Phosphate regulation in Streptomyces coelicolor and Streptomyces lividans: transcriptomic analysis of phoP and Ppk mutants.

Nutritional limitation and other stresses are known to induce the production of secondary metabolites in Streptomyces. The two-component regulatory system (PhoR/PhoP) and the enzyme polyphosphate kinase, Ppk, play an important role in adaptation of growth in conditions of phosphate limitation and mutations in both systems have been linked to increased production of antibiotics in Streptomyces lividans. To further characterize the above mentioned links phoP and ppk null mutations were generated in the prototrophic wild-type strain, MT1110, of the model streptomycete, Streptomyces coelicolor A(3)2. All strains were cultivated in 1.5 L batch fermenters using a chemically defined phosphate-limited minimal medium; metabolite and antibiotic assays were conducted alongside the transcriptomic analysis, sampling at several time points throughout cultivation. Parallel studies were performed with S. lividans TK24, a closely related streptomycete, using equivalent phoP and ppk mutant derivatives. However, the S. lividans studies were conducted with surface grown cultures, on complex R2YE medium, either phosphate limited or replete. Qualitative assessment of pigmented antibiotic production by the S. lividans mutants agreed with previous published results, with both mutants displaying enhanced pigmented antibiotic synthesis relative to the wild-type. In contrast, the S. coelicolor ppk mutant displayed significantly reduced production of pigmented antibiotics relative to the wild-type parent strain, irrespective of whether the mutant was cultivated in the minimal medium or complex R2YE medium. In the S. coelicolor experiments metabolite assays confirmed that cultures became phosphate-depleted during the batch cultivation, with the ppk mutant showing the slowest rate of depletion. From the microarray-based transcriptomic analysis, certain members of the PhoP regulon (phoR, phoP, pstS and pstC) were down-regulated in the phoP mutants, alongside ppk, consistent with their regulation by PhoP. A potential link between phosphate and nitrogen metabolism in S. coelicolor is suggested by the finding that a number of genes involved in glutamine synthesis and regulation (including glnA, glnD, glnR and glnRII) were transiently up-regulated in a phoP mutant. Furthermore, some genes involved in ATP generation (the atp operon) were also transiently up-regulated in the phoP mutant. A novel two component regulatory system (SCO4155 and SCO4156) was massively over expressed in the S. coelicolor phoP mutant, in addition to an adjacent gene, SCO4157, which encodes a homologue of the DegP/HtrA protease. A SCO4157 disruption mutant was shown to precociously hyper-produce undecylprodigiosin under phosphate limited conditions. It is speculated that the up-regulation of this system represents a PhoP-independent compensatory response to phosphate starvation. The transcriptomic analysis has enabled a greater understanding of the potential roles of PhoP and Ppk during phosphate limitation, and their involvement in antibiotic synthesis. This study has identified a large number of novel genes potentially involved in phosphate metabolism and scavenging and opens the way for a more focussed functional analysis of their respective roles