engleski

In silico studies of modular biosynthetic clusters

Modular biosynthetic clusters represent an extremely rich source of biologically active compounds that find wide-ranging applications. Their biosynthetic pathways consist of successive polymerization steps where simple building blocks get incorporated into a growing chain. This is made possible by fascinating enzymes operating in assembly line fashion. The two major classes are polyketide synthases (PKS) and non-ribosomal peptide synthetases (NRPS). They are organized in modules, each module being responsible for the introduction of one additional building block. The vast majority of useful secondary metabolites (antibiotics being the most important) have been detected by screening of "wild" isolates obtained from soil and other habitats. Recent studies revealed a plethora of uncultivable microorganisms in both soil and marine environments. Such a metagenomic approach is showing great perspective in isolation of novel biocatalysts from the uncultured microbiota. A new software tool (ClustScan) for rapid genome and metagenome gene clusters scanning and annotation was developed. An important aim of this work was the prediction of the chemical structures of products and, in particular their stereochemistry. By analysing known cluster sequences, it was found that the stereochemistry of the methyl groups was determined by the ketoreductase domains and not the ketosynthase domains as previously believed. ClustScan proved its utility by rapidly annotating PKS/NRPS gene clusters in genomes of Sacc. erythraea and S. scabies. It was used in annotation of PKS clusters of the slime mould Dictyostelium discoideum and the analysis of a hybrid PKS-NRPS gene-cluster from the J. Craig Venter Institute Global Ocean Sampling (GOS) Expedition metagenomic dataset. The genome sequence of the starlet sea anemone N. vectensis was searched for shikimic acid pathway genes, which are not known to be present in animals. Surprisingly, two genes were detected that had probably been acquired by horizontal gene transfer (HGT) from dinoflagellates and bacteria respectively. This analysis also detected bacterial sequences that might belong to an unidentified endosymbiont. We also studied two known endosymbionts C. ruddii and B. aphidicola both found in aphids and showed that there was considerable gene loss compared to free-living bacteria.

Polyketide synthases; non-ribosomal peptide synthetases; modular biosynthetic gene-clusters; in silico studies

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