engleski

The Dictyostelium discoideum genome and its polyketide synthase genes

Polyketides are important chemical substances for both pharmaceutical and agro-industries. Today, polyketide antibiotics, antifungals, antiparasitics, animal growth promotants, natural insecticides, immunosuppressives, cytostatics and anticholesterolemics are in commercial use. Polyketides are synthesized by Type I modular and Type II iterative polyketide synthases (PKS's) in bacteria, Type I iterative PKS's in fungi and by chalcone synthases in plants (The nature of polyketide antibiotic synthesis will be explained at the poster with an animated cartoon). As soil organisms that exist in a world of bacteria, fungi, nematodes, and other potential predators, the Dictyostelia should also have a rich chemical repertoire. The genome of Dictyostelium discoideum is exceptionally rich in polyketide synthase genes (PKS) encoded by more then 40 recognizable genes spread on all six chromosomes. At least one of the PKSs is dedicated to the synthesis of Differentiation Inducing Factor, as shown by Rob Kay and his collaborators. We know of no other organisms with as many PKS genes. We are using bioinformatics and gene expression approaches to confirm existing and to detect novel PKS genes. This sequence and expression information was used to ask how the PKS genes of Dictyostelium evolved. Similarity searches revealed all forty three known putative PKS genes present in the dictyBase. These were analyzed further using an approach based on hidden Markov models implemented within the HMMER program. Additional analyses showed that 3 dictyBase pairs of PKS genes (6 genes) could be combined into 3 single genes. In addition, 3 novel genes have been identified. Therefore, our analysis also revealed 43 PKS genes in total. PKS proteins are highly modular. 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 polyketide synthase. In about half of the genes, there is an additional domain translated downstream of the ACP. In two genes, these domains show homology to chalcone synthases, which creates a novel structure. Thirty-two of the PKS genes occur in thirteen potential gene-clusters (containing 2-5 genes each). At present we do not know whether any of the putative clustered PKS genes represent an individual biosynthetic pathway. Twelve single genes were found and they resemble Type I iterative genes. We have constructed a phylogenetic tree by neighbor joining of the KS domain sequences. This showed that the D. discoideum sequences formed a separate but very diverse group with distances between extreme members nearly as great as the distance to bacterial and fungal sequences. Many of the retrieved PKS genes are transcribed. We found expressed sequence tags for many PKS genes in cDNA libraries and we have recovered information on transcription of others by examining gene array experiments. Real time PCR techniques using primers to the 3' ends of the genes were performed with 10 selected PKS genes to obtain their time course of expression. All ten genes tested showed different expression patterns during growth and development.

polyketides; PKS genes; phylogeny; gene expression; Dictyostelium discoideum genome

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