Unusual regulatory mechanism for a Streptomyces multidrug resistance gene, ptr, involving three homologous protein-binding sites overlapping the promoter region.

A promoter controlling expression of the pristinamycin multidrug resistance gene (ptr), originally isolated from Streptomyces pristinaespiralis, is inducible by many toxic compounds in various Streptomyces species. Studies of ptr promoter control were carried out in the heterologous host, Streptomyces lividans. In S. lividans, a regulatory protein or a protein complex (Pip), identified by its ability to bind to the ptr promoter in gel-retardation experiments, was induced by pristinamycin I (PI). In situ copper-phenanthroline footprinting analysis identified three (A, B, and C) similar Pip-binding sites having the sequence GTACA(C/G)CGTA(C/T). These sites overlapped with functionally important regions of the promoter: the 'A' site overlapped with the -35 hexamer, 'B' overlapped with the -10 hexamer and 'C' was located between the transcription start site and the Shine-Dalgarno sequence. A GT-AG dinucleotide mutation was introduced at positions 8-9 of the consensus sequence to generate seven variant promoters: three mutated in one of the three sites, three mutated in two sites, and one mutated in all three sites. Whereas these promoters had reduced antibiotic (PI)-induced activity, their levels of expression in the absence of PI was higher. This suggested an unusual regulatory mechanism in which Pip could act either as an activator or repressor. Gel shift experiments revealed Pip or its homologues in many other Streptomyces species, suggesting that it is widely employed in the regulation of antibiotic resistance genes and perhaps secondary metabolism.