The Distribution and Diversity of LuxI/LuxR Quorum Sensing Systems in Proteobacteria (Pseudomonadota)

Abstract

In Pseudomonadota (formerly Proteobacteria), the N-acyl homoserine lactone (AHL) quorum sensing (QS) system involves LuxI/LuxR modules, where LuxI synthesizes AHLs and LuxR-AHL regulates target gene expression. Despite extensive characterization in many bacterial species, the distribution, genomic organization, and taxonomic comprehensiveness of LuxI/R systems remains unexplored at scale. In this study, we present the first large-scale, genome-wide assessment of LuxI/R QS systems across over 30,000 publicly available genomes at chromosome-level and manually curated spanning 938 genera. Using pfam-based domain annotation, we mapped the distribution, occurrence, and copy number of LuxI/R homologs. LuxI/R systems were identified in [~]32% of surveyed genera, with notable enrichment in symbiotic and plant-associated taxa such as Rhizobium, Burkholderia, and Pseudomonas, and remarkable conservation in pathogenic taxa such as Yersinia, Aeromonas, and Acinetobacter. Conversely, entire genera, including Escherichia, Salmonella, and Klebsiella, among others, lacked LuxI/R systems across all sequenced strains, suggesting evolutionary loss, niche-specific signaling strategies, or reliance on alternative currently unknown communication systems. Our results also revealed genera with multiple, non-redundant and taxonomically not-related LuxI/R pairs per genome, indicating modular architectures and unpredictable events of horizontal gene transfer events and genetic arrangements. This study delineates the complex distribution and conservation patterns of LuxI/R circuits, providing a resource for future studies into AHL-mediated QS regulation, and microbial community interactions across diverse environments. HighlightsO_LILuxI/LuxR quorum-sensing systems show an uneven distribution across Pseudomonadota (formerly Proteobacteria) and evolved through expansion, conservation, and loss, reflecting diverse ecological strategies C_LIO_LIAmong [~]31,815 high-quality Proteobacterial genomes, 6,400 (20.1%), corresponding to C_LIO_LI[~]303 genera ([~]32%), encoded at least one complete LuxI/LuxR pair. C_LIO_LIMultiple, highly variable LuxI/R copies, up to seven per genome, reveal extensive horizontal gene transfer and mosaic evolutionary histories, especially in rhizobial and plant-associated taxa. C_LIO_LIPhylogenetic analyses distinguish genera with conserved QS architectures from those with fragmented, lineage-independent LuxI/R repertoires, possibly highlighting diverse ecological pressures shaping QS. C_LI