Advertisement

Activation of fungal silent gene clusters: A new avenue to drug discovery

  • Axel A. Brakhage
  • Julia Schuemann
  • Sebastian Bergmann
  • Kirstin Scherlach
  • Volker Schroeckh
  • Christian Hertweck
Part of the Progress in Drug Research book series (PDR, volume 66)

Abstract

The ongoing exponential growth of DNA sequence data will lead to the discovery of many natural-product biosynthesis pathways by genome mining for which no actual product has been characterised. In many cases, these clusters remain silent under laboratory conditions. New technologies based on genetic engineering are available to induce silent genes. Heterologous expression of a silent gene cluster under the control of defined promoters can be applied. Alternatively, promoters of biosynthesis genes within the genome can be exchanged by defined promoters. Most promising, however, is the activation of pathway-specific regulatory genes, which was recently demonstrated. Such regulatory genes are present in many secondary metabolite gene clusters. This approach is rendered feasible by the fact that all of the genes encoding the large number of enzymes required for the synthesis of a typical secondary metabolite are clustered and that in some cases, a single regulator controls the expression of all members of a gene cluster to a certain extent. The advantage of this technique is that only a small gene needs to be handled, and that an ectopic integration is sufficient, bypassing all limitations of homologous recombination. Most conveniently, this strategy can trigger the concerted expression of all pathway genes. The vast amount of DNA sequences in the public database represents only the beginning of this new genomics era. The activation of these gene clusters by genetic engineering will lead to the discovery of many so far unknown products and therefore represents a novel avenue to drug discovery.

Keywords

Gene Cluster Biosynthetic Gene Cluster Extender Unit NONRIBOSOMAL Peptide Genome Mining 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. 1.
    Clardy J, Walsh C (2004) Lessons from natural molecules. Nature 432: 829–837PubMedCrossRefGoogle Scholar
  2. 2.
    Khosla C (1997) Harnessing the biosynthetic potential of modular polyketide synthases. Chem Rev 97: 2577–2590PubMedCrossRefGoogle Scholar
  3. 3.
    Sieber SA, Marahiel MA (2005) Molecular mechanisms underlying nonribosomal peptide synthesis: approaches to new antibiotics. Chem Rev 105: 715–738PubMedCrossRefGoogle Scholar
  4. 4.
    Yin J, Straight PD, Hrvatin S, Dorrestein PC, Bumpus SB, Jao C, Kelleher NL, Kolter R, Walsh CT (2007) Genome-wide high-throughput mining of natural-product biosynthetic gene clusters by phage display. Chem Biol 14: 303–312PubMedCrossRefGoogle Scholar
  5. 5.
    McAlpine JB, Bachmann BO, Piraee M, Tremblay S, Alarco AM, Zazopoulos E, Farnet CM (2005) Microbial genomics as a guide to drug discovery, structural elucidation: ECO-02301, a novel antifungal agent, as an example. J Nat Prod 68: 493–496PubMedCrossRefGoogle Scholar
  6. 6.
    Peric-Concha N, Long PF (2003) Mining the microbial metabolome: a new frontier for natural product lead discovery. Drug Discov Today 8: 1078–1084PubMedCrossRefGoogle Scholar
  7. 7.
    Bode HB, Bethe B, Hofs R, Zeeck A (2002) Big effects from small changes: possible ways to explore nature’s chemical diversity. Chembiochem 3: 619–627PubMedCrossRefGoogle Scholar
  8. 8.
    Walsh CT, Chen H, Keating TA, Hubbard BK, Losey HC, Luo L, Marshall CG, Miller DA, Patel HM (2001) Tailoring enzymes that modify nonribosomal peptides during and after chain elongation on NRPS assembly lines. Curr Opin Chem Biol 5: 525–534PubMedCrossRefGoogle Scholar
  9. 9.
    Cane DE (1997) Introduction: Polyketide and nonribosomal polypeptide biosynthesis. From collie to coli. Chem Rev 97: 2463–2464PubMedCrossRefGoogle Scholar
  10. 10.
    Cane DE, Walsh CT (1999) The parallel and convergent universes of polyketide synthases and nonribosomal peptide synthetases. Chem Biol 6: R319–325PubMedCrossRefGoogle Scholar
  11. 11.
    Paitan Y, Alon G, Orr E, Ron EZ, Rosenberg E (1999) The first gene in the biosynthesis of the polyketide antibiotic TA of Myxococcus xanthus codes for a unique PKS module coupled to a peptide synthetase. J Mol Biol 286: 465–474PubMedCrossRefGoogle Scholar
  12. 12.
    Silakowski B, Schairer HU, Ehret H, Kunze B, Weinig S, Nordsiek G, Brandt P, Blocker H, Hofle G, Beyer S et al (1999) New lessons for combinatorial biosynthesis from myxobacteria. The myxothiazol biosynthetic gene cluster of Stigmatella aurantiaca DW4/3-1. J Biol Chem 274: 37391–37399PubMedCrossRefGoogle Scholar
  13. 13.
    Wenzel SC, Kunze B, Hofle G, Silakowski B, Scharfe M, Blocker H, Muller R (2005) Structure and biosynthesis of myxochromides S1–3 in Stigmatella aurantiaca: evidence for an iterative bacterial type I polyketide synthase and for module skipping in nonribosomal peptide biosynthesis. Chembiochem 6: 375–385PubMedCrossRefGoogle Scholar
  14. 14.
    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
  15. 15.
    Liu W, Christenson SD, Standage S, Shen B (2002) Biosynthesis of the enediyne antitumor antibiotic C-1027. Science 297: 1170–1173PubMedCrossRefGoogle Scholar
  16. 16.
    Menzella HG, Reid R, Carney JR, Chandran SS, Reisinger SJ, Patel KG, Hopwood DA, Santi DV (2005) Combinatorial polyketide biosynthesis by de novo design and rearrangement of modular polyketide synthase genes. Nat Biotechnol 23: 1171–1176PubMedCrossRefGoogle Scholar
  17. 17.
    Lautru S, Deeth RJ, Bailey LM, Challis GL (2005) Discovery of a new peptide natural product by Streptomyces coelicolor genome mining. Nat Chem Biol 1: 265–269PubMedCrossRefGoogle Scholar
  18. 18.
    Zazopoulos E, Huang K, Staffa A, Liu W, Bachmann BO, Nonaka K, Ahlert J, Thorson JS, Shen B, Farnet CM (2003) A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Nat Biotechnol 21: 187–190PubMedCrossRefGoogle Scholar
  19. 19.
    Bode HB, Muller R (2005) The impact of bacterial genomics on natural product research. Angew Chem Int Ed Engl 44: 6828–6846PubMedCrossRefGoogle Scholar
  20. 20.
    Brendel N, Partida-Martinez LP, Scherlach K, Hertweck C (2007) A cryptic PKS-NRPS gene locus in the plant commensal Pseudomonas fluorescens Pf-5 codes for the biosynthesis of an antimitotic rhizoxin complex. Org Biomol Chem 5: 2211–2213PubMedCrossRefGoogle Scholar
  21. 21.
    Challis GL (2007) A widely distributed bacterial pathway for siderophore biosynthesis independent of nonribosomal peptide synthetases. Chembiochem 8: 1477CrossRefGoogle Scholar
  22. 22.
    Gross H, Stockwell VO, Henkels MD, Nowak-Thompson B, Loper JE, Gerwick WH (2007) The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters. Chem Biol 14: 53–63PubMedCrossRefGoogle Scholar
  23. 23.
    Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR, Batzoglou S, Lee SI, Basturkmen M, Spevak CC, Clutterbuck J et al (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumigatus and A. oryzae. Nature 438: 1105–1115PubMedCrossRefGoogle Scholar
  24. 24.
    Machida M, Asai K, Sano M, Tanaka T, Kumagai T, Terai G, Kusumoto K, Arima T, Akita O, Kashiwagi Y et al (2005) Genome sequencing and analysis of Aspergillus oryzae. Nature 438: 1157–1161PubMedCrossRefGoogle Scholar
  25. 25.
    Nierman WC, Pain A, Anderson MJ, Wortman JR, Kim HS, Arroyo J, Berriman M, Abe K, Archer DB, Bermejo C et al (2005) Genomic sequence of the pathogenic and allergenic filamentous fungus Aspergillus fumigatus. Nature 438: 1151–1156PubMedCrossRefGoogle Scholar
  26. 26.
    Cramer RA Jr, Stajich JE, Yamanaka Y, Dietrich FS, Steinbach WJ, Perfect JR (2006) Phylogenomic analysis of non-ribosomal peptide synthetases in the genus Aspergillus. Gene 383: 24–32PubMedCrossRefGoogle Scholar
  27. 27.
    Bok JW, Hoffmeister D, Maggio-Hall LA, Murillo R, Glasner JD, Keller NP (2006) Genomic mining for Aspergillus natural products. Chem Biol 13: 31–37PubMedCrossRefGoogle Scholar
  28. 28.
    Scherlach K, Hertweck C (2006) Discovery of aspoquinolones A-D, prenylated quinoline-2-one alkaloids from Aspergillus nidulans, motivated by genome mining. Org Biomol Chem 4: 3517–3520PubMedCrossRefGoogle Scholar
  29. 29.
    van den Broek P, Pittet A, Hajjaj H (2001) Aflatoxin genes and the aflatoxigenic potential of Koji moulds. Appl Microbiol Biotechnol 57: 192–199PubMedCrossRefGoogle Scholar
  30. 30.
    Zhang Y-Q, Wilkinson H, Keller NP, Tsitsigiannis DI (2004) Secondary metabolite gene clusters. In: Z An (ed): Handbook of Industrial Microbiology. Marcel Dekker, New York, 355–386Google Scholar
  31. 31.
    Bergmann S, Schuemann J, Scherlach K, Lange C, Brakhage AA, Hertweck C (2007) Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans. Nat Chem Biol 3: 213–217PubMedCrossRefGoogle Scholar
  32. 32.
    Sims JW, Fillmore JP, Warner DD, Schmidt EW (2005) Equisetin biosynthesis in Fusarium heterosporum. Chem Commun (Camb) 2: 186–188CrossRefGoogle Scholar
  33. 33.
    Song Z, Cox RJ, Lazarus CM, Simpson TT (2004) Fusarin C biosynthesis in Fusarium moniliforme and Fusarium venenatum. Chembiochem 5: 1196–1203PubMedCrossRefGoogle Scholar
  34. 34.
    Kennedy J, Turner G (1996) delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase is a rate limiting enzyme for penicillin production in Aspergillus nidulans. Mol Gen Genet 253: 189–197PubMedCrossRefGoogle Scholar
  35. 35.
    Waring RB, May GS, Morris NR (1989) Characterization of an inducible expression system in Aspergillus nidulans using alcA and tubulin-coding genes. Gene 79: 119–130PubMedCrossRefGoogle Scholar
  36. 36.
    Eley KL, Halo LM, Song Z, Powles H, Cox RJ, Bailey AM, Lazarus CM, Simpson TJ (2007) Biosynthesis of the 2-pyridone tenellin in the insect pathogenic fungus Beauveria bassiana. Chembiochem 8: 289–297PubMedCrossRefGoogle Scholar
  37. 37.
    Schmidt K, Riese U, Li Z, Hamburger M (2003) Novel tetramic acids and pyridone alkaloids, militarinones B, C and D, from the insect pathogenic fungus Paecilomyces militaris. J Nat Prod 66: 378–383PubMedCrossRefGoogle Scholar

Copyright information

© Birkhäuser Verlag, Basel (Switzerland) 2008

Authors and Affiliations

  • Axel A. Brakhage
    • 1
  • Julia Schuemann
    • 2
  • Sebastian Bergmann
    • 1
  • Kirstin Scherlach
    • 2
  • Volker Schroeckh
    • 1
  • Christian Hertweck
    • 2
  1. 1.Molecular and Applied Microbiology, Leibniz-Institute for Natural Product Research and Infection Biology (HKI)Friedrich Schiller UniversityJenaGermany
  2. 2.Biomolecular Chemistry, Leibniz-Institute for Natural Product Research and Infection Biology (HKI)Friedrich Schiller UniversityJenaGermany

Personalised recommendations