Project description:Actinomycete genomes contain a plethora of orphan gene clusters encoding unknown secondary metabolites, and representing a huge unexploited pool of chemical diversity. The explosive increase in genome sequencing and the massive advance of bioinformatic tools have revolutionized the rationale for natural product discovery from actinomycetes. In this context, we applied a genome mining approach to discover a group of unique catecholate-hydroxamate siderophores termed as qinichelins from Streptomyces sp. MBT76. Quantitative proteomics statistically correlated a gene cluster of interest (qch) to its unknown chemotype (qinichelin), after which structural elucidation of isolated qinichelin was assisted by bioinformatics analysis and verified by MS2 and NMR experiments. Strikingly, intertwined functional crosstalk among four separately located gene clusters was implicated in the biosynthesis of qinichelins.
Project description:Streptomyces has the largest repertoire of natural product biosynthetic gene clusters (BGCs), yet developing a universal engineering strategy for each Streptomyces species is challenging. Given that some Streptomyces species have larger BGC repertoires than others, we hypothesized that a set of genes co-evolved with BGCs to support biosynthetic proficiency must exist in those strains, and that their identification may provide universal strategies to improve the productivity of other strains. We show here that genes co-evolved with natural product BGCs in Streptomyces can be identified by phylogenomics analysis. Among the 597 genes that co-evolved with polyketide BGCs, 11 genes in the “coenzyme” category have been examined, including a gene cluster encoding for the co-factor pyrroloquinoline quinone (PQQ). When the pqq gene cluster was engineered into 11 Streptomyces strains, it enhanced production of 16,385 metabolites, including 36 known natural products with up to 40-fold improvement and several activated silent gene clusters. This study provides a new engineering strategy for improving polyketide production and discovering new biosynthetic gene clusters.
