The purpose of this chapter is to describe simple ways to identify
these LuxR solos, detect their ligands, and study their regulon.
The LuxR regulatory family is large and consists of several
subfamilies, one being the AHL-binding QS-LuxRs. Proteins of
the QS-LuxR subfamily are about 250 amino acids long and have
two domains bridged by a short linker region. One is an autoindu-
cer (AHL)-binding domain located at theN-terminus [9, 10] and
the other is a DNA-binding helix-turn-helix (HTH) domain posi-
tioned at theC-terminus [11–13]. The two domains can function
independently of each other. These proteins bind to an inverted
DNA repeat recognition sequence that consists of a conserved
20 bp palindrome site calledluxbox [14–17]. QS LuxR-type
proteins can act as either a transcriptional activator or a repressor
[1]. In the case of activation, binding to the AHL brings about a
conformational change that allows the HTH domain to bind DNA
atluxboxes of its target genes, which then allows the LuxR/
autoinducer complex to recruit RNA polymerase [18] and activate
transcription [19]. When the protein is a repressor, it is bound to
target promoters in the absence of the cognate AHL, thereby
blocking access to RNA polymerase. When AHL concentrations
reach quorum threshold concentrations and bind to the LuxR-type
protein, conformational changes cause it to release the promoter
and in turn relieve repression [20]. Structural analysis of TraR of
Agrobacterium tumefaciens[19, 21] and SdiA ofEscherichia coli
[22] revealed that the AHL-binding cavity is composed of five-
stranded antiparallelβ-sheets with threeα-helices on each side.
AHL binding to some QS-LuxRs is crucial for their folding and
stability and the absence of AHLs leads to fast degradation by
proteases [23].
Surprisingly, QS-LuxRs display rather low homology in their
primary structure; however almost all share nine highly conserved
amino acid residues [3, 19]. Six of these residues are hydrophobic
or aromatic and form the cavity of the AHL-binding domain and
three are in the HTH domain. Evolutionarily, two distinct groups
of QS-LuxRs are emerging; one group is found in proteobacteria
from different divisions (α,β, andγ) and the second is found only in
γ-proteobacteria. Interestingly, proteins from the first family
behave as activators whereas members of the second group are
mainly repressors [16]. The latter could have evolved relatively
recently probably at the divergence of the Xanthomonadsand
Xylellas, which lack QS LuxI/R homologs, but before the diver-
gence of the pseudomonads which harbors them [24].
Many sequenced proteobacterial genomes have evidence of the
widespread presence of QS-related LuxR AHL sensors/regulators
which lack a cognate LuxI AHL synthase [4, 6, 7]. These unpaired
QS LuxR family proteins have been called orphans and more
recently solos [5, 8] and possess the typical modular structure
having an acyl-homoserine lactone-binding domain at theirN-146 Vittorio Venturi et al.