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  • Review Article
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Combinatorial biosynthesis of reduced polyketides

Nature Reviews Microbiology volume 3, pages 925–936 (2005)Cite this article

Key Points

  • The reduced polyketides are a medicinally important group of metabolites, which are assembled in bacteria on gigantic multienzyme polyketide synthases (PKSs). These PKSs typically contain a single enzymatic domain for each step in polyketide construction, and so appear to be 'modular', on the genetic level at least.

  • The division-of-labour organization of the PKSs suggests that they might be genetically engineered to produce polyketide analogues, with potential as drug candidates. The idea of rearranging PKS components in as many ways as possible to generate large libraries of new compounds is known as 'combinatorial biosynthesis'.

  • Although genetic engineering has been shown repeatedly to work in practice, generating over 200 novel structures, many experiments produce low yields of the expected novel polyketides, or fail entirely. The goal of truly combinatorial engineering, though theoretically achievable, remains distant.

  • Therefore, a central goal in the field is to obtain a significantly deeper understanding of the operation and three-dimensional architecture of the PKSs to increase the efficiency of engineering experiments. Sequencing of additional gene clusters has revealed that PKSs are far more diverse and complex than initially appreciated.

  • Other important research areas include developing heterologous hosts for polyketide production, which are capable of post-translational modification of PKS proteins and which contain all of the necessary small-molecule precursors; improving the genetic tools required to manipulate and transfer large PKS genes and gene clusters; and identifying PKS domains and post-PKS tailoring enzymes which are inherently suited to combinatorial applications, due to their relaxed substrate specificities.

  • Significant progress has been made in all of these areas; of particular note are the first high-resolution structures of individual PKS components and the metabolic engineering of E. coli for polyketide production. Advances in engineering strategies have also resulted in a biological route to the important antiparasitic agent ivermectin.

Abstract

The bacterial multienzyme polyketide synthases (PKSs) produce a diverse array of products that have been developed into medicines, including antibiotics and anticancer agents. The modular genetic architecture of these PKSs suggests that it might be possible to engineer the enzymes to produce novel drug candidates, a strategy known as 'combinatorial biosynthesis'. So far, directed engineering of modular PKSs has resulted in the production of more than 200 new polyketides, but key challenges remain before the potential of combinatorial biosynthesis can be fully realized.

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Figure 1: Classes of polyketide metabolites and representative structures.
Figure 2: The modular polyketide synthase (PKS) paradigm.
Figure 3: Direct production of ivermectin-like drugs by genetic engineering of the avermectin polyketide synthase (PKS).
Figure 4: The 'double helical' model for modular polyketide synthases (PKSs).
Figure 5: Post-polyketide-synthase elaboration of a polyketide library.

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References

  1. Walsh, C. Where will new antibiotics come from? Nature Rev. Microbiol. 1, 65–70 (2003).

    Article  CAS  Google Scholar 

  2. Malpartida, F. & Hopwood, D. A. Molecular cloning of the whole biosynthetic pathway of a Streptomyces antibiotic and its expression in a heterologous host. Nature 309, 462–464 (1984).

    Article  CAS  PubMed  Google Scholar 

  3. Cortés, J., Haydock, S. F., Roberts, G. A., Bevitt, D. J. & Leadlay, P. F. An unusually large multifunctional polypeptide in the erythromycin-producing polyketide synthase of Saccharopolyspora erythraea. Nature 348, 176–178 (1990).

    Article  PubMed  Google Scholar 

  4. Donadio, S., Staver, M. J., McAlpine, J. B., Swanson, S. J. & Katz, L. Modular organization of genes required for complex polyketide biosynthesis. Science 252, 657–679 (1991). References 3 and 4 report the first sequencing of a modular PKS gene.

    Article  Google Scholar 

  5. Bartel, P. L. et al. Biosynthesis of anthraquinones by interspecies cloning of actinorhodin biosynthesis genes in streptomycetes: clarification of actinorhodin gene functions. J. Bacteriol. 172, 4816–4826 (1990).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. McDaniel, R., Ebert-Khosla, S., Hopwood, D. A. & Khosla, C. Engineered biosynthesis of novel polyketides. Science 262, 1546–1550 (1993).

    Article  CAS  PubMed  Google Scholar 

  7. Khosla, C. & Zawada, R. J. Generation of polyketide libraries via combinatorial biosynthesis. Trends Biotechnol. 14, 335–341 (1996).

    Article  CAS  PubMed  Google Scholar 

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

    Article  PubMed  Google Scholar 

  9. Kao, C. M., Luo, G. L., Katz, L., Cane, D. E. & Khosla, C. Manipulation of macrolide ring size by directed mutagenesis of a modular polyketide synthase. J. Am. Chem. Soc. 117, 9105–9106 (1995).

    Article  Google Scholar 

  10. Oliynyk, M., Brown, M. J., Corté s, J., Staunton, J. & Leadlay, P. F. A hybrid modular polyketide synthase obtained by domain swapping. Chem. Biol. 3, 833–839 (1996).

    Article  CAS  PubMed  Google Scholar 

  11. Donadio, S. & Sosio, M. Strategies for combinatorial biosynthesis with modular polyketide synthases. Comb. Chem. High Throughput Screen. 6, 489–500 (2003).

    Article  CAS  PubMed  Google Scholar 

  12. Weber, T., Welzel, K., Pelzer, S., Vente, A. & Wohlleben, W. Exploiting the genetic potential of polyketide producing streptomycetes. J. Biotechnol. 106, 221–232 (2003).

    Article  CAS  PubMed  Google Scholar 

  13. Weissman, K. J. Understanding and exploiting PKS modularity. Phil. Trans. R. Soc. Lond. A 362, 2671–2690 (2004).

    Article  CAS  Google Scholar 

  14. Gaisser, S. et al. Direct production of ivermectin-like drugs after domain exchange in the avermectin polyketide synthase of Streptomyces avermitilis. Org. Biomol. Chem. 1, 2840–2847 (2003). Describes the engineered biosynthesis of ivermectin, a valuable antiparasitic drug.

    Article  CAS  PubMed  Google Scholar 

  15. Patel, K. et al. Engineered biosynthesis of geldanamycin analogs for Hsp90 inhibition. Chem. Biol. 11, 1625–1633 (2004).

    Article  CAS  PubMed  Google Scholar 

  16. Starks, C. M., Zhou, Y., Liu, F. & Licari, P. J. Isolation and characterization of new epothilone analogues from recombinant Myxococcus xanthus fermentations. J. Nat. Prod. 66, 1313–1317 (2003).

    Article  CAS  PubMed  Google Scholar 

  17. Kohli, R. M. & Walsh, C. T. Enzymology of acyl chain macrocyclization in natural product biosynthesis. Chem. Commun. (Camb.) 3, 297–307 (2003).

    Article  CAS  Google Scholar 

  18. Ogasawara, Y. et al. Cloning, sequencing, and functional analysis of the biosynthetic gene cluster of macrolactam antibiotic vicenistatin in Streptomyces halstedii. Chem. Biol. 11, 79–86 (2004).

    CAS  PubMed  Google Scholar 

  19. Aparicio, J. F., Caffrey, P., Gil, J. A. & Zotchev, S. B. Polyene antibiotic biosynthesis gene clusters. Appl. Microbiol. Biotechnol. 61, 179–188 (2003).

    Article  CAS  PubMed  Google Scholar 

  20. Kim, C. G., Yu, T. W., Fryhle, C. B., Handa, S. & Floss, G. 3-Amino-5-hydroxybenzoic acid synthase, the terminal enzyme in the formation of the precursor of mC7N units in rifamycin and related antibiotics. J. Biol. Chem. 273, 6030–6040 (1998).

    Article  CAS  PubMed  Google Scholar 

  21. Oliynyk, M. et al. Analysis of the biosynthetic gene cluster for the polyether antibiotic monensin in Streptomyces cinnamonensis and evidence for the role of monB and monC genes in oxidative cyclization. Mol. Microbiol. 49, 1179–1190 (2003).

    Article  CAS  PubMed  Google Scholar 

  22. Ahlert, J. et al. The calicheamicin gene cluster and its iterative type I enediyne PKS. Science 297, 1173–1176 (2002).

    Article  CAS  PubMed  Google Scholar 

  23. Liu, W., Christenson, S. D., Standage, S. & Shen, B. Biosynthesis of the enediyne antitumor antibiotic C-1027. Science 297, 1170–1173 (2002).

    Article  CAS  PubMed  Google Scholar 

  24. Piel, J. et al. Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei. Proc. Natl Acad. Sci. USA 101, 16222–16227 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Gerth, K., Pradella, S., Perlova, O., Beyer, S. & Müller, R. Myxobacteria: proficient producers of novel natural products with various biological activities — past and future biotechnological aspects with the focus on the genus Sorangium. J. Biotechnol. 106, 233–253 (2003).

    Article  CAS  PubMed  Google Scholar 

  26. El-Sayed, A. K. et al. Characterization of the mupirocin biosynthesis gene cluster from Pseudomonas fluorescens NCIMB 10586. Chem. Biol. 10, 419–430 (2003).

    Article  CAS  PubMed  Google Scholar 

  27. Challis, G. L. & Hopwood, D. A. Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc. Natl Acad. Sci. USA 100, 14555–14561 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  28. Firn, R. D. & Jones, C. G. Natural products — a simple model to explain chemical diversity. Nat. Prod. Rep. 20, 382–391 (2003).

    Article  CAS  PubMed  Google Scholar 

  29. Staunton, J. & Weissman, K. J. Polyketide biosynthesis: a millennium review. Nat. Prod. Rep. 18, 380–416 (2001).

    Article  CAS  PubMed  Google Scholar 

  30. Smith, S., Witkowski, A. & Joshi, A. K. Structural and functional organization of the animal fatty acid synthase. Prog. Lipid Res. 42, 289–317 (2003). References 23 and 30 report the gene sequence of a PKS responsible for assembling an enediyne-type polyketide.

    Article  CAS  PubMed  Google Scholar 

  31. Stinear, T. P. et al. Giant plasmid-encoded polyketide synthases produce the macrolide toxin of Mycobacterium ulcerans. Proc. Natl Acad. Sci. USA 101, 1345–1349 (2004). Reports the sequencing and analysis of the mycolactone PKS.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  32. Caffrey, P. Conserved amino acid residues correlating with ketoreductase stereospecificity in modular polyketide synthases. Chembiochem 4, 654–657 (2003). Identifies residues in KR domains that can be used to predict the direction of ketoreduction.

    Article  CAS  PubMed  Google Scholar 

  33. Yu, T. W. et al. The biosynthetic gene cluster of the maytansinoid antitumor agent ansamitocin from Actinosynnema pretiosum. Proc. Natl Acad. Sci. USA 99, 7968–7963 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  34. Stratigopoulos, G., Bate, N. & Cundliffe, E. Positive control of tylosin biosynthesis: pivotal role of TylR. Mol. Microbiol. 54, 1326–1334 (2004).

    Article  CAS  PubMed  Google Scholar 

  35. Pfeifer, B. A. & Khosla, C. Biosynthesis of polyketides in heterologous hosts. Microbiol. Mol. Biol. Rev. 65, 106–118 (2001).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  36. Weissman, K. J., Hong, H., Oliynyk, M., Siskos, A. P. & Leadlay, P. F. Identification of a phosphopantetheinyl transferase for erythromycin biosynthesis in Saccharopolyspora erythraea. Chembiochem 5, 116–125 (2004).

    Article  CAS  PubMed  Google Scholar 

  37. Pfeifer, B., Hu, Z., Licari, P. & Khosla, C. Process and metabolic strategies for improved production of Escherichia coli-derived 6-deoxyerythronolide B. Appl. Environ. Microbiol. 68, 3287–3292 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  38. Rix, U., Fischer, C., Remsing, L. L. & Rohr, J. Modification of post-PKS tailoring steps through combinatorial biosynthesis. Nat. Prod. Rep. 19, 542–580 (2002).

    Article  CAS  PubMed  Google Scholar 

  39. Cane, D. E., Walsh, C. T. & Khosla, C. Harnessing the biosynthetic code: combinations, permutations and mutations. Science 282, 63–68 (1998).

    Article  CAS  PubMed  Google Scholar 

  40. Martin, C. J. et al. Heterologous expression in Saccharopolyspora erythraea of a pentaketide synthase derived from the spinosyn polyketide synthase. Org. Biomol. Chem. 1, 4144–4147 (2003).

    Article  CAS  PubMed  Google Scholar 

  41. Rowe, C. J. et al. Engineering a polyketide with a longer chain by insertion of an extra module into the erythromycin-producing polyketide synthase. Chem. Biol. 8, 475–485 (2001).

    Article  CAS  PubMed  Google Scholar 

  42. Long, P. F. et al. Engineering specificity of starter unit selection by the erythromycin-producing polyketide synthase. Mol. Microbiol. 43, 1215–1225 (2002).

    Article  CAS  PubMed  Google Scholar 

  43. 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 

  44. Petkovič, H. et al. A novel erythromycin, 6-desmethyl erythromycin D, made by substituting an acyltransferase domain of the erythromycin polyketide synthase. J. Antibiot. 56, 543–551 (2003). References 38 and 44 are comprehensive reviews on advances in the understanding and manipulation of post-PKS enzymes.

    Article  Google Scholar 

  45. Reeves, C. D. et al. Production of hybrid 16-membered macrolides by expressing combinations of polyketide synthase genes in engineered Streptomyces fradiae hosts. Chem. Biol. 11, 1465–1472 (2004).

    Article  CAS  PubMed  Google Scholar 

  46. Xue, Q., Ashley, G., Hutchinson, C. R. & Santi, D. V. A multiplasmid approach to preparing large libraries of polyketides. Proc. Natl Acad. Sci. USA 96, 11740–11745 (1999). Reports an important step towards combinatorial PKS engineering.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  47. Rodriguez, E. & McDaniel, R. Combinatorial biosynthesis of antimicrobials and other natural products. Curr. Opin. Chem. Biol. 4, 526–534 (2001).

    CAS  Google Scholar 

  48. Ranganathan, A. et al. Knowledge-based design of bimodular and trimodular polyketide synthases based on domain and module swaps: a route to simple statin analogues. Chem. Biol. 6, 731–741 (1999).

    Article  CAS  PubMed  Google Scholar 

  49. Watanabe, K., Wang, C. C., Boddy, C. N., Cane, D. E. & Khosla, C. Understanding substrate specificity of polyketide synthase modules by generating hybrid multimodular synthases. J. Biol. Chem. 278, 42020–42026 (2003).

    Article  CAS  PubMed  Google Scholar 

  50. Holzbaur, I. E. et al. Molecular basis of Celmer's rules: role of the ketosynthase domain in epimerisation and demonstration that ketoreductase domains can have altered product specificity with unnatural substrates. Chem. Biol. 8, 329–340 (2001).

    Article  CAS  PubMed  Google Scholar 

  51. Weissman, K. J. et al. The molecular basis of Celmer's rules: the stereochemistry of the condensation step in chain extension on the erythromycin polyketide synthase. Biochemistry 36, 13849–13855 (1997).

    Article  CAS  PubMed  Google Scholar 

  52. Tsuji, S. Y., Wu, N. & Khosla, C. Intermodular communication in polyketide synthases: comparing the role of protein–protein interactions to those in other multidomain proteins. Biochemistry 40, 2317–2325 (2001).

    Article  CAS  PubMed  Google Scholar 

  53. McDaniel, R., Welch, M. & Hutchinson, C. R. Genetic approaches to polyketide antibiotics. Chem. Rev. 105, 543–558 (2005).

    Article  CAS  PubMed  Google Scholar 

  54. Müller, R. Don't classify polyketide synthases. Chem. Biol. 11, 4–6 (2004).

    Article  PubMed  Google Scholar 

  55. Shen, B. Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms. Curr. Opin. Chem. Biol. 7, 285–295 (2003).

    Article  CAS  PubMed  Google Scholar 

  56. 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 

  57. Salomon, C. E., Magarvey, N. A. & Sherman, D. H. Merging the potential of microbial genetics with biological and chemical diversity: an even brighter future for marine natural product drug discovery. Nat. Prod. Rep. 21, 105–121 (2004).

    Article  CAS  PubMed  Google Scholar 

  58. 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 

  59. Õmura, S. et al. Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc. Natl Acad. Sci. USA 298, 12215–12220 (2001).

    Article  Google Scholar 

  60. Courtois, S. et al. Recombinant environmental libraries provide access to microbial diversity for drug discovery from natural products. Applied Environ. Microbiol. 69, 49–55 (2003). Describes a method for accessing microbial diversity from soil samples without cultivation.

    Article  CAS  Google Scholar 

  61. Ginolhac, A. et al. Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones. Appl. Environ. Microbiol. 70, 5522–5527 (2004).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  62. Piel, J. A polyketide synthase-peptide synthetase gene cluster from an uncultured bacterial symbiont of Paederus beetles. Proc. Natl Acad. Sci. USA 92, 14002–14007 (2002).

    Article  CAS  Google Scholar 

  63. Rascher, A. et al. Cloning and characterisation of a gene for geldanamycin production in Streptomyces hygroscopicus NRRL 3602. FEMS Microbiol. Lett. 218, 223–230 (2003).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

  65. Ayuso, A. et al. A novel actinomycete strain de-replication approach based on the diversity of polyketide synthase and nonribosomal peptide synthetase biosynthetic pathways. Appl. Microbiol. Biotechnol. 67, 795–806 (2005).

    Article  CAS  PubMed  Google Scholar 

  66. Ayuso-Sacido, A. & Genilloud, O. New PCR primers for the screening of NRPS and PKS-I systems in actinomycetes: detection and distribution of these biosynthetic gene sequences in major taxonomic groups. Microb. Ecol. 49, 10–24 (2004).

    Article  CAS  PubMed  Google Scholar 

  67. Edwards, D. J. et al. Structure and biosynthesis of the jamaicamides, new mixed polyketide-peptide neurotoxins from the marine cyanobacterium Lyngbya majuscula. Chem. Biol. 11, 817–833 (2004).

    Article  CAS  PubMed  Google Scholar 

  68. Snyder, R. V. et al. Polyketide synthase genes from marine dinoflagellates. Mar. Biotechnol. 5, 1–12 (2003).

    Article  CAS  Google Scholar 

  69. Strohl, W. R., Bartel, P. L., Li, Y., Connors, N. C. & Woodman, R. H. Expression of polyketide biosynthesis and regulatory genes in heterologous streptomycetes. J. Indust. Microbiol. 7, 163–174 (1991).

    Article  CAS  Google Scholar 

  70. Kao, C. M., Katz, L. & Khosla, C. Engineered biosynthesis of a complete macrolactone in a heterologous host. Science 265, 509–512 (1994). Reports the first biosynthesis of a polyketide macrolactone in the heterologous host Streptomyces coelicolor.

    Article  CAS  PubMed  Google Scholar 

  71. Rodriguez, E. et al. Rapid engineering of polyketide overproduction by gene transfer to industrially optimised strains. J. Ind. Microbiol. Biotechnol. 30, 480–488 (2003).

    Article  CAS  PubMed  Google Scholar 

  72. Sosio, M. et al. Artificial chromosomes for antibiotic-producing actinomycetes. Nature Biotechnol. 18, 343–345 (2000).

    Article  CAS  Google Scholar 

  73. Tao, M. F., Zhou, X. F., Kieser, T. & Deng, Z. X. Construction of a temperature inducible shuttle expression vector and its application in Streptomyces. Sheng Wu Gong Cheng Xue Bao 18, 420–423 (2002).

    CAS  PubMed  Google Scholar 

  74. Wilkinson, C. J. et al. Increasing the efficiency of heterologous promoters in actinomycetes. J. Mol. Microbiol. 4, 417–426 (2002).

    CAS  Google Scholar 

  75. Lambalot, R. H. et al. A new enzyme superfamily — the phosphopantetheinyl transferases. Chem. Biol. 3, 923–926 (1996). Describes a large family of proteins responsible for post-translational transfer of 4′-phosphopantetheine.

    Article  CAS  PubMed  Google Scholar 

  76. Quadri, L. E. et al. Characterization of Sfp, a Bacillus subtilis phosphopantetheinyl transferase for peptidyl carrier protein domains in peptide synthetases. Biochemistry 37, 1585–1595 (1998).

    Article  CAS  PubMed  Google Scholar 

  77. Rodriguez, E. et al. Engineered biosynthesis of 16-membered macrolides that require methoxymalonyl-ACP precursors in Streptomyces fradiae. Appl. Microbiol. Biotechnol. 66, 85–91 (2004).

    Article  CAS  PubMed  Google Scholar 

  78. Tang, L., Fu, H., Betlach, M. & McDaniel, R. Elucidating the mechanism of chain termination switching in the picromycin/methymycin polyketide synthase. Chem. Biol. 6, 553–558 (1999).

    Article  CAS  PubMed  Google Scholar 

  79. Shah, S. et al. Cloning, characterization, and heterologous expression of a polyketide synthase and P-450 oxidase involved in the biosynthesis of the antibiotic oleandomycin. J. Antibiot. 53, 502–508 (2000).

    Article  CAS  Google Scholar 

  80. Volchegursky, Y., Hu, Z., Katz, L. & McDaniel, R. Biosynthesis of the anti-parasitic agent megalomicin: transformation of erythromycin to megalomicin in Saccharopolyspora erythraea. Mol. Microbiol. 37, 752–762 (2000).

    Article  CAS  PubMed  Google Scholar 

  81. Tang, L. et al. Cloning and heterologous expression of the epothilone gene cluster. Science 287, 640–642 (2000). Describes the production of epothilone in the heterologous host E. coli.

    Article  CAS  PubMed  Google Scholar 

  82. He, J. & Hertweck, C. Iteration as programmed event during polyketide assembly; molecular analysis of the aureothin biosynthesis gene cluster. Chem. Biol. 10, 1225–1232 (2003).

    Article  CAS  PubMed  Google Scholar 

  83. 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). Describes the production of 6-dEB in an adapted strain of E. coli.

    Article  CAS  PubMed  Google Scholar 

  84. Roberts, G. A., Staunton, J. & Leadlay, P. F. Heterologous expression in Escherichia coli of an intact multienzyme component of the erythromycin-producing polyketide synthase. Eur. J. Biochem. 214, 305–311 (1993).

    Article  CAS  PubMed  Google Scholar 

  85. Kennedy, J., Murli, S. & Kealey, J. T. 6-Deoxyerythronolide B analogue production in Escherichia coli through metabolic pathway engineering. Biochemistry 42, 14342–14348 (2003).

    Article  CAS  PubMed  Google Scholar 

  86. Pfeifer, B. A., Wang, C. C., Walsh, C. T. & Khosla, C. Biosynthesis of yersiniabactin, a complex polyketide-nonribosomal peptide, using Escherichia coli as a heterologous host. Appl. Environ. Microbiol. 69, 6698–6702 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  87. Watanabe, K., Rude, M. A., Walsh, C. T. & Khosla, C. Engineered biosynthesis of an ansamycin polyketide precursor in E. coli. Proc. Natl Acad. Sci. USA 100, 9774–9778 (2003).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  88. Peiru, S., Menzella, H. G., Rodriguez, E., Carney, J. & Gramajo, H. Production of the potent antibacterial polyketide erythromycin C in Escherichia coli. Appl. Environ. Microbiol. 71, 2539–2547 (2005).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

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

    Article  CAS  PubMed  Google Scholar 

  90. Kumar, P., Koppisch, A. T., Cane, D. E. & Khosla, C. Enhancing the modularity of the modular polyketide synthases: transacylation in modular polyketide synthases catalyzed by malonyl-CoA:ACP transacylase. J. Am. Chem. Soc. 125, 14307–143112 (2003).

    Article  CAS  PubMed  Google Scholar 

  91. Gokhale, R. S., Tsuji, S. Y., Cane, D. E. & Khosla, C. Dissecting and exploiting intermodular communication in polyketide synthases. Science 284, 482–485 (1999).

    Article  CAS  PubMed  Google Scholar 

  92. Tang, L., Fu, H. & McDaniel, R. Formation of functional heterologous complexes using subunits from the picromycin, erythromycin and oleandomycin polyketide synthases. Chem. Biol. 7, 77–84 (2000).

    Article  CAS  PubMed  Google Scholar 

  93. Zhang, Y., Buchholz, F., Muyrers, J. P. & Stewart, A. F. A new logic for DNA engineering using recombination in Escherichia coli. Nature Genet. 20, 123–128 (1998).

    Article  CAS  PubMed  Google Scholar 

  94. Gust, B. et al. λ Red-mediated genetic manipulation of antibiotic-producing Streptomyces. Adv. Appl. Microbiol. 54, 107–128 (2004).

    Article  CAS  PubMed  Google Scholar 

  95. Wenzel, S. C., Gross, F., Zhang, Y., Fu., J., Stewart, A. F. & Muller, R. Heterologous expression of a myxobacterial natural products assembly line in pseudomonads via Red/ET recombineering. Chem. Biol. 13, 349–356 (2005).

    Article  CAS  Google Scholar 

  96. Kim, B. S., Sherman, D. H. & Reynolds, K. A. An efficient method for creation and functional analysis of libraries of hybrid type I polyketide synthases. Protein Eng. Des. Sel. 17, 277–284 (2004). Describes a directed evolution approach to PKS engineering.

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  98. Staunton, J. et al. Evidence for a double-helical structure for modular polyketide synthases. Nature Struct. Biol. 3, 188–192 (1996). Describes a model for the modular polyketide synthases.

    Article  CAS  PubMed  Google Scholar 

  99. Tsai, S. C. et al. Crystal structure of the macrocycle-forming thioesterase domain of the erythromycin polyketide synthase: versatility from a unique substrate channel. Proc. Natl Acad. Sci. USA 98, 14808–14813 (2001). Reports the first crystal structure for a PKS domain.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  100. Tsai, S. C., Lu, H., Cane, D. E., Khosla, C. & Stroud, R. M. Insights into channel architecture and substrate specificity from crystal structures of two macrocycle-forming thioesterases of modular polyketide synthases. Biochemistry 41, 12598–12606 (2002).

    Article  CAS  PubMed  Google Scholar 

  101. Tsuji, S. Y., Cane, D. E. & Khosla, C. Selective protein–protein interactions direct channeling of intermediates between polyketide synthase modules. Biochemistry 40, 2326–2331 (2001).

    Article  CAS  PubMed  Google Scholar 

  102. Broadhurst, R. W., Nietlispach, D., Wheatcroft, M. P., Leadlay, P. F. & Weissman, K. J. The structure of docking domains in modular polyketide synthases. Chem. Biol. 10, 723–731 (2003). Reports the NMR solution structure of a PKS docking-domain complex.

    Article  CAS  PubMed  Google Scholar 

  103. Milne, J. L. S. et al. Molecular architecture and mechanism of an icosahedral pyruvate dehydrogenase complex: a multifunctional catalytic machine. EMBO J. 21, 5587–5598 (2002).

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  104. Leadlay, P. & Baerga-Ortiz, A. Mammalian fatty acid synthase: closure on a textbook mechanism? Chem. Biol. 10, 101–103 (2003).

    Article  CAS  PubMed  Google Scholar 

  105. Kim, C. Y. et al. Reconstituting modular activity from separated domains of 6-deoxyerythronolide B synthase. Biochemistry 43, 13892–13898 (2004).

    Article  CAS  PubMed  Google Scholar 

  106. Marsden, A. F. A. et al. Stereospecific acyl transfers on the erythromycin-producing polyketide synthase. Science 263, 373–380 (1994).

    Article  Google Scholar 

  107. Beck, B. J., Aldrich, C. C., Fecik, R. A., Reynolds, K. A. & Sherman, D. H. Substrate recognition and channeling of monomodules from the pikromycin polyketide synthase. J. Biol. Chem. 278, 42020–42026 (2003).

    Article  CAS  Google Scholar 

  108. Cane, D. E., Kudo, F., Kinoshita, K. & Khosla, C. Precursor-directed biosynthesis: biochemical basis of the remarkable selectivity of the erythromycin polyketide synthase toward unsaturated triketides. Chem. Biol. 9, 131–142 (2002).

    Article  CAS  PubMed  Google Scholar 

  109. Aggarwal, R., Caffrey, P., Leadlay, P. F., Smith, C. J. & Staunton, J. The thioesterase of the erythromycin-producing polyketide synthase: mechanistic studies in vitro to investigate its mode of action and substrate specificity. J. Chem. Soc., Chem. Commun. 1519–1520 (1995).

  110. Haydock, S. F. et al. Divergent sequence motifs correlated with the substrate specificity of (methyl)malonyl-CoA:acyl carrier protein transacylase domains in modular polyketide synthases. FEBS Lett. 274, 246–248 (1995). Describes sequence motifs in AT activities that can be used to predict their substrate specificity.

    Article  Google Scholar 

  111. Kao, C. M. et al. Alcohol stereochemistry in polyketide backbones is controlled by the β-ketoreductase domains of modular polyketide synthases. J. Am. Chem. Soc. 120, 2478–2479 (1998).

    Article  CAS  Google Scholar 

  112. Kao, C. M. et al. Gain-of-function mutagenesis of the erythromycin polyketide synthase. 2. Engineered biosynthesis of an eight-membered ring tetraketide lactone. J. Am. Chem. Soc. 119, 11339–11340 (1997).

    Article  CAS  Google Scholar 

  113. Reid, R. et al. A model of structure and catalysis for ketoreductase domains in modular polyketide synthases. Biochemistry 42, 72–79 (2003).

    Article  CAS  PubMed  Google Scholar 

  114. Hong, Y. -S. et al. Inactivation of the carbamoyltransferase gene refines post-polyketide synthase modification steps in the biosynthesis of the antitumor agent geldanamycin. J. Am. Chem. Soc. 126, 11142–11143 (2004).

    Article  CAS  PubMed  Google Scholar 

  115. Butler, A. R., Bate, N., Kiehl, E. E., Kirst, H. A. & Cundliffe, E. Genetic engineering of aminodeoxyhexose biosynthesis in Streptomyces fradiae. Nature Biotechnol. 20, 713–716 (2002).

    Article  CAS  Google Scholar 

  116. Gaisser, S. et al. A defined system for hybrid macrolide biosynthesis in Saccharopolyspora erythraea. Mol. Microbiol. 36, 391–401 (2000).

    Article  CAS  PubMed  Google Scholar 

  117. Gaisser, S. et al. Parallel pathways for oxidation of 14-membered polyketide macrolactones in Saccharopolyspora erythraea. Mol. Microbiol. 44, 771–781 (2002).

    Article  CAS  PubMed  Google Scholar 

  118. Tang, L. & McDaniel, R. Construction of desosamine containing polyketide libraries using a glycosyltransferase with broad specificity. Chem. Biol. 8, 547–555 (2001). Describes an approach to creating libraries of engineered, bioactive polyketides.

    Article  CAS  PubMed  Google Scholar 

  119. Ziermann, R. & Betlach, M. Recombinant polyketide synthesis in Streptomyces: engineering of improved host strains. Biotechniques 26, 106–110 (1999).

    Article  CAS  PubMed  Google Scholar 

  120. Desai, R. P., Rodriguez, E., Galazzo, J. L. & Licari, P. Improved bioconversion of 15-fluoro-6-deoxyerythronolide B to 15-fluoro-erythromycin A by overexpression of the eryK gene in Saccharopolyspora erythraea. Biotechnol. Prog. 20, 1660–1665 (2004).

    Article  CAS  PubMed  Google Scholar 

  121. Lee, S. K. et al. The role of erythromycin C-12 hydroxylase, EryK, as a substitute for PikC hydroxylase in pikromycin biosynthesis. J. Bioorg. Chem. 32, 549–449 (2004).

    Article  CAS  Google Scholar 

  122. Gaisser, S. et al. New erythromycin derivatives from Saccharopolyspora erythraea using sugar O-methyltransferases from the spinosyn biosynthetic gene cluster. Mol. Microbiol. 41, 1223–1231 (2001).

    Article  CAS  PubMed  Google Scholar 

  123. Xue, Y., Wilson, D., Zhao, L., Liu, H. & Sherman, D. H. Hydroxylation of macrolactones YC-17 and narbomycin is mediated by the PikC-encoded cytochrome P450 in Streptomyces venezualae. Chem. Biol. 5, 661–667 (1998).

    Article  CAS  PubMed  Google Scholar 

  124. Zhang, Q. & Sherman, D. H. Isolation and structure determination of novamethymycin, a new bioactive metabolite of the methymycin biosynthetic pathway in Streptomyces venezualae. J. Nat. Prod. 64, 1147–1150 (2001).

    Google Scholar 

  125. Yoon, Y. J. et al. Generation of multiple bioactive macrolides by hybrid modular polyketide synthases in Streptomyces venezuelae. Chem. Biol. 9, 203–214 (2002).

    Article  CAS  PubMed  Google Scholar 

  126. Yang, M. et al. Probing the breadth of macrolide glycosyltransferases: in vitro remodeling of a polyketide antibiotic creates active bacterial uptake and enhances potency. J. Am. Chem. Soc. 127, 9336–9337 (2005).

    Article  CAS  PubMed  Google Scholar 

  127. Spiteller, P. et al. The post-polyketide synthase modification steps in the biosynthesis of the antitumor agent ansamitocin in Actinosynnema pretiosum. J. Am. Chem. Soc. 125, 14236–14237 (2003).

    Article  CAS  PubMed  Google Scholar 

  128. Walsh, C. T. Polyketide and nonribosomal peptide antibiotics: modularity and versatility. Science 303, 1805–1810 (2004).

    Article  CAS  PubMed  Google Scholar 

  129. Kohli, R. M., Burke, M. D., Tao, J. & Walsh, C. T. Chemoenzymatic route to macrocyclic hybrid peptide/polyketide-like molecules. J. Am. Chem. Soc. 125, 7160–7161 (2003).

    Article  CAS  PubMed  Google Scholar 

  130. Bloom, J. D. et al. Evolving strategies for enzyme engineering. Curr. Opin. Struct. Biol. 15, 1–6 (2005).

    Article  CAS  Google Scholar 

  131. Powell, K. A. et al. Directed evolution and biocatalysis. Angew. Chem. Int. Ed. Engl. 40, 3948–3959 (2001).

    Article  CAS  PubMed  Google Scholar 

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

    Article  CAS  Google Scholar 

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Acknowledgements

The authors wish to thank the Royal Society Dorothy Hodgkin Fellowship and the Biotechnology and Biological Sciences Research Council for support.

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Authors and Affiliations

  1. Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK

    Kira J. Weissman & Peter F. Leadlay

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DATABASES

Entrez

Bacillus subtilis

Escherichia coli

Streptomyces avermitilis

Streptomyces coelicolor

Swiss-Prot

Sfp

FURTHER INFORMATION

Kira J. Weissman's homepage

Peter F. Leadlay's homepage

Glossary

SCAFFOLD

The backbone atoms of a molecule, on which functionality is displayed.

MACROCYCLIZATION

Formation of a large macrolactone or macrolactam ring.

DIFFUSIVE LOADING

Binding of a substrate at an enzyme active site by diffusion through the cytoplasm.

LINKERS

Sequences of amino acids that adopt no fixed structure and that covalently join certain enzymatic domains within PKS modules.

METAGENOMIC

Genetic material obtained from an environmental sample.

LOADING DIDOMAIN

Consists of domains, minimally an acyl-transferase–acyl-carrier protein didomain, which initiate biosynthesis by selection of a starter unit.

DOCKING DOMAINS

Sequences of amino acids at the end of polyketide-synthase subunits which adopt distinct three-dimensional structures and are putatively involved in mediating protein–protein recognition between the multienzymes.

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Weissman, K., Leadlay, P. Combinatorial biosynthesis of reduced polyketides. Nat Rev Microbiol 3, 925–936 (2005). https://doi.org/10.1038/nrmicro1287

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