Cultivation dependent formation of siderophores by Gordonia rubripertincta CWB2.

• Genome mining reveals a desferrioxamine biosynthetic gene cluster. • Transcriptomics confirms Fe-dependent regulation of desferrioxamine biosynthesis. • Fe-limitation induces siderophore and citrate production and secretion. • Metal stress in succinate containing medium results in high siderophore yields. • First verified siderophore from a Gordonia species: desferrioxamine E. Herein we demonstrate cultivation-dependent siderophore production by the actinomycete Gordonia rubripertincta CWB2. The strain produces mostly citrate, but also desferrioxamine E (DFOE) and new hydroxamate-type siderophores. The production of hydroxamate-like siderophores is influenced by cultivation conditions, for example available carbon sources or presence of metals, such as the rare earth erbium or the heavy metal lead. By cultivation with succinate and extraction with an adsorbing resin (XAD) we purified the G. rubripertincta CWB2 siderophores (yield up to 178 mg L−1). The respective workflow comprises genome mining, cultivation, and overproduction strategies, a rapid screening procedure, as well as traditional structure enrichment and structure elucidation methods. This combination of methods allows the discovery of new natural products with metal complexation capacity, also for lanthanides of commercial value. G. rubripertincta CWB2 carries a desferrioxamine-like biosynthetic gene cluster. Its transcription was proven by a transcriptomic approach comparing expression levels of the selected gene cluster during cultivation in iron-depleted and repleted media. Further investigation of the siderophores of this desferrioxamine producing Actinobacterium could lead to new structures. [ABSTRACT FROM AUTHOR]