Diverse control of metabolism and other cellular processes in Streptomyces coelicolor by the PhoP transcription factor: genome-wide identification of in vivo targets

Abstract

Streptomycetes sense and respond to the stress of phosphate starvation via the two-component PhoR–PhoP signal transduction system. To identify the in vivo targets of PhoP we have undertaken a chromatin-immunoprecipitation-on-microarray analysis of wild-type and phoP mutant cultures and, in parallel, have quantified their transcriptomes. Most (ca. 80%) of the previously in vitro characterized PhoP targets were identified in this study among several hundred other putative novel PhoP targets. In addition to activating genes for phosphate scavenging systems PhoP was shown to target two gene clusters for cell wall/extracellular polymer biosynthesis. Furthermore PhoP was found to repress an unprecedented range of pathways upon entering phosphate limitation including nitrogen assimilation, oxidative phosphorylation, nucleotide biosynthesis and glycogen catabolism. Moreover, PhoP was shown to target many key genes involved in antibiotic production and morphological differentiation, including afsS, atrA, bldA, bldC, bldD, bldK, bldM, cdaR, cdgA, cdgB and scbR-scbA. Intriguingly, in the PhoP-dependent cpk polyketide gene cluster, PhoP accumulates substantially at three specific sites within the giant polyketide synthase-encoding genes. This study suggests that, following phosphate limitation, Streptomyces coelicolor PhoP functions as a ‘master’ regulator, suppressing central metabolism, secondary metabolism and developmental pathways until sufficient phosphate is salvaged to support further growth and, ultimately, morphological development.

The master regulator PhoP coordinates phosphate and nitrogen metabolism, respiration, cell differentiation and antibiotic biosynthesis: comparison in Streptomyces coelicolor and Streptomyces avermitilis

“…Allenby et al 19 reported the presence of a 9 nucleotides motif in 150 out of 333 PhoP-ChIP enriched sequences. This motif appear to correspond to core DRus.…”

“…In fact, when PhoP binds to the − 35 region of the promoters of PhoP-regulated genes, it acts as an activator by recruiting RNA polymerase to the promoter regions, whereas when it binds to the − 10 regions, or inside the open reading frame, usually it works as a repressor by preventing transcription. [19][20][21] THE pho REGULON: PhoP-REGULATED GENES Transcriptomic studies, footprinting assays and in vivo expression studies with reporter genes allowed the initial identification of about 50 genes, which are regulated by PhoP and form the core of the pho regulon. 17 A list of relevant genes regulated by PhoP is shown in Table 1 and a summary of downregulated and upregulated genes is shown in Figure 2.…”

“…New approaches using chromatin immunoprecipitation (ChIP-on-chip) have enlarged the scope of these studies. 19 Phosphate scavenging, transport, storage and mobilization Rodríguez-García et al, 4 in phosphate shift-down experiments using transcriptomic and proteomic analysis, discovered that the primary response to phoP deletion in S. coelicolor was the increase in expression of many genes that are involved in phosphate scavenging, transport, storage and mobilization. The primary targets of PhoP regulation were genes encoding phosphatases, including phoA, phoC, the phospholipase phoD 15 and the phytase-encoding gene, phyA.…”

“…PHO boxes have been identified in the promoter region of the pstSCAB cluster 5 and an internal PHO box has been proposed. 19 In addition, one of the pit genes, pitH2, which encodes a low-affinity phosphate transport system, is also upregulated by PhoP. 16 Another enzyme involved in phosphate storage and mobilization that is upregulated by PhoP after phosphate depletion is the polyphosphate kinase encoded by the ppk gene.…”

GntR family regulator SCO6256 is involved in antibiotic production and conditionally regulates the transcription of myo-inositol catabolic genes in Streptomyces coelicolor A3(2)

“…The regulation of CDA biosynthesis is poorly understood, except some twocomponent systems are characterized as its regulators. AbsA2 and PhoP repress the transcription of cdaR (Sheeler et al, 2005;Allenby et al, 2012), while AfsQ1 activates its transcription via binding upstream of cdaR (Wang et al, 2013). Other regulators, such as AbrA2, AbrC3 and NsdA, have been proved to affect CDA production indirectly (Yepes et al, 2011;Li et al, 2006).…”