RRNPP_detector

RRNPP_detector predicts peptide-based RRNPP quorum sensing systems in genomes and mobilomes (chromosomes, plasmids, and bacteriophages) of gram-positive bacteria, identifying regulators of processes such as virulence, sporulation, biofilm formation, conjugation, and lysogeny.

Key Features:

• Novelty Detection: Utilizes a signature based on multiple criteria common across experimentally validated RRNPP QSS families rather than relying on sequence homology, enabling identification of novel RRNPP systems.
• Broad Applicability: Analyzes chromosomes, plasmids, and bacteriophages from gram-positive bacteria to detect RRNPP QSSs across genomic and mobile element contexts.
• Discovery Potential: Application to complete genomes from NCBI revealed up to a 7.5-fold increase in the diversity of known RRNPP QSSs.

Scientific Applications:

• Pathway Regulation: Identification of RRNPP QSSs supports study of their roles in regulating virulence, sporulation, biofilm formation, conjugation, and lysogeny.
• Genomic Insights: Detects alternative secretion modes for candidate QSS propeptides and identifies "bilingual" bacteriophages and plasmids that may carry multiple quorum sensing languages.
• Biosynthetic Gene Clusters: Predicts chromosomal and plasmidic biosynthetic-gene-clusters that are regulated by QSSs, informing the genetic basis of secondary metabolite production.

Methodology:

RRNPP_detector applies a signature-based approach using criteria derived from known RRNPP systems and avoids sequence-homology searches to predict RRNPP QSSs in target genomes and mobilomes.