Network rewiring of a pneumococcal communication system promotes stress adaptation in a globally successful lineage

Cell-cell communication (CCC) systems regulate bacterial behaviors and shape social interactions within microbial communities. In Streptococcus pneumoniae, several CCC systems coordinate intra- and inter-strain signaling, yet the genetic plasticity of their components and regulons remains underexplored. Here, we investigate a divergent allelic variant of the TprA/PhrA CCC system, a regulator-pheromone pair widely conserved in S. pneumoniae. We characterize PhrA1.2, the second most prevalent PhrA pheromone, as a non-signaling variant found in the globally distributed GPSC6 lineage, with presence in isolates dating back to the 1960s. In GPSC6, PhrA1.2 co-occurs with TprA1.2, a truncated transcriptional regulator carrying premature stop codons that eliminate the predicted pheromone-binding domain. Functional assays show that PhrA1.2 is non-functional, both when paired with the truncated TprA1.2 and when paired with the canonical regulator allele TprA1.1. Unexpectedly, despite its truncation, TprA1.2 activates genes involved in oxidative stress responses, including those related to iron-sulfur cluster formation and redox homeostasis. Loss of tprA1.2 impairs growth and increases hydrogen peroxide sensitivity, while in vivo experiments reveal a fitness defect during nasopharyngeal colonization. Together, our findings show that the TprA1.2 allele represents a regulator that has lost its communication component while modifying its regulon. This variant promotes adaptation to oxidative stress and contributes to colonization, demonstrating circuit rewiring of a peptide-regulator CCC system in an epidemiologically relevant S. pneumoniae lineage.