Mechanism underlying the DNA-binding preferences of the Vibrio cholerae and vibriophage VP882 VqmA quorum-sensing receptors

Quorum sensing is a chemical communication process that bacteria use to coordinate group behaviors. In the global pathogen Vibrio cholerae, one quorum-sensing receptor and transcription factor, called VqmA (VqmA(Vc)), activates expression of the vqmR gene encoding the small regulatory RNA VqmR, which represses genes involved in virulence and biofilm formation. Vibriophage VP882 encodes a VqmA homolog called VqmA(Phage) that activates transcription of the phage gene qtip, and Qtip launches the phage lytic program. Curiously, VqmA(Phage) can activate vqmR expression but VqmA(Vc) cannot activate expression of qtip. Here, we investigate the mechanism underlying this asymmetry. We find that promoter selectivity is driven by each VqmA DNA-binding domain and key DNA sequences in the vqmR and qtip promoters are required to maintain specificity. A protein sequence-guided mutagenesis approach revealed that the residue E194 of VqmA(Phage) and A192, the equivalent residue in VqmA(Vc), in the helix-turn-helix motifs contribute to promoter-binding specificity. A genetic screen to identify VqmA(Phage) mutants that are incapable of binding the qtip promoter but maintain binding to the vqmR promoter delivered additional VqmA(Phage) residues located immediately C-terminal to the helix-turn-helix motif as required for binding the qtip promoter. Surprisingly, these residues are conserved between VqmA(Phage) and VqmA(Vc). A second, targeted genetic screen revealed a region located in the VqmA(Vc) DNA-binding domain that is necessary to prevent VqmA(Vc) from binding the qtip promoter, thus restricting DNA binding to the vqmR promoter. We propose that the VqmA(Vc) helix-turn-helix motif and the C-terminal flanking residues function together to prohibit VqmA(Vc) from binding the qtip promoter.