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Evidence-Based Complementary and Alternative Medicine
Volume 2011, Article ID 384572, 11 pages
http://dx.doi.org/10.1155/2011/384572
Review Article

Genome-Based Studies of Marine Microorganisms to Maximize the Diversity of Natural Products Discovery for Medical Treatments

School of Life Science and Biotechnology, Dalian University of Technology, Linggong Road 2, Dalian 116024, China

Received 15 January 2011; Revised 15 April 2011; Accepted 3 June 2011

Copyright © 2011 Xin-Qing Zhao. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. E. L. Cooper, “Drug discovery, CAM and natural products,” Evidence-Based Complementary and Alternative Medicine, vol. 1, pp. 215–217, 2004. View at Google Scholar
  2. P. Bhadury, B. T. Mohammad, and P. C. Wright, “The current status of natural products from marine fungi and their potential as anti-infective agents,” Journal of Industrial Microbiology and Biotechnology, vol. 33, no. 5, pp. 325–337, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  3. A. T. Bull and J. E. M. Stach, “Marine actinobacteria: new opportunities for natural product search and discovery,” Trends in Microbiology, vol. 15, no. 11, pp. 491–499, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  4. P. G. Williams, “Panning for chemical gold: marine bacteria as a source of new therapeutics,” Trends in Biotechnology, vol. 27, no. 1, pp. 45–52, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  5. A. C. Jones, L. Gu, C. M. Sorrels, D. H. Sherman, and W. H. Gerwick, “New tricks from ancient algae: natural products biosynthesis in marine cyanobacteria,” Current Opinion in Chemical Biology, vol. 13, no. 2, pp. 216–223, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  6. T. A. Gulder and B. S. Moore, “Chasing the treasures of the sea—bacterial marine natural products,” Current Opinion in Microbiology, vol. 12, no. 3, pp. 252–260, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  7. A. M. S. Mayer, A. D. Rodríguez, R. G. S. Berlinck, and N. Fusetani, “Marine pharmacology in 2007-8: marine compounds with antibacterial, anticoagulant, antifungal, anti-inflammatory, antimalarial, antiprotozoal, antituberculosis, and antiviral activities; Affecting the immune and nervous system, and other miscellaneous mechanisms of action,” Comparative Biochemistry and Physiology Part C, vol. 153, no. 2, pp. 191–222, 2011. View at Publisher · View at Google Scholar · View at PubMed
  8. A. M. S. Mayer, K. B. Glaser, C. Cuevas et al., “The odyssey of marine pharmaceuticals: a current pipeline perspective,” Trends in Pharmacological Sciences, vol. 31, no. 6, pp. 255–265, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  9. F. A. Villa and L. Gerwick, “Marine natural product drug discovery: leads for treatment of inflammation, cancer, infections, and neurological disorders,” Immunopharmacology and Immunotoxicology, vol. 32, no. 2, pp. 228–237, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  10. A. L. Waters, R. T. Hill, A. R. Place, and M. T. Hamann, “The expanding role of marine microbes in pharmaceutical development,” Current Opinion in Biotechnology, vol. 21, no. 6, pp. 780–786, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  11. T. L. Simmons, E. Andrianasolo, K. McPhail, P. Flatt, and W. H. Gerwick, “Marine natural products as anticancer drugs,” Molecular Cancer Therapeutics, vol. 4, no. 2, pp. 333–342, 2005. View at Google Scholar · View at Scopus
  12. H. Luesch, R. E. Moore, V. J. Paul, S. L. Mooberry, and T. H. Corbett, “Isolation of dolastatin 10 from the marine cyanobacterium Symploca species VP642 and total stereochemistry and biological evaluation of its analogue symplostatin 1,” Journal of Natural Products, vol. 64, no. 7, pp. 907–910, 2001. View at Publisher · View at Google Scholar · View at Scopus
  13. W. Fenical, P. R. Jensen, and X. C. Cheng, “Halimide, a cytotoxic marine natural product, and derivatives thereof,” WO/1999/048889, The Regents of the University of California, September 1999. View at Google Scholar
  14. S. K. Davidson, S. W. Allen, G. E. Lim, C. M. Anderson, and M. G. Haygood, “Evidence for the biosynthesis of bryostatins by the bacterial symbiont “Candidatus Endobugula sertula” of the bryozoan Bugula neritina,” Applied and Environmental Microbiology, vol. 67, no. 10, pp. 4531–4537, 2001. View at Publisher · View at Google Scholar · View at Scopus
  15. R. H. Feling, G. O. Buchanan, T. J. Mincer, C. A. Kauffman, P. R. Jensen, and W. Fenical, “Salinosporamide A: a highly cytotoxic proteasome inhibitor from a novel microbial source, a marine bacterium of the new genus Salinospora,” Angewandte Chemie International Edition, vol. 42, no. 3, pp. 355–357, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  16. W. H. Gerwick, L. T. Tan, and N. Sitachitta, “Nitrogen-containing metabolites from marine cyanobacteria,” in The Alkaloids: Chemistry and Biology, G. A. Cordell, Ed., vol. 57, pp. 75–184, Academic Press, San Diego, Calif, USA, 2001. View at Google Scholar
  17. M. E. Rateb and R. Ebel, “Secondary metabolites of fungi from marine habitats,” Natural Product Reports, vol. 28, no. 2, pp. 290–344, 2011. View at Publisher · View at Google Scholar · View at PubMed
  18. K. Liolios, I. A. Chen, K. Mavromatis et al., “The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata,” Nucleic Acids Research, vol. 38, no. 1, pp. D346–D354, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  19. K. Liolios, K. Mavromatis, N. Tavernarakis, and N. C. Kyrpides, “The Genomes On Line Database (GOLD) in 2007: status of genomic and metagenomic projects and their associated metadata,” Nucleic Acids Research, vol. 36, no. 1, pp. D475–D479, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  20. Moore, “Microbial Genome Sequencing Project,” http:// http://camera.calit2.net/microgenome.
  21. A. C. Jones, E. A. Monroe, E. B. Eisman, L. Gerwick, D. H. Sherman, and W. H. Gerwick, “The unique mechanistic transformations involved in the biosynthesis of modular natural products from marine cyanobacteria,” Natural Product Reports, vol. 27, no. 7, pp. 1048–1065, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  22. K. Engelhardt, K. F. Degnes, and S. B. Zotchev, “Isolation and characterization of the gene cluster for biosynthesis of the thiopeptide antibiotic TP-1161,” Applied and Environmental Microbiology, vol. 76, no. 21, pp. 7093–7101, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  23. Y. Ding, J. R. de Wet, J. Cavalcoli et al., “Genome-based characterization of two prenylation steps in the assembly of the stephacidin and notoamide anticancer agents in a marine-derived Aspergillus sp,” Journal of the American Chemical Society, vol. 132, no. 36, pp. 12733–12740, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  24. S. D. Bentley, K. F. Chater, A. M. Cerdeño-Tárraga et al., “Complete genome sequence of the model actinomycete Streptomyces coelicolor A3(2),” Nature, vol. 417, no. 6885, pp. 141–147, 2002. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  25. H. Ikeda, J. Ishikawa, A. Hanamoto et al., “Complete genome sequence and comparative analysis of the industrial microorganism Streptomyces avermitilis,” Nature Biotechnology, vol. 21, no. 5, pp. 526–531, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  26. M. Oliynyk, M. Samborskyy, J. B. Lester et al., “Complete genome sequence of the erythromycin-producing bacterium Saccharopolyspora erythraea NRRL23338,” Nature Biotechnology, vol. 25, no. 4, pp. 447–453, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  27. D. W. Udwary, L. Zeigler, R. N. Asolkar et al., “Genome sequencing reveals complex secondary metabolome in the marine actinomycete Salinispora tropica,” Proceedings of the National Academy of Sciences of the United States of America, vol. 104, no. 25, pp. 10376–10381, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  28. Y. Ohnishi, J. Ishikawa, H. Hara et al., “Genome sequence of the streptomycin-producing microorganism Streptomyces griseus IFO 13350,” Journal of Bacteriology, vol. 190, no. 11, pp. 4050–4060, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  29. X. J. Wang, Y. J. Yan, B. Zhang et al., “Genome sequence of the milbemycin-producing bacterium Streptomyces bingchenggensis,” Journal of Bacteriology, vol. 192, no. 17, pp. 4526–4527, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  30. J. Y. Song, H. Jeong, D. S. Yu et al., “Draft genome sequence of Streptomyces clavuligerus NRRL 3585, a producer of diverse secondary metabolites,” Journal of Bacteriology, vol. 192, no. 23, pp. 6317–6318, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  31. N. Ichikawa, A. Oguchi, H. Ikeda et al., “Genome sequence of kitasatospora setae NBRC 14216T: an evolutionary snapshot of the family Streptomycetaceae,” DNA Research, vol. 17, no. 6, pp. 393–406, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  32. M. Nett, H. Ikeda, and B. S. Moore, “Genomic basis for natural product biosynthetic diversity in the actinomycetes,” Natural Product Reports, vol. 26, no. 11, pp. 1362–1384, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  33. D. E. Cane, C. T. Walsh, and C. Khosla, “Harnessing the biosynthetic code: combinations, permutations, and mutations,” Science, vol. 282, no. 5386, pp. 63–68, 1998. View at Publisher · View at Google Scholar · View at Scopus
  34. H. G. Floss, “Combinatorial biosynthesis-potential and problems,” Journal of Biotechnology, vol. 124, no. 1, pp. 242–257, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  35. L. Du, C. Sánchez, and B. Shen, “Hybrid peptide-polyketide natural products: biosynthesis and prospects toward engineering novel molecules,” Metabolic Engineering, vol. 3, no. 1, pp. 78–95, 2001. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  36. P. R. Jensen, P. G. Williams, D.-C. Oh, L. Zeigler, and W. Fenical, “Species-specific secondary metabolite production in marine actinomycetes of the genus Salinispora,” Applied and Environmental Microbiology, vol. 73, no. 4, pp. 1146–1152, 2007. View at Publisher · View at Google Scholar · View at PubMed
  37. J. F. Martin, “Clusters of genes for the biosynthesis of antibiotics: regulatory genes and overproduction of pharmaceuticals,” Journal of Industrial Microbiology, vol. 9, no. 2, pp. 73–90, 1992. View at Google Scholar · View at Scopus
  38. A. Hornung, M. Bertazzo, A. Dziarnowski et al., “A genomic screening approach to the structure-guided identification of drug candidates from natural sources,” ChemBioChem, vol. 8, no. 7, pp. 757–766, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  39. T. Toyomasu, A. Kaneko, T. Tokiwano et al., “Biosynthetic gene-based secondary metabolite screening: a new diterpene, methyl phomopsenonate, from the fungus Phomopsis amygdali,” Journal of Organic Chemistry, vol. 74, no. 4, pp. 1541–1548, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  40. E. Zazopoulos, K. Huang, A. Staffa et al., “A genomics-guided approach for discovering and expressing cryptic metabolic pathways,” Nature Biotechnology, vol. 21, no. 2, pp. 187–190, 2003. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  41. L. C. Foulston and M. J. Bibb, “Microbisporicin gene cluster reveals unusual features of lantibiotic biosynthesis in actinomycetes,” Proceedings of the National Academy of Sciences of the United States of America, vol. 107, no. 30, pp. 13461–13466, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  42. I. Borodina, J. Siebring, J. Zhang et al., “Antibiotic overproduction in Streptomyces coelicolor A3(2) mediated by phosphofructokinase deletion,” Journal of Biological Chemistry, vol. 283, no. 37, pp. 25186–25199, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  43. I. Borodina, P. Krabben, and J. Nielsen, “Genome-scale analysis of Streptomyces coelicolor A3(2) metabolism,” Genome Research, vol. 15, no. 6, pp. 820–829, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  44. M. Castro-Melchor, S. Charaniya, G. Karypis, E. Takano, and W. S. Hu, “Genome-wide inference of regulatory networks in Streptomyces coelicolor,” BMC Genomics, vol. 11, no. 1, article 578, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  45. S. G. van Lanen and B. Shen, “Microbial genomics for the improvement of natural product discovery,” Current Opinion in Microbiology, vol. 9, no. 3, pp. 252–260, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  46. H. Gross, “Strategies to unravel the function of orphan biosynthesis pathways: recent examples and future prospects,” Applied Microbiology and Biotechnology, vol. 75, no. 2, pp. 267–277, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  47. J. B. McAlpine, “Advances in the understanding and use of the genomic base of microbial secondary metabolite biosynthesis for the discovery of new natural products,” Journal of Natural Products, vol. 72, no. 3, pp. 566–572, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  48. H. Gross, “Genomic mining—a concept for the discovery of new bioactive natural products,” Current Opinion in Drug Discovery and Development, vol. 12, no. 2, pp. 207–219, 2009. View at Google Scholar · View at Scopus
  49. J. E. Velásquez and W. A. van der Donk, “Genome mining for ribosomally synthesized natural products,” Current Opinion in Chemical Biology, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  50. A. L. Lane and B. S. Moore, “A sea of biosynthesis: marine natural products meet the molecular age,” Natural Product Reports, vol. 28, no. 2, pp. 411–428, 2011. View at Publisher · View at Google Scholar · View at PubMed
  51. J. E. Velásquez and W. A. van der Donk, “Genome mining for ribosomally synthesized natural products,” Current Opinion in Chemical Biology, vol. 15, pp. 11–12, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  52. A. S. Eustáquio, S. J. Nam, K. Penn et al., “The discovery of salinosporamide K from the marine bacterium “Salinispora pacifica” by Genome mining gives insight into pathway evolution,” ChemBioChem, vol. 12, no. 1, pp. 61–64, 2011. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  53. S. Lautru, R. J. Deeth, L. M. Bailey, and G. L. Challis, “Discovery of a new peptide natural product by Streptomyces coelicolor genome mining,” Nature Chemical Biology, vol. 1, no. 5, pp. 265–269, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  54. C. Corre, L. Song, S. O'Rourke, K. F. Chater, and G. L. Challis, “2-Alkyl-4-hydroxymethylfuran-3-carboxylic acids, antibiotic production inducers discovered by Streptomyces coelicolor genome mining,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 45, pp. 17510–17515, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  55. L. C. Blasiak and J. Clardy, “Discovery of 3-formyl-tyrosine metabolites from Pseudoalteromonas tunicata through heterologous expression,” Journal of the American Chemical Society, vol. 132, no. 3, pp. 926–927, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  56. S. Bergmann, J. Schümann, K. Scherlach, C. Lange, A. A. Brakhage, and C. Hertweck, “Genomics-driven discovery of PKS-NRPS hybrid metabolites from Aspergillus nidulans,” Nature Chemical Biology, vol. 3, no. 4, pp. 213–217, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  57. M. Gottelt, S. Kol, J. P. Gomez-Escribano, M. Bibb, and E. Takano, “Deletion of a regulatory gene within the cpk gene cluster reveals novel antibacterial activity in Streptomyces coelicolor A3(2),” Microbiology, vol. 156, no. 8, pp. 2343–2353, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  58. H. Gross, V. O. Stockwell, M. D. Henkels, B. Nowak-Thompson, J. E. Loper, and W. H. Gerwick, “The genomisotopic approach: a systematic method to isolate products of orphan biosynthetic gene clusters,” Chemistry and Biology, vol. 14, no. 1, pp. 53–63, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  59. A. L. McClerren, L. E. Cooper, C. Quan, P. P. Thomas, N. L. Kelleher, and W. A. van der Donk, “Discovery and in vitro biosynthesis of haloduracin, a two-component lantibiotic,” Proceedings of the National Academy of Sciences of the United States of America, vol. 103, no. 46, pp. 17243–17248, 2006. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  60. P. D. Schloss and J. Handelsman, “Metagenomics for studying unculturable microorganisms: cutting the Gordian knot,” Genome Biology, vol. 6, no. 8, article 229, 2005. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  61. S. F. Brady, L. Simmons, J. H. Kim, and E. W. Schmidt, “Metagenomic approaches to natural products from free-living and symbiotic organisms,” Natural Product Reports, vol. 26, no. 11, pp. 1488–1503, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  62. A. Uria and J. Piel, “Cultivation-independent approaches to investigate the chemistry of marine symbiotic bacteria,” Phytochemistry Reviews, vol. 8, no. 2, pp. 401–414, 2009. View at Publisher · View at Google Scholar · View at Scopus
  63. C. Gurgui and J. Piel, “Metagenomic approaches to identify and isolate bioactive natural products from microbiota of marine sponges,” Methods in Molecular Biology, vol. 668, pp. 247–264, 2010. View at Google Scholar
  64. J. C. Venter, K. Remington, J. F. Heidelberg et al., “Environmental genome shotgun sequencing of the Sargasso Sea,” Science, vol. 304, no. 5667, pp. 66–74, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  65. J. Piel, D. Hui, G. Wen et al., “Antitumor polyketide biosynthesis by an uncultivated bacterial symbiont of the marine sponge Theonella swinhoei,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 46, pp. 16222–16227, 2004. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  66. S. Sudek, N. B. Lopanik, L. E. Waggoner et al., “Identification of the putative bryostatin polyketide synthase gene cluster from “Candidatus Endobugula sertula”, the uncultivated microbial symbiont of the marine bryozoan Bugula neritina,” Journal of Natural Products, vol. 70, no. 1, pp. 67–74, 2007. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  67. K. M. Fisch, C. Gurgui, N. Heycke et al., “Polyketide assembly lines of uncultivated sponge symbionts from structure-based gene targeting,” Nature Chemical Biology, vol. 5, no. 7, pp. 494–501, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  68. H. Zhang, B. A. Boghigian, J. Armando, and B. A. Pfeifer, “Methods and options for the heterologous production of complex natural products,” Natural Product Reports, vol. 28, no. 1, pp. 125–151, 2011. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  69. F. O. Glöckner and I. Joint, “Marine microbial genomics in Europe: current status and perspectives: minireview,” Microbial Biotechnology, vol. 3, no. 5, pp. 523–530, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  70. A. Starcevic, J. Zucko, J. Simunkovic, P. F. Long, J. Cullum, and D. Hranueli, “ClustScan: an integrated program package for the semi-automatic annotation of modular biosynthetic gene clusters and in silico prediction of novel chemical structures,” Nucleic Acids Research, vol. 36, no. 21, pp. 6882–6892, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  71. M. H. T. Li, P. M. U. Ung, J. Zajkowski, S. Garneau-Tsodikova, and D. H. Sherman, “Automated genome mining for natural products,” BMC Bioinformatics, vol. 10, article 185, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  72. S. Anand, M. V. R. Prasad, G. Yadav et al., “SBSPKS: structure based sequence analysis of polyketide synthases,” Nucleic Acids Research, vol. 38, no. 2, pp. W487–W496, 2010. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  73. E. Esquenazi, C. Coates, L. Simmons, D. Gonzalez, W. H. Gerwick, and P. C. Dorrestein, “Visualizing the spatial distribution of secondary metabolites produced by marine cyanobacteria and sponges via MALDI-TOF imaging,” Molecular BioSystems, vol. 4, no. 6, pp. 562–570, 2008. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  74. S. B. Bumpus, B. S. Evans, P. M. Thomas, I. Ntai, and N. L. Kelleher, “A proteomics approach to discovering natural products and their biosynthetic pathways,” Nature Biotechnology, vol. 27, no. 10, pp. 951–956, 2009. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus
  75. A. Siegl, J. Kamke, T. Hochmuth et al., “Single-cell genomics reveals the lifestyle of Poribacteria, a candidate phylum symbiotically associated with marine sponges,” ISME Journal, vol. 5, no. 1, pp. 61–70, 2011. View at Publisher · View at Google Scholar · View at PubMed · View at Scopus