Archives of Microbiology

, Volume 187, Issue 2, pp 87–99 | Cite as

A cryptic type I polyketide synthase (cpk) gene cluster in Streptomyces coelicolor A3(2)

  • Krzysztof Pawlik
  • Magdalena Kotowska
  • Keith F. Chater
  • Katarzyna Kuczek
  • Eriko Takano
Original Paper


The chromosome of Streptomyces coelicolor A3(2), a model organism for the genus Streptomyces, contains a cryptic type I polyketide synthase (PKS) gene cluster which was revealed when the genome was sequenced. The ca. 54-kb cluster contains three large genes, cpkA, cpkB and cpkC, encoding the PKS subunits. Insilico analysis showed that the synthase consists of a loading module, five extension modules and a unique reductase as a terminal domain instead of a typical thioesterase. All acyltransferase domains are specific for a malonyl extender, and have a B-type ketoreductase. Tailoring and regulatory genes were also identified within the gene cluster. Surprisingly, some genes show high similarity to primary metabolite genes not commonly identified in any antibiotic biosynthesis cluster. Using western blot analysis with a PKS subunit (CpkC) antibody, CpkC was shown to be expressed in S. coelicolor at transition phase. Disruption of cpkC gave no obvious phenotype.


Streptomyces Polyketide biosynthesis Post-polyketide modifications Antibiotic biosynthesis 





Acyl carrier protein




6-Deoxyerythronolide synthase


Enoyl reductase






Mannitol soya flour medium


Non-ribosomal peptide synthetase


Polyketide synthase


Supplemented minimal medium


Terminal reductase


  1. Aparicio JF, Molnar I, Schwecke T, Konig A, Haydock SF, Khaw L, Staunton J, Leadlay PF (1996) Organization of the biosynthetic gene cluster for rapamycin in Streptomyces hygroscopicus: analysis of the enzymatic domains in the modular polyketide synthase. Gene 169:9–16PubMedCrossRefGoogle Scholar
  2. Bate N, Butler AR, Gandecha AR, Cundliffe E (1999) Multiple regulatory genes in the tylosin biosynthetic cluster of Streptomyces fradiae. Chem Biol 6:617–624PubMedCrossRefGoogle Scholar
  3. Bentley SD, Chater KF, Cerdeno-Tarraga AM, Challis GL, Thomson NR, James KD, Harris DE, Quail MA, Kieser H, Harper D, Bateman A, Brown S, Chandra G, Chen CW, Collins M, Cronin A, Fraser A, Goble A, Hidalgo J, Hornsby T, Howarth S, Huang CH, Kieser T, Larke L, Murphy L, Oliver K, O’Neil S, Rabbinowitsch E, Rajandream MA, Rutherford K, Rutter S, Seeger K, Saunders D, Sharp S, Squares R, Squares S, Taylor K, Warren T, Wietzorrek A, Woodward J, Barrell BG, Parkhill J, Hopwood DA (2002) Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature 417:141–147PubMedCrossRefGoogle Scholar
  4. Black T, Wolk C (1994) Analysis of a Het- mutation in Anabaena sp. strain PCC 7120 implicates a secondary metabolite in the regulation of heterocyst spacing. J Bacteriol 176:2282–2292PubMedGoogle Scholar
  5. Brautaset T, Sekurova ON, Sletta H, Ellingsen TE, StrLm AR, Valla S, Zotchev SB (2000) Biosynthesis of the polyene antifungal antibiotic nystatin in Streptomyces noursei ATCC 11455: analysis of the gene cluster and deduction of the biosynthetic pathway. Chem Biol 7:395–403PubMedCrossRefGoogle Scholar
  6. Broadhurst RW, Nietlispach D, Wheatcroft MP, Leadlay PF, Weissman KJ (2003) The structure of docking domains in modular polyketide synthases. Chem Biol 10:723–731PubMedCrossRefGoogle Scholar
  7. Caffrey P (2003) Conserved Amino Acid Residues Correlating With Ketoreductase Stereospecificity in Modular Polyketide Synthases. ChemBioChem 4:649–662CrossRefGoogle Scholar
  8. Caffrey P(2005) The stereochemistry of ketoreduction. Chem Biol 12:1060–1062PubMedCrossRefGoogle Scholar
  9. Casqueiro J, Gutierrez S, Banuelos O, Hijarrubia MJ, Martin JF(1999) Gene targeting in Penicillium chrysogenum: disruption of the lys2 gene leads to penicillin overproduction. J Bacteriol 181:1181–1188PubMedGoogle Scholar
  10. Cerdeno AM, Bibb MJ, Challis GL (2001) Analysis of the prodiginine biosynthesis gene cluster of Streptomyces coelicolor A3(2): new mechanisms for chain initiation and termination in modular multienzymes. Chem Biol 8:817–829PubMedCrossRefGoogle Scholar
  11. Challis GL, Hopwood DA (2003) Synergy and contingency as driving forces for the evolution of multiple secondary metabolite production by Streptomyces species. Proc Natl Acad Sci USA 100(Suppl 2):14555–14561PubMedCrossRefGoogle Scholar
  12. Cho YH, Kim EJ, Chung HJ, Choi JH, Chater KF, Ahn BE, Shin JH, Roe JH (2003) The pqrAB operon is responsible for paraquat resistance in Streptomyces coelicolor. J Bacteriol 185:6756–6763PubMedCrossRefGoogle Scholar
  13. Donadio S, Katz L (1992) Organization of the enzymatic domains in the multifunctional polyketide synthase involved in erythromycin formation in Saccharopolyspora erythraea. Gene 111: 51–60PubMedCrossRefGoogle Scholar
  14. Faust B, Hoffmeister D, Weitnauer G, Westrich L, Haag S, Schneider P, Decker H, Kunzel E, Rohr J, Bechthold A (2000) Two new tailoring enzymes, a glycosyltransferase and an oxygenase, involved in biosynthesis of the angucycline antibiotic urdamycin A in Streptomyces fradiae Tu2717. Microbiology 146:147–154PubMedGoogle Scholar
  15. Feitelson JS, Malpartida F, Hopwood DA (1985) Genetic and biochemical characterization of the red gene cluster of Streptomyces coelicolor A3(2). J Gen Microbiol 131: 2431–2441PubMedGoogle Scholar
  16. Ginolhac A, Jarrin C, Robe P, Perriere G, Vogel TM, Simonet P, Nalin R. (2005) Type I polyketide synthases may have evolved through horizontal gene transfer. J Mol Evol 60:716–725PubMedCrossRefGoogle Scholar
  17. Gokhale RS, Tsuji SY, Cane DE, Khosla C (1999) Dissecting and exploiting intermodular communication in polyketide synthases. Science 284:482–485PubMedCrossRefGoogle Scholar
  18. Han L, Yang K, Kulowski K, Wendt-Pienkowski E, Hutchinson CR, Vining LC (2000) An acyl-coenzyme A carboxylase encoding gene associated with jadomycin biosynthesis in Streptomyces venezuelae ISP5230. Microbiology 146: 903–910PubMedGoogle Scholar
  19. Haydock SF, Aparicio JF, Molnar I, Schwecke T, Khaw LE, Konig A, Marsden AF, Galloway IS, Staunton J, Leadlay PF (1995) Divergent sequence motifs correlated with the substrate specificity of (methyl)malonyl-CoA:acyl carrier protein transacylase domains in modular polyketide synthases. FEBS Lett 374: 246–248PubMedCrossRefGoogle Scholar
  20. Hesketh AR, Chandra G, Shaw AD, Rowland JJ, Kell DB, Bibb MJ, Chater K.F (2002). Primary and secondary metabolism, and post-translational protein modifications, as portrayed by proteomic analysis of Streptomyces coelicolor. Mol Microbiol 46: 917–932PubMedCrossRefGoogle Scholar
  21. Huang J, Shi J, Molle V, Sohlberg B, Weaver D, Bibb MJ, Karoonuthaisiri N, Lih CJ, Kao C, Buttner MJ, Cohen SN. (2005) Cross-regulation among disparate antibiotic biosynthetic pathways of Streptomyces coelicolor. Mol Microbiol 58:1276–1287PubMedCrossRefGoogle Scholar
  22. Ikeda H, Ishikawa J, Hanamoto A, Shinose M, Kikuchi H, Shiba T, Sakaki Y, Hattori M, Omura S (2003) Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat Biotechnol 21: 526–531PubMedCrossRefGoogle Scholar
  23. Ikeno S, Aoki D, Hamada M, Hori M, Tsuchiya KS. (2006) DNA sequencing and transcriptional analysis of the kasugamycin biosynthetic gene cluster from Streptomyces kasugaensis M338-M1. J Antibiot 59: 18–28PubMedCrossRefGoogle Scholar
  24. Ishikawa J, Hotta K (1999) FramePlot: a new implementation of the frame analysis for predicting protein-coding regions in bacterial DNA with a high G + C content. FEMS Microbiol Lett 174: 251–253PubMedCrossRefGoogle Scholar
  25. Kieser T, Bibb MJ, Buttner MJ, Chater KF, Hopwood DA (2000) Practical streptomyces genetics. The John Innes Foundation, Norwich, UKGoogle Scholar
  26. Konz D, Marahiel MA (1999) How do peptide synthetases generate structural diversity? Chem Biol 6:R39–R48PubMedCrossRefGoogle Scholar
  27. Kotowska M, Pawlik K, Butler AR, Cundliffe E, Takano E, Kuczek K (2002) Type II thioesterase from Streptomyces coelicolor A3(2). Microbiology 148:1777–1783PubMedGoogle Scholar
  28. Kuczek K, Pawlik K, Kotowska M, Mordarski M. (1997) Streptomyces coelicolor DNA homologous with acyltransferase domains of type I polyketide synthase gene complex. FEMS Microbiol Lett 157: 195–200PubMedCrossRefGoogle Scholar
  29. Lau J, Fu H, Cane DE, Khosla C (1999) Dissecting the role of acyltransferase domains of modular polyketide synthases in the choice and stereochemical fate of extender units. Biochemistry 38:1643–1651PubMedCrossRefGoogle Scholar
  30. Li A, Piel J (2002) A gene cluster from a marine Streptomyces encoding the biosynthesis of the aromatic spiroketal polyketide griseorhodin A. Chem Biol 9:1017–1026PubMedCrossRefGoogle Scholar
  31. Liu W, Shen B (2000) Genes for production of the enediyne antitumor antibiotic C-1027 in Streptomyces globisporus are clustered with the cagA gene that encodes the C-1027 apoprotein. Antimicrob Agents Chemother 44:382–392PubMedCrossRefGoogle Scholar
  32. Liu W, Christenson SD, Standage S, Shen B (2002) Biosynthesis of the enediyne antitumor antibiotic C-1027. Science 297:1170–1173PubMedCrossRefGoogle Scholar
  33. Liu W, Nonaka K, Nie L, Zhang J, Christenson SD, Bae J, Van Lanen SG, Zazopoulos E, Farnet CM, Yang CF, Shen B (2005) The neocarzinostatin biosynthetic gene cluster from S. carzinostaticus ATCC 15944 involving two iterative type I polyketide synthases. Chem Biol 12:293–302PubMedCrossRefGoogle Scholar
  34. Lombo F, Brana AF, Salas JA, Mendez C (2004) Genetic organization of the biosynthetic gene cluster for the antitumor angucycline oviedomycin in Streptomyces antibioticus ATCC 11891. ChemBioChem 5:1181–1187PubMedCrossRefGoogle Scholar
  35. Matsuno K, Yamada Y, Lee CK, Nihira T (2004) Identification by gene deletion analysis of barB as a negative regulator controlling an early process of virginiamycin biosynthesis in Streptomyces virginiae. Arch Microbiol 181:52–59PubMedCrossRefGoogle Scholar
  36. Otsuka M, Ichinose K, Fujii I, Ebizuka Y (2004) Cloning, sequencing, and functional analysis of an iterative type I polyketide synthase gene cluster for biosynthesis of the antitumor chlorinated polyenone neocarzilin in “Streptomyces carzinostaticus”. Antimicrob Agents Chemother 48:3468–3476PubMedCrossRefGoogle Scholar
  37. Reid R, Piagentini M, Rodriguez E, Ashley G, Viswanathan N, Carney J, Santi DV, Hutchinson CR, McDaniel R. (2003) A model of structure and catalysis for ketoreductase domains in modular polyketide synthases. Biochemistry 42:72–79PubMedCrossRefGoogle Scholar
  38. Rodriguez E, Gramajo H (1999) Genetic and biochemical characterization of the alpha and beta components of a propionyl–CoA carboxylase complex of Streptomyces coelicolor A3(2). Microbiology 145:3109–3119PubMedGoogle Scholar
  39. Rodriguez E, Banchio C, Diacovich L, Bibb MJ, Gramajo H (2001) Role of an essential acyl coenzyme A carboxylase in the primary and secondary metabolism of Streptomyces coelicolor A3(2). Appl Environ Microbiol 67:4166–4176PubMedCrossRefGoogle Scholar
  40. Rudd BA, Hopwood DA (1979) Genetics of actinoorhodin biosynthesis by Streptomyces coelicolor A3(2). J Gen Microbiol 114:35–43PubMedGoogle Scholar
  41. Sambrook J, Fritsch EF, Maniatis T (1989) Moleculer cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, New YorkGoogle Scholar
  42. Shen B (2003) Polyketide biosynthesis beyond the type I, II and III polyketide synthase paradigms. Curr Opin Chem Biol 7:285–295PubMedCrossRefGoogle Scholar
  43. Silakowski B, Nordsiek G, Kunze B, Blocker H, Muller R (2001) Novel features in a combined polyketide synthase/non-ribosomal peptide synthetase: the myxalamid biosynthetic gene cluster of the myxobacterium Stigmatella aurantiaca Sga15. Chem Biol 8:59–69PubMedCrossRefGoogle Scholar
  44. Siskos AP, Baerga-Ortiz A, Bali S, Stein V, Mamdani H, Spiteller D, Popovic B, Spencer JB, Staunton J, Weissman KJ, Leadlay PF. (2005) Molecular basis of Celmer’s rules: stereochemistry of catalysis by isolated ketoreductase domains from modular polyketide synthases. Chem Biol 12:1145–1153PubMedCrossRefGoogle Scholar
  45. Staunton J, Weissman KJ (2001) Polyketide biosynthesis:a millennium review. Nat Prod Rep 18:380–416PubMedCrossRefGoogle Scholar
  46. Takano E (2006) gamma-Butyrolactones: Streptomyces signalling molecules regulating antibiotic production and differentiation. Curr Opin Microbiol 9:1–8CrossRefGoogle Scholar
  47. Takano E, Chakraburtty R, Nihira T, Yamada Y, Bibb MJ (2001) A complex role for the gamma-butyrolactone SCB1 in regulating antibiotic production in Streptomyces coelicolor A3(2). Mol Microbiol 41:1015–1028PubMedCrossRefGoogle Scholar
  48. Takano E, Kinoshita H, Mersinias V, Bucca G, Hotchkiss G, Nihira T, Smith CP, Bibb M, Wohlleben W, Chater K (2005) A bacterial hormone (the SCB1) directly controls the expression of a pathway-specific regulatory gene in the cryptic type I polyketide biosynthetic gene cluster of Streptomyces coelicolor. Mol Microbiol 56:465–479PubMedCrossRefGoogle Scholar
  49. Wang L, Vining LC (2003) Control of growth, secondary metabolism and sporulation in Streptomyces venezuelae ISP5230 by jadW(1), a member of the afsA family of gamma-butyrolactone regulatory genes. Microbiology 149:1991–2004PubMedCrossRefGoogle Scholar
  50. Weber T, Welzel K, Pelzer S, Vente A, Wohlleben W (2003) Exploiting the genetic potential of polyketide producing streptomycetes. J Biotechnol 106:221–232PubMedCrossRefGoogle Scholar
  51. Wendt-Pienkowski E, Huang Y, Zhang J, Li B, Jiang H, Kwon H, Hutchinson CR, Shen B (2005) Cloning, sequencing, analysis, and heterologous expression of the fredericamycin biosynthetic gene cluster from Streptomyces griseus. J Am Chem Soc 127:16442–16452PubMedCrossRefGoogle Scholar
  52. Wietzorrek A, Bibb M (1997) A novel family of proteins that regulates antibiotic production in streptomycetes appears to contain an OmpR-like DNA-binding fold. Mol Microbiol 25:1181–1184PubMedCrossRefGoogle Scholar
  53. Yadav G, Gokhale RS, Mohanty D (2003) Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J Mol Biol 328:335–363PubMedCrossRefGoogle Scholar
  54. Yonaha K, Nishie M, Aibara S. (1992) The primary structure of omega-amino acid: pyruvate aminotransferase. J Biol Chem 267:12506–12510PubMedGoogle Scholar
  55. Yu TW, Hopwood DA (1995) Ectopic expression of the S. coelicolor whiE genes for polyketide spore pigment synthesis and their interaction with the act genes for actinorhodin biosynthesis. Microbiology 141:2779–2791PubMedCrossRefGoogle Scholar
  56. Yu TW, Bai L, Clade D, Hoffmann D, Toelzer S, Trinh K, Xu J, Moss S, Leistner E, Floss HG. (2002) The biosynthetic gene cluster of the maytansinoid antitumor agent ansamitocin from Actinosynnema pretiosum. Proc Natl Acad Sci USA 99:7968–7973PubMedCrossRefGoogle Scholar
  57. Zhu G, LaGier MJ, Stejskal F, Millership JJ, Cai X, Keithly JS (2002) Cryptosporidium parvum: the first protist known to encode a putative polyketide synthase. Gene 298:79–89PubMedCrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Krzysztof Pawlik
    • 1
  • Magdalena Kotowska
    • 1
  • Keith F. Chater
    • 2
  • Katarzyna Kuczek
    • 1
  • Eriko Takano
    • 2
    • 3
  1. 1.Institute of Immunology and Experimental TherapyPolish Academy of SciencesWroclawPoland
  2. 2.John Innes Centre Norwich Research Park NorwichUK
  3. 3.Department of Microbial Physiology, Groningen Biomolecular Sciences and Biotechnology Institute (GBB)University of GroningenHarenThe Netherlands

Personalised recommendations