Mechanism underlying the DNA-binding preferences of theVibrio choleraeand vibriophage VP882 VqmA quorum-sensing receptors
Authors: Duddy Olivia P. , Huang Xiuliang , Silpe Justin E. , Bassler Bonnie L. 
Published: April 2021

ABSTRACTQuorum sensing is a chemical communication process that bacteria use to coordinate group behaviors. In the global pathogenVibrio cholerae, one quorum-sensing receptor and transcription factor, called VqmA (VqmAVc), activates expression of thevqmRgene encoding the small regulatory RNA VqmR, which represses genes involved in virulence and biofilm formation. Vibriophage VP882 encodes a VqmA homolog called VqmAPhagethat activates transcription of the phage geneqtip, and Qtip launches the phage lytic program. Curiously, VqmAPhagecan activatevqmRexpression but VqmAVccannot activate expression ofqtip. Here, we investigate the mechanism underlying this asymmetry. We find that promoter selectivity is driven exclusively by each VqmA DNA-binding domain and key DNA sequences in thevqmRandqtippromoters are required to maintain specificity. A protein sequence-guided mutagenesis approach revealed that the residue E194 of VqmAPhageand A192, the equivalent residue in VqmAVc, in the helix-turn-helix motifs contribute to promoter-binding specificity. A genetic screen to identify VqmAPhagemutants that are incapable of binding theqtippromoter but maintain binding to thevqmRpromoter delivered additional VqmAPhageresidues located immediately C-terminal to the helix-turn-helix motif as required for binding theqtippromoter. Surprisingly, these residues are conserved between VqmAPhageand VqmAVc. A second, targeted genetic screen revealed a region located in the VqmAVcDNA-binding domain as necessary to prevent VqmAVcfrom binding theqtippromoter, thus restricting DNA-binding to thevqmRpromoter. We propose that the VqmAVchelix-turn-helix motif and the C-terminal flanking residues function together to prohibit VqmAVcfrom binding theqtippromoter.AUTHOR SUMMARYBacteria use a chemical communication process called quorum sensing (QS) to orchestrate collective behaviors. Recent studies demonstrate that bacteria-infecting viruses, called phages, also employ chemical communication to regulate collective activities. Phages can encode virus-specific QS-like systems, or they can harbor genes encoding QS components resembling those of bacteria. The latter arrangement suggests the potential for chemical communication across domains, i.e., between bacteria and phages. Ramifications stemming from such cross-domain communication are not understood. Phage VP882 infects the global pathogenVibrio cholerae, and “eavesdrops” onV. choleraeQS to optimize the timing of its transition from living as a parasite to killing the host, and moreover, to manipulateV. choleraebiology. To accomplish these feats, phage VP882 relies on VqmAPhage, the phage-encoded homolog of theV. choleraeVqmAVcQS receptor and transcription factor. VqmAVc, by contrast, is constrained to the control of onlyV. choleraegenes and is incapable of regulating phage biology. Here, we discover the molecular mechanism underpinning the asymmetric transcriptional preferences of the phage-encoded and bacteria-encoded VqmA proteins. We demonstrate how VqmA transcriptional regulation is crucial to the survival and persistence of both the pathogenV. cholerae, and the phage that preys on it.