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Mining and engineering natural-product biosynthetic pathways

Nature Chemical Biology volume 3, pages 379–386 (2007)Cite this article

Abstract

Natural products continue to fulfill an important role in the development of therapeutic agents. In addition, with the advent of chemical genetics and high-throughput screening platforms, these molecules have become increasingly valuable as tools for interrogating fundamental aspects of biological systems. To access the vast portion of natural-product structural diversity that remains unexploited for these and other applications, genome mining and microbial metagenomic approaches are proving particularly powerful. When these are coupled with recombineering and related genetic tools, large biosynthetic gene clusters that remain intractable or cryptic in the native host can be more efficiently cloned and expressed in a suitable heterologous system. For lead optimization and the further structural diversification of natural-product libraries, combinatorial biosynthetic engineering has also become indispensable. However, our ability to rationally redesign biosynthetic pathways is often limited by our lack of understanding of the structure, dynamics and interplay between the many enzymes involved in complex biosynthetic pathways. Despite this, recent structures of fatty acid synthases should allow a more accurate prediction of the likely architecture of related polyketide synthase and nonribosomal peptide synthetase multienzymes.

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Figure 1
Figure 2
Figure 3: Combinatorial assembly of PKS modules through synthetic biology.
Figure 4: The fungal FAS is another biomolecular motor.
Figure 5
Figure 6: General two-step strategy for the transglycosylation of calicheamicin using the native glycosyltransferase CalG1.
Figure 7: Production of the antimalarial drug precursor artemisinic acid in engineered yeast and its chemical conversion to the active species artemisinin.

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References

  1. Newman, D.J., Cragg, G.M. & Snader, K.M. Natural products as a source of new drugs over the period 1981–2002. J. Nat. Prod. 66, 1002–1037 (2003).

    Article  Google Scholar 

  2. Spring, D.R. Chemical genetics to chemical genomics: small molecules offer big insights. Chem. Soc. Rev. 34, 472–482 (2005).

    Article  CAS  PubMed  Google Scholar 

  3. Koehn, F.E. & Carter, G.T. The evolving role of natural products in drug discovery. Nature Rev. Drug Discov. 4, 206–220 (2005).

    Article  CAS  Google Scholar 

  4. Wilkinson, B. & Bachmann, B.O. Biocatalysis in pharmaceutical preparation and alteration. Curr. Opin. Chem. Biol. 10, 169–176 (2006).

    Article  CAS  PubMed  Google Scholar 

  5. Ro, D.-K. et al. Production of the antimalarial drug precursor artemisinic acid in engineered yeast. Nature 440, 940–943 (2006).

    Article  CAS  PubMed  Google Scholar 

  6. Wang, J. et al. Platensimycin is a selective FabF inhibitor with potent antibiotic properties. Nature 441, 358–361 (2006).

    Article  CAS  PubMed  Google Scholar 

  7. Bentley, S.D. et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417, 141–147 (2002).

    Article  PubMed  Google Scholar 

  8. Oliynyk, M. et al. Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL2338. Nat. Biotechnol. 25, 447–453 (2007).

    Article  CAS  PubMed  Google Scholar 

  9. Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  10. Ostash, B.B., Saghatelian, A. & Walker, S. A streamlined metabolic pathway for the biosynthesis of moenomycin A. Chem. Biol. 14, 257–267 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Song, L. et al. Type III polyketide synthase β-ketoacyl-ACP starter unit and ethylmalonyl-CoA extender unit selectivity discovered by Streptomyces coelicolor genome mining. J. Am. Chem. Soc. 128, 14754–14755 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. McAlpine, J.B. et al. Microbial genomics as a guide to drug discovery and structural elucidation: ECO-02301, a novel antifungal agent, as an example. J. Nat. Prod. 68, 493–496 (2005).

    Article  CAS  PubMed  Google Scholar 

  13. Lautru, S., Deeth, R.J., Bailey, L.M. & Challis, G.L. Discovery of a new peptide product by Streptomyces coelicolor genome mining. Nat. Chem. Biol. 1, 265–269 (2005).

    Article  CAS  PubMed  Google Scholar 

  14. Zazopoulos, E. et al. A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Nat. Biotechnol. 21, 187–190 (2003).

    Article  CAS  PubMed  Google Scholar 

  15. Bachmann, B.O., McAlpine, J.B., Zazopolous, E., Farnet, C.M. & Piraee, M. Farnesyl dibenzodiazopines, their production with microorganisms, and their use as antitumor, antibacterial and antiinflammatory agents. Patent Cooperation Treaty patent WO2004065591 (2004).

  16. Bergmann, S. et al. Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat. Chem. Biol. 3, 213–217 (2007).

    Article  CAS  PubMed  Google Scholar 

  17. Camilli, A. & Bassler, B.L. Bacterial small-molecule signalling pathways. Science 311, 1113–1116 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  18. Amann, R.I., Ludwig, W. & Schleifer, K.-H. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol. Rev. 59, 143–169 (1995).

    CAS  PubMed  PubMed Central  Google Scholar 

  19. Brady, S.F. & Clardy, J. Palmitoylputrescine, an antibiotic isolated from the heterologous expression of DNA extracted from bromeliad tank water. J. Nat. Prod. 67, 1283–1286 (2004).

    Article  CAS  PubMed  Google Scholar 

  20. Brady, S.F. & Clardy, J. Cloning and heterologous expression of isocyanide biosynthetic genes from environmental DNA. Angew. Chem. Int. Ed. Engl. 44, 7063–7065 (2005).

    Article  CAS  PubMed  Google Scholar 

  21. Pfeifer, B.A., Admiraal, S.J., Gramajo, H., Cane, D.E. & Khosla, C. Biosynthesis of complex polyketides in a metabolically engineered strain of E. coli. Science 291, 1790–1792 (2001).

    Article  CAS  PubMed  Google Scholar 

  22. Watanabe, K. et al. Total biosynthesis of antitumor nonribosomal peptides in Escherichia coli. Nat. Chem. Biol. 2, 423–428 (2006).

    Article  CAS  PubMed  Google Scholar 

  23. Schmidt, E.W. et al. Patellamide A and C biosynthesis by a microcin-like pathway in Prochloron didemni, the cyanobacterial symbiont of Lissoclinum patella. Proc. Natl. Acad. Sci. USA 102, 7315–7320 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Long, P.F., Dunlap, W.C., Battershill, C.N. & Jaspars, M. Shotgun cloning and heterologous expression of the patellamide gene cluster as a strategy to achieved sustained metabolite production. ChemBioChem 6, 1760–1765 (2005).

    Article  CAS  PubMed  Google Scholar 

  25. Wenzel, S.C. et al. Heterologous expression of a myxobacterial natural products assembly line in Pseudomonads via Red/ET recombineering. Chem. Biol. 12, 349–356 (2005).

    Article  CAS  PubMed  Google Scholar 

  26. Gross, F. et al. Metabolic engineering of Pseudomonas putida for methylmalonyl-CoA biosynthesis to enable complex heterologous secondary metabolite formation. Chem. Biol. 13, 1253–1264 (2006).

    Article  CAS  PubMed  Google Scholar 

  27. Richardson, S.M., Wheelan, S.J., Yarrington, R.M. & Boeke, J.D. GeneDesign: rapid, automated design of multikilobase synthetic genes. Genome Res. 16, 550–556 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Kodumal, S.J. et al. Total synthesis of long DNA sequences: synthesis of a contiguous 32-kb polyketide synthase gene cluster. Proc. Natl. Acad. Sci. USA 101, 15573–15578 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  29. Menzella, H.G. et al. Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes. Nat. Biotechnol. 23, 1171–1176 (2005).

    Article  CAS  PubMed  Google Scholar 

  30. Moss, S.J., Martin, C.J. & Wilkinson, B. Loss of co-linearity by modular polyketide synthases: a mechanism for the evolution of chemical diversity. Nat. Prod. Rep. 21, 575–593 (2004).

    Article  CAS  PubMed  Google Scholar 

  31. Heathcote, M.L., Staunton, J. & Leadlay, P.F. Role of type II thioesterases: evidence for removal of short acyl chains produced by aberrant decarboxylation of chain extender units. Chem. Biol. 8, 207–220 (2001).

    Article  CAS  PubMed  Google Scholar 

  32. Yeh, E., Kohli, R.M., Bruner, S.D. & Walsh, C.T. Type II thioesterase restores activity of a NRPS module stalled with an aminoacyl-S-enzyme that cannot be elongated. ChemBioChem 5, 1290–1293 (2004).

    Article  CAS  PubMed  Google Scholar 

  33. Uguru, G.C. et al. Active-site modifications of adenylation domains lead to hydrolysis of upstream nonribosomal peptidyl thioester intermediates. J. Am. Chem. Soc. 126, 5032–5033 (2004).

    Article  CAS  PubMed  Google Scholar 

  34. Arnold, F.H. Fancy footwork in the sequence-space shuffle. Nat. Biotechnol. 24, 328–330 (2006).

    Article  CAS  PubMed  Google Scholar 

  35. Yoshikuni, Y., Ferrin, T.E. & Keasling, J.D. Designed divergent evolution of enzyme function. Nature 440, 1078–1082 (2006).

    Article  CAS  PubMed  Google Scholar 

  36. Stachelhaus, T., Schneider, A. & Maraheil, M.A. Rational design of peptide antibiotics by targeted replacement of bacterial and fungal domains. Science 269, 69–72 (1995).

    Article  CAS  PubMed  Google Scholar 

  37. Cortés, J. et al. Repositioning of a domain in a modular polyketide synthase to promote specific chain length cleavage. Science 268, 1487–1489 (1995).

    Article  PubMed  Google Scholar 

  38. Donadio, S., Staver, M.J., McAlpine, J.B., Swanson, S.J. & Katz, L. Modular organization of genes required for complex polyketide biosynthesis. Science 252, 675–679 (1991).

    Article  CAS  PubMed  Google Scholar 

  39. Maier, T., Jenni, S. & Ban, N. Architecture of a mammalian fatty acid synthase at 4.5Å resolution. Science 311, 1258–1262 (2006).

    Article  CAS  PubMed  Google Scholar 

  40. Jenni, S., Leibundgut, M., Maier, T. & Ban, N. Architecture of a fungal fatty acid synthase at 5 Å resolution. Science 311, 1263–1267 (2006).

    Article  CAS  PubMed  Google Scholar 

  41. Tang, Y., Kim, C.-Y., Mathews, I.I., Cane, D.E. & Khosla, C. The 2.7-Å crystal structure of a 194-kDa homodimeric fragment of the 6-deoxyerythronolide B synthase. Proc. Natl. Acad. Sci. USA 103, 11124–11129 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  42. Jenni, S., Leibundgut, M., Boehringer, D., Frick, C. & Ban, N. Structural basis for substrate delivery by acyl carrier protein in the yeast fatty acid synthase. Science 316, 288–290 (2007).

    Article  PubMed  Google Scholar 

  43. Weissman, K.J. The structural basis for docking in modular polyketide biosynthesis. ChemBioChem 7, 485–494 (2006).

    Article  CAS  PubMed  Google Scholar 

  44. Hahn, M. & Stachelhaus, T. Harnessing the potential of communication-mediating domains for the biocombinatorial synthesis of nonribosomal peptides. Proc. Natl. Acad. Sci. USA 103, 275–280 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  45. Koglin, A. et al. Conformational switches modulate protein interactions in peptide antibiotic synthetases. Science 312, 273–276 (2006).

    Article  CAS  PubMed  Google Scholar 

  46. Qiao, C., Wilson, D.J., Bennett, E.M. & Aldrich, C.C. A Mechanism-based aryl carrier protein/thiolation domain affinity probe. J. Am. Chem Soc. 129, 6350–6351 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Worthington, A.S., Rivera, H., Jr., Torpey, J.W., Alexander, M.D. & Burkart, M.D. Mechanism-based protein cross-linking probes to investigate carrier protein-mediated biosynthesis. ACS Chem. Biol. 1, 687–691 (2006).

    Article  CAS  PubMed  Google Scholar 

  48. Miao, V. et al. Genetic engineering in Streptomyces roseosporus to produce hybrid lipopeptide antibiotics. Chem. Biol. 13, 269–276 (2006).

    Article  CAS  PubMed  Google Scholar 

  49. Nguyen, K.T. et al. Combinatorial biosynthesis of novel antibiotics related to daptomycin. Proc. Natl. Acad. Sci. USA 103, 17462–17467 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  50. Kopp, F., Grünewald, J., Mahlert, C. & Marahiel, M.A. Chemoenzymatic design of acidic lipopeptide hybrids: new insights into the structure-activity relationship of daptomycin and A54145. Biochemistry 45, 10474–10481 (2006).

    Article  CAS  PubMed  Google Scholar 

  51. Wilcoxen, K.M., Leman, L.J., Weinberger, D.A., Huang, Z-Z. & Ghadiri, M.R. Biomimetic catalysis of intermodular aminoacyl transfer. J. Am. Chem. Soc. 129, 748–749 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  52. Leman, L.J., Weinberger, D.A., Huang, Z.-Z., Wilcoxen, K.M. & Ghadiri, M.R. Functional and mechanistic analyses of biomimetic aminoacyl transfer reactions in de novo designed coiled coil peptides via rational active site engineering. J. Am. Chem. Soc. 129, 2959–2966 (2007).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  53. Chan, Y.A. et al. Hydroxymalonyl-acyl carrier protein (ACP) and aminomalonyl-ACP are two additional type I polyketide synthase extender units. Proc. Natl. Acad. Sci. USA 103, 14349–14354 (2006).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  54. Reeves, C.D. et al. Alteration of the substrate specificity of a modular polyketide synthase acyltransferase domain through site-directed mutagenesis. Biochemistry 40, 15464–15470 (2001).

    Article  CAS  PubMed  Google Scholar 

  55. Del Vecchio, F. et al. Active-site residue, domain and module swaps in modular polyketide synthases. J. Ind. Microbiol. Biotechnol. 30, 489–494 (2003).

    Article  CAS  PubMed  Google Scholar 

  56. Baerga-Ortiz, A. et al. Directed mutagenesis alters the stereochemistry of catalysis by isolated ketoreductase domains from the erythromycin polyketide synthase. Chem. Biol. 13, 277–285 (2006).

    Article  CAS  PubMed  Google Scholar 

  57. Weist, S. & Sussmuth, R.D. Mutational biosynthesis—a tool for the generation of structural diversity in the biosynthesis of antibiotics. Appl. Microbiol. Biotechnol. 68, 141–150 (2005).

    Article  CAS  PubMed  Google Scholar 

  58. Weissman, K.J. Mutasynthesis—uniting chemistry and genetics for drug discovery. Trends Biotechnol. 25, 139–142 (2007).

    Article  CAS  PubMed  Google Scholar 

  59. Li, S.M. & Heide, L. New aminocoumarin antibiotics from genetically engineered Streptomyces strains. Curr. Med. Chem. 12, 419–427 (2005).

    Article  CAS  PubMed  Google Scholar 

  60. Thibodeaux, C.J., Melancon, C.E. & Liu, H-W. Unusual sugar biosynthesis and natural product glycodiversification. Nature 446, 1008–1016 (2007).

    Article  CAS  PubMed  Google Scholar 

  61. Rodriguez, L. et al. Engineering deoxysugar biosynthetic pathways from antibiotic-producing microorganisms, a tool to produce novel glycosylated bioactive compounds. Chem. Biol. 9, 721–729 (2002).

    Article  CAS  PubMed  Google Scholar 

  62. Hoffmeister, D. et al. Engineered urdamycin glycosyltransferases are broadened and altered in substrate specificity. Chem. Biol. 9, 287–295 (2002).

    Article  CAS  PubMed  Google Scholar 

  63. Zhang, C. et al. Exploiting the reversibility of natural product glycosyltransferase-catalyzed reactions. Science 313, 1291–1294 (2006).

    Article  CAS  PubMed  Google Scholar 

  64. McCoy, E. & O'Connor, S.E. Directed biosynthesis of alkaloid analogs in the medicinal plant Catharanthus roseus. J. Am. Chem. Soc. 128, 14276–14277 (2006).

    Article  CAS  PubMed  Google Scholar 

  65. Chen, S., Galan, M.C., Coltharp, C. & O'Connor, S.E. Redesign of a central enzyme in alkaloid biosynthesis. Chem. Biol. 13, 1137–1141 (2006).

    Article  CAS  PubMed  Google Scholar 

  66. Zhang, Y. et al. Using unnatural protein fusions to engineer resveratrol biosynthesis in yeast and mammalian cells. J. Am. Chem. Soc. 128, 13030–13031 (2006).

    Article  CAS  PubMed  Google Scholar 

  67. Breinbauer, R., Vetter, I.R. & Waldmann, H. From protein domains to drug candidates—natural products as guiding principles in the design and synthesis of compound libraries. Angew. Chem. Int. Ed. 41, 2879–2890 (2002).

    Google Scholar 

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Acknowledgements

J.M. thanks the Biotechnology and Biological Sciences Research Council for support of biosynthetic engineering research through grants and studentships (36/B12126 and BB/C503662). S. Moss (Biotica) and M. Gregory (Biotica) are also acknowledged for proofreading the manuscript.

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Authors and Affiliations

  1. Barrie Wilkinson is at Biotica, Chesterford Research Park, Little Chesterford, Essex CB10 1XL, UK. barrie.wilkinson@biotica.com,

    Barrie Wilkinson

  2. Jason Micklefield is at the School of Chemistry and Manchester Interdisciplinary Biocentre, The University of Manchester, 131 Princess Street, Manchester M1 7ND, UK. j.micklefield@manchester.ac.uk,

    Jason Micklefield

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Competing interests

B.W. works for and has financial interests in Biotica, a drug discovery company that uses biosynthetic engineering technology. J.M. has no competing financial interests.

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Wilkinson, B., Micklefield, J. Mining and engineering natural-product biosynthetic pathways. Nat Chem Biol 3, 379–386 (2007). https://doi.org/10.1038/nchembio.2007.7

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