The TetR-like regulator SCO4385 and Crp-like regulator SCO3571 modulate heterologous production of antibiotics in Streptomyces coelicolor M512
Heterologous expression in well-studied model strains is a  routinely applied method to investigate biosynthetic pathways. Here, we pursue a comparative approach of large-scale DNA-affinity-capturing assays coupled with semi-quantitative mass spectrometry, to identify putative regulatory proteins from Streptomyces coelicolor M512, that bind to the heterologously expressed biosynthetic gene clusters of the liponucleoside antibiotics caprazamycin and liposidomycin. Both gene clusters share an almost identical genetic arrangement, including the location of promoter regions, as detected by RNA-sequencing. A total of 2214 proteins were trapped at the predicted promoter regions, with only three binding to corresponding promoters in both gene clusters. Among these, overexpression of a yet uncharacterized TetR-family regulator, SCO4385, increased caprazamycin but not liposidomycin production. Protein-DNA interaction experiments using biolayer-interferometry confirmed the binding of Sco4385 to Pcpz10 and PlpmH at different locations within both promoter regions, which might explain its functional variance. Sequence alignment allowed the determination of a consensus sequence present in both promoter regions,  to which Sco4385 was experimentally shown to bind. Furthermore, we show that overexpression of the Crp regulator Sco3571 leads to a three-fold increase in caprazamycin and liposidomycin production yields, possibly due to an increased expression of a precursor pathway. Overall design: RNA-seq of the heterologously expressed caprazamycin and liposidomycin biosynthetic gene cluster in Streptomyces coelicolor M512 after 2 days and 4 days of growth.