SHP/Rgg systems belong to the RRNPP transcriptional regulator superfamily, which is involved in cell–cell communication mechanisms. Their study in streptococci has highlighted their role in regulating diverse biological processes, such as biofilm formation or modulation of virulence in pathogenic streptococci, and the production of post-translationally modified peptides in Streptococcus thermophilus, a key bacterium in yogurt manufacturing. Early investigations described a simple regulatory mechanism, with a single Rgg regulator controlling a specific target in response to its cognate SHP signaling peptide. However, more recent studies have revealed cross-interactions between multiple SHP/Rgg systems, suggesting a more complex organization. In this context, S. thermophilus represents a particularly relevant model due to the remarkable accumulation of SHP/Rgg systems in its genome.

The aim of this thesis was to characterize the complete set of interactions between SHP/Rgg systems in S. thermophilus.

First, an in silico analysis at the scale of the salivarius group which includes S. thermophilus, Streptococcus salivarius, and Streptococcus vestibularis was conducted to catalogue SHP/Rgg systems. We observed that S. thermophilus exhibits a significantly higher abundance of these systems. Given that the emergence of S. thermophilus is more recent than that of S. salivarius, these findings suggest that this accumulation did not result from simple conservation from S. salivarius but rather from acquisitions via horizontal gene transfer from streptococci outside the salivarius group.

Experimentally, we demonstrated that the major SHPs are indeed secreted and detectable by LC–MS/MS in culture supernatants. For the first time, we monitored the joint dynamics of SHPs and their targets (RiPPs) throughout bacterial growth. Our results show that SHPs are synchronously secreted, accumulate, and are reimported before gradually disappearing. The study of three RiPPs revealed that they are also secreted synchronously, but unlike SHPs, they persist in the supernatant.

Next, to explore interactions between SHP/Rgg systems, we constructed translational fusions between the promoters of target operons and a luciferase reporter gene in various genetic contexts, with or without complementation using synthetic SHPs. This approach enabled the reconstruction of the complete regulatory network of these systems in S. thermophilus, revealing interactions that primarily occur through SHPs. We demonstrated that, within a single cell, different SHPs can interact with the same transcriptional regulator.

Furthermore, for one of the targets of these SHP/Rgg systems, we identified an original co-regulatory mechanism involving two regulators from distinct RRNPP families. Detailed investigation of this target led to the discovery of a previously undescribed RiPP whose modified structure remains to be elucidated.

Overall, this work challenges the traditional linear and independent view of SHP/Rgg quorum-sensing mechanisms and emphasizes the importance of considering these systems as interconnected and dynamic communication networks within the bacterial cell. This revised perspective is essential in the context of fine-tuning these systems, as in Streptococcus pneumoniae, a pathogenic streptococcus that has also accumulated numerous SHP/Rgg systems.