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Polyketide genes in Dictyostelium discoideum genome

The social amoeba (cellular slime mould) Dictyostelium discoideum is an important model organism for studies in development, cell communication and, more recently, evolution [1]. Yet, one aspect of the life of these organisms has been ignored: like other soil micro-organisms they should produce a complex chemical repertoire. The genome sequence was recently completed showing around 12, 500 genes in a relatively small genome of 34 Mb. The organism is exceptionally rich in polyketide synthases (PKS) encoded by more than 40 recognizable genes spread on all six chromosomes [2, http://dictybase.org/]. We know of no other organisms with as many PKS genes [3]. Therefore, we have started with the analysis of the potential PKS genes using bioinformatics methods. The putative PKS genes were initially identified using BLAST [http://www.ncbi.nlm.nih.gov/blast/], with the erythromycin KS4 domain [3] as a query against the translated D. discoideum genome sequence. In order to recover potentially new PKS genes the dicyBase version 2.5 was used. A knowledge based resource for analysis of non-ribosomal peptide synthetases and polyketide synthases [http://www.nii.res.in/nrps-pks.html] was used to retrieve PKS domain sequences for building custom profiles. The current version of HMMER [http://hmmer.wustl.edu/] and the current release of the Pfam database [http://www.sanger.ac.uk/Software/Pfam/] were used for profile analysis. All PKS protein sequences were extracted from dictyBase and searched against the entire Pfam database locally. From the 45 PKS genes identified, 29 occur in 12 potential gene-clusters (containing 2-5 genes each), which might correspond to the biosynthetic pathways of different natural products. The genes show a similar domain structure to Type I PKS genes except that they contain two additional conserved amino acid stretches (of 450-1500 and 300-600 amino acids) of unknown function that does not show any homology to any known protein. No loading domains could be identified, which suggests there might be a novel initiation mechanism. Sixteen of the genes resemble Type I iterative genes, but no Type II genes were found. In this poster we will present the use of bioinformatics approaches to analyse two conserved amino acid sequences of unknown function with detailed sequence annotation using Artemis [http://www.sanger.ac.uk/Software/ Artemis/]. Detailed annotation of all genes showed that they encoded β -ketoacylsynthase (KS), acyltransferase (AT), dehydratase (DH), methyltransferase (MT), enoylreductase (ER), ketoreductase (KR) and acyl carrier protein (ACP) domains expected in a PKS [3]. [1] R.H. Kessin, Dictyostelium - evolution, cell biology, and the development of multicellularity, Cambridge Univ. Press, Cambridge, 2001, pp. 1-294. [2] L. Eichinger, J.A. Pachebat, G. Glockner, M.A. Rajandream, R., Sucgang et al., Nature 435 (2005) 43-57. [3] D. Hranueli, J. Cullum, B. Basrak, P. Goldstein, P.F. Long, Curr. Med. Chem. 12 (2005) 1697-1704.

Dictyostelium discoideum; genome; gene annotation; gene expression; phylogeny; natural products; polyketides

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