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Bioinformatics Advance Access originally published online on July 27, 2007
Bioinformatics 2007 23(19):2543-2549; doi:10.1093/bioinformatics/btm381
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Polyketide synthase genes and the natural products potential of Dictyostelium discoideum

J. Zucko 1,5, N. Skunca 1, T. Curk 2, B. Zupan 2,3, P.F. Long 4, J. Cullum 5, R.H. Kessin 6 and D. Hranueli 1,*

1Faculty of Food Technology and Biotechnology, University of Zagreb, Pierottijeva 6, 10000 Zagreb, Croatia, 2Faculty of Computer and Information Science, University of Ljubljana, Trzaska cesta 25, SI-1001 Ljubljana, Slovenia, 3Department of Molecular and Human Genetics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA, 4The School of Pharmacy, University of London, 29/39 Brunswick Square, London WC1N 1AX, UK, 5Department of Genetics, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany and 6Department of Anatomy and Cell Biology, Columbia University, 630 West 168th Street, 10032 New York, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The genome of the social amoeba Dictyostelium discoideum contains an unusually large number of polyketide synthase (PKS) genes. An analysis of the genes is a first step towards understanding the biological roles of their products and exploiting novel products.

Results: A total of 45 Type I iterative PKS genes were found, 5 of which are probably pseudogenes. Catalytic domains that are homologous with known PKS sequences as well as possible novel domains were identified. The genes often occurred in clusters of 2–5 genes, where members of the cluster had very similar sequences. The D.discoideum PKS genes formed a clade distinct from fungal and bacterial genes. All nine genes examined by RT–PCR were expressed, although at different developmental stages. The promoters of PKS genes were much more divergent than the structural genes, although we have identified motifs that are unique to some PKS gene promoters.

Contact: dhranueli{at}pbf.hr

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Dmitrij Frishman

Received on May 15, 2007; revised on July 9, 2007; accepted on July 10, 2007

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