Mining the microbial metabolome: A new frontier for natural product lead discovery

Drug Discovery Today

Volumn 8, Issue 23, 2003, Pages 1078-1084

  Perić Concha, Nataša ^a   Long, Paul F ^a  

^a UNIVERSITY OF LONDON   (United Kingdom)

Author keywords

Chemical Biology; Drug Discovery; Metabolomics; Metagenome; Microbiology; Pharmaceutical Science; Polyketides; Streptomyces

Indexed keywords

DRUG METABOLITE; ERYTHROMYCIN; LACTONE DERIVATIVE; TRANSFER RNA;

ACTINOMYCES; BIOINFORMATICS; CHEMICAL STRUCTURE; COMBINATORIAL CHEMISTRY; DATA BASE; DNA LIBRARY; DRUG INDUSTRY; DRUG RESEARCH; ESCHERICHIA COLI; FERMENTATION; GENE CLUSTER; GENE SEQUENCE; GENETIC ENGINEERING; GENOME; METABOLITE; MICROBIAL METABOLISM; MICROBIOLOGICAL PHENOMENA AND FUNCTIONS; MICROFLORA; MOLECULAR MODEL; NEAR INFRARED SPECTROSCOPY; NONHUMAN; POLYMERASE CHAIN REACTION; REVIEW; STREPTOMYCES;

BIOLOGICAL FACTORS; DRUG INDUSTRY; GENOME, BACTERIAL; HUMANS; MULTIGENE FAMILY;

EID: 1642453829     PISSN: 13596446     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1359-6446(03)02901-5     Document Type: Review

References (46)

1. Newman D.J., et al. The influence of natural products upon drug discovery. Nat. Prod. Rep. 17:2000;215-234.
2. Subramaniam S. Productivity and attrition: key challenges for biotech and pharma. Drug Discov. Today. 8:2003;513-515.
3. Hopwood D.A. The Streptomyces genome - be prepared! Nat. Biotechnol. 21:2003;505-506.
4. Rondon M., et al. The Earth's bounty: assessing and accessing soil microbial diversity. Trends Biotechnol. 17:1999;403-409.
5. Lindpainter K. Pharmacogenetics and pharmacogenomics in drug discovery and development: an overview. Clin. Chem. Lab. Med. 41:2003;398-410.
6. Workman P. The opportunities and challenges of personalized genome-based molecular therapies for cancer: targets, technologies, and molecular chaperones. Cancer Chemother. Pharmacol. 52:(Suppl. 1):2003;S45-S56.
7. Moran G.J., Mount J. Update on emerging infections: news from the Centers for Disease Control and Prevention. Ann. Emerg. Med. 41:2003;148-151.
8. Beggs M., Long A.C. High throughput genomics and drug discovery - parallel universes or a continuum? Drug Discov. World. 3:2002;75-80.
9. Ausman, D.J. (2001) Screening's age of insecurity. Modern Drug. Discov. May, 32-39.
10. Mueller-Kuhrt L. Putting nature back into drug discovery. Nat. Biotechnol. 21:2003;602.
11. Walters W.P., Namchuk M. Designing screens: how to make your hits a hit. Nat. Rev. Drug Discov. 2:2003;259-266.
12. Donadio S., et al. Targets and assays for discovering novel antibacterial agents. J. Biotechnol. 99:2002;175-185.
13. Geysen H.M., et al. Combinatorial compound libraries for drug discovery: an ongoing challenge. Nat. Rev. Drug Discov. 2:2003;222-230.
14. Rondon M.R., et al. Cloning the soil metagenome: a strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2000;2541-2547.
15. Lazzarini A. Rare genera of actinomycetes as potential producers of new antibiotics. Antonie Van Leeuwenhoek. 78:2000;399-405.
16. Brandao P.F., et al. Dereplication for biotechnology screening: PyMS analysis and PCR-RFLP-SSCP (PRS) profiling of 16S rRNA genes of marine and terrestrial actinomycetes. Appl. Microbiol. Biotechnol. 58:2002;77-83.
17. Oberreuter H., et al. Intraspecific diversity of Brevibacterium linens, Corynebacterium glutamicum and Rhodococcus erythropolis based on partial 16S rDNA sequence analysis and Fourier-transform infrared (FT-IR) spectroscopy. Microbiology. 148:2002;1523-1532.
18. Mazza P., et al. Diversity of Actinoplanes and related genera isolated from an Italian soil. Microb. Ecol. 45:2003;362-372.
19. Cropp T.A., et al. Recent developments in the production of novel polyketides by combinatorial biosynthesis. Biotechnol. Genet. Eng. Rev. 19:2002;159-172.
20. Staunton J., Weissman K.J. Polyketide biosynthesis: a millennium review. Nat. Prod. Rep. 18:2001;380-416.
21. Mendez C., Salas J.A. Altering the glycosylation pattern of bioactive compounds. Trends Biotechnol. 19:2001;449-456.
22. Schwarzer D., et al. Non-ribosomal peptides: from genes to products. Nat. Prod. Rep. 20:2003;275-287.
23. Moore B.S., Piel J. Engineering biodiversity with type II polyketide synthase genes. Antonie Van Leeuwenhoek. 78:2000;391-398.
24. Beck B.J., et al. Iterative chain elongation by a pikromycin monomodular polyketide synthase. J. Am. Chem. Soc. 125:2003;4682-4683.
25. Aparicio J.F., et al. Polyene antibiotic biosynthesis gene clusters. Appl. Microbiol. Biotechnol. 61:2003;179-188.
26. Austin M.B., Noel J.P. The chalcone synthase superfamily of type III polyketide synthases. Nat. Prod. Rep. 20:2003;79-110.
27. McDaniel R., et al. Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel "unnatural" natural products. Proc. Natl. Acad. Sci. U. S. A. 96:1999;1846-1851.
28. Ikeda H., et al. Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis. Nat. Biotechnol. 21:2003;526-531.
29. Bentley S.D., et al. Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2). Nature. 417:2002;141-147.
30. Cole S.T., et al. Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence. Nature. 393:1998;537-544.
31. Cole S.T., et al. Massive gene decay in the leprosy bacillus. Nature. 409:2001;1007-1011.
32. Garnier T., et al. The complete genome sequence of {Mycobacterium bovis. Proc. Natl. Acad. Sci. U. S. A. 100:2003;7877-7882.
33. Sosio M., et al. Multiple peptide synthetase gene clusters in actinomycetes. Mol. Gen. Genet. 264:2000;213-221.
34. Yadav G., et al. SEARCHPKS: a program for detection and analysis of polyketide synthase domains. Nucleic Acids Res. 31:2003;3654-3658.
35. Zazopoulos E., et al. A genomics-guided approach for discovering and expressing cryptic metabolic pathways. Nat. Biotechnol. 21:2003;187-190.
36. Hopwood D.A., et al. Genetics of antibiotic production in Streptomyces coelicolor A3(2), a model streptomycete. Biotechnology. 28:1995;65-102.
37. Handelsman J., et al. Molecular biological access to the chemistry of unknown soil microbes: a new frontier for natural products. Chem. Biol. 5:1998;R245-R249.
38. Berry A.E., et al. Isolation of high molecular weight DNA from soil for cloning into BAC vectors. FEMS Microbiol. Lett. 223:2003;15-20.
39. Liles M.R., et al. A census of rRNA genes and linked genomic sequences within a soil metagenomic library. Appl. Environ. Microbiol. 69:2003;2684-2691.
40. Alduina R., et al. Artificial chromosome libraries of Streptomyces coelicolor A3(2) and Planobispora rosea. FEMS Microbiol. Lett. 218:2003;181-186.
41. Wang G.Y., et al. Novel natural products from soil DNA libraries in a streptomycete host. Org. Lett. 2:2000;2401-2404.
42. MacNeil I.A., et al. Expression and isolation of antimicrobial small molecules from soil DNA libraries. J. Mol. Microbiol. Biotechnol. 3:2001;301-308.
43. Gillespie D.E., et al. Isolation of antibiotics turbomycin A and B from a metagenomic library of soil microbial DNA. Appl. Environ. Microbiol. 68:2002;4301-4306.
44. Wilkinson C.J., et al. Increasing the efficiency of heterologous promoters in actinomycetes. J. Mol. Microbiol. Biotechnol. 4:2002;417-426.
45. Allen J., et al. High-throughput classification of yeast mutants for functional genomics using metabolic footprinting. Nat. Biotechnol. 21:2003;692-696.
46. Vaidyanathan S., et al. Assessment of near-infrared spectral information for rapid monitoring of bioprocess quality. Biotechnol. Bioeng. 74:2001;376-388.