Skip to main content
SpringerLink
Log in

MapsiDB: an integrated web database for type I polyketide synthases

  • Original Paper
  • Published:
Bioprocess and Biosystems Engineering Aims and scope Submit manuscript

Abstract

Polyketides have diverse biological activities, including pharmacological functions such as antibiotic, antitumor and agrochemical properties. They are biosynthesized from short carboxylic acid precursors by polyketide synthases (PKSs). As natural polyketide products include many clinically important drugs and the volume of data on polyketides is rapidly increasing, the development of a database system to manage polyketide data is essential. MapsiDB is an integrated web database formulated to contain data on type I polyketides and their PKSs, including domain and module composition and related genome information. Data on polyketides were collected from journals and online resources and processed with analysis programs. Web interfaces were utilized to construct and to access this database, allowing polyketide researchers to add their data to this database and to use it easily.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2

Similar content being viewed by others

References

  1. Silakowski B, Schairer HU, Ehret H, Kunze B, Weinig S, Nordsiek G, Brandt P, Blöcker H, Höfle G, Beyer S, Müller R (1999) New lessons for combinatorial biosynthesis from myxobacteria. The myxothiazol biosynthetic gene cluster of Stigmatella aurantiaca DW4/3–1. J Biol Chem 274:37391–37399

    Article  CAS  Google Scholar 

  2. Kakavas SJ, Katz L, Stassi D (1997) Identification and characterization of the niddamycin polyketide synthase genes from Streptomyces caelestis. J Bacteriol 179:7515–7522

    CAS  Google Scholar 

  3. Ikeda H, Nonomiya T, Usami M, Ohta T, Omura S (1999) Organization of the biosynthetic gene cluster for the polyketide antihelmintic macrolide avermectin in Streptomyces avermitilis. Proc Natl Acad Sci USA 96:9509–9514

    Article  CAS  Google Scholar 

  4. Omura S, Ikeda H, Ishikawa J, Hanamoto A, Takahashi C, Shinose M, Takahashi Y, Horikawa H, Nakazawa H, Osonoe T, Kikuchi H, Shiba T, Sakaki Y, Hattori M (2001) Genome sequence of an industrial microorganism Streptomyces avermitilis: deducing the ability of producing secondary metabolites. Proc Nat Acad Sci USA 98:12215–12220

    Article  CAS  Google Scholar 

  5. Aparicio JF, Caffrey P, Marsden AFA, Staunton J, Leadlay PF (1994) Limited proteolysis and active-site studies of the first multienzyme component of the erythromycin-producing polyketide synthase. J Biol Chem 269:8524–8528

    CAS  Google Scholar 

  6. Floss HG, Yu TW (1999) Lessons from the rifamycin biosynthetic gene cluster. Curr Opin Chem Biol 3:592–597

    Article  CAS  Google Scholar 

  7. Cheng YQ, Tang GL, Shen B (2003) Type I polyketide synthase requiring a discrete acyltransferase for polyketide biosynthesis. Proc Natl Acad Sci USA 100:3149–3154

    Article  CAS  Google Scholar 

  8. Rawlings BJ (2001) Type I polyketide biosynthesis in bacteria (part A-erythromycin biosynthesis). Nat Prod Rep 18:190–227

    Article  CAS  Google Scholar 

  9. Rawlings BJ (2001) Type I polyketide biosynthesis in bacteria (part B). Nat Prod Rep 18:231–281

    Article  CAS  Google Scholar 

  10. Staunton J, Weissman KJ (2001) Polyketide biosynthesis: a millennium review. Nat Prod Rep 18:380–416

    Article  CAS  Google Scholar 

  11. Cane DE (1997) Introduction: polyketide and nonribosomal polypeptide biosynthesis. Chem Rev 97:2463–2706

    Article  CAS  Google Scholar 

  12. Funa N, Ohnishi Y, Fujii I, Shibuya M, Ebizuka Y, Horinouchi S (1999) A new pathway for polyketide synthesis in microorganisms. Nature 400:897–899

    Article  CAS  Google Scholar 

  13. Moore BS, Hopke JN (2001) Discovery of a new bacterial polyketide biosynthetic pathway. ChemBioChem 2:35–38

    Article  CAS  Google Scholar 

  14. Wiesmann KE, Cortes J, Brown MJ, Cutter AL, Staunton J, Leadlay PF (1995) Polyketide synthesis in vitro on a modular polyketide synthase. Chem Biol 2:583–589

    Article  CAS  Google Scholar 

  15. Gaitatzis M, Silakowski B, Kunze B, Nordsiek G, Blöcker H, Höfle G, Müller R (2002) The biosynthesis of the aromatic myxobacterial electron transport inhibitor stigmatellin is directed by a novel type of modular polyketide synthase. J Biol Chem 277:13082–13090

    Article  CAS  Google Scholar 

  16. Shen B, Hutchinson CR (1996) Deciphering the mechanism for the assembly of aromatic polyketides by a bacterial polyketide synthase. Proc Natl Acad Sci USA 93:6600–6604

    Article  CAS  Google Scholar 

  17. Yadav G, Gokhale RS, Mohanty D (2003) Computational approach for prediction of domain organization and substrate specificity of modular polyketide synthases. J Mol Biol 328:335–363

    Article  CAS  Google Scholar 

  18. Ansari MZ, Yadav G, Gokhale RS, Mohanty D (2004) NRPS-PKS: a knowledge-based resource for analysis of NRPS/PKS megasynthases. Nucleic Acids Res 32:W405–W413

    Article  CAS  Google Scholar 

  19. MAPSI. http://gate.smallsoft.co.kr:8080/pks

  20. McDaniel R, Thamchaipenet A, Gustafsson C, Fu H, Betlach M, Betlach M, Ashley G (1999) Multiple genetic modifications of the erythromycin polyketide synthase to produce a library of novel “unnatural” natural products. Proc Natl Acad Sci USA 96:1846–1851

    Article  CAS  Google Scholar 

  21. McDaniel R, Kao CM, Hwang SJ, Khosla C (1997) Engineered intermodular and intramodular polyketide synthase fusions. Chem Biol 4:667–674

    Article  CAS  Google Scholar 

  22. Eddy SR (1998) Profile hidden Markov models. Bioinformatics 14:755–763

    Article  CAS  Google Scholar 

  23. Ronning CM, Fedorova ND, Bowyer P, Coulson R, Goldman G, Kim HS, Turner G, Wortman JR, Yu J, Anderson MJ, Denning DW, Nierman WC (2005) Genomics of Aspergillus fumigatus. Rev Iberoam Micol 22(4):223–228

    Article  Google Scholar 

  24. Galagan JE, Calvo SE, Cuomo C, Ma LJ, Wortman JR et al (2005) Sequencing of Aspergillus nidulans and comparative analysis with A. fumitatus and A. oryzae. Nature 438:1105–1115

    Article  CAS  Google Scholar 

  25. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    CAS  Google Scholar 

  26. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTALW: 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

    Article  CAS  Google Scholar 

  27. NCBI. http://www.ncbi.nlm.nih.gov

Download references

Acknowledgments

This research was financially supported by Ministry of Education, Science, and Technology and Korea Industrial Technology Foundation through the Human Resource Training Project, and by Ministry of Knowledge Economy grants from the Intelligence Bioinformatics and Application Center at the Korea Research Institute of Bioscience and Biotechnology.

Author information

Authors and Affiliations

  1. SmallSoft Co., Ltd., Jang-Dong 59-5, Yusung-Gu, Daejeon, 305-343, South Korea

    Hongseok Tae & Kiejung Park

  2. Department of Pharmaceutical Engineering, Sunmoon University, Asan, 336-708, South Korea

    Jae Kyung Sohng

Authors
  1. Hongseok Tae
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Jae Kyung Sohng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Kiejung Park
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Kiejung Park.

Additional information

MapsiDB is available at http://gate.smallsoft.co.kr:8080/pks/mapsidb.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Tae, H., Sohng, J.K. & Park, K. MapsiDB: an integrated web database for type I polyketide synthases. Bioprocess Biosyst Eng 32, 723–727 (2009). https://doi.org/10.1007/s00449-008-0296-3

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00449-008-0296-3

Keywords

Search

Navigation