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.

Nazrin A. Aziz,Huan You Gan,AndrÃ© O. Hudson,Michael A. Savka,Han Ming Gan,Nurul H. Ahmad

doi:10.3389/fcimb.2014.00188

Nazrin A. Aziz, Huan You Gan + Show 4 more

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https://doi.org/10.3389/fcimb.2014.00188

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Abstract

Here we report the draft genomes and annotation of four N-acyl homoserine lactone (AHL)-producing members from the family Sphingomonadaceae. Comparative genomic analyses of 62 Sphingomonadaceae genomes were performed to gain insights into the distribution of the canonical luxI/R-type quorum sensing (QS) network within this family. Forty genomes contained at least one luxR homolog while the genome of Sphingobium yanoikuyae B1 contained seven Open Reading Frames (ORFs) that have significant homology to that of luxR. Thirty-three genomes contained at least one luxI homolog while the genomes of Sphingobium sp. SYK6, Sphingobium japonicum, and Sphingobium lactosutens contained four luxI. 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 Sphingobium and one Sphingomonas genome(s) contain three convergently oriented genes composed of two tandem luxR genes proximal to one luxI (luxR-luxR-luxI). Interestingly, luxI solos were identified in two Sphingobium 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 luxI/R circuitry and genome-based taxonomical description of the available sphingomonad genomes to date indicating that the presence of luxR solos and luxI solos are not an uncommon feature in members of the Sphingomonadaceae family.

Highlights

Members of the Sphingomonadaceae family are Gram-negative glycosphingolipid-containing bacteria that belong to the α-4 subclass of proteobacteria (Yabuuchi et al, 1990)
Culture extracts prepared from each of the four sphingomonads strains in this study chosen for whole genome sequencing activated at least two acyl homoserine lactone (AHL)-dependent whole cell bacterial biosensors (Supplemental Table 1)
Rr 2-17 isolated from grapevine tumor provided the first glimpse of quorum sensing (QS) ability in the genus Novosphingobium (Gan et al, 2009)

Summary

Introduction

Members of the Sphingomonadaceae family are Gram-negative glycosphingolipid-containing bacteria that belong to the α-4 subclass of proteobacteria (Yabuuchi et al, 1990). This family possesses a variety of metabolic capabilities that are potentially advantageous pertaining to a variety of bioremediation capabilities (White et al, 1996). It was shown that the biphenyland naphthalene-degrading Sphingomonas aromaticivorans F199 strain and other sphingomonads that degrade additional xenobiotic compounds contain large plasmids encoding the catabolic pathways (Romine et al, 1999; Ogramab et al, 2000; Basta et al, 2004, 2005).

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