Large-Scale Identification of Known and Novel RRNPP Quorum-Sensing Systems by RRNPP_Detector Captures Novel Features of Bacterial, Plasmidic, and Viral Coevolution

Abstract

Gram-positive Firmicutes bacteria and their mobile genetic elements (plasmids, bacteriophages) encode peptide-based quorum sensing systems (QSSs) that orchestrate behavioral transitions as a function of population densities. In their simplest form, termed “RRNPP”, these QSSs are composed of two adjacent genes: a communication propeptide and its cognate intracellular receptor. RRNPP QSSs notably regulate social/competitive behaviors such as virulence or biofilm formation in bacteria, conjugation in plasmids or lysogeny in temperate bacteriophages. However, the genetic diversity and the prevalence of these communication systems, together with the breadth of behaviors they control, remain largely under-appreciated. To better assess the impact of density-dependency on microbial community dynamics and evolution, we developed the RRNPP_detector software, which predicts known and novel RRNPP QSSs in chromosomes, plasmids and bacteriophages of Firmicutes. Applying RRNPP_detector against available complete genomes of viruses and Firmicutes, we identified a rich repertoire of RRNPP QSSs from 11 already-known subfamilies and 21 novel high-confidence candidate subfamilies distributed across a vast diversity of taxa. The analysis of high-confidence RRNPP subfamilies notably revealed 14 subfamilies shared between chromosomes/plasmids/phages, 181 plasmids and 82 phages encoding multiple communication systems, phage-encoded QSSs predicted to dynamically modulate bacterial behaviors, and 196 candidate biosynthetic gene clusters under density-dependent regulation. Overall, our work enhances the field of quorum sensing research and reveals novel insights into the co-evolution of gram-positive bacteria and their mobile genetic elements.

Structural phylogenetics unravels the evolutionary diversification of communication systems in gram-positive bacteria and their viruses

“…Last, the biological processes controlled by these communication systems are not linked to cellular dormancy or viral latency, but rather to the production of virulence factors and antimicrobials 21 . This is mirrored by the substantial number of syntenic biosynthetic gene clusters (BGCs) predicted to be regulated by TprA and Rgg members (Figure 2a) 19 .…”

“…Once a quorum of cells, plasmids or viruses is met, communication peptides get frequently internalized within cells and binds to the tetratricopeptide repeats (TPRs) of cognate intracellular receptors, leading to gene or protein activation or inhibition, facilitating a coordinated response beneficial for a dense population. The density-dependent regulations of RRNPPA systems control behaviors like bacterial virulence, biofilm formation, sporulation, competence, conjugation and bacteriophage lysis/lysogeny decisions [17][18][19][20][21] . Although these receptors were identified in the early 1990s 29,30 , their evolutionary history is unclear due to frequent mutations and transfers, making sequence comparisons challenging 28,31,32 .…”

“…Subfamilies with experimental validation of at least one member are highlighted in color. Other subfamilies correspond to high-confidence candidate subfamilies detected with RRNPP_detector in 19 . Biological processes experimentally shown to be regulated in a density-dependent manner by a QS system are displayed for each validated subfamily.…”

“…Biological processes experimentally shown to be regulated in a density-dependent manner by a QS system are displayed for each validated subfamily. Subfamilies in gray correspond to novel, high-confidence candidate RRNPPA subfamilies from 19 . A star mapped to a leaf indicates a predicted regulation of an adjacent biosynthetic gene cluster by the corresponding QS system.…”

“…These proteins allow gram-positive bacteria, their plasmids and their viruses to assess their population density and regulate key biological processes accordingly. These communication systems have been shown to regulate virulence, biofilm formation, sporulation, competence, solventogenesis, antibiotic resistance or antimicrobial production in bacteria [17][18][19][20][21] , conjugation in conjugative elements, lysis/lysogeny decision in bacteriophages 22 and host manipulation by mobile genetic elements (MGEs) 19,23 . Accordingly, the RRNPPA family has a substantial impact on human societies as it connects to the virulence and transmissibility of pathogenic bacteria and the spread of antimicrobial resistance genes through horizontal gene transfers.…”