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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

Gan, Han Ming, Gan, Huan You, Ahmad, Nurul H, Aziz, Nazrin A, Hudson, André O and Savka, Michael A 2015, 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, Frontiers in cellular and infection microbiology, vol. 4, pp. 1-14, doi: 10.3389/fcimb.2014.00188.

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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
Formatted 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
Author(s) Gan, Han MingORCID iD for Gan, Han Ming orcid.org/0000-0001-7987-738X
Gan, Huan You
Ahmad, Nurul H
Aziz, Nazrin A
Hudson, André O
Savka, Michael A
Journal name Frontiers in cellular and infection microbiology
Volume number 4
Article ID 188
Start page 1
End page 14
Total pages 14
Publisher Frontiers Media
Place of publication Lausanne, Switzerland
Publication date 2015-01
ISSN 2235-2988
Keyword(s) Novosphingobium
Sphingomonadaceae
luxI/R
luxR solos
phylogenetic
quorum-sensing
whole genome sequencing
amino acid sequence
bacterial proteins
evolution, molecular
gene expression regulation, bacterial
genetic variation
genome, bacterial
phylogeny
quorum sensing
repressor proteins
sequence alignment
trans-activators
transcription factors
Summary 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.
Language eng
DOI 10.3389/fcimb.2014.00188
Field of Research 060309 Phylogeny and Comparative Analysis
HERDC Research category C1.1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2015, Gan, Gan, Ahmad, Aziz, Hudson and Savka
Free to Read? Yes
Use Rights Creative Commons Attribution licence
Persistent URL http://hdl.handle.net/10536/DRO/DU:30101928

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Every reasonable effort has been made to ensure that permission has been obtained for items included in DRO. If you believe that your rights have been infringed by this repository, please contact drosupport@deakin.edu.au.