Inducible expression of (pp)pGpp synthetases in Staphylococcus aureus is associated with activation of stress response genes

Abstract

The stringent response is characterized by the synthesis of the messenger molecules pppGpp, ppGpp or pGpp (here collectively designated (pp)pGpp). The phenotypic consequences resulting from (pp)pGpp accumulation vary among species and can be mediated by different underlying mechanisms. Most genome-wide analyses have been performed under stress conditions, which often mask the immediate effects of (pp)pGpp-mediated regulatory circuits. In Staphylococcus aureus, (pp)pGpp can be synthesized via the RelA-SpoT-homolog, RelSau upon amino acid limitation or via one of the two small (pp)pGpp synthetases RelP or RelQ upon cell wall stress. We used RNA-Seq to compare the global effects in response to induction of the synthetase of rel-Syn (coding for the enzymatic region of RelSau) or relQ without the need to apply additional stress conditions. Induction of rel-Syn resulted in changes in the nucleotide pool similar to induction of the stringent response via the tRNA synthetase inhibitor mupirocin: a reduction in the GTP pool, an increase in the ATP pool and synthesis of pppGpp, ppGpp and pGpp. Induction of all three enzymes resulted in similar changes in the transcriptome. However, RelQ was less active than Rel-Syn and RelP, indicating strong restriction of its (pp)pGpp-synthesis activity in vivo. (pp)pGpp induction resulted in the downregulation of many genes involved in protein and RNA/DNA metabolism. Many of the (pp)pGpp upregulated genes are part of the GTP sensitive CodY regulon and thus likely regulated through lowering of the GTP pool. New CodY independent transcriptional changes were detected including genes involved in the SOS response, iron storage (e.g. ftnA, dps), oxidative stress response (e.g., perR, katA, sodA) and the psmα1–4 and psmß1-2 operons coding for cytotoxic, phenol soluble modulins (PSMs). Analyses of the ftnA, dps and psm genes in different regulatory mutants revealed that their (pp)pGpp-dependent regulation can occur independent of the regulators PerR, Fur, SarA or CodY. Moreover, psm expression is uncoupled from expression of the quorum sensing system Agr, the main known psm activator. The expression of central genes of the oxidative stress response protects the bacteria from anticipated ROS stress derived from PSMs or exogenous sources. Thus, we identified a new link between the stringent response and oxidative stress in S. aureus that is likely crucial for survival upon phagocytosis.

Crosstalk between guanosine nucleotides regulates cellular heterogeneity in protein synthesis during nutrient limitation

“…The different protein synthesis activity of strains carrying a mutation in one of the genes encoding a (pp)pGpp synthase (Figs 1, 3C) is consistent with previous reports that SAS enzymes differ between themselves and also with RelA in the guanosine nucleotide that they preferentially produce (18,(29)(30)(31). Our observations demonstrate that each particular product differs in its in vivo function, thereby extending previous observations that ppGpp and pppGpp can differ in their effect on gene transcription in E. coli (32).…”

Crosstalk between guanosine nucleotides regulates cellular heterogeneity in protein synthesis during nutrient limitation

“…Strains carrying single mutations in one of the three genes encoding a (pp)pGpp synthase (Δ sasA , Δ sasB , relA ; Figs 1 and 3C ) exhibit different protein synthesis activity, consistent with previous reports that SAS enzymes differ between themselves and also with RelA in the guanosine nucleotide that they preferentially produce [ 14 , 30 – 32 ]. Our experiments thereby extend previous observations that ppGpp and pppGpp can differ in their effect on gene transcription in E .…”

Global Transcriptomic Response of Staphylococcus aureus to Virulent Bacteriophage Infection

“…Moreover, purine synthesis is associated with (p)ppGpp alarmone level [ 44 ]. The accumulation of (p)ppGpp can lead to the inhibition of transcription, translation, and premature cell death [ 45 , 46 ], following which the bacteriophage does not multiply effectively within the cell. In turn, the studied vB_SauM-515A1 bacteriophage is able to reduce the level of (p)ppGpp alarmone by expressing the hmzG gene.…”