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Streptococcus pyogenes, or Group A Streptococcus, is a Gram-positive bacterium that can be both a human commensal and pathogen. Central to this dichotomy are temperate bacteriophages that incorporate into the bacterial genome as a prophage. These genetic elements encode both the phage proteins as well as toxins harmful to the human host. One such conserved phage protein paratox (Prx) is always found encoded adjacent to the toxin genes and this linkage is preserved during transduction. Within Streptococcus pyogenes, Prx functions to inhibit the quorum-sensing ComRS receptor-signal pair that is the master regulator of natural competence, or the ability to uptake endogenous DNA. Specifically, Prx directly binds and inhibits the receptor ComR by unknown mechanism. To understand how Prx inhibits ComR at the molecular level we pursued an X-ray crystal structure of Prx bound to ComR. The structural data supported by solution X-ray scattering data demonstrate that Prx induces a conformational change in ComR to directly access the DNA binding domain. Furthermore, electromobility shift assays and competition binding assays reveal that Prx effectively uncouples the inter-domain conformational change that is required for activation of ComR by the signaling molecule XIP. Although to our knowledge the molecular mechanism of quorum-sensing inhibition by Prx is unique, it is analogous to the mechanism employed by the phage protein Aqs1 in Pseudomonas aeruginosa. Together, this demonstrates an example of convergent evolution between Gram-positive and Gram-negative phages to inhibit quorum-sensing, and highlights the versatility of small phage proteins.

Streptococcus pyogenes is a causative agent of pharyngitis and necrotizing fasciitis. Key to its pathogenicity are numerous prophages spread throughout its genome that encode deadly toxins. These prophages also encode several proteins whose biological function is unknown. Of particular interest is the conserved phage protein paratox (Prx), which is genetically linked to phage toxin genes. Our past results have shown that Prx expression is regulated by the natural competence ComRS quorum sensing pathway, and that Prx itself is a negative regulator of ComRS. Prx directly binds the transcription factor and quorum sensing receptor ComR and inhibits its ability to bind DNA by an unknown mechanism. As ComR undergoes a significant conformational change upon binding the peptide pheromone XIP, we hypothesize that Prx employs a novel mechanism of protein‐protein binding and inhibition. Using a combination of structural biology and biochemistry, including X‐ray crystallography, small‐angle X‐ray scattering (SAXS), and various fluorescence assays, we have been able to elucidate the molecular details of how Prx manipulates the conformation of ComR to prevent activation by the XIP pheromone. Our results not only reveal a dynamic protein‐protein binding mechanism, but further demonstrate the myriad roles that phage proteins have evolved to regulate the pathways of their hosts for self‐preservation.

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