Crossregulation of rapamycin and elaiophylin biosynthesis by RapH in Streptomyces rapamycinicus

Rapamycin is an important macrocyclic antibiotic produced by Streptomyces rapamycinicus. In the rapamycin biosynthetic gene cluster (BGC), there are up to five regulatory genes, which have been shown to play important roles in the regulation of rapamycin biosynthesis. Here, we demonstrated that the rapamycin BGC-situated LAL family regulator RapH co-ordinately regulated the biosynthesis of both rapamycin and elaiophylin. We showed that rapH overexpression not only resulted in enhanced rapamycin production but also led to increased synthesis of another type I polyketide antibiotic, elaiophylin. Consistent with this, rapH deletion resulted in decreased production of both antibiotics. Through real-time RT-PCR combined with β-glucuronidase reporter assays, four target genes controlled by RapH, including rapL (encoding a lysine cyclodeaminase)/rapH in the rapamycin BGC and ela3 (encoding a LuxR family regulator)/ela9 (encoding a hypothetical protein) in the elaiophylin BGC, were identified. A relatively conserved signature sequence recognized by RapH, which comprises two 4-nt inverted repeats separated by 8-nt, 5'-GTT/AC-N8-GTAC-3', was defined. Taken together, our findings demonstrated that RapH was involved in co-ordinated regulation of two disparate BGCs specifying two unrelated antibiotics, rapamycin and elaiophylin. These results further expand our knowledge of the regulation of antibiotic biosynthesis in S. rapamycinicus. KEY POINTS: • The cluster-situated regulator RapH controlled the synthesis of two antibiotics. • Four promoter regions recognized by RapH were identified. • A 16-nt signature DNA sequence essential for RapH regulation was defined.