University of Zagreb. Faculty of Food Technology and Biotechnology. Department of Biochemical Engineering. Section for Bioinformatics.
Abstract
Ameboidna protozoa Dictyostelium discoideum je važan modelni organizam za istraživanje razvoja stanica i evolucije. Nedavno završeno sekvenciranje genoma amebe D. discoideum (6 kromosoma - 34 Mb) pokazalo je oko 12.500 gena, među kojima je više od 40 gena s genetičkom uputom za poliketidsintaze (PKS). Do sada nije poznat niti jedan drugi organizam s toliko mnogo gena PKS. Zbog toga je, u ovom diplomskom radu, bioinformatičkim pristupom započeta analiza gena PKS. Od 45 prepoznatih gena PKS, 29 se nalazi unutar 12 potencijalnih genskih nakupina, od po 2-5 gena, koje možda odgovaraju biosintetskim putovima za različite prirodne produkte. Šesnaest je gena PKS pojedinačno. Svi su geni po strukturi slični genima PKS ponavljajućeg tipa I, osim što sadržavaju dva dodatna sačuvana područja aminokiselina (450-1500 i 300-600 aminokiselina) nepoznatih funkcija koje ne pokazuju sličnost ni s jednim poznatim proteinom. Nije prepoznata niti jedna domena odgovorna za početak sinteze poliketida, što upućuje na mogući novi mehanizam početka sinteze. Nije prepoznat niti jedan gen PKS tipa II. Provedena je detaljna analiza dvaju sačuvanih područja aminokiselina nepoznatih funkcija i njihova anotacija. Utvrđeno je da one sadržavaju domene metiltransferaze i dehidrataze. Dakle, opsežna je anotacija svih gena PKS pokazala da se oni sastoje od tipičnih domena: β-ketoacilsintaze, aciltransferaze, dehidrataze, metiltransferaze, alkenreduktaze, ketoreduktaze i maloga polipeptida nosača acila, očekivanih u svim genima PKS. Pored toga, provedena je analiza domena s aciltransferaznom aktivnošću i filogenetska analiza evolucije gena PKS u genomu amebe D. discoideum.The social amoeba (cellular slime mould) Dictyostelium discoideum is an important model organism for studies of development and evolution. 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. Up till now there is no other organism with as many PKS genes. Therefore, in this diploma thesis the analysis of potential PKS genes using bioinformatics methods was started. 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. Sixteen genes are individual genes. All genes show similar domain structure to Type I iterative PKS genes except that they contain two additional conserved amino acid stretches (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 and no Type II genes were found. Detailed analysis of two conserved amino acid sequences of unknown function showed the presence of methyltransferase and dehydratase domains. The annotation of all genes showed that they encode β-ketoacylsynthase, acyltransferase, dehydratase, methyltransferase, enoylreductase, ketoreductase and acyl carrier protein domains expected in all PKSs. In addition to that, the analysis of AT domains and phylogenetic analysis of PKS gene evolution in the D. discoideum genome were done
