S9: Strategies for the identification and sequencing of promising antibiotic-producing actinomycetes

Streptomycetes are a major source of antimicrobials, making these filamentous organisms an important asset in the fight against the continouously emerging multiply drug resistant bacteria. The morphological development of the Streptomyces colony, whereby the organism degrades its vegetative mycelium to produce aerial hyphae and spores, coincides with complex chemical differentiation to initiate secondary metabolism. As a first step towards drug discovery we seek to wake up and identify so-called sleeping antibiotic biosynthetic clusters in actinomycetes, and for this we need to understand the signals that trigger secondary metabolism in the organisms' habitat. We identified N-acetylglucosamine as one major signal for the onset of sleeping antibiotics, which effects derepression of the DasR regulon, which includes many clusters for antibiotics and yet unknown secondary metabolites (Rigali et al. (2008), EMBO Rep 9: 670-675). We have built up an actinomycete strain collection from remote areas, and this actinomycete library is mined using these and other expression technologies currently being developed in our laboratory. Following activity tests against a range of different multi-drug resistant (Gram-negative) clinical isolates, next-gen sequencing is applied to obtain the full genome sequences of the most promising producer strains. We are currently mining these sequences in combination with metabolic and bioactivity profiling to identify the bioactive compounds. Our most recent advances in terms of waking up sleeping antibiotics and the pros and cons of high-throughput genome sequencing as a tool for drug discovery will be discussed.