Impact of Streptococcus pyogenes prophage Φ1207.3 on bacterial host response to stress conditions

The SOS response is an inducible system activated by some bacterial species in the presence of stressful conditions and extensive DNA damage. Streptococci lack a canonical SOS response, but an SOS-like response was reported in some species. The mef(A)-msr(D)-carrying prophage Ф1207.3 of Streptococcus pyogenes contains a DNA region, spanning from orf6 to orf11, showing homology to characterized streptococcal SOS-like cassettes. In the present thesis, the impact of prophage Φ1207.3 SOS-like cassette on bacterial host response to stress conditions was evaluated. Isogenic derivatives of Hex mismatch repair-proficient S. pneumoniae R6 strain were constructed and used to study if the Φ1207.3 SOS-like cassette confers an SOS-mutagenesis phenotype. Survival and mutation rate assays were carried out using a UV-C LED instrument for which we designed and 3D-printed customized equipment, consisting of an instrument support and swappable-autoclavable mini-plates and lids. The presence of Φ1207.3 SOS-like cassette increased bacterial survival and mutation rate upon UV-C light exposure. Then, isogenic derivatives of Hex mismatch repair-deficient S. pneumoniae Rx1 strain were constructed and tested in survival and mutation rate assays. The SOS-like response activated by the Φ1207.3 prophage increases bacterial survival and mutation rate also in the absence of Hex mismatch repair system and upon treatment with UV-C light or mitomycin C. Dual RNA sequencing was used to investigate gene expression in both Φ1207.3 prophage and S. pneumoniae R6 host in response to UV-C light stress. An increase of the SOS-like cassette genes was observed upon UV-C light exposure, the level of expression correlated with the exposure time. Regarding the bacterial host genome, analysis of differentially expressed genes revealed a notable up-regulation of genes involved in nutrient transport. RNA sequencing results were confirmed by quantitative Real Time PCR experiments.