Identification of Novel Bioactive Compounds from the Metagenome of the Marine Sponge Haliclona simulans

Handbook of Molecular Microbial Ecology II: Metagenomics in Different Habitats

Volumn , Issue , 2011, Pages 553-562

  Lejon, David P H ^a   Kennedy, Jonathan ^a   Dobson, Alan D W ^a  

^a UNIVERSITY COLLEGE CORK   (Ireland)

Author keywords

Functional metagenomics based approach; Haliclona simulans, metabolic diversity; Novel bioactive compounds

Indexed keywords

EID: 84870553359     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9781118010549.ch52     Document Type: Chapter

References (47)

1. Altschul SF, Madden TL, Schaffer AA, Zhang JH, Zhang Z, et al. 1997. Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25:3389-3402.
2. Blunt JW, Copp BR, Munro MH, Northcote PT, Prinsep MR. 2006. Marine natural products. Nat. Prod. Rep. 23:26-78.
3. Brady SF. 2007. Construction of soil environmental DNA cosmid libraries and screening for clones that produce biologically active small molecules. Nat. Protoc. 2:1297-1305.
4. Brady SF, Simmons L, Kim JH, Schmidt EW. 2009. Metagenomic approaches to natural products from free-living and symbiotic organisms. Nat. Prod. Rep. 26:1488-1503.
5. Cragg GM, Grothaus PG, Newman DJ. 2009. Impact of natural products on developing new anti-cancer agents. Chem. Rev. 109:3012-3043.
6. Duckworth A. 2009. Farming sponges to supply bioactive metabolites and bath sponges: A review. Mar. Biotechnol. 11:669-679.
7. Dunlap WC, Battershill CN, Liptrot CH, Cobb RE, Bourne DG, et al. 2007. Biomedicinals from the phytosymbionts of marine invertebrates: A molecular approach. Methods 42:358-376.
8. Felsenstein J. 1989. PHYLIP-Phylogeny Inference Package (Version 3.2). Cladistics 5:164-166.
9. Ferrer M, Beloqui A, Timmis KN, Golyshin PN. 2009. Metagenomics for mining new genetic resources of microbial communities. J. Mol. Microbiol. Biotechnol. 16:109-123.
10. Fieseler L, Horn M, Wagner M, Hentschel U. 2004. Discovery of the novel candidate phylum "Poribacteria" in marine sponges. Appl. Environ. Microbiol. 70:3724-3732.
11. Garson MJ, Flowers AE, Webb RI, Charan RD, McCaffrey EJ. 1998. A sponge/dinoflagellate association in the haplosclerid sponge Haliclona sp.: Cellular origin of cytotoxic alkaloids by Percoll density gradient fractionation. Cell Tissue Res. 293:365-373.
12. Handelsman J. 2004. Metagenomics: Application of genomics to uncultured microorganisms. Microbiol. Mol. Biol. Rev. 68:669-685.
13. Hardeman F, Sjoling S. 2006. Metagenomic approach for the isolation of a novel low-temperature-active lipase from uncultured bacteria of marine sediment. In International Conference on Alpine and Polar Microbiology, Innsbruck, Austria, pp. 524-534.
14. Heath C, Hu XP, Cary SC, Cowan D. 2009. Identification of a novel alkaliphilic esterase active at low temperatures by screening a metagenomic library from Antarctic desert soil. Appl. Environ. Microbiol. 75:4657-4659.
15. Hentschel U, Usher KM, Taylor MW. 2006. Marine sponges as microbial fermenters. FEMS Microbiol. Ecol. 55:167-177.
16. Hoffmann F, Larsen O, Thiel V, Rapp HT, Pape T, et al. 2005. An anaerobic world in sponges. Geomicrobiol. J. 22:1-10.
17. Imhoff JF, Trüper HG. 1976. Marine sponges as habitats of anaerobic phototrophic bacteria. Microb. Ecol. 3:1-9.
18. Jeong H, Yim JH, Lee C, Choi SH, Park YK, et al. 2005. Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent. Nucleic Acids Res. 33:7066-7073.
19. Jones BV, Sun F, Marchesi JR. 2007. Using skimmed milk agar to functionally screen a gut metagenomic library for proteases may lead to false positives. Lett. Appl. Microbiol. 45:418-420.
20. Kennedy J, Marchesi JR, Dobson ADW. 2007. Metagenomic approaches to exploit the biotechnological potential of the microbial consortia of marine sponges. Appl. Environ. Microbiol. 75:11-20.
21. Kennedy J, Marchesi JR, Dobson ADW. 2008a. Marine metagenomics: Strategies for the discovery of novel enzymes with biotechnological applications from marine environments. Microb. Cell Fact. 7:27.
22. Kennedy J, Codling CE, Jones BV, Dobson ADW, Marchesi JR. 2008b. Diversity of microbes associated with the marine sponge, Haliclona simulans, isolated from Irish waters and identification of polyketide synthase genes from the sponge metagenome. Environ. Microbiol. 10:1888-1902.
23. Kim UJ, Shizuya H, de Jong PJ, Birren B, Simon MI. 1992. Stable propagation of cosmid sized human DNA inserts in an F factor based vector. Nucleic Acids Res. 20:1083-1085.
24. Kobayashi J, Ishibashi M. 1993. Bioactive metabolites of symbiotic marine microorganisms. Chem. Rev. 93:1753-1769.
25. Lammle K, Zipper H, Breuer M, Hauer B, Buta C, et al. 2007. Identification of novel enzymes with different hydrolytic activities by metagenome expression cloning. J. Biotechnol. 127:575-592.
26. Lee DG, Jeon JH, Jang MK, Kim NY, Lee JH, et al. 2007. Screening and characterization of a novel fibrinolytic metalloprotease from a metagenomic library. Biotechnol. Lett. 29:465-472.
27. Lee S-W, Won K, Lim HK, Kim J-C, Choi GJ, et al. 2004. Screening for novel lipolytic enzymes from uncultured soil microorganisms. Appl. Microbiol. Biotechnol. 65:720-726.
28. Lorenz P, Eck J. 2005. Metagenomics and industrial applications. Nat. Rev. Microbiol. 3:510-516.
29. Martinez A, Kolvek SJ, Yip CLT, Hopke J, Brown KA, et al. 2004. Genetically modified bacterial strains and novel bacterial artificial chromosome shuttle vectors for constructing environmental libraries and detecting heterologous natural products in multiple expression hosts. Appl. Environ. Microbiol. 70:2452-2463.
30. Molinski TF, Dalisay DS, Lievens SL, Saludes JP. 2009. Drug development from marine natural products. Nat. Rev. Drug Discov. 8:69-85.
31. Munro MH, Blunt JW, Dumdei EJ, Hickford SJ, Lill RE, et al. 1999. The discovery and development of marine compounds with pharmaceutical potential. J. Biotechnol. 70:15-25.
32. Newman DJ, Hill RT. 2005. New drugs from marine microbes: The tide is turning. In Annual Meeting of the Society-for-Industrial- Microbiology, Chicago, IL, pp. 539-544.
33. Piel J. 2009. Metabolites from symbiotic bacteria. Nat. Prod. Rep. 26:338-362.
34. Rondon MR, August PR, Bettermann AD, Brady SF, Grossman TH, et al. 2000. Cloning the soil metagenome: A strategy for accessing the genetic and functional diversity of uncultured microorganisms. Appl. Environ. Microbiol. 66:2541-2547.
35. Schmidt EW. 2005. From chemical structure to environmental biosynthetic pathways: Navigating marine invertebrate-bacteria associations. Trends Biotechnol. 23:437-440.
36. Sipkema D, Franssen MCR, Osinga R, Tramper J, Wijffels RH. 2005. Marine sponges as pharmacy. Mar. Biotechnol. 7:142-162.
37. Snyder RV, Gibbs PDL, Palacios A, Abiy L, Dickey R, et al. 2003. Polyketide synthase genes from marine dinoflagellates. Mar. Biotechnol. 5:1-12.
38. Stierle AC, Cardellina JH, Singleton FL. 1988. A marine micrococcus produces metabolites as cribed to the sponge Tedania ignis. Experientia 44:1021-1021.
39. Tamura K, Nei M, Kumar S. 2004. Prospects for inferring very large phylogenies by using the neighbor-joining method. Proc. Natl. Acad. Sci. USA 101:11030-11035.
40. Taylor MW, Radax R, Steger D, Wagner M. 2007. Spongeassociated microorganisms: Evolution, ecology, and biotechnological potential. Microbiol. Mol. Biol. Rev. 71:295-347.
41. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:4673-4680.
42. Usher KM, Fromont J, Sutton DC, Toze S. 2004. The biogeography and phylogeny of unicellular cyanobacterial symbionts in sponges from Australia and the Mediterranean. Microb. Ecol. 48:167-177.
43. Waschkowitz T, Rockstroh S, Daniel R. 2009. Isolation and characterization of metalloproteases with a novel domain structure by construction and screening of metagenomic libraries. Appl. Environ. Microbiol. 75:2506-2516.
44. Webster NS, Negri AP, Munro M, Battershill CN. 2004. Diverse microbial communities inhabit Antarctic sponges. Environ. Microbiol. 6:288-300.
45. Webster NS, Taylor MW, Behnam F, Lücker S, Rattei T, et al. 2010. Deep sequencing reveals exceptional diversity and modes of transmission for bacterial sponge symbionts. Environ. Microbiol. 12:2070-2082.
46. Wijffels RH. 2008. Potential of sponges and microalgae for marine biotechnology. Trends Biotechnol. 26:26-31.
47. Yu SJ, Deng ZW, Proksch P, Lin WH. 2006. Oculatol, oculatolide, and A-nor sterols from the sponge Haliclona oculata. J. Nat. Prod. 69:1330-1334.