The biosynthesis of membrane lipids is an essential pathway for virtually all bacteria. Despite its potential importance for the development of novel antibiotics, little is known about the underlying signaling mechanisms that allow bacteria to control their membrane lipid composition within narrow limits. Recent studies disclosed an elaborate feed-forward system that senses the levels of malonyl-CoA and modulates the transcription of genes that mediate fatty acid and phospholipid synthesis in many Gram-positive bacteria including several human pathogens. A key component of this network is FapR, a transcriptional regulator that binds malonyl-CoA, but whose mode of action remains enigmatic. We report here the crystal structures of FapR from Staphylococcus aureus (SaFapR) in three relevant states of its regulation cycle. The repressor-DNA complex reveals that the operator binds two SaFapR homodimers with different affinities, involving sequence-specific contacts from the helix-turn-helix motifs to the major and minor grooves of DNA. In contrast with the elongated conformation observed for the DNA-bound FapR homodimer, binding of malonyl-CoA stabilizes a different, more compact, quaternary arrangement of the repressor, in which the two DNA-binding domains are attached to either side of the central thioesterase-like domain, resulting in a non-productive overall conformation that precludes DNA binding. The structural transition between the DNA-bound and malonyl-CoA-bound states of SaFapR involves substantial changes and large (>30 Å) inter-domain movements; however, both conformational states can be populated by the ligand-free repressor species, as confirmed by the structure of SaFapR in two distinct crystal forms. Disruption of the ability of SaFapR to monitor malonyl-CoA compromises cell growth, revealing the essentiality of membrane lipid homeostasis for S. aureus survival and uncovering novel opportunities for the development of antibiotics against this major human pathogen.
An opportunistic Gram-positive pathogen, Staphylococcus aureus is a major threat to humans and animals, being responsible for a variety of infections ranging from mild superficial to severe infections such as infective endocarditis, septic arthritis, osteomyelitis and sepsis. The increasing resistance of S. aureus against most current antibiotics emphasizes the need to develop new approaches to control this important pathogen. The lipid biosynthetic pathway is one appealing target actively pursued to develop anti-Staphylococcal agents. Despite its potential biomedical importance, however, little is known about the signaling mechanisms that allow S. aureus to control its phospholipid content. In order to shed light on this fundamental mechanism, we studied S. aureus FapR (SaFapR) a transcription factor that senses the levels of malonyl-CoA, a key intermediate in fatty acid biosynthesis, and modulates the expression of genes involved in fatty acid and phospholipid biosynthesis. Our studies of SaFapR uncovered the mechanistic basis of a complex biological switch that controls membrane lipid homeostasis in S. aureus. We also discovered that disruption of the ability of SaFapR to recognize malonyl-CoA, the ligand that controls SaFapR binding to DNA, compromises S. aureus viability, thus revealing new opportunities for the development of antibiotics against this major human pathogen.