title: Discovery of the rhizopodin biosynthetic gene cluster in Stigmatella aurantiaca Sg a15 by genome mining.
abstract: The field of bacterial natural product research is currently undergoing a paradigm change concerning the discovery of natural products. Previously most efforts were based on isolation of the most abundant compound in an extract, or on tracking bioactivity. However, traditional activity-guided approaches are limited by the available test panels and frequently lead to the rediscovery of already known compounds. The constantly increasing availability of bacterial genome sequences provides the potential for the discovery of a huge number of new natural compounds by in silico identification of biosynthetic gene clusters. Examination of the information on the biosynthetic machinery can further prevent rediscovery of known compounds, and can help identify so far unknown biosynthetic pathways of known compounds. By in silico screening of the genome of the myxobacterium Stigmatella aurantiaca Sg a15, a trans-AT polyketide synthase/non-ribosomal peptide synthetase (PKS/NRPS) gene cluster was identified that could not be correlated to any secondary metabolite known to be produced by this strain. Targeted gene inactivation and analysis of extracts from the resulting mutants by high performance liquid chromatography coupled to high resolution mass spectrometry (HPLC-HRMS), in combination with the use of statistical tools resulted in the identification of a compound that was absent in the mutants extracts. By matching with our in-house database of myxobacterial secondary metabolites, this compound was identified as rhizopodin. A detailed analysis of the rhizopodin biosynthetic machinery is presented in this manuscript.
authors.affiliation: Helmholtz-Institut für Pharmazeutische Forschung Saarland, Helmholtz Zentrum für Infektionsforschung and Pharmazeutische Biotechnologie, Universität des Saarlandes, Postfach 151150, 66041 Saarbrücken, Germany.
authors.forename: Dominik
authors.initials: D
authors.lastname: Pistorius
authors.forename: Rolf
authors.initials: R
authors.lastname: Müller
mesh_terms: D001688:Biological Products / Q000737:chemistry / Q000378:metabolism*; D053898:Biosynthetic Pathways / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D018942:Macrolides; D010080:Oxazoles / Q000737:chemistry / Q000378:metabolism*; D010453:Peptide Synthases / Q000235:genetics* / Q000378:metabolism; D020606:Stigmatella aurantiaca / Q000201:enzymology* / Q000235:genetics / Q000378:metabolism
chemical_list: D001688:Biological Products; D018942:Macrolides; D010080:Oxazoles; C081739:rhizopodin; D010453:Peptide Synthases; C104385:non-ribosomal peptide synthase