Structural basis for operator and antirepressor recognition by Myxococcus xanthus CarA repressor

Abstract

SummaryBlue light induces carotenogenesis in Myxococcus xanthus. The carB operon encodes all but one of the structural genes involved, and its expression is regulated by the CarA-CarS repressor-antirepressor pair. In the dark, CarA-operator binding represses carB. CarS, produced on illumination, interacts physically with CarA to dismantle the CarA-operator complex and activate carB. Both operator and CarS bind to the autonomously folded N-terminal domain of CarA, CarA(Nter), which in excess represses carB. Here, we report the NMR structure of Car-A(Nter), and map residues that interact with operator and CarS by NMR chemical shift perturbations, and in vivo and in vitro analyses of site-directed mutants. We show CarA(Nter) adopts the wingedhelix topology of MerR-family DNA-binding domains, and conserves the majority of the helix-turn-helix and wing contacts with DNA. Tellingly, helix a2 in CarA, a key element in operator DNA recognition, is also critical for interaction with CarS, implying that the CarA-CarS protein-protein and the CarA-operator protein-DNA interfaces overlap. Thus, binding of CarA to operator and to antirepressor are mutually exclusive, and CarA may discern structural features in the acidic CarS protein that resemble operator DNA. Repressor inactivation by occluding the DNAbinding region may be a recurrent mechanism of action for acidic antirepressors.

ExsD Inhibits Expression of thePseudomonas aeruginosaType III Secretion System by Disrupting ExsA Self-Association and DNA Binding Activity

“…Antiactivators from other systems (non-AraC targets) function by one of three mechanisms: preventing self-association of the activator (5), occluding the DNA binding domain from interacting with DNA (19,22,24), or inducing conformational changes that alter the structure of the DNA binding domain (6). ExsD inhibits ExsA-dependent transcription by employing at least two of these mechanisms.…”

Light-dependent gene regulation by a coenzyme B 12 -based photoreceptor

“…S1B). Besides their autonomously stable, N-terminal DNA-binding domains (CarANt and CarHNt, respectively) that recognize the same operator (12,19,20), CarA and CarH have C-terminal domains (CarACt and CatHCt, respectively) with a B 12 -binding motif of the type found in enzymes like methionine synthase (6,12,(21)(22)(23). However, only CarH requires B 12 for its repressor activity (12).…”

“…S1A) (13). CarS is an antirepressor with an SH3-domain topology that mimics operator DNA to specifically target the DNA recognition helix of the MerR-type DNA-binding winged-helix domain of two paralogous repressors, CarA and CarH, to counteract their binding to operator (18,19). In the dark, these two repressors down-regulate the promoter P B that drives expression of the carB-carA gene cluster, where the remaining carotenogenic genes are grouped (Fig.…”

QsIA disrupts LasR dimerization in antiactivation of bacterial quorum sensing

“…Antiactivators from several systems seem to occupy sites on the transcription factors that would otherwise coordinate specific base contacts on the DNA, thereby precluding or inhibiting binding of the transcription factor to its target elements (29)(30)(31). However, unlike those antiactivators, QsIA uses a unique mechanism by which QsIA interacts with LasR LBD and hence disrupts the LasR dimerization, which is essential for LasR-DNA interaction.…”