The biosynthesis of natural products: the characterisation and manipulation of AtrA, an evolutionarily conserved transcription factor

The current need for new antibiotics clinically is well documented. A variety of approaches are being taken to meet this need including the renewed mining of Streptomyces natural products using methodologies that provide greater depth and target antibiotic-resistant pathogens. One key area is the development of culture conditions that induce the production of a wider range of Streptomyces natural products. This “secondary” metabolism is known to be regulated by numerous transduction systems but for many, if not most, the actual regulatory signal has yet to be identified. The identification of the signals for transduction systems may allow the development of media or growth conditions that extend the range of Streptomyces natural products identifiable by laboratory-based screens. The greatest benefit is likely to be derived from the manipulation of transduction systems that are evolutionarily conserved and have regulons covering multiple Streptomyces natural products. Previous work identified that the production of actinorhodin by S. coelicolor, a well-established model for understanding the regulation of secondary metabolism is regulated by AtrA, (SCO4118) a member of the TetR family of one-component, signal transducers. Moreover, AtrA has subsequently been shown to be evolutionarily conserved and regulate the production of secondary metabolites in several species beyond S. coelicolor. The first part of this thesis identifies by a combination of bioinformatics, chromatin immunoprecipitation and transcriptomics that the regulon of AtrA in S. coelicolor is broad and AtrA regulation extends to secondary metabolism beyond the production of actinorhodin. The mutagenesis of a selection of the members of the AtrA regulon of S. coelicolor is also described. The second part describes the investigation of the signal transduced by S. coelicolor AtrA, which encompassed an analysis of actinorhodin. This work made the unexpected finding that S. coelicolor produces non-specific inhibitors of DNA: protein interactions. It is speculated that such inhibitions may provide an undescribed mechanism for quelling general transcription as part of the developmental cycle of streptomycetes.