Polyketide synthase genes and the natural products potential of Dictyostelium discoideum

• Published in: Bioinformatics 2007-10, Vol.23 (19), p.2543-2549
• Main Authors: Zucko, J., Skunca, N., Curk, T., Zupan, B., Long, P.F., Cullum, J., Kessin, R.H., Hranueli, D.
• Format: Article
• Language: English
• Subjects: Amino Acid Sequence; Amoeba; Animals; Biological and medical sciences; Biological Products - metabolism; Chromosome Mapping - methods; Dictyostelium - physiology; Dictyostelium discoideum; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Molecular Sequence Data; Multigene Family - physiology; Polyketide Synthases - chemistry; Polyketide Synthases - physiology; Protein Structure, Tertiary; Sequence Analysis, Protein - methods; Sequence Homology, Amino Acid
• ISSN: 1367-4803; 1460-2059; 1367-4811
• DOI: 10.1093/bioinformatics/btm381

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: [e-mail] Supplementary information: Supplementary data are available at Bioinformatics online.