation domain of multifunctional peptide synthetases. Chem Biol 3:913–921
    [Google Scholar]
  33. Stachelhaus T., Mootz H. D., Bergendahl V., Marahiel M. A. 1998; Peptide bond formation in nonribosomal peptide biosynthesis. Catalytic role of the condensation domain. J Biol Chem 273:22773–22781
    [Google Scholar]
  34. Stachelhaus T., Mootz H. D., Marahiel M. A. 1999; The specificity-conferring code of adenylation domains in nonribosomal peptide synthetases. Chem Biol 6:493–505
    [Google Scholar]
  35. Yakimov M. M., Giuliano L., Timmis K. N., Golyshin P. N. 2000; Recombinant acylheptapeptide lichenysin: high level of production by Bacillus subtilis cells. J Mol Microbiol Biotechnol 2:217–224
    [Google Scholar]
  36. Zhang Y., Buchholz F., Muyrers J. P. P., Stewart F. 1998; A new logic for DNA engineering using recombination in Escherichia coli . Nat Genet 20:123–128
    [Google Scholar]
  37. Zhou Z., Lai J. R., Walsh C. T. 2006; Interdomain communication between the thiolation and thioesterase domains of EntF explored by combinatorial mutagenesis and selection. Chem Biol 13:869–879
    [Google Scholar]
/content/journal/micro/10.1099/mic.0.2008/020685-0
Loading
/content/journal/micro/10.1099/mic.0.2008/020685-0
Loading

Data & Media loading...

This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error