(p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition

Fatty acid biosynthesis (FASII) enzymes have been considered as valid targets for antimicrobial drug development against the human pathogen Staphylococcus aureus. However, our findings showed that incorporation of compensatory host fatty acids confers FASII antibiotic adaptation that compromises prospective treatments. Adaptation to anti-FASII drugs is preceded by a non-replicative latency period. Here we investigated the factors that dictate the duration of latency prior to adaptation outgrowth, and identify stringent response as a regulator of both FASII and adaptation to FASII inhibition. We first show that (p)ppGpp induction inhibits malonyl-CoA synthesis, and constitutes a second regulator of FASII and phospholipid synthesis in S. aureus, in addition to the FapR repressor. We then show that anti-FASII treatment triggers transient (p)ppGpp induction during the anti-FASII latency phase, with a concomitant reduction of FapR regulon expression. This effect is reversed upon adaptive outgrowth. Using three different sensors, we give evidence that anti-FASII treatment shifts the distribution of malonyl-CoA between its interactants, FapR and FabD, increasing expression of phospholipid synthesis genes plsX and plsC during outgrowth. We conclude that (p)ppGpp pools dictate malonyl-CoA availability in S. aureus FASII regulation, and contribute to latency prior to anti-FASII adaptation. A combinatory approach, coupling a (p)ppGpp inducer and an anti-FASII, blocks S. aureus growth, opening perspectives for bi-therapy treatment.