AUTHOR=Gan Han Ming , Gan Huan You , Ahmad Nurul H. , Aziz Nazrin A. , Hudson André O. , Savka Michael A. 

TITLE=Whole genome sequencing and analysis reveal insights into the genetic structure, diversity and evolutionary relatedness of luxI and luxR homologs in bacteria belonging to the Sphingomonadaceae family

JOURNAL=Frontiers in Cellular and Infection Microbiology

VOLUME=4

YEAR=2015

URL=https://www.frontiersin.org/journals/cellular-and-infection-microbiology/articles/10.3389/fcimb.2014.00188

DOI=10.3389/fcimb.2014.00188

ISSN=2235-2988

ABSTRACT=<p>Here we report the draft genomes and annotation of four <italic>N</italic>-acyl homoserine lactone (AHL)-producing members from the family <italic>Sphingomonadaceae</italic>. Comparative genomic analyses of 62 <italic>Sphingomonadaceae</italic> genomes were performed to gain insights into the distribution of the canonical <italic>luxI/R</italic>-type quorum sensing (QS) network within this family. Forty genomes contained at least one <italic>luxR</italic> homolog while the genome of <italic>Sphingobium yanoikuyae</italic> B1 contained seven Open Reading Frames (ORFs) that have significant homology to that of <italic>luxR</italic>. Thirty-three genomes contained at least one <italic>luxI</italic> homolog while the genomes of <italic>Sphingobium</italic> sp. SYK6, <italic>Sphingobium japonicum</italic>, and <italic>Sphingobium lactosutens</italic> contained four <italic>luxI</italic>. Using phylogenetic analysis, the sphingomonad LuxR homologs formed five distinct clades with two minor clades located near the plant associated bacteria (PAB) LuxR solo clade. This work for the first time shows that 13 <italic>Sphingobium</italic> and one <italic>Sphingomonas</italic> genome(s) contain three convergently oriented genes composed of two tandem <italic>luxR</italic> genes proximal to one <italic>luxI</italic> (<italic>luxR-luxR-luxI</italic>). Interestingly, <italic>luxI</italic> solos were identified in two <italic>Sphingobium</italic> species and may represent species that contribute to AHL-based QS system by contributing AHL molecules but are unable to perceive AHLs as signals. This work provides the most comprehensive description of the <italic>luxI/R</italic> circuitry and genome-based taxonomical description of the available sphingomonad genomes to date indicating that the presence of <italic>luxR</italic> solos and <italic>luxI</italic> solos are not an uncommon feature in members of the <italic>Sphingomonadaceae</italic> family.</p>