Genomic characterization of bacteria from the ultra-oligotrophic Madison aquifer: insight into the archetypical LuxI/LuxR and identification of novel LuxR solos

Abstract

Objectives To characterize the bacterial community of Wind Cave’s Madison aquifer through whole-genome sequencing, and to better understand the bacterial ecology by identifying genes involved in acyl-homoserine lactone (AHL) based quorum-sensing (QS) systems. Results Genome-based taxonomic classification revealed the microbial richness present in the pristine Madison aquifer. The strains were found to span eleven genera and fourteen species, of which eight had uncertain taxonomic classifications. The genomes of strains SD129 and SD340 were found to contain the archetypical AHL QS system composed of two genes, luxI and luxR. Surprisingly, the genomes of strains SD115, SD129, SD274 and SD316 were found to contain one to three luxR orphans (solos). Strain SD129, besides possessing an archetypical AHL QS luxI-luxR pair, also contained two luxR solos, while strain SD316 contained three LuxR solos and no luxI-luxR pairs. The ligand-binding domain of two LuxR solos, one each from strains SD129 and SD316, were found to contain novel substitutions not previously reported, thus may represent two LuxR orphans that detection and response to unknown self-produced signal(s), or to signal(s) produced by other organisms.

Insights into Adaptive Mechanisms of Extreme Acidophiles Based on Quorum Sensing/Quenching-Related Proteins

“…The AI-1 system is one major QS type which has been characterized widely. Meanwhile, the related LuxI/LuxR and their homologues are focused on and examined extensively via in silico analyses ( 41 , 42 ). Using the domain-based strategy and key residue comparison, we found that an adjacent LuxI/R homolog pair was carried by most A. ferrooxidans and A. thiooxidans strains, similar to the distribution of the AfeI/AfeR system based on sequence BLAST analysis ( 22 ).…”

“…For the stringent identification of putative LuxI/R homologs, a profile Hidden Markov model (HMM)-based similarity search (E value, <1e-5) was conducted to scan for the signature protein family (Pfam) domain contained in reported LuxI (PF00765, autoinducer synthase) and LuxR (PF03472, autoinducer-binding domain), respectively. In addition, three signature domains, IPR016181 (acyl-CoA N-acyltransferase), IPR001690 (autoinducer synthase), and IPR018311 (autoinducer synthesis, conserved site), are universally present in the functionally validated LuxIs, while a canonical LuxR always contains four signature domains, IPR005143 (autoinducer-binding domain), IPR036388 (winged helix-turn-helix DNA-binding domain), IPR016032 (signal transduction response regulator, C-terminal effector), and IPR000792 (transcription regulator LuxR, C-terminal) ( 41 ). To further verify the high confidence of LuxI/R homologs, the shortlisted proteins were subsequently subjected to InterProScan 5 ( 62 ) for conserved domain architecture searching.…”