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Databases of the thiotemplate modular systems (CSDB) and their in silico recombinants (r-CSDB)

  • Natural Products
  • Published:
Journal of Industrial Microbiology & Biotechnology

Abstract

Modular biosynthetic clusters are responsible for the synthesis of many important pharmaceutical products. They include polyketide synthases (PKS clusters), non-ribosomal synthetases (NRPS clusters), and mixed clusters (containing both PKS and NRPS modules). The ClustScan database (CSDB) contains highly annotated descriptions of 170 clusters. The database has a hierarchical organization, which allows easy extraction of DNA and protein sequences of polypeptides, modules, and domains as well as an organization of the annotation so as to be able to predict the product chemistry to view it or export it in a standard SMILES format. The recombinant ClustScan database contains information about predicted recombinants between PKS clusters. The recombinants are generated by modeling homologous recombination and are associated with annotation and prediction of product chemistry automatically generated by the model. The database contains over 20,000 recombinants and is a resource for in silico approaches to detecting promising new compounds. Methods are available to construct the corresponding recombinants in the laboratory.

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Acknowledgments

This work was supported by the grant 09/5 (to D.H.) from the Croatian Science Foundation, Republic of Croatia and by a cooperation grant of the German Academic Exchange Service (DAAD) and the Ministry of Science, Education and Sports, Republic of Croatia (to D.H. and J.C.). It was also supported by the Leverhulme Trust; Japanese Bio-Industry Association and The School of Pharmacy, University College London (to P.F.L.).

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Author notes

  1. Ida Trninic Ruzic

    Present address: Croatian Accreditation Agency, Vukovarska 78, 10000, Zagreb, Croatia

Authors and Affiliations

  1. Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000, Zagreb, Croatia

    Janko Diminic, Jurica Zucko, Ida Trninic Ruzic, Ranko Gacesa, Daslav Hranueli & Antonio Starcevic

  2. Institute of Pharmaceutical Science, King’s College London, 150 Stamford Street, London, SE1 9NH, UK

    Paul F. Long

  3. Department of Chemistry, King’s College London, 150 Stamford Street, London, SE1 9NH, UK

    Paul F. Long

  4. Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653, Kaiserslautern, Germany

    John Cullum

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  1. Janko Diminic
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Correspondence to Antonio Starcevic.

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Diminic, J., Zucko, J., Ruzic, I.T. et al. Databases of the thiotemplate modular systems (CSDB) and their in silico recombinants (r-CSDB). J Ind Microbiol Biotechnol 40, 653–659 (2013). https://doi.org/10.1007/s10295-013-1252-z

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