Hyperphosphorylation of the Group A Streptococcal Control of Virulence Regulator Increases Promoter Occupancy Specifically at Virulence Factor-Encoding Genes

The control of virulence two-component gene regulatory system (CovRS) is critical to the pathogenesis of many medically important streptococci. In emm1 group A streptococci (GAS), CovR directly binds the promoters of numerous GAS virulence factor-encoding genes. Elimination of CovS phosphatase activity increases CovR phosphorylation (CovR;P) levels and abrogates GAS virulence. Given the emm type-specific diversity of CovRS function, in this study we used chromatin immunoprecipitation sequencing (ChIPseq) to define global CovR DNA occupancy in the wild-type emm3 strain MGAS10870 (medium CovR;P) and its CovS phosphatase-negative derivative 10870-CovS-T284A (high CovR;P). In the wild-type emm3 strain, 89% of the previously identified emm1 CovR binding sites present in the emm3 genome were also enriched; additionally, we ascertained unique CovR binding, primarily to genes in mobile genetic elements and other sites of interstrain chromosomal differences. Elimination of CovS phosphatase activity specifically increased CovR occupancy at the promoters of a broad array of CovR repressed virulence factor-encoding genes, including those encoding the key GAS regulator Mga and M protein. However, a limited number of promoters had augmented enrichment at low CovR;P levels. Differential motif searches using sequences enriched at high versus low CovR;P levels revealed two distinct binding patterns. At high CovR;P, a pseudopalindromic AT-rich consensus sequence (WTWTTATAAWAAAAWNATDA) consistent with CovR binding as a dimer was determined. Conversely, sequences specifically enriched at low CovR;P contained isolated ATTARA motifs suggesting an interaction with a monomer. These data extend understanding of global CovR DNA occupancy beyond emm1 GAS and provide a mechanism for previous observations regarding hypovirulence induced by CovS phosphatase abrogation.

Automated summary

The CovRS gene regulatory system plays a critical role in the pathogenesis of many streptococci. In this study, the researchers used chromatin immunoprecipitation sequencing (ChIPseq) to investigate the global DNA occupancy of CovR in emm3 group A streptococci. They found that elimination of CovS phosphatase activity increased CovR occupancy at the promoters of virulence factor-encoding genes, including the key regulator Mga and M protein. The study also identified different binding patterns of CovR at high and low phosphorylation levels, suggesting a dimeric and monomeric interaction, respectively.